The Phenotype of SDHB Germline Mutation Carriers
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
SUPPLEMENTARY FIGURES and TABLES Genetic Hallmarks of Recurrent/Metastatic Adenoid Cystic Carcinoma
SUPPLEMENTARY FIGURES AND TABLES Genetic Hallmarks Of Recurrent/Metastatic Adenoid Cystic Carcinoma SUPPLEMENTARY FIGURES Figure S1. Flow diagram of study design. Figure S2. Primary and recurrent/metastatic adenoid cystic carcinoma distribution by anatomic site. Figure S3. Variant allelic frequency (VAF) density histogram for NOTCH1 mutations observed in recurrent/metastatic adenoid cystic carcinoma (R/M ACC). Figure S4. Downsampling analysis of R/M MSK-IMPACT cohort (n=94) to simulate mutation detection at 100x coverage. Figure S5. Representative PyClone plots demonstrating intratumoral heterogeneity quantified as number of genomically distinct subclonal populations in adenoid cystic carcinoma. Figure S6. MRI of the neck with contrast of adenoid cystic carcinoma of right parotid gland involving masseter muscle and ascending ramus. Figure S7. Histologic confirmation of 6 representative distant metastatic sites of a single case with parotid adenoid cystic carcinoma. Figure S8. Fluorescence in situ hybridization (FISH) of distant lung metastatic lesions in a single case of parotid adenoid cystic carcinoma. Figure S9. Two-way plots of cancer cell fraction in a single case of parotid adenoid cystic carcinoma, comparing primary tumor with eight metastatic lesions. Figure S10. Multiregion clonal evolution heatmap analysis of two breast adenoid cystic carcinoma cases with transformation to high grade triple-negative breast cancer (TNBC) histology. SUPPLEMENTARY TABLES Table S1. Study distribution of primary and recurrent/metastatic (R/M) adenoid cystic carcinoma (ACC) cases. Mixed entails head and neck, lung, and breast disease sites. Table S2. Top gene alteration incidence by tumor site (includes primary and recurrent/metastatic cases). Table S3. Top gene alteration incidence of recurrent/metastatic adenoid cystic carcinoma (R/M ACC) cases comparing primary site with distant metastatic site. -
Next-Generation Sequencing for Identifying a Novel/De Novo
Martínez-Hernández et al. BMC Medical Genomics (2019) 12:68 https://doi.org/10.1186/s12920-019-0528-1 CASE REPORT Open Access Next-generation sequencing for identifying a novel/de novo pathogenic variant in a Mexican patient with cystic fibrosis: a case report Angélica Martínez-Hernández1, Julieta Larrosa2, Francisco Barajas-Olmos1, Humberto García-Ortíz1, Elvia C. Mendoza-Caamal3, Cecilia Contreras-Cubas1, Elaheh Mirzaeicheshmeh1, José Luis Lezana4 and Lorena Orozco1* Abstract Background: Mexico is among the countries showing the highest heterogeneity of CFTR variants. However, no de novo variants have previously been reported in Mexican patients with cystic fibrosis (CF). Case presentation: Here, we report the first case of a novel/de novo variant in a Mexican patient with CF. Our patient was an 8-year-old male who had exhibited the clinical onset of CF at one month of age, with steatorrhea, malabsorption, poor weight gain, anemia, and recurrent respiratory tract infections. Complete sequencing of the CFTR gene by next generation sequencing (NGS) revealed two different variants in trans, including the previously reported CF-causing variant c.3266G > A (p.Trp1089*, W1089*), that was inherited from the mother, and the novel/ de novo CFTR variant c.1762G > T (p.Glu588*). Conclusion: Our results demonstrate the efficiency of targeted NGS for making a rapid and precise diagnosis in patients with clinically suspected CF. This method can enable the provision of accurate genetic counselling, and improve our understanding of the molecular basis of genetic diseases. Keywords: Cystic fibrosis, Next generation sequencing, P.Trp1089*, P.Glu588*, Novel/de novo variant Background been detected, with the deletion of phenylalanine at pos- Cystic fibrosis (CF, MIM# 219700) is the most common ition 508 (c.1521_1523delCTT, p.Phe508del, F508del) autosomal recessive disorder among Caucasians. -
Multi-Omics Analysis Defines Core Genomic Alterations in Pheochromocytomas and Paragangliomas
