The 4th Joint Spring Conference 7-9 March 2016 The City Hall, Cardiff Civic Centre
Abstract Booklet
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Oral Presentations
(Arranged alphabetically by lead author)
Risk factors for the presence of pathogenic APC and biallelic MUTYH mutations in patients with multiple adenomas
S.W. ten Broeke.1 S.S. Badal 1, T. van Wezel 2, H. Morreau 2, F.J. Hes 1, H.F. Vasen 3,4, C.M. Tops 1, M. Nielsen 1
1 Department of Clinical Genetics, Leiden University Medical Centre, the Netherlands. 2 Department of Pathology, Leiden University Medical Centre, the Netherlands. 3 The Netherlands Foundation for the Detection of Hereditary Tumours, Leiden, the Netherlands. 4 Department of Gastroenterology, Leiden University Medical Centre, the Netherlands.
Background. Patients with multiple colorectal adenomas may carry germline mutations in the APC or MUTYH gene. The aims of this study were (1) to assess the proportion of patients with an APC-mutation or bi-allelic MUTYH mutations in patients with multiple adenomas and (2) to identify risk factors that predict the finding of mutations.
Methods. We performed mutation analysis of the APC gene and/or MUTYH gene in a nationwide cohort of 2151 patients ascertained from Dutch family cancer clinics between 1992 and 2015. The following risk factors of a pathogenic germline mutation were analysed using logistic regression analysis: cumulative adenoma count, age of CRC diagnosis, age of adenoma detection, family history for CRC and year of mutation analysis.
Results. The presence of APC mutations increases with adenoma count (adenoma count between brackets): (0) 2%, (1-9) 1%, (10-19) 1%, (20-49) 8%, (50-99) 12%, (100<) 71%. Bi- allelic MUTYH-mutations were most common in individuals with 50-99 adenomas: (0) 1%, (1- 9) 3% , (10-19) 2%, (20-49) 7 % , (50-99) 16%, (>100) 7% . Adenoma count and younger age at adenoma detection were associated with a pathogenic mutation. Family history of CRC was not a predictive factor. A lower age at CRC diagnosis decreased the odds of finding an APC mutation (OR: 0.45). The detection rate of APC and bi-allelic MUTYH mutations declines from 54% before 2004 to 14% after 2004.
Discussion. Adenoma count and younger age at adenoma detection are the main predictive factors of finding a mutation. The mutation detection rate of both MUTYH and APC mutations was very low in patients with <20 adenomas; APC-mutations were most often found in patients with >100 adenoma and MUTYH-mutations in those with 50-99 adenomas. Adenoma count is more important in the selection of patients for germline mutation screening than family history of CRC. Our findings have an important impact on referral policy.
UNC80 mutations lead to Intellectual Disability with persistent Hypotonia, Encephalopathy, and Growth Retardation, without true Facial Dysmorphism
Jan Maarten Cobben.1,18 Asbjorg Stray-Pedersen, 2,3,18 Trine E. Prescott, 4,18 Sora Lee, 5 Chunlei Cang, 5 Kimberly Aranda, 5 Sohnee Ahmed, 6 Marielle Alders, 7 Thorsten Gerstner, 8 Kathinka Aslaksen, 9 Martine Tetreault, 10 Wen Qin, 11 Taila Hartley, 11 Shalini N. Jhangiani, 1,16 Donna M. Munzy, 1,16 Maja Tarailo-Graovac, 12 Clara DM van Karnebeek, 13 Care4Rare Canada Consortium, Baylor Hopkins Centre for Mendelian Genomics, James R. Lupski, 1,14,15,16 Dejian Ren, 5 Grace Yoon. 6,7
(1)Department of Pediatrics; (7)Department of Clinical Genetics, AMC University Hospital, Amsterdam, the Netherlands (2)Department of Molecular and Human Genetics; (14)Department of Pediatrics; (15)Department of Molecular and Human Genetics (16) Human Genome Sequencing Centre, Baylor College of Medicine, Houston, USA (3)Norwegian National Newborn Screening (4)Department of Medical Genetics, Oslo Univeristy Hospital, Olso, Norway (5)Department of Biology, Univeristy of Pensylvania, Philadelphia, USA (6)Hospital for Sick Children; (17)Division of Neurology Univeristy of Toronto, Toronto, Canada (8)Department of Pediatrics, Sorlandet Hospital, Arendal, Norway (10)Department of Human Genetics, McGill Univeristy, Montreal, Canada (11)The Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Canada (12)Department of Medical Genetics; (13)Department of Pediatrics, University of British Columbia, Vancouver, Canada (18) These authors contributed equally to this work.
UNC80 is a large component of the NALCN sodium-leak channel complex that regulates the basal excitability of the nervous system. Loss-of-function mutations of NALCN cause infantile hypotonia with psychomotor retardation and characteristic facies (IHPRF). It appears that UNC80 mutations are associated with a comparable clinical picture: We report four individuals from three unrelated families with homozygous missense or compound heterozygous truncating mutations in UNC80 with persistent hypotonia, encephalopathy, growth failure, and severe intellectual disability. There appears to be no true facial dysmorphism. HEK293T cells transfected with an expression plasmid containing the c.5098C>T (p.Pro1700Ser) UNC80 mutation found in one individual showed markedly decreased NALCN channel currents compared to controls. Our findings further demonstrate the importance of normal basal ionic conductance components like UNC80, for normal human neurodevelopment.
Strategy to Knockout Type V Collagen Using the CRISPR-Cas9n System
Andrea Cordaro 1, Paul Nistor 2, C. Maeve Caldwell 2
1 Medical Student, University of Bristol, Bristol, BS8 1TH, United Kingdom 2 Regenerative Medicine Laboratory, University of Bristol, Bristol, BS8 1TH, United Kingdom
Clustered, regularly interspaced, short palindromic repeat (CRISPR) RNA-guided nucleases have recently emerged as powerful gene editing tools with high specificity, efficiency and simple customization. Ehlers-Danlos syndrome is a connective tissue disease in which deficiency of type V collagen, a component of extracellular matrix, creates morphologically abnormal collagen fibrils. We present a strategy using the CRISPR-Cas9 nickase (Cas9n) system to knockout type V collagen in embryonic and iPS cell lines. The Cas9n mutant is a more specific system compared to its wildtype Cas9 counterpart. Cas9n effects a double- stranded break at a target genomic locus by requiring two simultaneous single-stranded nicks, thus minimizing off-target mutagenesis. In this strategy, two Cas9ns each complexed with a 20 nucleotide RNA-guide bind to a complementary locus on exon 2 of the col5A1 gene to create two single-stranded breaks. The exon 2 target locus contains a TAA stop codon that is out-of-frame. Therefore, a repair single-stranded oligodeoxynucleotide (ssODN) with homology arms to the target locus is substituted into the exon by homology directed repair (HDR), causing the TAA stop codon to become in-frame. This allows for the mRNA construct to be subject to nonsense-mediated decay, inducing a gene knockout. Gene editing was focused in exon 2 of col5A1 in one embryonic and two iPS cell lines. Two addgene plasmids were modified for the expression of cas9n and the insertion of RNA guides and two RNA oligos were created, complementary to the sense and anti-sense target strands of exon 2. A 54 nucleotide repair ssODN was also constructed, with homology arms flanking the site of alteration. Results were confirmed by gel electrophoresis and sequencing analysis. This strategy is important for the study of the molecular mechanism of Ehlers-Danlos syndrome in vitro and as a model for a broad range of specific gene knockouts.
Selectively targeting TSC1/2 deficient cells by exploiting endoplasmic reticulum stress
D. Mark. Davies. 1,2 Charlotte E. Johnson 2, Rachel Errington 2, Henry, McCann 2, Julian R. Sampson 2, Andrew R. Tee 2,
1: Department of Oncology, South Wales Cancer Centre, Singleton Hospital, Swansea SA2 8QA, UK. 2: Institute of Cancer and Genetics, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
The mammalian/mechanistic target of rapamycin complex 1(mTORC1) pathway is frequently hyper-activated in tumours of patients with tuberous sclerosis and in sporadic cancers mTORC1 regulates many processes, such as cell growth, proliferation, metastasis, autophagy, metabolism and angiogenesis. Recently, mTOR inhibitors, which normalise aberrant mTORC1 signalling, have been licensed for the treatment of tuberous sclerosis. However, an alternative approach to normalising mTORC1 signalling is to exploit abnormal cellular stress that arises from mTORC1 activation. We have demonstrated that TSC1/2 deficient cells exhibit abnormal endoplasmic reticulum stress and this can be selectively targeted using a clinically useable drug, nelfinavir. We have further shown that this selective toxicity can be enhanced by combing nelfinavir with other drugs that target cell survival mechanisms. These drug combinations represent potential novel approaches to the treatment of tuberous sclerosis and other tumour predisposition syndromes characterised by hyper activation of mTORC1 signalling, as well as sporadic cancers.
High yield of causative mutations by whole exome sequencing in selected individuals with childhood cancer
Illja Diets.1 Marjolijn Jongmans 1,2, Esme Wannders 1, Arjen Mensenkamp 1, Marjolijn Ligtenberg 1, Eveline Kamping 1, Peter Hoogerbrugge 3, Maran Oldenrode-Berends 4, David Koolen 1, Gijs Santen 5, Dylan Mordaunt 6, Antonis Kattamis 7, Agata Pastorczak 8, Anneke Vulto-van Silfhout 1, Eveline de Bont 9, Jan Loeffen 10, Roland Kuiper 1, Nicoline Hoogerbrugge 1
1 Department of Human Genetics, Radboud University Medical Centre and Radboud Institute for Molecular Life Science, Nijmegen, the Netherlands. 2 Department of Medical Genetics, University Medical Centre Utrecht, NL 3 Department of Pediartic Oncology, Princes Maxima Centre, The Bilt, NL. 4 Department of Genetics, University Medical Centre Groningen, Groningen, NL 5 Department of Clinical Genetics, Leiden University Medical Centre, Leiden, NL. 6 Department of Genetics and Molecular Pathology, SA Pathology, Women’s and Children’s Hospital, North Adelaide, Australia. 7 First Department of Pediatrics, Athens University Medical School, Athens, Greece. 8 Department of Pediatrics, Athens University Medical School, Athens, Greece. 8 Department of Pediactrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Poland. 9 Department of Pediactric Oncology and Hematology, Beatrix Children’s Hospital, University Medical Centre Groningen, NL. 10 Department of Pediactric Oncology and Hematology, Sophia Children’s Hospital, Erasmus Medical Centre, Rotterdam, NL
Childhood cancer predisposition shows extensive genetic heterogeneity with currently over 100 predisposing conditions described and likely many to be identified. Recognition of genetic predisposition in a child with cancer may lead to better treatment choices and surveillance options. We applied whole exome sequencing on germline DNA of children and their parents. These children were diagnosed with cancer and had at least one of the following features: intellectual disability (ID) or congenital anomalies, adult type of cancer, a family history for childhood cancer or multiple primary malignancies. All included cases remained undiagnosed after consultation by a clinical geneticist and often multiple genetic tests. Analysis of the first 25 patients resulted in a high yield of causative mutations (Table 1). Five patients carried mutations in the known cancer genes TP53, DICER1 (n=3) and ETV6. In three children, exome sequencing revealed syndromes that likely contributed to their malignancy (EP300 based Rubinstein Taybi syndrome in a girl with AML; ARID1A based Coffin Siris syndrome and ACTB based Baraitser Winter syndrome in two boys with ALL). In addition, we identified novel candidate genes for childhood cancer. For instance, in a girl with lymphoma and congenital anomalies of the kidney (CAKUT) and uterus a de novo E4F1 mutation (p.Arg90*) was found, which could explain both conditions. E4F1 is a binding partner of HNF1β, a gene known to be involved in CAKUT. In addition, E4F1 is a key posttranslational regulator of p53. Our study shows the value of exome sequencing in the field of childhood cancer predisposition, both to facilitate the diagnosis of known syndromes as well as to trace novel genes involved in cancer susceptibility.
Table 1. Results of whole exome sequencing of the first 25 patients Solved Strong candidate No candidate Analysis or Total (%) gene found gene found validation ongoing 1. ID/congenital anomalies 4 3 4 10 21 (46.6) 2. Multiple primary cancers 2 3 1 3 9 (20) 3. Family history 3 2 2 6 13 (28.9) 4. Adult type of cancer 0 1 0 1 2 (4.4) Total 9 9 7 20 45 (100)
SMAD2 Mutations are associated with arterial aneurysms and dissections
Dimitra Micha 1, Dong-chuan Guo 2, Yvonne Hilhorst-Hofstee 3, Fop van Kooten 4, Dian Atmaja 1,5, Eline Overwater 1,6, Ferdy K. Cayami 1,5, Ellen S. Regalado 2, Jiddeke M. van de Kamp 1, Rene van Uffelen 7, Hanka Venselaar 8, Sultana M.H. Faradz 5, Gerrit Vriend 8, Marjan M. Weiss 1, Erik A. Sistermans 1, Alessandra Maugeri 1, Dianna M. Milewicz 2, Gerard Pals 1, Fleur S. van Dijk 1,9,10
1 Department of Clinical Genetics, Centre for Connective Tissue Research, VU University Medical Centre, P.O. Box 7057, 1007 MB Amsterdam, NL. 2 Department of Internal Medicine, University of Texas Health Science Centre at Houston, Houston, Texas, USA. 3 Department of Clinical Genetics, Leiden University Medical Centre, PO Box 9600 2300 RC, Leiden, NL 4 Department of Neurology, Erasmus Medical Centre, PO Box 2040, 3000 CA, Rotterdam, NL. 5 Centre for Biomedical Research, Faculty of Medicine, Diponegoro University Jln Prof H Soedarto, P.O. Box 1269, Semarang, Central Java, Indonesia. 6 Department for Clinical Genetics, Academic Medical Centre, P.O. Box 22660, 1100 DD, AmsterdamNL 7 Department for Respiratory Medicine, Albert Schweitzer Hospital, 3318 AT Dordrecht, NL 8 Centre for Molecular and Bimolecular Genetics (CMBI), P.O. Box 9101, 6500 HB, Nijmegen, NL *Correspondence: [email protected] 9 Department of Clinical Genetics, University Medical Centre Groningen, P.O. Box 30.001, Groningen, NL 10 North West Thames Regional Genetics Service, London North West Healthcare NHS Trust, Harrow, UK.
We report three families with arterial aneurysms and dissections in which variants predicted to be pathogenic were identified in SMAD2. Moreover, one variant occurred de novo in a proband with unaffected parents. Recently, a fourth variant was identified. SMAD2 is a strong candidate gene for arterial aneurysms and dissections given its role in the TGF-β signaling pathway. Furthermore, although SMAD2 and SMAD3 probably have functionally distinct roles in cell signaling, they are structurally very similar. Our findings indicate that SMAD2 mutations are associated with arterial aneurysms and dissections and are in accordance with the observation that patients with pathogenic variants in genes encoding proteins involved in the TGF-β signaling pathway exhibit arterial aneurysms and dissections as key features.
Characterising STAT3 signaling as a therapeutic target for vascularized tumours and Tuberous sclerosis
K.M. Dodd, E. Rad, N.T.F Green, A.R. Tee
Cancer and Genetics, Institute of Medical Genetics, Heath Park, Cardiff, CF14 4XN, UK.
Tuberous sclerosis (TSC) is a rare inherited tumour-predisposition disorder affecting approximately 1 in 10,000 live births. Mutation to either the TSC1 or TSC2 genes results in the development of benign tumours in multiple organ systems. The tumours which present with TSC are heavily vascularized due to constitutive activation of the mammalian target of rapamycin signaling (mTOR) pathway. Cell line models for TSC therefore provide a useful model for studying the process of tumour angiogenesis and the mTORC1 signalling pathway, which is thought to be upregulated in a number of sporadic cancers as well as TSC. We utilize cell line models for TSC to investigate key signaling mechanisms driving the activity of HIF-1α, a hypoxia induced transcription factor which promotes vascularization, increased glucose metabolism, metastasis and cell survival. Elevation of HIF is reported in a number of different cancer cell types, and is downstream of several tumour suppressors and oncogenes, making it an appealing therapeutic target for both a number of sporadic cancers and TSC. We demonstrate that inhibition of STAT3 with the curcumin analogue FLLL31 can block the migration of TSC associated (AML) angiomyolipoma-derived cell lines, this inhibition is further enhanced by co-treatment with the mTOR kinase inhibitor KU-0063794, indicating that STAT3 drives migration of these cells via mTOR-dependent and -independent mechanisms. Furthermore, knockdown of STAT3 in these AML-derived cells also significantly reduced average tumour spheroid volume in soft agar. Further investigation into this signalling pathway has revealed that the transcription factor Nf- kB is also upregulated in TSC2-/- cell lines and is driving STAT3 activity in this setting. Our results demonstrate that TSC-loss induces expression of a network of transcription factors promoting tumour growth, including STAT3, Nf-KB and HIF-1α. Our data indicates that targeting NF-kB/STAT3 in combination with mTORC1 may enhance the anti-tumourigenic efficacy of rapalogues currently utilised in cancer therapy. To demonstrate the wider implications of this work, we replicated this work in cell line models for neurofibromatosis type 1 (NF-1). Results indicate that STAT3 knockdown or inhibition with FLLL31 can block cell migration and invasion, as well as tumour spheroid formation of cell lines derived from NF-1 associated malignant peripheral nerve sheath tumours (MPNSTs). This work indicates that STAT3 may be an appealing therapeutic target for a wide range of tumour types.
Understanding mechanisms behind renal cancer development
E.A.Dunlop 1, M. Naven 2, S. Rundel 1,2, K. Ashelford 2, S. Edkins 2, J.R. Sampson 1, A.R. Tee 1.
1 Division of Cancer and Genetics, Cardiff University, Cardiff, CF14 4XN, UK.
2 Wales Gene Park, Institute of Medical Genetics, Cardiff University, Cardiff, CF14 4XN, UK.
The genetic condition, Birt-Hogg-Dubé (BHD) Syndrome is characterised by the development of fibrofolliculomas, lung cysts and renal cancer. Renal cancer is the most life-threatening manifestation of BHD syndrome and is estimated to affect up to one third of BHD patients. In contrast to other monogenic disorders which cause renal cancer, the renal tumours associated with BHD syndrome are histologically diverse, with chromophobe, hybrid chromophobe/oncocytoma, clear cell, oncocytoma and papillary subtypes all observed. The average age of onset of renal cancer in BHD patients is 50 years (Shuch et al., 2014), over 13 years younger than the average onset of sporadic renal cancer.
Folliculin (FLCN) is the tumour suppressor gene responsible for BHD syndrome. We have previously shown that loss of FLCN results in PGC-1α-mediated mitochondrial biogenesis and increased ROS production (Yan et al., 2014). We hypothesise that renal cancer development occurs earlier in BHD patients than in the general population due to accelerated genetic damage which may be in part due to elevated levels of ROS caused by loss of FLCN function. The random nature of the increased genetic damage, increased genetic instability or decreased DNA repair occurring in FLCN-deficient cells could account for the different histological tumour subtypes observed in BHD patients.
As it takes time for these genetic changes to occur and renal cancer to develop in BHD patients, we wanted to investigate how the genetic landscape of FLCN-deficient cells alters over time. We monitored FLCN-expressing and –deficient human kidney cells immediately following FLCN-knockdown and following one year of continuous tissue culture. We then assessed these cells for alterations in DNA damage markers by western blotting and for changes in gene expression through RNAseq using next generation sequencing technology. We found that after one year in culture, FLCN-deficient cells harbour elevated levels of DNA damage compared to control cells. They also exhibit a markedly different gene expression profile. We observe gene expression changes previously linked to FLCN loss, such as are over-represented in the dataset, which fits with the reported role of FLCN in cell-cell adhesion. Further analysis of the genetic changes observed following long-term FLCN knockdown will give us a better understanding of mechanisms underlying renal cancer development.
Prostate cancer genome-wide association study from 89,000 men using the OncoArray chip identifies more than 30 novel prostate cancer susceptibility loci.
Rosalind A. Eeles 1. Fredrick R. Schumacher 2, Ali A. Al Olama 3, Sonja I. Berndt 4, Fredrik Wikland 5, David V. Conti 2, Mahbubl Ahmed 1, Sara Benlloch 3, Kenneth Muir 6, Artitaya Lophatananon 6, Douglas F. Easton 3, Peter Kraft 7, Stephen J. Chanock 4, Brian E. Henderson 2, Zsofia Kote-Jarai 1, Christopher A. Haiman 2. On Behalf of the Elucidating Loci Involved in Prostate Cancer Susceptibility (ELLIPSE), Prostate Cancer Assoccation Group to Investigate Cancer Associated Alterations (PRACTICAL), Cancer of the Prostate in Sweden (CAPS), Breast and Prostate Cancer Cohort Consortium (BPC3) and Prostate Cancer Genome-wide Association Study of Uncommon Susceptibility loci (PEGASUS)
1 The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK. 2 University of South California, USA. 3 University of Cambridge, UK. 4 NIH, USA. 5 Karolinska, Stockholm, Sweden. 6 University of Manchester, UK. 7 University of Harvard, USA.
Genome-wide association studies (GWAS) and fine-mapping efforts have identified 112 loci associated with prostate cancer susceptibility to date. Combined multiplicatively, these loci explain 33% of the familial relative risk for prostate cancer among populations of European ancestry. In order to identify novel prostate cancer susceptibility loci we conducted a GWAS involving 53,000 prostate cancer cases and 36,000 controls using the OncoArray that includes a 260K GWAS backbone and a custom portion of 310K SNPs developed from previous GWAS and fine-mapping studies of multiple cancer types (http://epi.grants.cancer.gov/oncoarray/). Following standard quality control procedures, the prostate cancer OncoArray genotyped data were imputed using the October 2014 release of the 1000 genomes project data as a reference and analysed by participating study for overall and advanced prostate cancer using logistic regression. The study-specific results were combined using inverse variance fixed effect meta- analysis. Regions surrounding previously associated variants (+/- 500kb of the reported index variant) were excluded to identify novel associations. In the OncoArray meta-analysis, we identified more than 30 novel loci significantly associated (P<5.0x10-8) with overall prostate cancer risk, including loci associated with advanced (Gleason ≥8, death from prostate cancer, PSA>100, or disease stage “Distant – outside the pelvis”), or early-onset (≤55 years of age) prostate cancer. These results provide further insight into the underlying mechanisms of prostate cancer carcinogenesis and will improve the utility of genetic risk scores for targeted screening and prostate cancer prevention. It is expected that these results combined with fine mapping analyses will yield a genetic profile of about 150 SNPs for large scale genotyping in such translational studies in 2016.
Use of multiple SNP testing to predict breast cancer risk in a familial screening clinic
D.G. Evans *1,2, A. Brentnall *3, H. Byers 2, E. Harkness 1, P. Stavrinos 2, A. Howell 1, W. Newman 1, J. Cuzick 3.
1 Genesis Breast Cancer Prevention Centre and Nightingale Breast Screening Centre, Univeristy Hospital of South Manchester, Southmoor Road, Wythenshawe, Manchester, M23 9LT, UK. 2 Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, University of Manchester and Central Manchester Foundation Trust, Manchester, M13 9WL. UK. 3 Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, EC1M 6BQ, UK.
Introduction: Familial-risk clinics have been set up across the developed world to offer intensive screening and preventive strategies. Whilst genetic testing for BRCA1/2 provides important risk information for a minority of women, use of common genetic variants associated with variation in breast cancer risk has not yet been implemented but may have relevance to a much larger number of women. Methods: A case-control study was designed to assess the effects of the first 18 single nucleotide polymorphisms identified through genome wide association studies on breast cancer incidence. Pre-defined polygenic risk scores for the general population (SNP18), BRCA1 (SNP3) and BRCA2 carriers (SNP13) were obtained by multiplying normalised risk estimates for each allele to provide an overall score. The observed / expected odds of breast cancer was estimated by logistic regression and discrimination was measured by the area under the receiver operating characteristic (AUC). A prospective sub-sample was used to assess women without breast cancer at entry to the clinic, and analysis of the non-BRCA carriers was also tested after adjustment for expected absolute risk from the Tyrer-Cuzick model. Results. SNP18 genotyping was performed in 2,055 samples including 451 women with breast cancer (364 prospective). SNP18 was a predictor in the non-BRCA1/2 group (inter-quartile range odds ratio 1.55 (95%CI 1.30-1.87), AUC 0.59 (0.55-0.62), O/E 96%). The risk ratio from upper to lower quintile of polygenic risk score was 2.1 fold. Findings were similar for women in the prospective sub-sample, and unaffected by adjustment for risk from classical risk factors. There was some evidence to support the use of SNP3 (BRCA1 carriers, AUC 0.62 (95%CI 0.55 – 0.70)) and SNP12 (BRCA2 carriers, AUC 0.55 (0.48-0.62)), but the general population weights in SNP18 performed worse for these groups (BRCA1 AUC 0.52 (0.44–0.59), BRCA2 AUC 0.53 (0.45- 0.60)). Conclusion SNP18 is ready to be used to refine risk assessment for women already at increased risk due to their family history, without BRCA1/2 mutations. Different weightings are required for women with BRCA1/2 mutations.
A network analysis of genes with de novo mutations in polymicrogyria patients
Katherine A. Fawcett 1, David Sims 1, Thomas Cushion 2, Daniela T. Pilz 2,3, Andrew E. Fry 2,4.
1 MRC Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3PT, UK. 2 Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN. 3 Clinical Genetics, West of Scotland Genetic Services, Queen Elizabeth University Hospital, 1345 Govan Road, Glasgow, G51 4TF. 5 Institute of Medical Genetics, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK.
Polymicrogyria (PMG) is a clinically and genetically heterogeneous malformation of cortical development characterised by excessive small gyri and disruption of normal cortical layering. In recent years a range of single gene and chromosomal disorders have been identified in PMG patients. This has led to improved knowledge of the disease and the biological pathways underlying normal brain development. However, in the majority of cases the cause of PMG is still unknown. We exome sequenced 57 parent-offspring trios (PMG patients and their unaffected parents) and identified 68 de novo variants, of which six were in known polymicrogyria genes. We assessed whether the de novo variants hit genes demonstrating higher than expected levels of mutational constraint within healthy human populations. We also exploited gene networks constructed using gene annotation, gene co-expression and protein-protein interaction datasets to examine the connectivity between these genes and known PMG genes. We found that genes in which the de novo variants resided were enriched for constrained genes (genes that carry fewer-than-expected missense variants in a control population). Furthermore, genes carrying de novo variants in PMG patients were more connected to each other within gene networks than would be expected by chance. Novel genes carrying predicted deleterious de novo variants were significantly clustered within the networks. Moreover, a subset of the candidate genes were individually more connected to known PMG genes than expected by chance. We found that, after excluding pathogenic mutations in known PMG genes, there remained a trend towards enrichment of constrained genes suggesting that further genes causing PMG remain to be identified. However, the paucity of genes hit in multiple patients in our exome data is further evidence that PMG is a genetically heterogeneous disorder. Sequencing of additional patient cohorts and/or analysis of variants in relevant functional models will be necessary to confirm a causative role for the novel variants identified in our study.
Visualising phenotypic and genomic relationships with DECIPHER – A community endeavour to map the Clinical Genome Firth HV, Bevan AP, Brent S, Hutton B, Perrett D, Swaminathan G, Wright CF, Hurles, ME.
1Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambs CB10 1SA UK 2 Dept of Medical Genetics, Cambridge University Hospitals Foundation Trust, Cambridge CB2 2QQ UK
DECIPHER (http:///decipher.sanger.ac.uk) was established in 2004 to serve the genetics community and has grown to become a major global platform for the visualization of phenotypic and genomic relationships. DECIPHER is unique in displaying all scales of genomic variation, from single base pair to megabases is size, in a single interface and has now developed an exciting visualisation of phenotypic relationships.
DECIPHER promotes flexible data-sharing; it enables the extent of sharing to be tailored so that it is proportionate to the clinical or scientific need to facilitate diagnosis or discovery. DECIPHER is a global community with 242 projects (9 in the Netherlands and 70 in the UK). There are 6 consortia within DECIPHER enabling more limited sharing (including the DDD consortium linking all 23 UK Clinical Genetics services and the NHS consortium). More than 32,000 patient records are shared via consortia, including >110,000 phenotypes and their associated genomic variants. There are >18,500 patient records with open-access consent that are searchable via the openly available search engine on the homepage that enables searching of phenotype terms and genomic coordinates using single terms or more advanced searches. Search is customized and for logged-in users will also include any data in project or consortia of which they are members. Since its inception, DECIPHER has facilitated more than 900 publications in the peer-reviewed scientific literature.
DECIPHER has facilitated key exchanges between UK and Dutch clinical geneticists enabling closer interaction between the two communities. Over recent years, DECIPHER has widened its remit from developmental disorders to Rare Disease, including hereditary cancer. DECIPHER is a pioneering partner in the Global Alliance for Global Health (GA4GH) initiative and has been driving development of the Matchmaker exchange Application Programming Interface (API) enabling a query initiated in DECIPHER to also search connected databases (currently PhenomeCentral and GeneMatcher).
A major development in DECIPHER for 2016 is the Phenotype browser built using Human Phenotype Ontology (HPO) terms enabling the relationship between phenotypes, genes and genomic variants to be explored and analysed computationally and the rich patient resource in DECIPHER to be visualised and queried from both a phenotypic and genomic perspective. A demonstration will be given during the presentation.
The Development of a Clinical Screening Instrument for Tumor Predisposition Syndromes in Childhood Cancer Patients: protocol for a prospective, observational, multi-center study (TuPS)
Saskia M.J. Hopman 1,2, Floor A.M. Postema 2, Corianne A.J.M de Borgie 3, Johannes H.M. Merks 2, Raoul C.M. Hennekam 4.
1 Department of Genetics, University Medical Centre Utrecht, the Netherlands 2 Department of Pediatric Oncology, Emma Children’s Hospital/ Academic Medical Centre Amsterdam, the Netherlands 3 Clinical Research Unit, Clinical Methodology, University of Amsterdam, the Netherlands 4 Department of Pediatrics, Emma Children’s Hospital/ Academic Medical Centre, Amsterdam, the Netherlands
Background Identification of a tumor predisposition syndrome (TPS) in patients who have cancer in childhood is paramount for optimal care. A screening instrument may serve as a standard screen for genetic counselling. It can guarantee that in each child with cancer the presence of a TPS is considered. Such a screening instrument should be based on the manifestations of known TPS. We have developed a screening instrument consisting of 2D and 3D picture series and a screening form for manifestations not visible in the picture series1. The screening instrument can be completed by a research nurse, genetic counsellor or treating physician and remotely reviewed by a clinical geneticist. Here we describe the protocol for the TuPS study, a prospective multi-center study for validation of the screening instrument.
Aim 1: To assess prospectively the clinical validity (focusing on sensitivity) of an observational screening instrument for tumor predisposition syndromes in childhood cancer patients. 2: To use 3D facial analyses in childhood cancer patients to identify additional (patterns of) morphological abnormalities with predictive value to improve the screening instrument.
Outcome measurements For aim 1, the primary outcome measurement in the assessment of the screening instrument will be sensitivity. A sensitivity of 94% or higher will be considered as clinically relevant. The secondary outcome measurements are the specificity, positive predictive value, negative predictive value, the inter-observer variability and the separate contribution of all aspects of the tool separately to the decision of the clinical geneticist when assessing the tool. For aim 2 the outcome measurement will be positive predictive value of individual morphological abnormalities and their weight within the overall assessment of the instrument.
Methodology and design All children newly diagnosed with a childhood cancer in the Netherlands within a period of 2 years (sample size 1000 patients) will be evaluated by two clinical geneticists using the screening instrument. Children with a positive screening result (suspected for a TPS) will follow regular clinical genetic diagnostics. From the series of patients with a negative screening result (not suspected for a TPS), a random sample of patients will be assigned to additional full clinical genetic evaluation in order to determine false negatives.
1: Hopman et al. Eur J Cancer. 2013 Oct;49(15):3247-54
Remark: the development of the screening instrument was submitted as an abstract and selected for a poster for the UK-NL joint meeting 2014.
NF1 genetic testing: where have we got to?
D.G. Evans 1,2, N. Bowers 2, E. Burkitt-Wright 2, S. Garg 2, V. Scott-Kitching 2, M. Penman- Splitt 3, A. Dobbie 4, E. Howard 2, J. Ealing 2, G. Vassalo 2, A.J. Wallace 2, Northern UK NF1 Research Network, S.M. Huson 2
1 Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester Academic Health Sciences Centre (MAHSC), Institute of Human Development, University of Manchester; 2 Neurofibromatosis Centre, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Central Manchester University Hospital NHS Foundation Trust Manchester, M13 9WL, UK; 3 Northern Genetic Service, Centre for Life, Newcastle; 4 Yorkshire Genetic Service, Chapel Allerton Hospital, Leeds.
[email protected] Introduction – The NHS has commissioned a national complex NF1 service since 2009. As part of the service we provide an RNA based mutation analysis for NF1, a DNA based analysis for SPRED1 and melanocyte/schwann cell culture to assist in counseling mosaic patients. We present the outcomes of testing and discuss their implications for future practice. Methods – The RNA based technique used was that developed by Messiaen and colleagues (Human Mutation 2000; 15:541-5).The outcome of testing of individuals from 04/09 to 12/15 were analyzed. Mutation detection rates depending on family history and clinical presentation (whether they met NIH diagnostic criteria or had a pigmentary phenotype) were compared. Statistical anaslysis was carried out using chi square testing with two tailed Fisher’s exact test. Results- RNA analysis was carried out on 361 NF1 affected individuals who fulfilled NIH criteria with at least one non pigmentary criterion. Potentially causative variants in the NF1 gene were identified in 166/171 (97.08%-95% CI 94.56-99.6%) of familial cases compared to 182/190 (95.8%-95% CI 92.93-98.65%) of sporadic samples (p=0.58). A total of 41/348 (11.8%) of samples had mutations only classifiable with RNA analysis. Of the thirteen cases with no identified mutation two had a dysembryoplastic neuroepithelial tumour (DNET) identified on MRI of the brain both associated with epilepsy. The presence of DNET in 2/13 (15%) negative screens versus 2/348 (0.6% -Relative Risk of 0.004) with mutations is highly significant (p=0.007).44/71 individuals (62%) aged <20 with 6+ CAL and no non pigmentary NF1 criterion had an RNA sample assessed. Six of this group (10.5%) had SPRED1 mutations. Missense mutations in the NF1 gene were found more frequently than SPRED1 mutations in patients with pigmentary only phenotypes regardless of family history. Furthermore the mutation type was significantly different in those with pigmentary only phenotypes with 76.5% (13/17 in this analysis) of cases having non-truncating mutations compared with only 13.6% (17/125) of cases with neurofibromas. Six individuals with mosaic NF1 and negative analysis on lymphocytes have undergone biopsy of CAL patches, five for genetic counselling and one for diagnostic purposes. The causative mutation has been found in 3/3 where results are available at time of submission. In exceptional cases, clinical assessment challenged the initial laboratory report and was correct. Conclusion – RNA based testing has proven to be more specific and sensitive than DNA based techniques. The detection rate in sporadic and familial cases was similar- the only mosaic cases detected all had a segmental phenotype. Using the detection rates reported here, a normal RNA based test gives only a 1/9 likelihood of still having NF1 compared with a 1/6 chance using DNA based NF1 testing. The improved detection of RNA based techniques combined with increasing clinical indications (clinically relevant genotype-phenotype correlation, cord blood testing vs. clinical follow-up to allow early diagnosis of affected individuals, PGD and free foetal DNA testing for pregnancies with affected Fathers) mean we offer mutation testing to all newly diagnosed individuals and families with no previous mutation analysis.