ARTICLE Received 11 Aug 2014 | Accepted 5 Dec 2014 | Published 27 Jan 2015 DOI: 10.1038/ncomms7044 OPEN Multi-omics analysis defines core genomic alterations in pheochromocytomas and paragangliomas Luis Jaime Castro-Vega1,2,*, Eric Letouze´3,*, Nelly Burnichon1,2,4,*, Alexandre Buffet1,2,4, Pierre-He´lie Disderot1,2, Emmanuel Khalifa1,2,4,Ce´line Loriot1,2, Nabila Elarouci3, Aure´lie Morin1,2,Me´lanie Menara1,2, Charlotte Lepoutre-Lussey1,2,5,Ce´cile Badoual1,2,6, Mathilde Sibony2,7, Bertrand Dousset2,8,9,10, Rossella Libe´2,9,10,11,12, Franck Zinzindohoue2,13, Pierre Franc¸ois Plouin1,2,5,12,Je´roˆme Bertherat2,9,10,11,12, Laurence Amar1,2,5, Aure´lien de Reynie`s3, Judith Favier1,2,y & Anne-Paule Gimenez-Roqueplo1,2,4,12,y Pheochromocytomas and paragangliomas (PCCs/PGLs) are neural crest-derived tumours with a very strong genetic component. Here we report the first integrated genomic examination of a large collection of PCC/PGL. SNP array analysis reveals distinct copy-number patterns associated with genetic background. Whole-exome sequencing shows a low mutation rate of 0.3 mutations per megabase, with few recurrent somatic mutations in genes not previously associated with PCC/PGL. DNA methylation arrays and miRNA sequencing identify DNA methylation changes and miRNA expression clusters strongly associated with messenger RNA expression profiling. Overexpression of the miRNA cluster 182/96/183 is specific in SDHB-mutated tumours and induces malignant traits, whereas silencing of the imprinted DLK1-MEG3 miRNA cluster appears as a potential driver in a subgroup of sporadic tumours. -
Crystal Structure of Bacterial Succinate:Quinone Oxidoreductase Flavoprotein Sdha in Complex with Its Assembly Factor Sdhe
Crystal structure of bacterial succinate:quinone oxidoreductase flavoprotein SdhA in complex with its assembly factor SdhE Megan J. Mahera,1, Anuradha S. Heratha, Saumya R. Udagedaraa, David A. Dougana, and Kaye N. Truscotta,1 aDepartment of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia Edited by Amy C. Rosenzweig, Northwestern University, Evanston, IL, and approved February 14, 2018 (received for review January 4, 2018) Succinate:quinone oxidoreductase (SQR) functions in energy me- quinol:FRD), respectively (13, 15). The importance of this protein tabolism, coupling the tricarboxylic acid cycle and electron transport family, in normal cellular metabolism, is manifested by the iden- chain in bacteria and mitochondria. The biogenesis of flavinylated tification of a mutation in human SDHAF2 (Gly78Arg), which is SdhA, the catalytic subunit of SQR, is assisted by a highly conserved linked to an inherited neuroendocrine disorder, PGL2 (10). Cur- assembly factor termed SdhE in bacteria via an unknown mecha- rently, however, the role of SdhE in flavinylation remains poorly nism. By using X-ray crystallography, we have solved the structure understood. To date, three different modes of action for SdhE/ of Escherichia coli SdhE in complex with SdhA to 2.15-Å resolution. Sdh5 have been proposed, suggesting that SdhE facilitates the Our structure shows that SdhE makes a direct interaction with the binding and delivery of FAD (13), acts as a chaperone for SdhA flavin adenine dinucleotide-linked residue His45 in SdhA and main- (10), or catalyzes the attachment of FAD (10). Moreover, the re- tains the capping domain of SdhA in an “open” conformation. -
Inhibition of Mitochondrial Complex II in Neuronal Cells Triggers Unique
www.nature.com/scientificreports OPEN Inhibition of mitochondrial complex II in neuronal cells triggers unique pathways culminating in autophagy with implications for neurodegeneration Sathyanarayanan Ranganayaki1, Neema Jamshidi2, Mohamad Aiyaz3, Santhosh‑Kumar Rashmi4, Narayanappa Gayathri4, Pulleri Kandi Harsha5, Balasundaram Padmanabhan6 & Muchukunte Mukunda Srinivas Bharath7* Mitochondrial dysfunction and neurodegeneration underlie movement disorders such as Parkinson’s disease, Huntington’s disease and Manganism among others. As a corollary, inhibition of mitochondrial complex I (CI) and complex II (CII) by toxins 1‑methyl‑4‑phenylpyridinium (MPP+) and 3‑nitropropionic acid (3‑NPA) respectively, induced degenerative changes noted in such neurodegenerative diseases. We aimed to unravel the down‑stream pathways associated with CII inhibition and compared with CI inhibition and the Manganese (Mn) neurotoxicity. Genome‑wide transcriptomics of N27 neuronal cells exposed to 3‑NPA, compared with MPP+ and Mn revealed varied transcriptomic profle. Along with mitochondrial and synaptic pathways, Autophagy was the predominant pathway diferentially regulated in the 3‑NPA model with implications for neuronal survival. This pathway was unique to 3‑NPA, as substantiated by in silico modelling of the three toxins. Morphological and biochemical validation of autophagy markers in the cell model of 3‑NPA revealed incomplete autophagy mediated by mechanistic Target of Rapamycin Complex 2 (mTORC2) pathway. Interestingly, Brain Derived Neurotrophic Factor -
High-Efficiency CRISPR/Cas9 Mutagenesis of the White Gene in the Milkweed Bug Oncopeltus Fasciatus
| INVESTIGATION High-Efficiency CRISPR/Cas9 Mutagenesis of the white Gene in the Milkweed Bug Oncopeltus fasciatus Katie Reding and Leslie Pick1 Department of Entomology, University of Maryland, College Park, Maryland 20742 ORCID IDs: 0000-0003-2067-4232 (K.R.); 0000-0002-4505-5107 (L.P.) ABSTRACT In this manuscript, we report that clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 is highly efficient in the hemipteran Oncopeltus fasciatus. The white gene is well characterized in Drosophila where mutation causes loss of eye pigmentation; white is a reliable marker for transgenesis and other genetic manipulations. Accordingly, white has been targeted in a number of nonmodel insects to establish tools for genetic studies. Here, we generated mutations in the Of-white (Of-w) locus using CRISPR/Cas9. We found that Of-w is required for pigmentation throughout the body of Oncopeltus, not just the ommatidia. High rates of somatic mosaicism were observed in the injected generation, reflecting biallelic mutations, and a high rate of germline mutation was evidenced by the large proportion of heterozygous G1s. However, Of-w mutations are homozygous lethal; G2 homozygotes lacked pigment dispersion throughout the body and did not hatch, precluding the establishment of a stable mutant line. Embryonic and parental RNA interference (RNAi) were subsequently performed to rule out off-target mutations producing the observed phenotype and to evaluate the efficacy of RNAi in ablating gene function compared to a loss-of-function mutation. RNAi knockdowns phe- nocopied Of-w homozygotes, with an unusual accumulation of orange granules observed in unhatched embryos. This is, to our knowledge, the first CRISPR/Cas9-targeted mutation generated in Oncopeltus. -
Cfdna Deconvolution Via NIPT of a Pregnant Woman After Bone Marrow
Zhu et al. Human Genomics (2021) 15:14 https://doi.org/10.1186/s40246-021-00311-w PRIMARY RESEARCH Open Access cfDNA deconvolution via NIPT of a pregnant woman after bone marrow transplant and donor egg IVF Jianjiang Zhu1 , Feng Hui2, Xuequn Mao1, Shaoqin Zhang1, Hong Qi1* and Yang Du2* Abstract Cell-free DNA is known to be a mixture of DNA fragments originating from various tissue types and organs of the human body and can be utilized for several clinical applications and potentially more to be created. Non-invasive prenatal testing (NIPT), by high throughput sequencing of cell-free DNA (cfDNA), has been successfully applied in the clinical screening of fetal chromosomal aneuploidies, with more extended coverage under active research. In this study, via a quite unique and rare NIPT sample, who has undergone both bone marrow transplant and donor egg IVF, we investigated the sources of oddness observed in the NIPT result using a combination of molecular genetics and genomic methods and eventually had the case fully resolved. Along the process, we devised a clinically viable process to dissect the sample mixture. Eventually, we used the proposed scheme to evaluate the relatedness of individuals and the demultiplexed sample components following modified population genetics concepts, exemplifying a noninvasive prenatal paternity test prototype. For NIPT specific applicational concern, more thorough and detailed clinical information should therefore be collected prior to cfDNA-based screening procedure like NIPT and systematically reviewed when an abnormal report is obtained to improve genetic counseling and overall patient care. Keywords: NIPT, Target sequencing, Fetal fraction, IVF, Transplant, Prenatal diagnostic Introduction establishment of circulating tumor DNA (ctDNA) in the Cell-free DNA (cfDNA) is known to be a mixture from plasma of cancer patients [4]. -
Genetic Testing for Reproductive Carrier Screening and Prenatal Diagnosis
Medical Coverage Policy Effective Date ............................................. 7/15/2021 Next Review Date ......................................12/15/2021 Coverage Policy Number .................................. 0514 Genetic Testing for Reproductive Carrier Screening and Prenatal Diagnosis Table of Contents Related Coverage Resources Overview ........................................................ 2 Genetics Coverage Policy ............................................ 2 Genetic Testing Collateral File Genetic Counseling ...................................... 2 Recurrent Pregnancy Loss: Diagnosis and Treatment Germline Carrier Testing for Familial Infertility Services Disease .......................................................... 3 Preimplantation Genetic Testing of an Embryo........................................................... 4 Preimplantation Genetic Testing (PGT-A) .. 5 Sequencing–Based Non-Invasive Prenatal Testing (NIPT) ............................................... 5 Invasive Prenatal Testing of a Fetus .......... 6 Germline Mutation Reproductive Genetic Testing for Recurrent Pregnancy Loss ...... 6 Germline Mutation Reproductive Genetic Testing for Infertility ..................................... 7 General Background .................................... 8 Genetic Counseling ...................................... 8 Germline Genetic Testing ............................ 8 Carrier Testing for Familial Disease ........... 8 Preimplantation Genetic Testing of an Embryo.......................................................... -