Experience of participation in a therapeutic drug trial for neonatal patients with X-linked Hypohidrotic Ectodermal Dysplasia (XLHED)
A.Kamath 1 ,I. Tully 1, P. Kandaswamy 2, N. Thomas 2, K. Burke 2, A. Clarke 1,3
1 Institute of Medical Genetics, University Hospital of Wales, CF14 4PY, UK 2 Department of Paediatrics, University Hospital of Wales, CF14 4PY, UK 3 Cardiff University, Cardiff, CF10 3XQ, UK
Background: X-linked Hypohidrotic Ectodermal Dysplasia (XLHED), the most common ectodermal dysplasia is caused by Ectodysplasin A (EDA) gene mutations. The EDA Receptor (EDAR) binds specifically the A1 isoform of EDA (EDA-A1) for signal transmission.1 Affected males present with abnormalities of the skin, teeth, hair and secretory glands.
Methods: A phase two, open-label trial has recruited ten cases to assess the safety, pharmacokinetics and immunogenicity of postnatal administration of EDI200. This is a fully humanized EDA-A1 replacement molecule, linked to a human IgG/Fc sequence. Male infants, recruited between 48 hours and 14 days of age, with a genetically confirmed diagnosis of XLHED, are eligible to receive five doses over 14 days. We report on the experience of recruiting and treating two neonatal patients out of ten (globally).
Both at-risk males were identified antenatally, following confirmation of maternal carrier status, conferring 50% risk. The infants were admitted to the Children’s Hospital at about one week of age for a 21-day period, following confirmation of the genetic diagnosis.
The treatment was administered in 5 doses. Blood, urine tests and skin biopsies were taken to monitor the effects of the treatment. Immunogenicity and pharmacokinetics were measured after the first and final doses. Clinical reviews including ophthalmology, dermatology and neurodevelopmental assessments were undertaken.
Results: There were no apparent complications from the treatment in either patient. Both patients are being followed-up according to the protocol.
Discussion: In utero administration of the preparation has shown promising outcomes in animal models.2 Therefore, the next step, which may be more effective at ameliorating the effects of this condition, would be to attempt prenatal therapy if there are no apparent ill effects of the treatment in human neonates.
REFERENCES 1. YanM,WangLC, Hymowitz SG, Schilbach S, Lee J, Goddard A, de VosAM, Gao WQ, Dixit VM. 2000. Two-amino acid molecular switch in an epithelial morphogen that regulates binding to two distinct receptors. Science 290:523–527. 2. Gaide O, Schneider P. 2003. Permanent correction of an inherited ectodermal dysplasia with recombinant EDA. Nature Medicine 9 (5): 614-618
Technological innovation in hereditary cancer risk assessment
A.Kulkarni 1, A. Kenney 2, V. Tripathi 1, C. Compton 1, S. Rose 1, E. Haque 1, L. Izatt 1,
D. Ruddy 1, E. Clement 1, A. Shaw 1
1 Guy’s Regional Genetics Service, Guy’s Hospital, London, SE1 9RT, England 2 UBQO Limited, London, SW4 0AL, England
Guy’s Cancer Genetics guidelines are used across Southeast London, Kent & East Sussex and updated in line with national standards. However they are currently presented in ‘non- interactive’ 'pdf' format that is not always readily accessible. It is also difficult to ensure clinicians are using the most recent version of the guidelines.
The Cancer Genetics application (App), developed by Guy’s Clinical Genetics department and UBQO with funding from Guy’s and St Thomas’ Charity, provides streamlined hereditary cancer risk assessment and referral guidance for clinicians.
The aim is to address inequity in referrals and improve patient access to our service by targeting several key factors, including clinicians’ limited understanding of hereditary cancer, lack of time, confusion about where to refer patients and use of outdated guidance.
The App contains a risk assessment tool and succinct reference guide, enabling clinicians to easily decide who requires genetic assessment of their cancer risk and who can be managed in primary or secondary care. Patients thereby have quicker access to cancer surveillance, genetic counselling, pharmaco-prevention and surgical options.
Cancer Genetics is freely available on iOS and android platforms and via a public website. It is certified as a Class 1 medical device and a secure content management system allows quick central updates.
We will present the development process, user feedback and integration of the App into primary and secondary care. Our goal is that Cancer Genetics will promote timely, evidence- based management of those at risk of hereditary cancer.
Informing family members in hereditary tumour syndromes
Fred H. Menko, Annelien L. Bredenoord, Imke Christiaans, Lutgarde C.P. Govaerts, Marjolein Kriek, Mere C. van Maarle, Renske Oegema, M. Corrette Ploem, Fleur Vansenne, Margreet G. Ausems, Frederik J. Hes, Suzanna G.M. Frints, Jasper J. van der Smagt
Correspondence: Fred H. Menko, clinical geneticist, Family Cancer Clinic, Antoni van Leeuwenhoek, Netherlands Cancer Institute, Amsterdam, the Netherlands
National and international guidelines have been set up on informing at-risk relatives in families with hereditary tumour syndromes. However, unfortunately, in clinical practice relatives not rarely present with symptomatic cancer since they were either not informed or refrained from DNA testing and surveillance. In the Netherlands, in 2015, a front-page newspaper item on this issue has led to public interest in our ongoing debate with patient advocate organisations on current guidelines, the duties of patients and geneticists and the pros and cons of contacting family members initiated by the clinical genetics centres. In addition, the compilation of pedigrees and family data bases is a subject of debate, since under current Dutch legislation the family members involved might have a right to be informed that their personal data have been registered. Several ongoing projects are aimed at improving the procedure in which probands inform their relatives. In addition, it is a matter of debate if genetics centres could take on a proactive role and directly contact relatives at risk of disease. A new form of organisation would be needed if such a proactive role would seem to be the best way to proceed. The issue is pressing due to the changing landscape of DNA diagnostics with an expected increase in DNA testing due to next generation sequencing and testing for the purpose of treatment decisions. We discuss legal, ethical and social issues of informing at-risk relatives and the option of research projects aimed at the evaluation of various models suitable for implementation in clinical practice.
Heterozygous KIDINS220/ARMS nonsense variants cause spastic paraplegia, intellectual disability, nystagmus, and obesity
Dragana Josifova 1, Glen Monroe 2, Federico Tessedori 2,7*, Esther de Graaff 3, Bert van der Zwaag 2, Sarju Mehta 4, The DDD Study 5, Magdalena Harakalova 2, Karen Duran 2, Sanne Savelberg 2, Ies Nijman 3, Heinz Jungbluth 6, Casper Hoogenraad 3, Jeroen Bakkers 7,9, Nine Knoers 2, Helen Firth 4,5, Phil Beales 8, Gijs van Haaften 2**, Mieke van Haelst 2**#
1 Department of Clinical Genetics, Guys’ and St Thomas’ Hospital, London SE1 7EH, UK. 2 Department of Medical Genetics and Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht 3584 CX, NL 3 Division of Cell Biology, Faculty of Science, University of Utrecht 3584 CH, NL 4 Department of Clinical Genetics, Cambridge University NHS Foundation Trust, Addenbrooke’s Hospital, Cambridge CB2 0QQ 5 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1RQ, UK. 6 Department of Paediatric Neurolog, Evelina Children’s Hospital, Guys’ and St Thomas’ Hospital NHS Foundation Trust, London SE1 7EH, UK; Randall Division of Cell and Molecular Biophysics, Muscle Signaling Section, and Department of Basic and Clinical Neuroscience, IoPPN, King’s College, London, WC1N 1EH, UK. 7 Hubrecht Institute-KNAW and University Medical Centre Utrecht, Utrecht 3584 CT, NL 8 Genetics and Genomes Medicine Program, UCL Institute of Child Health, London WC1N 1EH, UK. 9 Department of Medical Physiology, University Medical Centre Utrecht, Utrecht 3584 CX, NL */** The authors wish it to be known that, in their opinion, the first three authors and the last two authors should be regarded as joint authors. # Corresponding author: Mieke M. van Haelst – [email protected]
We identified de novo nonsense variants in KIDINS220/ARMS in three unrelated patients with spastic paraplegia, intellectual deficit, nystagmus, and obesity. KIDINS220 (Kinase D ineracting substrate of 220 kDa), also known as ARMS (Ankyrin Repeat-rich Membrane Spanning) is an essential scaffold protein coordinating neurotrophin signal pathways in neurites and controls axonal and dendritic maturation. The spatiotemporal expression of different KIDINS220 isoforms is finely tuned in the mammalian brain, and knockout Kidins220 animals show developmental central nervous system anomalies. Molecular analysis of patients’ variants confirmed expression and translation of truncated transcripts. These transcripts are similar to recently characterized alternative terminal exon splice isoforms of KIDINS220 that function in a dominant negative manner on full-length (wild- type) KIDINS220 by aberrant localization in intracellular puncta in the cell body instead of neurite tips. In Zebrafish, functional tissue-specific expression studies in motor neurons using the wild-type or p.(Trp1350*) variant resulted in spasms.This was more evident in embryos expressing the mutant KIDINS220, confirming a functional link between spasticity and disruption of KIDINS220 levels and/or function. Our patients manifest similarities with MOMO Syndrome (Macrosomia, Obesity, Macrocephaly and Ocular abnormalities; OMIM 157980), however prenatal ventricular dilatation and spastic paraplegia are not features of this condition. KIDINS220 Sanger sequencing of ten MOMO patients did not yield any variants. We therefore suggest that our patients have a distinct syndrome characterized by Spastic paraplegia, Intellectual disability, Nystagmus and Obesity (SINO). In conclusion, we show here that de novo heterozygous truncating KIDINS220 variants cause SINO syndrome. This is the first report of KIDINS220 variants causing a human disease.
Classification and clinical management of Variants of Uncertain Significance in high penetrance cancer predisposition genes
S. Moghadasi 1, D.M. Eccles 2, P. Devilee 3, M.P.G. Vreeswijk 3, C.J. Asperen 1
1 Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2333ZA, the Netherlands 2 Faculty of Medicine, University of Southampton, Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, SO16 5YA, UK. 3 Department of Human Genetics, Leiden University Medical Centre, Leiden, 2333ZC, the Netherlands.
In 2008, the International Agency for Research on Cancer (IARC) proposed a system for classifying sequence variants in highly penetrant breast and colon cancer susceptibility genes, linked to clinical actions. This system uses a multifactorial likelihood model (MLM) to calculate the posterior probability that an altered DNA sequence is pathogenic. Variants between 5%- 94•9% are categorized as variants of uncertain significance (VUS) (class 3). This interval is wide and includes variants with a substantial difference in pathogenicity. We think that carriers of class 3 variants would benefit from a fine-tuning of this classification. To improve the clinical utility of the current classification system, we suggest a pragmatic adaptation to clinical practice. Our suggestion is that the laboratory specialists divide VUS class 3 into two subgroups: class 3A with a posterior probability of 0•05 to 0•499 and class 3B with a posterior probability of 0•5-0•949. We propose to communicate and test family members when the posterior probability of pathogenicity of a VUS is higher than 0•5 (i.e. category 3B) but no communication of variants in class 3A unless there is clinical benefit for counselee or for research. The purpose of the recommendations is to improve the clinical management of the counselees by a more precise classification of the variants without causing unnecessary stress for the counselees or additional costs for the health care system, while minimizing the risk of missing pathogenic mutations in clinical practice.
Our recommendations for classification and communication of the variants:
Our suggestion for communication with Class Posterior probability Description counselees Clearly not Class 1 <0·001 Do not communicate pathogenic Do not communicate Unlikely to be Class 2 0·001-0·049 (unless there is clinical benefit for counselee or pathogenic for research) Do NOT communicate Class 0·05-0·499 (unless there is clinical benefit for
3A
Class 3 - VUS counselee or for research) Class
0·05 0·949 0·5-0·949 Do communicate 3B Likely to be Class 4 0·95-0·99 Do communicate pathogenic Clearly Class 5 >0·99 Do communicate pathogenic
De novo loss of function mutations in USP9X cause a female specific recognizable syndrome with developmental delay and distinct congenital malformations
Margot R.F. Reijnders 1,21, Vasilio Zachariadis 2,21, Brooke Latour 1,3,21, Lachlan Jolly 4,21, Grazia M. Mancini 5, Rolph Pfundt 1, Ka Man Wu 1, Conny M.A. Van Ravenswaaji-Arts 6, Hermine E. Veenstra- Knol 6, Britt-Marie M. Anderlid 2,7, Stephen A. Wood 8, Sau Wei Cheung 9, Angela Barnicoat 10, Frank Probst 9, Pilar Magoulas 9, Sue Price 13, Alice S. Brooks 5, Helena Malmgren 2,7, Arja Harila-Saari 11, Carlo M. Marcelis 1, Maaike Vreeburg 12, Emma Hobson 13, V. Reid Sutton 9, Zornitza Stark 14, Julie Vogt 15, Nicola Cooper 16, Jiin Ying LIM 17, Angeline Hwei Meeng LAI 17, Deepti Domingo 18, Bruno Reversade 19, The DDD Study, Jozef Gecz 4, Christian Gilissen 1, Han G. Brunner 1,12, Usha Kini 20, 22, Ronald Roepman 1, 22*, Ann Nordgren 2, 7, 22, Tjitske Kleefstra 1, 22*.
1 Dept of Human Genetics, Radboud University Medical Centre, 6500 HB Nijmegen, NL. 2 Dept of Molecular Medicine and Surgery and Centre for Molecular Medicine, Karolinska Institute, 171 76 Stockholm, Sweden. 3 Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre 6500 HB Nijmegen, NL. 4 Neurogenetics, School of Medicine and the Robinson Research Institute, SA 5006 the University of Adelaide, Australia. 5 Dept of Clinical Genetics, Erasmus MC Sophia Children’s Hospital, 3000 CA Rotterdam, NL. 6 University of Groningen, University Medical Centre of Groningen 9700 RB Department of Genetics, Groningen, NL. 7 Dept of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden. 8 The Eskitis Institute for Drug Discovery, Griffith University, QLD 4111 Brisbane, Australia. 9 Dept for Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. 10 Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK. 11 Dept of Women’s and Children’s Health, Karolinska University Hospital, 171 76 Stockholm, Sweden. 12 Dept of Clinical Genetics, Maastricht University Medical Centre, 6202 AZ Maastricht, NL. 13 Dept of Clinical Genetics, Chapel Allerton Hospital, Leeds, LS7 4SA, UK. 14 Victorian Clinical Genetics Service, Murdoch Children’s Research Institute, Melbourne, VIC 3052 Australia. 15 West Midlands Regional Genetics Service, Clinical Genetics Unit, Birmingham Women’s Hospital, B15 2TG, UK. 16 Clinical Genetics Unit, Birmingham Women’s NHS Foundation Trust, Mindelsohn Way, Edgbaston, B15 2G, UK. 17 KK Women’s and Children’s Hospital, 229899 Singapore, Singapore. 18 School of Biological Sciences, the University of Adelaide, Adelaide 5000, Australia. 19 Institute of Medical Biology, A (*) STAR, 138648 Singapore, Singapore. 20 Dept of Clinical Genetics, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK. 21, 22 These authors contributed equally
Mutations in over a hundred genes have been reported to cause X-linked recessive intellectual disability (ID) mainly in males. In contrast, the number of identified X-linked genes in which de novo mutations specifically cause ID in females is limited. Here, we report seventeen females with de novo loss of function mutations in USP9X, encoding a highly conserved deubiquitinating enzyme. The females in our study have a specific phenotype that includes ID/developmental delay (DD), characteristic facial features, short stature and distinct congenital malformations comprising choanal atresia, anal abnormalities, post-axial polydactyly, heart defects, hypomastia, cleft palate/bifid uvula, progressive scoliosis and structural brain abnormalities. Four females from our cohort were identified by targeted genetic testing as their phenotype was suggestive for USP9X mutations. In several females pigment changes along Blaschko lines and body asymmetry were observed which is likely related to differential (escape from) X-inactivation between tissues. Expression studies on both mRNA and protein level in affected female-derived fibroblasts showed significant reduction of USP9X level, confirming the loss of function effect of the identified mutations. Given that some features of affected females are also reported in known ciliopathy syndromes, we examined the role of USP9X in the primary cilium and found that endogenous USP9X localizes along the length of the ciliary axoneme, indicating that its loss of function could indeed disrupt cilium-regulated processes. Absence of dysregulated ciliary parameters in affected female-derived fibroblasts however points towards spatiotemporal specificity of ciliary USP9X (dys-)function.
Imprinting: the Achilles heel of trio-based Exome sequencing
G.W.E. Santen 1, MAGEL2 Consortium, A. van Haeringen 1, E, Aten 1
1 Department of Clinical Genetics, Leiden University Medical Centre, Leiden, 2300 RC, the Netherlands.
The possibilities and application of molecular genetic diagnostics have increased immensely in the past decade, particularly in the field of rare intellectual disability (ID) syndromes. A frequently cited reason for parents to perform genetic diagnostics is to know their recurrence risk (RR) for a future pregnancy. The vast majority of ID has been shown to be caused by de novo mutations and thus results in a low RR. Mutations and chromosomal deletions in imprinted regions, although a rare cause of ID may result in a 50% RR.
Next generation sequencing is rapidly replacing classical molecular diagnostics. It has been shown that trio-based sequencing is an efficient way of finding causal mutations. None of the published large exome sequencing studies however report taking familial imprinted mutations explicitly into account in their filtering strategy, and imprinted causes of ID have not been identified in these studies.
We encountered a large family with 14 affected individuals from 5 nuclear families in two generations. All patients had severe intellectual disability and many of them displayed camptodactyly and hypotonia. There were dysmorphic features, but no syndromic diagnosis could be made by experienced clinical geneticists. Four of the patients died at young age due to various complications. Exome sequencing did not reveal any pathogenic mutation using standard analyses, but when the extraordinary pedigree of this family was taken into account a paternally inherited pathogenic frameshift mutation in MAGEL2 was identified. MAGEL2 is located in the imprinted Prader-Willi/Angelman region on chromosome 15. De novo truncating mutations in MAGEL2 on the paternal allele have been shown to cause a Prader-Willi-like phenotype in 4 patients. The diagnosis of Prader-Willi was considered in one of our patients, although it was not in the differential diagnosis for the other patients.
It is worrisome to realize that the causative mutation was only identified because of the extended pedigree of this family and would have been missed otherwise Clearly, this issue only arises when trio exome sequencing is performed, and not when only the affected individual is sequenced. To further investigate the scope of this potential pitfall we have looked for putatively truncating mutations in MAGEL2, UBE3A and KCNK9 in the ExAc database (accessed June 10th 2015) consisting of ~120.000 alleles. We identified 6 likely pathogenic alleles leading to an estimated carrier frequency of ~1/10.000. We therefore recommend that any trio-based sequencing analysis pipeline takes imprinted genes explicitly into account, displaying all variants, inherited or not, in this relatively limited number of genes.
SMC1A truncating mutations are associated with a severe epilepsy phenotype which is distinct from de Lange syndrome.
Suresh Somarathi 1, Joseph Symonds 2, Ajoy Sarkar 3, Tara Montgomery 4, Alan Donaldson 5, Anne Lampe 6, Peter Turnpenny 7, Shelagh Joss 2, Kay Metcalfe 1
1 Department of Genomic Medicine, Saint Mary’s Hospital Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK. 2 West Scotland Genetics Service, Level 1, Laboratory Medicine Building, South Glasgow University Hospital, 1345 Govan Road, Glasgow G51 4TF, UK. 3 Department of Clinical Genetics, Nottingham City Hospital, Nottingham University Hospitals NHS Trust, Nottingham, UK 2 4 Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, UK. 5 Department of Clinical Genetics, University Hospital Bristol NHS Trust, Saint Michael’s Hospital, Bristol, UK. 6 South East of Scotland Clinical Genetics Service, Molecular Medicine Centre, Western General Hospital, Edinburgh, UK. 7 Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital (Heavitree) Exeter, UK.
Background In frame mutations and missense mutations in the SMC1A gene (Structural Maintenance of Chromosomes 1A), which is a cohesion complex gene are reported to be responsible for about 4 to 6% of cases of Cornelia de Lange Syndrome (CDLS). Children affected with CDLS have distinct facial features, developmental delay, prenatal and postnatal growth retardation, abnormalities of hands and feet with variable involvement of other organs. Frameshift and nonsense mutations in SMC1A were not reported in association with CDLS previously and were assumed to be lethal. More recently loss of function mutations in the SMC1A gene have been reported in the literature (Goldstein JH et al., 2015; Lebrun N et al., 2015). Aim We report a series of 8 cases (7 cases from DDD study and another one who is a deceased twin of one of the subjects) in whom de novo loss of function mutations were identified including frameshift and nonsense mutations in the SMC1A gene. We analysed their clinical features to expand the clinical phenotype of these truncating types of SMC1A mutations. Discussion All the 7 cases have epilepsy and presented with clusters of epileptic seizures which are of multiple types and in some, showed poor response to treatment with anti-epileptic medication. Abnormalities of limb development were noticed in 3 subjects, which included clinodactyly and camptodactyly of fingers, 1-2 toe syndactyly of toes and deviation of halluces at metatarso- phalangeal joints. Mild facial asymmetry with unilateral ptosis was present in 1 subject. Deep set eyes with downward sloping palpebral fissures and widely spaced teeth were present in 1 subject. Ventricular septal defect (VSD) and Atrial septal defect (ASD) were present in 1 subject and a small intra-atrial connection was present in another subject. Hypotonia and cortical visual impairment were present in 2 subjects. One subject had bifid T6 Vertebra and choanal atresia. Symmetrical growth retardation and developmental delay was present in all the subjects. Conclusion The clinical phenotype of the patients with loss of function mutations in SMC1A appears to be different to the typical features of CDLS and appears to be a distinct clinical entity. It is important to note that none of these subjects were considered to have CDLS prior to the results from the DDD study. These observations are also supportive of SMC1A as a candidate gene in some patients with clusters of seizures and severe epilepsy.
Compound heterozygous NEK1 variants in two siblings with oral- facial-digital syndrome type II (Mohr syndrome)
Marijn F. Stokman* 1,2, Glen R. Monroe* 1,2, Isabelle F.P.M. Kappen* 1,3, Paulien A. Terhal 1, Marie-Jose H. van den Boogaarde 1, Sanne M.C. Savelberg 1,2, Lars T. van der Veken 1, Robert J.J. van Es 4, Susanne M. Lens 2,5, Rutger C. Hengeveld 2,5, Marijn A. Creton 4, Nard G. Janssen 4, Aebele B. Mink van der Molen 3, Michelle B. Ebbeling 6, Rachel H. Giles 7, Nine V. Knoers 1,2, Gijs Van Haaften 1,2 (* Shared First Authors)
1 Department of Genetics, University Medical Centre Utrecht, Utrecht, 3584 EA, the Netherlands 2 Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht 3584 CG, the Netherlands 3 Department of Plastic Surgery, University Medical Centre Utrecht, Utrecht 3584 CX, the Netherlands 4 Department of Oral and Maxillofacial Surgery and Special Dental Care, University Medical Centre Utrecht, Utrecht, 3584 CX, the Netherlands 5 Department of Molecular Cancer Research, University Medical Centre Utrecht, Utrecht, 3584 CG, the Netherlands 6 Department of Ophthalmology, University Medical Centre Utrecht, Utrecht, 3584 CX, the Netherlands 7 Department of Nephrology and Hypertension, Regenerative Medicine Centre, University Medical Centre Utrecht, Utrecht 3584 CT, the Netherlands
Background The oral-facial-digital (OFD) syndromes comprise a group of related disorders with a combination of oral, facial and digital anomalies. Variants in several ciliary genes have been associated with subtypes of OFD syndrome, yet in most OFD patients the underlying cause remains unknown. Objective To investigate the molecular basis of two brothers with OFD type II, Mohr syndrome. Methods We performed single nucleotide polymorphism (SNP)-array analysis on two brothers with features of OFD type II and their healthy parents to identify homozygous regions and candidate genes. Subsequently, we performed whole exome sequencing (WES) on the family. Candidate variants were confirmed with Sanger sequencing and alternative splicing was assessed with cDNA analysis. Immunocytochemistry was used to assess cilia number and length. Results Using WES we identified compound heterozygous variants in the NIMA (Never in Mitosis Gene A) - Related Kinase 1 gene (NEK1). The novel variant c.464G>C disturbs normal splicing in an essential region of the kinase domain. The nonsense variant c.1226G>A, p.Trp409*, results in nonsense-associated alternative splicing, removing the first coiled-coil domain of NEK1. Patient-derived fibroblasts showed severely reduced ciliation compared to control fibroblasts (18.0% vs. 48.9%, p<0.0001). There was no significant difference in cilia length. Conclusions We identified compound heterozygous deleterious variants in NEK1 in two brothers with Mohr syndrome. Ciliation in patient fibroblasts is drastically reduced, consistent with a ciliary defect pathogenesis. Our results establish NEK1 variants involved in the etiology of a subset of patients with OFD syndrome type II and support the consideration of including (routine) NEK1 analysis in patients suspected of OFD.
Genetic studies in Noncompaction Cardiomyopathy using Next Generation Sequencing
L.A. Verlooij 1, J.P. van Melle 2, R.A. de Boer 2, M.P. van der Berg 2, J.D.H. Jongbloed 1, Y.M. Hoedemaekers 1.
1 Department of Clinical Genetics, University Medical Centre, Groningen, 9700 RB, the Netherlands. 2 Department of Cardiology, University Medical Centre, Groningen, 9700 RB, the Netherlands
Background: Noncompaction cardiomyopathy (NCCM) is a myocardial disease, characterized by a thickened left ventricular wall with a two-layered structure, consisting of a thin compact epicardial layer and an excessively thickened non-compact endocardial layer. NCCM is genetic in 67% of the patients, yet in 50% of familial NCCM no genetic defect has been identified. Next Generation Sequencing (NGS) techniques now allow analysis of a large number of cardiomyopathy genes simultaneously, which may yield a higher mutation detection rate. Goal: The aim of this study is to delineate the prevalence and spectrum of genetic defects in NCCM patients in a tertiary referral Center in the Northern part of the Netherlands (Groningen), using NGS and thereby evaluating its value in diagnosing a genetic defect in NCCM. Methods: NGS was performed in 61 of 86 patients. The other 25 patients were (previously) tested for two to nine genes with Sanger sequencing. Results: In 30 of 86 patients (35%) a genetic defect (class 5 or 4) was detected by NGS. Eighteen (58%) of the genetic defects were found in sarcomeric genes. Mutations in MYH7 were the most common genetic defect (32%), followed by MYBPC3 (19%) and TTN (13%) (figure 1). NGS identified a large group of class 3 variations, 67% of the identified genetic defects, in 18 of 61 patients (30%) (figure 2). Conclusions: The prevalence of genetic defects in NCCM identified with NGS is comparable to the prevalence described previously. However, with NGS a large group of class 3 variations was identified. Part of these mutations may be re-classified as class 4 or 5 defects in the future, which may result in a higher mutation detection rate and spectrum of genetic defects in NCCM. Sarcomere mutations remain the most common identified genetic cause for NCCM. MYH7 (32%) MYBPC3 (19%) TTN (13%) DSP (6%) MYPN (6%) Other (23%) 02468 10 12 14 16 2 to 9 genes NGS 55 genes NGS 60 genes Class 5 Class 4 Class 3
Fetal imaging in the diagnosis of skeletal dysplasias and craniosynostosis – a case series
V. Ward 1, M. Irving 1, A. Beleza 1, S. Sankaran 2, G.J. Lee 3, C. Ridout 4, C. Ogilvie 5, K. Mann 5, D. Shears 6, J. Carmichael 7, M. Holder-Espinasse 1 1 Clinical Genetics, Guy’s and St Thomas’ NHS Foundation Trust, London, UK. 2 Maternal-Fetal Medicine, Guy’s and St Thomas’ NHS Foundation Trust, London, UK. 3 Neonatology, Guy’s and St Thomas’ NHS Foundation Trust, London, UK. 4 Molecular Genetics, Viapath, Guy’s and St Thomas’ NHS Foundation Trust, London, UK. 5 Genetics Laboratories, Guy’s and St Thomas’ NHS Foundation Trust, London, UK. 6 Clinical Genetics, Oxford University Hospital NHS Foundation Trust, Oxford, UK. 7 Paediatric Radiology, Guy’s and ST Thomas’ NHS Foundation Trust, London, UK.
There are more than 450 skeletal dysplasias ranging in severity and the degree of associated complications, and although individually rare, collectively they have a birth incidence of around 1 in 5000. Prenatal diagnosis is most often prompted by the finding of short long bones on routine ultrasound scanning or in cases with a family history of skeletal dysplasias. Specific diagnosis can be difficult and relies on clinical, radiological and molecular criteria.
Craniosynostosis, the premature fusion of the cranial sutures, has a prevalence of 1 in 2000 and around 15% of these are syndromic and are associated with other anomalies. Prenatal ultrasound diagnosis of craniosynostosis can be difficult and so a definite diagnosis relies on DNA testing.
The use of fetal MRI and fetal CT scan imaging has advantages over ultrasound imaging and can provide excellent tissue resolution and a greater field of view. Detailed imaging allows for a clear differential diagnosis to be established as early as possible, enabling further investigations such as molecular diagnostic testing to be considered to achieve a more precise diagnosis. This can allow for the distinction between lethal and non lethal dysplasias, and permit further discussions with parents around the prognosis and further management of these conditions.
We report 4 prenatal cases of Saethre-Chotzen and Carpenter syndromes, Hypochondrogenesis, and Metatropic dysplasia with their clinical, radiological and molecular features. We show the first UK case where fetal CT scan was performed as well as fetal MRI images to demonstrate the importance of fetal imaging in helping to reach a prenatal diagnosis and the impact it has on subsequent clinical management.
Poster Presentations
Poster Presentations, displayed alphabetically by lead author
1. Adrenocortical carcinoma in association with Birt-Hogg-Dube Syndrome J. Adlard. A. Anthoney, H. Lindsay, R. Robinson, R, Charlton, A. Kraus
2. Concurrent BRCA1 and PALB2 mutations identified on cancer gene panel testing J.Adlard. N. Camm, L. Mavrogiannis, S. Shepherd, R. Charlton.
3. RET variant p.Tyr791Phe: Low risk, but not no risk? J.Adlard. S. Gilbey, M. Lansdown, R. Brown, L. Mavrogiannis, R. Charlton.
4. A novel missense mutation in TRPV4 causing Spondometaphyseal Dysplasia, Kozlowski type and Metatropic Dysplasia R.A. Akilapa D.S Johnson , S.M. Kirwin
5. Results of a National Audit of Screening Advice given to Adults with PTEN Hamartoma Syndrome A.F. Brady , A. Taylor , K.L. Lachlan
6. Histological & molecular hallmarks of PMS2 associated tumours S.W. ten Broeke. T. van Wezel , E. Gomez Garcia , L.P. van Hest , T.G.W. Letteboer , J.W. Olderode- Berends , Th.A. van Os , L. Spruijt , J.F.J. Tromp , J.T.Wijnen , H. Morreau , M. Nielsen
7. Rib Anomalies in People with Congenital Heart Disease D.L. Brown, I.J. Wilson, M.J. Wright, J.J. O’Sullivan, J.A. Goodship, C. Gowdy
8. Perlecan (HSPG2) Mutations associated with Rolland Desbuquois Dyssegmental Dysplasia E. Clement, A. Calder, T. Cullup, E. Rosser
9. Antenatal diagnosis of Mosaic Trisomy 13: Dilemmas in management E. Craft, T. Mousa, A.O. Akuma, F. Bulock, P.Vasudevan
10. The utility of a Carrier Register to provide long term follow up for carriers of inherited cancer syndromes A.Dane, J. Wiggins, C. Moss., Z. Kemp, A. George
11. Are online personal health records useful for patients with genetic conditions to share information with family members? Selina Goodman, Professor Heather Skirton & Professor Ray Jones
12. A unique case of a mosaic genome-wide uniparental isodisomy in a newborn with Beckwith-Wiedemann syndrome Saskia M.J. Hopman, P.F.R. Hochstenbach, A.A. Verrijn Stuart , J.C. Giltay , L.T. van der Veken
13. Compound heterozygosity for two novel mutations in NTHL1 in an individual with adenomatous polyposis and multiple tumours S. Kenwrick, O. Spasic-Boskovic, A. Taylor, K. Brugger, H. Rai, S. Abbs, J. Wyke, M. Tischkowitz, E. Maher, J. Whitworth
14. Brain-thyroid-lung syndrome in a child caused by a deletion on chromosome 14 proximal of the NKX2.1 gene locus Mira Kharbanda, Sunia Khadouma, Jeremy Jones, Malcolm Donaldson, Joachim Pohlenz, Pia Hermanns
15. Mast syndrome (SPG21), a rare but recognizable phenotype Anneke Kievit, Esther Brusse, Margriet Collée, Erik-Jan Kamsteeg, Rick van Minkelen
16. KBG Syndrome: an emerging cause of developmental delay K.J. Low, T.Ashraf, N.L.E Canham, J. Clayton-Smith, C. Deshpande, A. Donaldson, R.B. Fisher, F.A. Flinter, N.C Foulds, K. Gibson, I. Hayes, A. Hills, S.E. Holder, M.D. Irving, S. Joss, E.C. Kivuva, K. Lachlan, A.C. Magee, V.P.M. McConnell, M. McEntagart, K. Metcalfe, T. Montgomery, R.A. Newbury-Ecob, F.J. Stewart, P.D. Turnpenny, J. Vogt, M. Williams , DDD Study, S.F. Smithson
17. Retrospective analysis of the prevalence of Beckwith-Wiedermann Syndrome in Northern Ireland R. Moore 1, D.Donnelly
18. Three generation family with atypical interstitial deletion within chromosome 22q11.21 R. Moore, V. McConnell
19. GSK2126458, a dual PI3K/mTOR inhibitor, is less effective than rapamycin for treatment of renal lesions in a genetically engineered Tsc2+/- mouse model Kalin Narov, Paulina Samsel, Jian Yang, Ashley Jones, Julian Sampson, Ming Hong Shen
20. Feingold syndrome with no Tracheo-oesophalgeal atresia C. Powell, E. Craft, P. Vasudevan
21. Genetic mechanisms associated with tuberous sclerosis and tuberous sclerosis-like phenotypes Meera Raja, Gemma Sharman, Laura Thomas, Angharad Walters, Peter Giles, Kevin Ashelford, Matthew Mort, James Colley, Julian Sampson
22. Histiocytoid Cardiomyopathy and Microphthalmia and Linear Skin Defects Syndrome: Phenotypes linked by truncating variants in NDUFB11 Gillian Rea, James S. Ware, Tessa Homfray, Jan Till, Ferran Roses-Noguer, Rachel Buchan, Sam Wilkinson, Alicja Wilk, Roddy Walsh, Shibu John, Shane McKee, Fiona J. Stewart, Victoria Murday, Robert W. Taylor, John Baksi, Piers Daubeney, Sanjay Prasad, Paul J.R. Barton, Stuart Cook
23. Audit of Tuberous Sclerosis Diagnostic assessment and surveillance in the Northern Region. Richardson, A. Henderson
24. A Clinical Audit of a Lynch Syndrome Referral Protocol Peter Risby, Dr. Verna Lavender
25. A single centre experience of tumour immunohistochemistry and mutation analysis in the investigation of Muir Torre Syndrome Katherine Schon, Ed Rytina, James Drummond, Stephen Abbs, Marc Tischkowitz
26. Genetic Mechanisms in Colorectal Polyposis Dr. E. Short, Dr. L. Thomas, Dr. P. Giles, Dr. J. Colley, Dr. K. Ashelford, Dr. M. Mort, Prof. J. Sampson.
27. Genetic Weight Watching C.T.R.M Stumple, D.A. Schott, T. Rinne, M.M. van Haelst, M.F. Stokman, E.C.M Mariman
28. Exome sequencing reveals distinct molecular mechanisms of duodenal and colorectal tumorigenesis in familial adenomatous polyposis and MUTYH-associated polyposis Laura E. Thomas, Joanna Hurley, Sian Jose, Kevin Ashelford, Matthew Mort, Shelley Idzizazyczk, Julie Maynard, Helena Leon Brito, Manon Harry, Angharad Walters, Sarah Jane Walton, Sunil Dolwani, Geraint Williams, Meleri Morgan, Susan Clark, Julian R. Sampson
29. Skin lesions and arthralgias in a large pedigree with a partially anakinra-responsive and possibly IL-18 driven NLRC4-related autoinflammatory disease C.M.L. Volker-Touw, H.D. de Koning, T. van Kempen, K. Oberndorff, J. Giltay, C.G.F. de Kovel, M. Boes, M.A.M. van Steensel, G.T.J. van Well, A. Simo, J. Frenkel, M.E. van Gijn
30. Audit of BRCA gene testing and demand for risk reducing mastectomy in Essex E. Williams, B. Hoskins, V. Ramakrishnan, L. Side
Adrenocortical carcinoma in association with Birt-Hogg-Dube Syndrome
J. Adlard. A. Anthoney, H. Lindsay, R. Robinson, R, Charlton, A. Kraus. Yorkshire Regional Genetics Service and Leeds Teaching Hospitals NHS Trust, LS7 4SA, UK.
Case The proband was a woman who had undergone left adrenalectomy at 42 years for a virilising adrenocortical tumour with raised testosterone levels and hirsuitism. Mitotic activity was low, but there was histological concern for an adrenal carcinoma, and the tumour recurred 4 years later. She had a past medical history of lung cysts and eight episodes of pneumothorax. No abnormal skin lesions were identified, but her sister was reported to have had skin lumps and a renal cyst. Her parents were smokers and had died of lung cancer in their 50s/60s.
Genetic testing was performed on a panel test. A frameshift FLCN mutation c.1250del; p.Phe417fs was identified consistent with Birt-Hogg-Dube syndrome. Her 24 year-old son carries the same mutation. He does not have skin lesions and a renal ultrasound was normal. However, he had respiratory symptoms and was found to have right lung bullae.
Discussion Adrenal tumours have very rarely been described in patients with Birt-Hogg-Dube syndrome of non-secretory and oncocytic subtype (Raymond et al 2014). Our case supports and extends a phenotype of adrenal tumours in Birt-Hogg-Dube syndrome. Adrenal tumours are recognised in other syndromes including Lynch, MEN1 and Li Fraumeni for which our patient screened negative.
Concurrent BRCA1 and PALB2 mutations identified on cancer gene panel testing
J.Adlard. N. Camm, L. Mavrogiannis, S. Shepherd, R. Charlton. Yorkshire Regional Genetics Service and Leeds Teaching Hospitals NHS Trust, LS7 4SA, UK.
Case The proband was diagnosed with ER positive, HER2 negative unilateral ductal breast cancer at 65 years. She had a family history meeting local criteria for BRCA1 and BRCA2 mutation testing which did not identify any pathogenic mutation.
10 months later, the proband's daughter was diagnosed with ER positive, HER2 negative unilateral ductal breast cancer at the age of 32. She was offered a wider panel test of breast cancer-associated genes which identified two pathogenic mutations: BRCA1 c.4165_4166del; p.Ser1389X and PALB2 c.2052del; p.Arg686fs.
The proband's husband had one paternal first cousin affected with breast cancer in her 50s. Testing confirmed he carries the BRCA1 mutation and his wife, the PALB2 mutation
Discussion Families with coincident BRCA1/2 and PALB2 mutations are rare (Ancot et al 2015; Downs et al 2015). It is likely that the risk for double heterozygotes is similar to the risk of the more penetrant gene (BRCA1) with some additional disease-specific risk (e.g. pancreas) from the other gene (PALB2). This case demonstrates potential value of extending breast cancer gene testing to panels, which provided likely explanations for the cancer history on both sides of the family. Further details of the pedigree, testing and management will be presented.
RET variant p.Tyr791Phe: Low risk, but not no risk?
J.Adlard. S. Gilbey, M. Lansdown, R. Brown, L. Mavrogiannis, R. Charlton. Leeds Teaching Hospitals NHS Trust, Leeds LS7 4SA, UK.
Cases We have identified two unrelated men diagnosed with isolated phaeochromocytoma in their 40s/50s as carrying the controversial RET gene variant c.2372A>T; p.Tyr791Phe. This variant was included in the European Molecular Genetics Quality Network laboratory assessment scheme in 2012. 65.5% of laboratories reported the variant as relevant for developing medullary thyroid cancer and 15% as a potential but debated risk, with the information to be used with caution. However, some research paper authors (Erlic et al 2010, Toledo et al 2015) have suggested that it has no pathogenic effect.
Both of our probands have had thyroid problems. The first had a left thyroid lobectomy prior to genetic testing for a multinodular goitre with no evidence of C-cell hyperplasia. The second proband had elevated serum calcitonin detected and abnormal thyroid imaging; total thyroidectomy was performed, with histology showing multinodular goitre and widespread C- cell hyperplasia.
Discussion The general population heterozygote frequency of this variant is about 0.8%. As MEN2 is rare (~1 in 35,000-100,000), the variant cannot be highly penetrant. However, the identification of both phaeochromocytoma and C-cell hyperplasia in an individual with RET p.Tyr791Phe is against this variant being completely benign. Further details and discussion will be presented.
A novel missense mutation in TRPV4 causing Spondometaphyseal Dysplasia, Kozlowski type and Metatropic Dysplasia
R.A. Akilapa 1 D.S Johnson 1, S.M. Kirwin 2
1 Sheffield Children’s Hospital NHS Foundation Trust, Sheffield, S10 2AH. UK.
2 Molecular Diagnostics Laboratory, 1600 Rockland Road, Wilmington, DE 19803, USA.
TRPV4 is a protein coding gene, important for calcium ion permeability. The encoded Non- selective cation channel is thought to be regulated by a calmodulin-dependent mechanism. Mutations in the gene are causative of a heterogeneous group of disorders including Spondometaphyseal Dysplasia Kozlowski type, Metatropic Dysplasia, Hereditary Motor and Sensory Neuropathy type IIC and Autosomal Dominant Bracyolmia. We report on a family harbouring a novel TRPV4 missense mutation in exon 16, that to our knowledge has not been previously published or recorded in the NCBI SNP or 1000 genome databases. The proband presents with clinical features consistent with a diagnosis of Spondomtephyseal Dyplasia Kozslowski type. Further family studies confirmed the mutation to be present in the proband’s daughter. X-rays were consistent with a diagnosis of Metatropic Dysplasia. The absence of this missense variation in unaffected family members adds further evidence to the pathogenicity of the mutation found. This report demonstrates the heterogeneity of pathology caused by identical mutations in TRPV4. It also broadens our understanding of this particular region of the gene, in particular the importance in calcium/calmodulin signalling which is known to be influenced by this domain.
Results of a National Audit of Screening Advice given to Adults with PTEN Hamartoma Syndrome
A.F. Brady 1, A. Taylor 2, K.L. Lachlan 3
1 North West Thames Regional Genetics Service, London North West Healthcare NHS Trust, Watford Road, Harrow, HA1 3UJ. 2 Cambridge University Hospitals NHS Foundation Trust, Addenbrooke’s Hospital, Cambridge, CB2 0QQ. 3 Wessex Clinical Genetics Service, University Hospitals Southampton NHS Trust, SO16 5YA.
We report the results of a national audit of screening advice given to adult patients with PTEN Hamartoma syndrome. Screening guidance was proposed by the Pan Thames Cancer Genetics Group and reviewed at the Spring Cancer Genetics Group meeting 2015.
Patients were included in the audit if they had a PTEN mutation (or likely pathogenic variant) or are at 50% risk, were 16 years or older at time last advice given, with most recent advice given between August 1st 2010 and August 1st 2015.
The audit aimed to establish a baseline for practice in the UK with a view to completing the audit loop in five years time.
Histological & molecular hallmarks of PMS2 associated tumours
S.W. ten Broeke.1 T. van Wezel 2, E. Gomez Garcia 3, L.P. van Hest 4, T.G.W. Letteboer 5, J.W. Olderode-Berends 6, Th.A. van Os 7, L. Spruijt 8, J.F.J. Tromp 1, J.T.Wijnen 1, H. Morreau 9, M. Nielsen 1
1 Department of Clinical Genetics, Leiden University Medical Centre, the Netherlands. 2 Department of Pathology, Leiden University Medical Centre, the Netherlands. 3 Department of Clinical Genetics, Maastricht University Medical Centre, the Netherlands. 4 Department of Clinical Genetics, VU Amsterdam, the Netherlands 5 Department of Clinical Genetics, University Medical Centre Utrecht, the Netherlands. 6 Department of Clinical Genetics, University Medical Centre Groningen, the Netherlands. 7 Department of Clinical Genetics, Academic Medical Centre, Amsterdam, the Netherlands. 8 Department of Clinical Genetics, Radboud University Medical Centre, the Netherlands. 9 Department of Pathology, Leiden University Medical Centre, the Netherlands.
Background Lynch syndrome (LS) related cancers have a different genetic background and histology compared with sporadic colorectal cancers (CRC) and show a different treatment response and survival. Definition of the genetic landscape and common mutational targets of these tumours might lead to better methods of detection and provide potential therapeutic targets. Up to now most studies on Lynch related tumours focussed on MLH1, MSH2 and MSH6 deficient tumours, but data on PMS2 related tumours is currently lacking, likely due to the previously hampered PMS2 mutation detection which has strongly improved in recent years. We now aim to unravel the histological and molecular hallmarks of PMS2 associated CRC compared with other Lynch and sporadic tumours.
Methods We obtained informed consent of PMS2 mutation carriers and were able to collect 21 CRCs for histological and molecular evaluation. Histological hallmarks were scored by an experienced pathologist. Moreover, to get an impression of the somatic tumour spectrum, we used the Ampliseq Cancer Hotspot panel (version 2) on isolated DNA from tumour samples. This panel covers mutation hotspots in 50 genes (~2800 COSMIC mutations) , including well known somatically mutated genes such as KRAS, APC and TP53. The results were compared with a control cohort of 23 sporadic CRCs that were tested in a diagnostic setting.
Results PMS2 associated CRCs showed a number of LS associated hallmarks: 81% were right-sided, 43% had Crohn’s like infiltrate (missing: 19%) and 81% (missing: 14%) showed microsatellite instability. However, a majority (63%, missing: 14%) hardly had any tumour infiltrating lymphocytes, a well-known hallmark of Lynch associated tumours. The molecular analysis showed a relatively low percentage of TP53 and APC mutations compared with controls and a high percentage of a specific FBXW7 mutation. Notably, 5/21 of CRCs had this c.1393C>T transition, where the controls had none. We also found a relatively rare KRAS hotspot mutation in exon 4 (c.436G>A, p.Ala146Thr) occurring three times in the PMS2 cohort but not in the control cohort. Lastly, we identified a possible germline SMAD4 mutation (c.1082G>A, p.Arg361His)(high allele frequency of 70%).
Discussion To our knowledge this is the first study to examine tumour characteristics of a cohort consisting solely of PMS2 mutation carriers. Several findings such as the specific KRAS and FBXW7 mutations might possibly help with the identification of PMS2 associated tumours. The finding of a less active immune response might negatively influence survival and treatment options, but this requires further investigation.
Rib Anomalies in People with Congenital Heart Disease
D.L. Brown 1,2, I.J. Wilson 2, M.J. Wright 1, J.J. O’Sullivan 2,3, J.A. Goodship 1,2, C. Gowdy .4
1 Northern Genetics Service, Newcastle upon Tyne, NE1 3BZ, UK. 2 Institute of Genetic Medicine, Newcastle University, NE1 3BZ, UK. 3 Department of Paediatric Cardiology, Freeman Hospital, Newcastle upon Tyne, NE1 4LP, UK. 4 Radiology Department, Royal Victoria Infirmary, Newcastle Upon Tyne, NE1 4LP, UK.
Background: Minor malformations are common in people with congenital heart disease (CHD). This study sought to determine the frequency and pattern of rib anomalies in people with congenital heart disease.
Materials and Methods: Plain chest x-rays (CXRs) taken for clinical purposes were reviewed in 767 people with congenital heart disease and 359 SCBU graduates without congenital heart disease. The radiologists’ reports were also reviewed. Cases with recognised syndromes (n=14), extracardiac malformations (n=6) and known offspring of diabetic mothers (n=4) were excluded; control CXRs with evidence of CHD (cardiomegaly, abnormal cardiac silhouette, pulmonary venous hypertension, sternal wires) (n=11) or an extracardiac malformation (n=9) were excluded. Rib changes secondary to thoracotomy were not considered as anomalies. The number of thoracic ribs was counted in CXRs showing C7 to L1 vertebrae. The presence of neonatal cervical ribs was assessed in images taken at 1000 days of age or less. A second interpreter reviewed 11% of cases’ images and 30% of controls’ images. Differences in interpretation were resolved by re-evaluation of CXRs by both interpreters together. Fisher’s exact test was used to calculate p values in R.
Results: People with CHD are more likely to have the combination of 11 pairs of thoracic ribs and other minor anomalies of ribs or vertebrae (p=0.017); and to have bilateral neonatal cervical ribs (p=0.00035). An asymmetric thoracic rib number in cases, with 11 on the right and 12 on the left approaches statistical significance (p=0.058). However, there is no significant difference between cases and controls having 12 thoracic ribs on the right and 11 on the left (p=0.18). Having 11 pairs of thoracic ribs and no other rib anomalies is not more common in cases than controls (p=0.13), nor is the presence of 13 pairs of thoracic ribs (p=0.16). Bilateral accessory cervical ribs are more common in controls (p= 0.0014).
Conclusions: Specific patterns of minor rib anomalies are common in people with congenital heart disease. Minor malformations are an important part of the phenotype which may provide useful clues to the genetic aetiology.
Perlecan (HSPG2) Mutations associated with Rolland Desbuquois Dyssegmental Dysplasia
E. Clement.1 A. Calder 2, T. Cullup 3, E. Rosser 1.
1 Department of Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK. 2 Department of Radiology, Great Ormond Street Hospital for Children NHS Trust Foundation, London, WC1N 3JH, UK. 3 North East Thames Regional Genetics Laboratory, Great Ormond Street Hospital for Children NHS Trust Foundation, London, WC1N 3JH, UK. [email protected]
Schwartz- Jampel syndrome is (SJS) is a rare autosomal recessive disorder characterized by abnormalities of the skeletal muscles, including muscle weakness, myotonia, bone dysplasia, joint contractures and short stature. Affected individuals often develop a typical ‘pinched’ facial appearance with small features and blepharophimosis. The range and severity of symptoms may vary from case to case. SJS is typically divided into 2 types. Type 1 is known to result from mutations in HSPG2 which encodes perlecan, a basement membrane component. SJS type 2 is associated with LIFR mutations.
The skeletal changes associated with type 1 SJS are usually relatively mild and fit into the chondrodysplasia spectrum. These may include platyspondyly with kyphoscoliosis, bowing of the long bones and hip dysplasia. HSPG2 mutations have also been described in Silverman- Handmaker dyssegmental dysplasia (DDSH), a more severe form of skeletal dysplasia associated with vertebral segmentation abnormalities, and short thick long bones. It is usually fatal in the neonatal period. Rolland Desbuquois dyssegmental dysplasia (DDRD) is described as a milder but distinct form of dyssegmental dysplasia, the genetic basis of which has not been described.
We report clinical and radiological features in 2 siblings now aged 4 and 1, born to first cousin parents who have clinical features of SJS but with skeletal changes consistent with DDRD. A homozygous splice site mutation has been identified on exome sequencing in HSPG2.
To our knowledge this is the first report of any genetic alteration in a case of DDRD and the first clinical report of a case of dyssegmental dysplasia associated with myotonia. HSPG2 mutations associated with DDSH are thought to be functionally null whereas those in SJS are thought to be associated with a reduction in protein. It is possible that our patients bridge the phenotypic spectrum of HSPG2-related disorders.
Antenatal diagnosis of Mosaic Trisomy 13: Dilemmas in management
E. Craft.1 T. Mousa,2 A.O. Akuma,3 F. Bulock,4 P.Vasudevan1
1 Consultant Geneticist, Clinical Genetics, Royal Leicester Infirmary, Leicester, LE1 5WW, England 2 Consultant Obseterian, Fetal Medicine Unit, Royal Leicester Infirmary, Leicester, LE1 5WW, England 3 Consultant Neonatalogist Neonatal Unit, Royal Leicester Infirmary, Leicester, LE1 5WW, England 4 Consultant Paedriatric Cardiology, Cardiology Department, Genfield General Hospital, Leicester.
Trisomy 13 is associated with severe developmental delay, failure to thrive, microcephaly and congenital heart defects. Due to limited life expectancy, medical intervention other than palliative care is not generally recommended. Approximately 5% of trisomy 13 cases are reported to be ‘mosaic’.
We present a male baby in whom an anterior diaphragmatic hernia was identified prenatally. Amniocentesis identified ‘mosaic trisomy 13’ (66% of cells showed abnormal male karyotype).
Due to limited information about the care and outcomes of mosaic trisomy the clinical outcome harder to predict and the parents decided to continue the pregnancy after prenatal counselling.
The baby was born at term in good condition with no apparent phenotypic features of trisomy 13 and had his surgical at 2 months of age with good result. At 15 months old he was making good developmental progress.
This case illustrates the limited predictive value of a laboratory report of mosaicism and ‘median survival time’ of Trisomy 13 in literature resulting in difficult clinical decision making and counselling. Ultimately, the clinical features of baby after birth, the uncertainty of chromosomal mosaicism and parental wishes were considered in management of this cases rather that limited descriptions of ‘mosaic trisomy 13’ in the literature.
The utility of a Carrier Register to provide long term follow up for carriers of inherited cancer syndromes
A.Dane,1 J. Wiggins, 1 C. Moss.,1 Z. Kemp1,2 A. George1,2
1 Royal Marsden NHS Foundation Trust, London, SW3 6JJ, United Kingdom 2 Institute for Cancer Research, Sutton, SM2 5NG, United Kingdom
The Cancer Genetics Unit at the Royal Marsden NHS Foundation Trust established a Carrier Register in 2013 to provide long term follow up for carriers of inherited cancer syndromes. The utility, costs, advantages and challenges of maintaining the Register will be discussed. The main aim of the Register is to monitor cancer surveillance, arrange referrals for screening and risk-reducing surgery, monitor cascade testing and offer follow up appointments as needed. Currently there are 1,233 BRCA mutation carriers, 118 Lynch syndrome (LS) carriers and 88 carriers of other inherited cancer syndromes on the Register. Carriers are entered on to the Register at point of genetic diagnosis with a future date set for notes review. BRCA carriers’ notes are reviewed at ages 30, 40 and 50. Notes for LS carriers and carriers of other inherited cancer syndromes are reviewed annually. In addition to its main aim, the Register has been useful for audit and research purposes including the NHS Breast Screening Programme audit, LS screening audit, identifying eligible CAPP3 patients, arranging a mail-out to all BRCA carriers about NICE guidelines on chemoprevention, and identifying potential patients for clinical trials, for example with PARP inhibitors.
Are online personal health records useful for patients with genetic conditions to share information with family members?
Selina Goodman 1, Professor Heather Skirton 1 & Professor Ray Jones 1
1 Plymouth University, Plymouth PL4 8AA UK
For many genetic conditions, a family can have many people at risk of the same disease. Therefore, for some patients it may be important to share information about the diagnosis with relatives to enable testing, better understanding and improved self-management. This could be supported through information provided electronically to patients, but this is still not commonly done, despite widespread use of electronic information by families to share information in other situations. Patient organised personal health records (PHRs) can provide this facility, allowing individuals to decide what they share and with whom. Prior to a planned intervention study to support patients at risk of familial colorectal cancer, we undertook a scoping exercise to determine types and current usage of PHRs. We compared how they differed in aspects (content, security, functionality, purpose and acceptance) relevant to users at risk of genetic conditions. We discuss key attributes of PHRs suitable for facilitating information exchange and highlight the importance of the healthcare professional’s approach to ensure successful adoption. These technologies have the potential to empower patients and their relatives. Genetic services need to address the integration of this technology into patient care, as its use has important implications for current and future clinical practice.
An unique case of a mosaic genome-wide uniparental isodisomy in a newborn with Beckwith-Wiedemann syndrome
Saskia M.J. Hopman 1, P.F.R. Hochstenbach 1, A.A. Verrijn Stuart 2, J.C. Giltay 1, L.T. van der Veken 1
1 Department of Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands. 2 Department of Endocrinology, University Medical Centre Utrecht, Utrecht, the Netherlands.
Background gwUPiDMosaicism for a cell line in which all chromosome pairs consists of two identical copies derived from only one of the parents, a so called genome-wide uniparental isodisomy (gwUPiD) is a rare phenomenon. Beckwith-Wiedemann syndrome Beckwith-Wiedemann syndrome (OMIM#130650) is characterized by prenatal and postnatal overgrowth, hemihyperplasia, macroglossia and an increased frequency of embryonic tumors. In 60-70% of the patients, an epigenetic error at either the H19DMR (imprinting control region, ICR1) or KvDMR (ICR2), controlling the appropriate allelic expression of the paternal IGF2 and maternal CDKN1C genes, causes the clinical phenotype. In 10-15% of cases, the cause is presence of two paternally derived copies of chromosome region 11p15, a so called paternal uniparental disomy (UPD) 11p15. A small percentage of cases are caused by maternal translocations/inversions or paternal duplications (2-3%) or mutation in CDKN1C (5-7%).
Clinical history We report on a newborn presenting with clinical characteristics of Beckwith-Wiedemann syndrome (BWS): high birth weight (~P80), facial dysmorphisms including ear lobe creases and nevus flammeus, umbilical hernia, diastastis recti, hepatomegaly and hypoglycemia due to hyperinsulinism. Molecular investigations To confirm clinical diagnosis, a methylation test was performed which showed hypermethylation of H19DMR, corresponding to a paternal UPD 11p. To exclude a chromosomal rearrangement, karyotyping and SNP-array analysis (Illumina CytoSNP-850k) were performed on DNA isolated from peripheral blood. SNP-array showed a gwUPiD in a high percentage of cells (>95%). No additional clinically relevant copy number alterations were observed and karyotyping showed a normal female karyotype. Since only mosaicism for gwUPiD can be compatible with life we decided to perform additional SNP-array analysis on saliva and urine derived DNA, which showed normal biparental contribution without any indication for the presence of gwUPiD cells.
Conclusion In conclusion, we present a rare case of BWS in a newborn caused by mosaic gwUPiD.
Compound heterozygosity for two novel mutations in NTHL1 in an individual with adenomatous polyposis and multiple tumours
S. Kenwrick 1, O. Spasic-Boskovic 1, A. Taylor 1, K. Brugger 1, H. Rai 1, S. Abbs 1, J. Wyke 2, M. Tischkowitz 1, E. Maher 1, J. Whitworth 3.
1 East Anglian Clinical Genetics Service. Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK. 2 Ipswich Hospital, Heath Road, Ipswich IP4 5PD, UK. 3 Cambridge University at Addenbrooke’s Hospital CB2 0QQ, UK.
A 62 year old male with Jewish ancestry presented with over 40 adenomatous polyps throughout the large bowel following an abnormal result on faecal occult blood screening. Family history was not consistent with dominant inheritance. He previously had a parotid gland tumour, aged 60, and shortly after his polyposis was detected, he developed acute myeloid leukaemia. APC, MutYH and GREM1 gene testing was normal. Interrogation of the NTHL1 gene using the Illumina Trusight panel revealed that he is a compound heterozygote for two truncating mutation, in trans, not previously described for cases of polyposis. These are present only one and 23 times, respectively in the EXAC database and are therefore likely pathogenic. Two previous reports describe three different NTHL1 mutations in four families (Weren et al. 2015; Rivera et al. 2015). The eight affected individuals all had multiple tumours but none presented with a parotid gland tumour, or AML. This report therefore extends the mutation as well as the tumour spectrum associated with NTHL1 polyposis. Whole genome sequencing of 96 individuals to date, from the Multiple Tumour Study, with a variety of multiple tumours, study did not reveal any additional cases with homozygosity or compound heterozygosity for NTHL1.
Brain-thyroid-lung syndrome in a child caused by a deletion on chromosome 14 proximal of the NKX2.1 gene locus
Mira Kharbanda 1, Sunia Khadouma 3, Jeremy Jones 2, Malcolm Donaldson 2, Joachim Pohlenz 3, Pia Hermanns 3.
1 West of Scotland Genetics Service, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK. 2 Royal Hospital for Sick Children, Glasgow, G51 4TF, UK. 3 Children’s Hospital, Mainz, Germany.
Brain-lung-thyroid syndrome (BLTS) is a rare disorder characterized by congenital hypothyroidism (CH), infant respiratory distress syndrome (IRDS) and benign hereditary chorea (BHC). BLTS is caused by mutations in NKX2.1, a transcription factor involved in thyroid, lung and central nervous system development.
In most previously published cases of BLTS, a point mutation or deletion of NKX2.1 has been identified. Here we present a BLTS patient without a NKX2.1 mutation. Using array-CGH, we identified a heterozygous 1 Mb deletion on chromosome 14, approximately 195,000 bp proximal to NKX2.1. The deleted region encompasses 3 genes: MBIP, BRMS1L and RALGAPA1. Currently, we are trying to determine whether NKX2.1 directly interacts with one of these 3 proteins or whether one of the proteins binds to the NKX2.1 gene promoter.
Three other patients with deletion proximal to NKX2.1 and features of BLTS have been described in the literature. The smallest common deleted region encompasses just MBIP (MUK-binding inhibitory protein). MBIP is expressed in the thyroid, lung and forebrain. Our aim is to clarify whether MBIP is involved in NKX2.1 gene expression or regulation. This finding will help identify new mechanisms of NKX2.1 regulation and provide a deeper understanding of possible causes of thyroid disorders.
Mast syndrome (SPG21), a rare but recognizable phenotype
Anneke Kievit 1, Esther Brusse 2, Margriet Collée 1, Erik-Jan Kamsteeg 3, Rick van Minkelen 1
1 Dept. Of Clinical Genetics and 2 Dept. of Neurology, Erasmus MC, 3000CA Rotterdam, The Netherlands, 3 Dept. of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, The Netherlands.
Introduction: Mast syndrome is an autosomal recessive complicated form of hereditary spastic paraplegia with dementia. It was first described among Old Order Amish. Subtle childhood abnormalities may be present, but the main features like spastic paraplegia, dementia develop in early aduthood. The disease is slowly progressive and cerebellar and extrapyramidal signs are also found in patients with advanced disease. Patients have a thin corpus callosum and white- matter abnormalities on MRI of the brain. Mutations were found in the acid-cluster protein of 33 kDa (ACP33) gene, which was designated “maspardin” (Mast syndrome, spastic paraplegia, autosomal recessive with dementia). Five new patients with Mast syndrome, due to mutations in the SPG21 gene, will be presented. Patients: Three Dutch patients (2 brothers and 1 sister) of a consanguineous sibship of 9, showed a normal early development and followed normal education. At the age of resp.20/35/45 years they started to have progressive motor problems, like problems with walking and frequent falls. Also fatigue, concentration problems, depression and regression. At the age of resp 54/50/55 years they became bedridden due to spasticity, dementia, incontinency, swallowing difficulties and were unable to speak. They had no epilepsy or vision problems. Neurological examination at the age of 50/43/50 years showed bipyramidal syndrome, dysarthria and ataxia and neuropsychological examination showed global cognitive impairment and deterioration. MRI of the brain showed supratentorial generalized atrophy and a thin corpus callosum but no white matter abnormalities. The eldest brother died at the age of 56 years.Two Saudi Arabian patients of a consanguineous sibship were diagnosed with Mast syndrome and showed the same phenotype. Methods: Clinical findings of the new Mast syndrome patients were collected and compared to those described before. Whole exome sequencing was performed using DNA of the siblings followed by homozygeous filtering of genes of the ROH and movement disorder panel consisting of 212 genes. Results: Clinical findings of all patients described and new, will be presented. Homozygous mutations were detected in the SPG21 gene in the new patients. Conclusions: Mast syndorme is a rare, but recognizable phenotype: there is a normal early development or a slight delay with progressive deterioration at adult age with pyramidal signs and cerebellar and extrapyramidal signs at a later stage, cognitive decline with dementia and psychiatric problems, a thin corpus callosum and supratentorial generalized atrophy of the brain leading to a bedridden status and dependency within 10-20 years after onset. The differential diagnostic considerations will be discussed and also the possible role of maspardin, which has been shown to localize to intracellular endosomal/trans-Golgi transportation vesicles and rather be involved in protein-protein interactions and in sorting and/or trafficking of molecules in the endosomal pathway, a crucial process for maintenance of neuron health.
KBG Syndrome: an emerging cause of developmental delay
K.J. Low 1, T.Ashraf 2, N.L.E Canham 3, J. Clayton-Smith 4,5, C. Deshpande 2, A. Donaldson 1, R.B. Fisher 6, F.A. Flinter 2, N.C Foulds 7, K. Gibson 8, I. Hayes 9, A. Hills 10, S.E. Holder 3, M.D. Irving 2, S. Joss 11, E.C. Kivuva 12, K. Lachlan 6, A.C. Magee 13, V.P.M. McConnell 13, M. McEntagart 14, K. Metcalfe 4, T. Montgomery 15, R.A. Newbury-Ecob 1, F.J. Stewart 13, P.D. Turnpenny 12, J. Vogt 16, M. Williams 9, DDD Study 17, S.F. Smithson 1.
1 UHBristol NHS Trust, Bristol, BS2 8EG, UK. 2 Guy’s and St Thomas’ NHS Trust, London, SE1 9RT, UK. 3 North West Thames Regional Genetics Service, Harrow, HA1 3UJ, UK. 4 Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester, M13 9WL, UK. 5 Institute of Human Development, University of Manchester, M13 9NT, UK. 6 Teesside Genetics Unit, The James Cook University Hospital, Middlesbrough, TS4 3BW, UK. 7 Wessex Clinical Genetics Service, Southampton, SO16 5YA, UK. 8 Genetic Health Service NZ, Christchurch Hospital, Christchurch, New Zealand. 9 Genetic Health Service NZ, Auckland Hospital, New Zealand, 10 Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, BS10 5NB, UK. 11 West of Scotland Department of Clinical Genetics, Glasgow G51 4TF, UK. 12 Royal Devon and Exeter Hospital, Exeter, EX1 2ED. 13 Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, BT9 7AB. 14 South West Thames Clinical Genetics Service, St George’s Hospital, London, SW17 0QT, UK. 15 Northern Genetics Service, Newcastle Upon Tyne, NE1 3BZ, UK. 16 West Midlands Regional Genetics Service, Birmingham, B15 2TG, UK. 17 Wellcome Trust Sanger Institute, Cambridgeshire, CB10 1SA, UK.
We describe 32 KBG patients from 27 families ascertained from both targeted gene sequencing and from exome sequencing (DDD study). The former involved ANKRD11 sequencing in patients who had a clinical diagnosis of KBG syndrome whilst the latter utilized whole exome sequencing in a group of children with developmental delay without a diagnosis. Our patients ranged from infancy to middle age enabling insight into the prognosis of KBG. In this cohort speech delay and learning difficulties were highly frequent but varied. Behavioural problems were also common. Macrodontia of permanent upper central incisors was the most common, but not universal, physical feature. Other clinical features included short stature, conductive hearing loss, severe and recurrent middle ear infection, subtle palatal abnormalities, infantile or persistent feeding difficulties. We identified a wide anterior fontanelle with delayed closure, a new feature to be described, in a fifth of the cohort. Previously described facial features of KBG syndrome were clearly recognisable in half the patients. Sanger sequencing of ANKRD11 confirmed mutations in all patients and we did not find any phenotype-genotype correlations. This study demonstrates that KBG syndrome is a significant Mendelian cause of developmental delay. By comparing the two diagnostic groups of patients we show that the clinical features can be subtle and non-specific making the diagnosis elusive. We therefore propose that ANKRD11 should be included on ‘developmental delay’ gene panels. We propose updated diagnostic criteria for KBG and a new summary of care recommendations for patients with the condition.
Retrospective analysis of the prevalence of Beckwith-Wiedermann Syndrome in Northern Ireland
R. Moore 1, D.Donnelly 2
1,2 Clinical Genetics Department, A Floor, Belfast City Hospital, 51 Lisburn Road, Belfast, BT9 7AB, Northern Ireland.
Background and Aims Genomic imprinting is the phenomenon whereby there is exclusive monoalleleic parent-of- origin specific gene expression. One of the most commonly recognised imprinted disorders (IDs) is Beckwith-Wiedemann syndrome (BWS). Epidemiological data on IDs is sparse. BWS is an overgrowth disorder characterised by abdominal wall defects, macroglossia, Wilm’s tumour, hemihypertrophy and neonatal hypoglycaemia. BWS is caused by disruption to a number of imprinted genes at 11p15. The aim of this study was to retrospectively analyse the prevalence of BWS within Northern Ireland. Within the study we looked at some of the features of BWS in relation to the molecular diagnosis.
Methods We used a search tool within our information management system to identify all patients in Northern Ireland with a molecular or clinical diagnosis of BWS between the period of January 1987 and February 2015.
Results 37 patients in total had a diagnosis of BWS. 26 patients had molecular confirmation. Of these 26 patients, 18 had hypomethylation of ICR2, 6 had paternal uniparental disomy (UPD), 1 had a duplication of ICR1 and 1 had a CDKN1C mutation. The live-birth prevalence of BWS was calculated to be 5.408 x 10-5 which equates to ~ 1 in 18,500. The majority of our patients were referred to the genetics service at birth. 17 patients had an omphalocoele. 17 patients had neonatal hypoglycaemia. 8 patients had hemihypertrophy, 4 of whom had UPD as the molecular diagnosis. 1 patient developed a Wilm’s tumour and 1 patient developed hepatoblastoma. Both of these patients also had UPD. 1 patient had an angiomyolipoma and maternal hypomethylation of ICR2 as the underlying molecular diagnosis.
Conclusions The live-birth prevalence of Beckwith-Wiedemann syndrome in Northern Ireland is ~ 1 in 18,500. This is lower than the few reported prevalence statistics. The 2 characteristic tumours of Wilm’s tumour and hepatoblastoma in our cohort of patients occurred in children with uniparental disomy which is in keeping with the risk reported in the literature. Hemihypertrophy was also seen more frequently in those with UPD.
Three generation family with atypical interstitial deletion within chromosome 22q11.21
R. Moore 1, V. McConnell 1
1 Clinical Genetics Department, A Floor, Belfast City Hospital, Belfast Health & Social Care Trust, 51 Lisburn Road, Belfast, BT9 7AB, Northern Ireland
We present a three generation family affected by an atypical interstitial deletion within chromosome 22q11.21 with a minimum size of approximately 686kb. The deletion interval involves only the distal part of the 22q11.2 deletion syndrome critical region (which includes Di George and velocardiofacial syndrome) and therefore does not contain the gene TBX1. To our knowledge >18 cases have been reported in the literature to date. The phenotype is variable and includes developmental delay, subtle dysmorphism and cardiac defects.
The 23 year old proband first presented to the genetics service at 27 weeks gestation with her first pregnancy after referral from rheumatology for assessment of joint hypermobility and radiological findings of high riding right patella and a left subluxed patella with bilateral effusions and normal echocardiogram, raising the possibility of a connective tissue disorder. Her clinical phenotype involves unusual dysmorphism including dysplastic ears, retrognathia, dental overcrowding, a high arched palate, long uvula, velvety skin and some keloid scar formation. Array-CGH at a resolution level of 60K detected an atypical interstitial deletion within chromosome 22q11.21 ~686kb. Other cardiac and genetic investigations and collagen studies which were completed will be presented.
Subsequent testing has shown the atypical interstitial deletion within chromosome 22q11.21 to be maternally inherited and has also been shown to be present in the proband’s daughter who had surgical repair of an umbilical hernia. Interestingly the proband’s mother has history of joint laxity and umbilical hernia. Within the family a number of others have been affected with umbilical hernia including; a maternal aunt, maternal grandmother and maternal great-grandmother. Segregation analysis of the hernia and clinical phenotype with the deletion is currently in progress within the family. Documenting the phenotype within this family will be important in expanding the knowledge on this unusual deletion. This case demonstrates that array CGH should be considered in referrals for assessment of possible connective tissue disorder when atypical phenotypic features are present.
GSK2126458, a dual PI3K/mTOR inhibitor, is less effective than rapamycin for treatment of renal lesions in a genetically engineered Tsc2+/- mouse model
Kalin Narov*, Paulina Samsel*, Jian Yang*, Ashley Jones, Julian Sampson, Ming Hong Shen (* Equal Contributors)
Institute of Medical Genetics, Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
Tuberous sclerosis (TSC) is a genetic tumour syndrome involving multiple organs. It is caused by mutations in the TSC1 or TSC2 gene that lead to aberrant activation of the mechanistic target of rapamycin (mTOR) signalling pathway. The allosteric mTOR inhibitor rapamycin and its analogues (rapalogues) have demonstrated some beneficial effects for treating TSC- associated tumours in both preclinical and clinical trials. However, some tumours have little response to treatment probably partly due to rapamycin induced activation of Akt. GSK2126458 is a highly potent and orally bioavailable dual ATP-competitive inhibitor of PI3K and mTOR, and may help to overcome problems caused by rapalogues. Preclinical studies have demonstrated broad anti-tumour activity of GSK2126458 in vitro and in vivo. Preliminary data from a phase 1 trial for advanced solid tumours suggested 2.5 mg as daily maximum tolerated dose (MTD) while several other phase 1 trials are still under way. In this study, we have assessed the therapeutic efficacy of GSK2126458 on renal lesions in a genetically engineered Tsc2+/ mouse model. We first determined 2 mg/kg of GSK2126458 for males and 1 mg/kg for females as the daily MTD. We treated Tsc2+/- mice from the age of 13 months with vehicle, rapamycin (4 mg/kg) and GSK2126458 (MTD) (n=9 per group) 5 times a week via intraperitoneal injection for two months. Tumour burden was estimated from total whole areas and cellular areas respectively of all lesions (cystic, papillary and solid) observed in 6 coronal sections at a150 µm interval prepared from each kidney of a mouse. Compared to vehicle, both rapamycin (P=0.0004 for whole areas; P=0.0006 for cellular areas) and GSK2126458 (P=0.002 for whole areas; P=0.010 for cellular areas) treated mice showed significant reduction in overall tumour burden but GSK2126458 was less effective than rapamycin (P=0.0643 for whole areas; P=0.0135 for cellular areas).
Feingold syndrome with no Tracheo-oesophalgeal atresia
C. Powell 1, E. Craft 2, P. Vasudevan 3.
1 Trust Grade Speciality Doctor, Clinical Genetics, Royal Leicester Infirmary, Leicester, LE1 5WW, UK. 2 Consultant Geneticist, Clinical Genetics, Royal Leicester Infirmary, Leicester, LE1 5WW, UK. 3 Consultant Geneticist, Clinical Genetics, Royal Leicester Infirmary, Leicester, LE1 5WW, UK.
Feingold syndrome is a genetic condition with autosomal dominant inheritance, characterised by microcephaly, mild-moderate learning disability, digit anomalies and trachea-oesophageal atresia, associated with a heterozygous mutation in the MYCN gene.
Our case is a 10 year old girl with mild learning and behavioural difficulties. Specifically, she has delayed motor and speech development, following an uneventful pregnancy and birth and requires educational support. No other health problems are known, including no gastrointestinal problems. Her mother also has mild learning difficulties.
Clinically, she has relative microcephlay (<0.4th centile), with a height and weight between 25th – 50th centiles. Bilateral 5th finger clindodactyly with a short middle phalanx. Thumb and toe anomalies were not evident. She had unremarkable palpebral fissures and jaw shape.
Her mother similarly has relative microcephaly (<3rd centile on adult chart). Her palpebral fissures are short and down-slanted. Her right thumb is distinctly hypoplastc and both fifth fingers have a short middle phalanx.
Her microarray identified a maternally inherited 1.2Mb deletion within 2p24.3; encompasses the entire MYCN gene that is associated with Feingold syndrome.
In summary we present a case of Feingold Syndrome in a mother and daughter, detected by microarray, highlighting the phenotypic variability and absence of tracheo-oesophalgeal atresia.
Genetic mechanisms associated with tuberous sclerosis and tuberous sclerosis-like phenotypes
Meera Raja 1, Gemma Sharman 1, Laura Thomas 1, Angharad Walters 1, Peter Giles 1, Kevin Ashelford 1, Matthew Mort 1, James Colley 1, Julian Sampson 1.
1 Institute of Medical Genetics, Cardiff University, UK.
Mutations in the TSC1 or TSC2 genes are identified in at approx. 90% of cases of tuberous sclerosis (TSC). Their identification is important for genetic counselling and as a resource to better understand the pathophysiology of TSC. The remaining patients are classified as no mutation identified (NMI). It is expected that a number of different genetic mechanisms may account for their phenotypes. They may have mutations in TSC1 or TSC2 that have escaped detection (e.g. mutations in un-screened promoters or untranslated regions, or low level mosaicism for conventional mutations), and/or there may be mutations in other genes that confer similar phenotypes to TSC.
This study employs targeted ultra deep sequencing (UDS) of the genomic TSC1 and TSC2 loci and, where this is negative, whole exome sequencing (WES) to identify the genetic causes of TSC and TSC-like phenotypes in NMI patients. Trios of samples (an affected proband and their unaffected parents) have been analysed to aid in novel, de novo variant detection. To date, 91 samples (29 trios and two duos) have been analysed by targeted UDS of the region containing TSC1 and TSC2, and 15 of these samples (5 trios) have been analysed by WES. Putative SNVs and indels were verified using a combination of PCR, COLD-PCR and Direct Sequencing. For 28 of the patients, RNA was also available and a TSC1 and TSC2 allelic imbalance assay is being undertaken.
UDS identified a likely pathogenic de novo TSC2 mutation (c.2590C>T; p.Q864X) in one patient. This mutation was mosaic; present in only 1% of alleles. UDS also identified two non- mosaic de novo mutations in TSC1: c.1498C>T; p.R500X in one patient, and c.1717C>T; p.Q573X in another patient. No imbalance of allelic expression has been detected in 3 of the 28 patients, further allelic imbalance assays are being undertaken. Additionally, further investigation of non-TSC1/2 de novo mutations identified by WES is being undertaken.
Histiocytoid Cardiomyopathy and Microphthalmia and Linear Skin Defects Syndrome: Phenotypes linked by truncating variants in NDUFB11
Gillian Rea 1,2,5, James S. Ware 1,2, Tessa Homfray 3, Jan Till 3, Ferran Roses-Noguer 3, Rachel Buchan 1,2, Sam Wilkinson 1,2, Alicja Wilk 1,2, Roddy Walsh 1,2, Shibu John 1,2, Shane McKee 5, Fiona J. Stewart 5, Victoria Murday 6, Robert W. Taylor 7, John Baksi 3, Piers Daubeney 3, Sanjay Prasad 1,3, Paul J.R. Barton 1,2, Stuart Cook 1,2,4.
1 NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London, SW3 6NP, UK. 2 National Heart and Lung Institute, Imperial College London, London SW3 6NP, UK. 3 Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK. 4 National Heart Centre Singapore, Singapore 169609, Singapore. 5 Department of Clinical Genetics, Belfast City Hospital, Belfast, BT9 7AB, UK. 6 Department of Clinical Genetics, NHS Greater Glasgow and Clyde, Southern General Hospital, Glasgow, G51 4TF, UK. 7 Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle Upon Tyne, NE2 4HH, UK.
Background: Mutations in NDUFB11, which encodes a component of the Mitochondrial Respiratory Chain (MRC) were recently reported to cause both Histiocytoid Cardiomyopathy (Histiocytoid CM) and Microphthalmia with Linear Skin Defects Syndrome (MLS syndrome). Histiocytoid CM is a rare, distinctive form of cardiomyopathy with ~ 150 cases reported worldwide, that predominantly affects females early in life and is characterized by arrhythmias and associated sudden death. MLS syndrome, also known as a MIDAS (microphthalmia, dermal aplasia, and sclerocornea syndrome, is a rare X-linked disorder with male lethality in utero, characterized by unilateral or bilateral microphthalmia and linear skin defects, along Blaschko lines, which are classically limited to the face and neck, present from birth, and heal with time, often leaving minimal scarring. Methods and results: Here we report a fourth case of Histiocytoid CM with a de novo nonsense mutation in NDUFB11 (ENST00000276062.8: c.262C>T; p.Arg88Ter), identified using Whole Exome Sequencing (WES) of a family trio. An identical mutation has been previously reported in association with MLS syndrome. Our case lacked the diagnostic features of MLS syndrome but detailed clinical comparison of the two cases revealed significant phenotypic overlap. Heterozygous mutations in HCCS and COX7B, which, like NDUFB1, encode proteins of the MRC, have also previously been identified in MLS syndrome including a case with features of both MLS syndrome and Histiocytoid CM. However, a systematic review of WES data from previously published Histiocytoid CM cases, alongside four additional cases presented here for the first time, did not identify any mutations in these genes. Conclusion: We conclude that NDUFB11 is a cause of both Histiocytoid CM and MLS, and that these disorders are allelic (genetically related). Screening for evidence of malignant arrhythmias and cardiomyopathy would be appropriate in individuals with MLS syndrome. Additional nuclear encoded mitochondrial or mitochondrial DNA genes are good candidates for further causes of both Histiocytoid CM and MLS syndrome.
Audit of Tuberous Sclerosis Diagnostic assessment and surveillance in the Northern Region. R. Richardson1, A. Henderson2 1,2 Northern Genetics Service, Institute of Genetic Medicine, Newcastle upon Tyne, NE1 3BZ, UK [email protected]
Background Tuberous Sclerosis Complex (TSC) is an autosomal dominantly inherited multisystem disorder. (1) Birth incidence is estimated at 1:5800 (2). Consensus guidelines were first proposed in 1999 (3) and were reviewed and an update published in 2013 (4). Level of adherence to these guidelines in the Northern Region was unknown. This audit reviewed management of the TSC patients in the Northern Region. Method Patients were identified via the Northern Genetics service (NGS) database. Additional patients were identified from a Paediatric TSC MDT meeting. NGS notes were reviewed. Newcastle Hospitals Trust records were reviewed where available. If no records existed in Newcastle Trust, and care was being received in another hospital, efforts were made to review those hospital notes. Up to 2013, the 1998 TSC consensus guidelines were used. From 2013 onwards, the 2013 guidelines were used. Results 101 patients were identified. 58 sets of notes were retrieved. 46 of which were included. 28 were diagnosed when 1999 guidelines applied. 4 were diagnosed when the 2013 guidelines applied. 41 had management/surveillance when the 1999 guideline applied. 45 had management/surveillance when the 2013 guideline applied Audit against the 1999 guidelines showed less than 50% adherence in: fundoscopy, ECG, skin assessment, annual BP, annual U&E (if PKD), pulmonary investigations Audit against the 2013 guidelines showed less than 50% adherence: in use of abdominal MRI for screening for AMLs , BP, GFR, counselling about Oestrogens use, assessment of teeth, MRI brain surveillance, TAND screening, LAM screening, skin surveillance, Cardiology and Ophthalmology follow up. Conclusions There is poor adherence to the consensus guidelines for diagnostic assessment and surveillance of TSC. It was also observed that there is no agreement as to which specialty coordinates overall care for TSC patients. Limitations Efforts were made to review all notes for patients, including NGS notes, Newcastle Hospital notes and relevant local hospital notes. General practice information was not sought and it is possible that some patients were receiving surveillance from their GP, which was not documented in hospital notes. In many cases, information was not documented, for example, asking about pulmonary or cardiac symptoms. The assumption was made therefore that this was not done.
References 1 Curatolo P ‘Tuberous sclerosis’. Lancet. 2008;372:657–668. 2 O'Callaghan ‘Prevalence of tuberous sclerosis estimated by capture-recapture analysis.’ Lancet. 1998;352:318–319. 3 Tuberous Sclerosis Consensus Conference: recommendations for diagnostic evaluation. National Tuberous Sclerosis Association. RoachES, DiMarioFJ, Kandt RS, Northrup H. Journal Child Neurology. 1999 Jun;14(6):401-7. 4 Tuberous Sclerosis Complex Surveillance and Management. Krueger, Northrup, International Tuberous Sclerosis Complex consensus group. Ped Neurology. Oct 2013 Volume 49, Issue 4, Pages 255–265
A Clinical Audit of a Lynch Syndrome Referral Protocol
Peter Risby 1, Dr. Verna Lavender 2,
1 Oxford Dept. of Clinical Genetics, Churchill Hospital, Oxford, OX5 1SU, UK. 2 Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0fl, UK.
Background Around 14% of patients with colorectal cancer have tumours that exhibit a deficiency in mismatch repair (MMR) genes1. Three percent of these patients have Lynch syndrome, where the MMR gene mutations are germline in origin. Lynch syndrome is associated with significant lifetime cancer risks2, so early diagnosis is required to optimise outcomes; however, previous identification of individuals with Lynch syndrome has depended on the use of family assessment-based guidelines, which fail to capture a significant proportion due to familial heterogeneity3. Routine MMR immunohistochemistry testing of resected primary colorectal cancers has, therefore, been practiced at a local NHS Trust since 20124. Method A clinical audit was conducted between 01.01.2014 and 31.12.2014 to identify compliance with the Lynch syndrome referral protocol. The Lynch syndrome referral protocol, developed by the local NHS Trust MMR Group, was used to develop the audit standard that all patients aged between 18 and 70 and treated with surgical resection for primary colorectal cancer and found to be mismatch repair deficient, should be referred to the clinical genetics service for counselling and potential investigation of germline mutations. De-identified binomial data were summarised using descriptive statistics to analyse the proportion of patients who were treated according to the Lynch syndrome referral protocol. Sub-analysis by age stratification was also conducted. Results 256 adult patients had resection of primary colorectal cancer at the local NHS Trust during the data collection period. Of the 256 patients, 130 (50.8 %) were aged 70 or under, 113 (87%) had MMR testing, and 10 (3.9%) had potentially clinically significant results. Of these ten patients, only three were referred to clinical genetics; two of which were found to have germline mutations (both were aged 50 - 70). Conclusions The majority of patients who met the Lynch syndrome referral protocol inclusion criteria (based on age, diagnosis and treatment) were referred for MMR testing and tested; however not all eligible patients were tested. A key area of improvement to ensure both compliance with the Lynch syndrome referral protocol and identification of all individuals with an MMR germline mutation, is referring suitable patients to the clinical genetics service for counselling and testing for germline mutations, as currently only 30% are referred. Although the proportion of patients with MMR (sporadic and germline) mutations is relatively low, the results have major clinical significance, informing decision making about both adjuvant treatments and familial screening (where germline mutations have been detected).
References 1. Guinney, J. et al (2015) The consensus molecular subtypes of colorectal cancer. Nature medicine. Advanced online publication. doi:10.1038/nm.3967 2. Vasen H, F, A. et al (2015) Clinical management of hereditary colorectal cancer syndromes. Nature Reviews Gastroenterology & Hepatology. 12 p88-97 3. Serrano, M. et al (2012) Bethesda criteria for microsatellite instability testing: impact on the detection of new cases of Lynch syndrome. Familial Cancer 11: 571-578. 4. Colling, R. et al (2015) Screening for Lynch syndrome and referral to clinical genetics by selective mismatch repair protein immunohistochemistry testing: an audit and cost analysis. Journal of Clinical Pathology 0: p1-4
A single centre experience of tumour immunohistochemistry and mutation analysis in the investigation of Muir Torre Syndrome
Katherine Schon 1, Ed Rytina 2, James Drummond 1, Stephen Abbs 1, Marc Tischkowitz 1,3
1 East Anglian Medical Genetics Service, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK. 2 Histopathology Department, Addenbrooke’s Hospital, Cambridge, CB1 0QQ, UK. 3 Department of Medical Genetics, University of Cambridge, CB2 0QQ, UK.
Introduction Sebaceous tumours are rare in the general population (prevalence <1%) but occur relatively frequently in Lynch syndrome (~9%) as part of Muir Torre Syndrome (MTS). Here we evaluate the diagnostic and genetic work up of sebaceous tumours in our region.
Methods Patients with sebaceous tumours were ascertained from the pathology database over a two year period (October 2012 to 2014). IHC results, clinical genetics notes and molecular genetics results were reviewed.
Results Of forty-five patients with sebaceous tumours, six were already diagnosed with MTS. 20/38 IHC results were abnormal and fourteen new referrals were made to Genetics with nine patients having genetic testing. A new MTS diagnosis was made in two patients (22%) with sebaceous adenomas: an 81 year old female with previous duodenal and endometrial cancer (MSH2) and a 56 year old female with a previous history of endometrial cancer (PMS2).
Discussion Making a diagnosis of MTS has significant implications for the patient and their family. Our experience shows that offering molecular testing to individuals with a sebaceous tumour and abnormal IHC has a good yield, detecting a pathogenic mutation in 22%. One individual had a mutation in PMS2, which has not previously been associated with MTS.
Genetic Mechanisms in Colorectal Polyposis
Dr. E. Short, Dr. L. Thomas, Dr. P. Giles, Dr. J. Colley, Dr. K. Ashelford, Dr. M. Mort, Prof. J. Sampson.
Institute of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XW, UK.
Background Familial Adenomatous Polyposis (FAP), MUTYH-Associated Polyposis (MAP) and Polymerase Proofreading-Associated Polyposis (PPAP) are syndromes of adenomatous polyposis, and are due to mutations in APC, MUTYH, POLE and POLD1. Up to 90% of patients with a phenotype of typical FAP (>100 adenomas) have a pathogenic APC germline mutation identified through sequencing of coding exons and deletion/duplication analysis via MLPA. Of those with a phenotype of attenuated FAP (AFAP) with 10-100 adenomas, an APC or MUTYH germline mutation is detected in only 10-50% of cases. The aim of this study is to identify novel constitutional mutations predisposing to multiple colorectal polyps (>10) when no mutation is identified (NMI) in APC or MUTYH during routine genetic diagnosis. Such currently undetected mutations may occur outside of the open reading frame (ORF) of the known polyposis-associated genes, such as in promoters, UTRs or introns, they may occur as conventional mutations at low frequency in mosaic cases or additional genes may be responsible for the phenotype.
Methods 60 patients with ≥ 10 colorectal polyps have been recruited. All are negative for APC/MUTYH mutations following sequence/dosage analysis of coding exons. Haloplex (Agilent) is being employed for targeted sequence capture of the genomic APC/MUTYH loci, and the ORFs of an additional 15 genes related to, or possibly related to, colorectal neoplasia (BMPR1A, CDH1, CHEK2, EPCAM, MLH1, MSH2, MSH6, PMS2, PTEN, SMAD4, STK11, TP53, POLE, POLD1, and AXIN2. This is followed by ultradeep sequencing (UDS) on a HiSeq (Illumina). Samples are also undergoing cDNA sequencing to screen for APC/MUTYH allelic imbalance (AI) and splicing abnormalities, and qPCR is being employed to assess APC/MUTYH gene expression. Samples that remain NMI following these tests undergo whole exome sequencing.
Results UDS and data analysis has been completed on 31 patients. Putative novel pathogenic variants have been identified in 3 patients in APC, AXIN2 and POLE. AI assays are in progress. So far 6/33 patients displayed AI in APC and 5/40 patients displayed AI in MUTYH. These findings are being confirmed with gene expression studies using qPCR. cDNA sequencing has been completed on 17 patients to date and there was no evidence of splicing abnormalities. Conclusions The identification of novel genetic variants or mechanisms responsible for colorectal polyposis may provide benefits for patients and their families through improved diagnosis and clinical genetic management.
Genetic Weight Watching
C.T.R.M Stumple 1, D.A. Schott 1,2, T. Rinne 3, M.M. van Haelst 4, M.F. Stokman 4, E.C.M Mariman 5
1 Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastrictt UMC + Maastricht; 2 Department of Pediatrics, Zuyderland Medical Centre, Heerlen; 3 Department of Human Genetics, Radboud University Medical Centre, Nijmegen; 4 Department of Genetics, University Medical Centre Utrecht; 5 Department of Human Biology, NUTRIM, Masstricht University Medical Centre, Masstricht, the Netherlands
A teenage boy born to American-Danish parents was presented with morbid obesity since the neonatal period. The cause of this extreme obesity was never found, despite all kinds of investigations (eg Prader-Willi syndrome) during childhood in several countries. The parents told that despite a diet since neonatal period and a very active life, there was no effect on his weight control. Anamnestic there was also an anosmia and no signs of pubertal development at age 11 years, leading to a clinical suspicion of Kallmann syndrome. Physical examination showed morbid obesity with acanthosis nigricans (sign of insulin resistance). He had a normal intelligence, without any dysmorphism and prepubertal Tanner stadia. Regular laboratory investigation for obesity showed no abnormalities, including OGTT and OSAS survey. Investigation of the Kallmann genes was normal. Recently, physical puberty started, excluding the clinical suspicion.
Exome sequencing revealed two compound heterozygous mutations in the ADCY3 gene; a truncating mutation and an in-frame deletion of an evolutionarily highly conserved amino acid located in the adenylyl cyclase domain of the ADCY3 protein. Mutations in this gene have not been associated with human genetic obesity so far, although previous GWAS studies showed that ADCY3 is a susceptibility locus for childhood body mass index.
Differential diagnosis, especially with Bardet-Biedl syndrome (BBS) will be discussed. Mutations in the ADCY3 gene have not been reported sofar in BBS.
Ciliopathies are a heterogeneous group of conditions due to mutations in genes coding for proteins with a function in primary and/or sensory cilia. Obesity and impairment of the olfactory system can be part of the symptoms. ACDY3 is used as a histological marker for cilia, because it is relatively highly expressed in cilia, where it functions in signal transduction. Considering the fact that the Adcy3 knockout-mouse is obese and has an impaired smell, mutations in the human ADCY3 gene can be regarded as possibly underlying the clinical condition of the presented patient. Causality of ADCY3 mutations will be further investigated using cilia assays in patient-derived cells.
Exome sequencing reveals distinct molecular mechanisms of duodenal and colorectal tumorigenesis in familial adenomatous polyposis and MUTYH-associated polyposis
Laura E. Thomas 1, Joanna Hurley 2, Sian Jose 1, Kevin Ashelford 1, Matthew Mort 1, Shelley Idzizazyczk 1, Julie Maynard 1, Helena Leon Brito 1, Manon Harry 1, Angharad Walters 1, Sarah Jane Walton 3, Sunil Dolwani 1, Geraint Williams 1, Meleri Morgan 4, Susan Clark 3, Julian R. Sampson 1.
1 Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff University CF14 4XN, UK. 2 Dept. of Gastroenterology, Prince Charles Hospital, Merthyr Tydfil, CF47 9DT, UK. Dept. of Surgery, St Marks Hospital, London, HA1 3UJ, UK. 4 Dept. of Pathology, University of Wales Hospital, Cardiff, CF14 4XN, UK.
Background With improved management of colorectal disease, duodenal cancer is becoming the leading cause of familial adenomatous polyposis (FAP)-associated mortality. The risks of duodenal polyposis and cancer in MUTYH-associated polyposis (MAP) are uncertain. Molecular studies of duodenal tumorigenesis in FAP and MAP are virtually non-existent and the underlying genetic mechanisms of adenoma development in both disease contexts remain unclear.
Methods This study utilised exome sequencing (Agilent, 50Mb SureSelect), targeted Sanger sequencing and array comparative genomic hybridisation (CGH) (Illumina, BlueGnome) to characterise somatic mutational events in 74 duodenal adenomas from patients with FAP (N=13) or MAP (N=13). The disease contexts were compared to each other and the duodenal findings to the reported somatic landscape in colorectal adenomas in FAP and MAP.
Results and Conclusions Significant differences in the underlying mutational spectra were identified between FAP and MAP duodenal adenomas, including the numbers of single nucleotide variants (SNVs) and the frequency of G>T transversions. Moreover, although both duodenal and colorectal adenomas were characterised by somatic APC and KRAS mutations, there were significant differences in the involvement of other driver genes, with multiple mutations in duodenal adenomas in genes affecting the hedgehog, HER and Cadherin signalling pathways. These mutations are largely absent from colorectal adenomas. These differences may be important in relation to the identification of molecular biomarkers for “high risk” duodenal adenomas and for strategies for pharmacological prevention or treatment of duodenal polyposis.
Skin lesions and arthralgias in a large pedigree with a partially anakinra-responsive and possibly IL-18 driven NLRC4-related autoinflammatory disease
C.M.L. Volker-Touw* 1, H.D. de Koning* 2, T. van Kempen 3, K. Oberndorff 4, J. Giltay 1, C.G.F. de Kovel 1, M. Boes 5, M.A.M. van Steensel 6, G.T.J. van Well 7, A. Simon 8, J. Frenkel* 9, M.E. van Gijn* 1.
1 Dept. of Medical Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands; 2 Dept. of Dermatology, Radboud University Medical Centre, Nijmegen, the Netherlands; 3 Dept. of Rheumatology and Clinical Immunology Laboratory of Translational Immunology (LTI) University Medical Centre Utrecht, the Netherlands. 4 Dept. of Pediatrics, Atrium-Orbis Medicla Centre, Sittard, the Netherlands; 5 Dept. of Pediatric Immunology and Laboratory of Translation Immunology (LTI) University Medical Centre, Utrecht, the Netherlands; 6 Dept. of Dermatology, Maastricht University Medical Centre, Maastricht, the Netherlands. 7 Dept. of Pediatrics, Maastricht University Medical Centre, Maastricht, the Netherlands. 8 Dept. of General Internal Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands. 9 Dept. of Pediatrics, University Medical Centre Utrecht, Utrecht, the Netherlands *These authors contributed equally.
Background: Autoinflammatory disorders (AID) are a heterogeneous group of diseases characterized by chronic or recurrent systemic sterile inflammation. The best-known subset of AIDs is mediated by IL-1β production. Recently, gain of function mutations in NLRC4 have been described in association with autoinflammatory disease. Methods: We performed whole exome sequencing in members of a large 6 generation pedigree with a hitherto unknown AID. Medical data were collected retrospectively. IL-1β and IL-18 concentrations were analyzed in plasma. Skin biopsies were obtained of lesional and uninvolved skin from three patients for routine histology and immunohistochemical staining of IL-1β and IL-17. Results: WES revealed a novel heterozygous p.Ser445Pro variant in NLRC4, which segregated with the 13 affected family members (LOD-score 3.58), and is located next to the recently described p.His443Pro pathogenic mutation. Prediction software programs (Sift, Polyphen) indicated pathogenic properties. The clinical phenotype was influenced by weather conditions, stress, and infection. Skin lesions included painful erythematous nodes on the shins and feet, bouts of urticarial skin rash, or a combination of both. Two patients presented with late-onset enterocolitis, one with a fulminant polyarthritis. In a subset of the patients, the clinical symptoms resolved promptly upon treatment with the IL-1 receptor antagonist anakinra. Plasma concentrations of IL-1β were normal, whereas IL-18 concentrations were extremely elevated in all patients, even without an inflammatory episode (median 4,324 pg/ml; ref. 0-34 pg/ml). Biopsies of lesional skin showed a non-specific lymphocytic-histiocytic infiltrate in the dermis, unlike the histology of previously described autoinflammatory skin diseases. IL-1β could not be detected, IL-17 was present in mast cells in both lesional and uninvolved skin. Conclusions: In this study we describe a novel variant in NLRC4 in a large pedigree with a possibly IL-18-driven and partially anakinra-responsive AID. We present for the first time the histopathological findings associated with mutations in NLRC4. The phenotype consisted of erythematous skin nodes, urticaria and arthralgias, with late-onset enterocolitis in two patients. Plasma IL-1β concentrations were normal. A lymphocytic-histiocytic infiltrate without IL-1β expression was identified in affected skin tissue, which enables differentiation from the phenotype observed in CAPS and Schnitzler’s syndrome.
Audit of BRCA gene testing and demand for risk reducing mastectomy in Essex
E. Williams 1, B. Hoskins 2, V. Ramakrishnan 3, L. Side 1 1 North East Thames Regional Genetic Service, Great Ormond Street Hospital, London, WC1N 3JH, UK. 2 North East Thames Regional Genetic Service Laboratory, Great Ormond Street Hospital, London, WC1N 3JH, UK. 3 St Andrews Centre for Plastic Surgery, Broomfield Hospital, Chelmsford, CM1 7ET, UK.
We established a risk-reducing mastectomy MDT (RRM MDT) in 2011, to ensure consistency of decision-making following requests for risk-reducing mastectomies by women in Essex. Meetings were initially held 3 times a year, but this was increased to quarterly in 2014 due to an increase in requests for surgery. Clinicians attending this meeting noticed an increase in numbers of patients discussed, particularly the number of BRCA1/2 gene mutation carriers. Currently the service does not have dedicated funding, so we conducted an audit to look at increasing demand for the service with a view to approaching commissioners for funding.
The key questions we addressed were, (1) whether the number of BRCA1/2 gene tests, and in particular predictive tests had increased; (2) whether the number of BRCA1/2 gene mutation carriers identified increased; (3) whether the number of women discussed at the RRM MDT increased, and (4) whether the number of BRCA1/2 gene mutation carriers requesting RRM increased.
As BRCA1/2 gene testing is arranged in-house, our genetics laboratory provided data about all BRCA1/2 genetic testing arranged between January 2013 and May 2015, including results. We undertook a notes review of all BRCA1/2 gene mutation carriers tested within this time frame to identify those living in Essex and those who had been referred for discussion at the Essex RRM MDT. Additionally, the RRM MDT discussion lists and patient proformas were reviewed to provide data since the inception of this meeting.
Our data showed an approximately two-fold increase in number of BRCA1/2 genetic tests requested over the reviewed timeframe. The number of predictive BRCA1/2 gene tests arranged has approximately doubled since January 2013. Furthermore, the number of BRCA1/2 gene mutation carriers identified has approximately doubled since January 2013. As the frequency of RRM MDT meetings has increased from three to four per year, we observed a concomitant increase in the number of women discussed. Finally, while the proportion of women requesting RRM was found to be about constant at a third, because the numbers of women identified as BRCA1/2 gene mutation carriers continues to increase, so does the total number of BRCA1/2 gene mutation carriers requesting RRM.
Meeting organisation by The Wales Gene Park