One in Three Highly Selected Greek Patients with Breast Cancer Carries A
Cancer genetics J Med Genet: first published as 10.1136/jmedgenet-2019-106189 on 12 July 2019. Downloaded from ORIGINAL ARTICLE One in three highly selected Greek patients with breast cancer carries a loss-of-function variant in a cancer susceptibility gene Florentia Fostira, 1 Irene Kostantopoulou,1 Paraskevi Apostolou,1 Myrto S Papamentzelopoulou,1 Christos Papadimitriou,2 Eleni Faliakou,3 Christos Christodoulou,4 Ioannis Boukovinas,5 Evangelia Razis,6 Dimitrios Tryfonopoulos,7 Vasileios Barbounis,8 Andromache Vagena,1 Ioannis S Vlachos,9 Despoina Kalfakakou, 1 George Fountzilas,10 Drakoulis Yannoukakos1 ► Additional material is ABSTRact individuals carrying such pathogenic variants (PVs) published online only. To view Background Gene panel testing has become the norm face an increased lifetime risk for cancer diagnoses.1 please visit the journal online (http:// dx. doi. org/ 10. 1136/ for assessing breast cancer (BC) susceptibility, but actual The implementation of BRCA1 and BRCA2 genetic jmedgenet- 2019- 106189). cancer risks conferred by genes included in panels are testing into clinical practice has enabled the identifi- not established. Contrarily, deciphering the missing cation of individuals at high risk and the application For numbered affiliations see hereditability on BC, through identification of novel of tailored management guidelines, significantly end of article. candidates, remains a challenge. We aimed to investigate improving both cancer prevention and survival.2 the mutation prevalence and spectra in a highly Mutations -
The Genetic Complexity of Prostate Cancer
G C A T T A C G G C A T genes Review The Genetic Complexity of Prostate Cancer Eva Compérat 1,2,3,*, Gabriel Wasinger 3 , André Oszwald 3 , Renate Kain 3 , Geraldine Cancel-Tassin 1 and Olivier Cussenot 1,4 1 CeRePP/GRC5 Predictive Onco-Urology, Sorbonne University, 75020 Paris, France; [email protected] (G.C.-T.); [email protected] (O.C.) 2 Department of Pathology, Hôpital Tenon, Sorbonne University, 75020 Paris, France 3 Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria; [email protected] (G.W.); [email protected] (A.O.); [email protected] (R.K.) 4 Department of Urology, Hôpital Tenon, Sorbonne University, 75020 Paris, France * Correspondence: [email protected]; Tel.: +33-658246024 Received: 28 September 2020; Accepted: 23 November 2020; Published: 25 November 2020 Abstract: Prostate cancer (PCa) is a major concern in public health, with many genetically distinct subsets. Genomic alterations in PCa are extraordinarily complex, and both germline and somatic mutations are of great importance in the development of this tumor. The aim of this review is to provide an overview of genetic changes that can occur in the development of PCa and their role in potential therapeutic approaches. Various pathways and mechanisms proposed to play major roles in PCa are described in detail to provide an overview of current knowledge. Keywords: prostate cancer; germline mutations; somatic mutations; PTEN; TMPRSS2; ERG; androgen receptors 1. Introduction Prostate cancer (PCa) is a major concern in public health, with more than 1.1 million cases worldwide detected every year [1]. -
Multiple Endocrine Neoplasia Type 2: an Overview Jessica Moline, MS1, and Charis Eng, MD, Phd1,2,3,4
GENETEST REVIEW Genetics in Medicine Multiple endocrine neoplasia type 2: An overview Jessica Moline, MS1, and Charis Eng, MD, PhD1,2,3,4 TABLE OF CONTENTS Clinical Description of MEN 2 .......................................................................755 Surveillance...................................................................................................760 Multiple endocrine neoplasia type 2A (OMIM# 171400) ....................756 Medullary thyroid carcinoma ................................................................760 Familial medullary thyroid carcinoma (OMIM# 155240).....................756 Pheochromocytoma ................................................................................760 Multiple endocrine neoplasia type 2B (OMIM# 162300) ....................756 Parathyroid adenoma or hyperplasia ...................................................761 Diagnosis and testing......................................................................................756 Hypoparathyroidism................................................................................761 Clinical diagnosis: MEN 2A........................................................................756 Agents/circumstances to avoid .................................................................761 Clinical diagnosis: FMTC ............................................................................756 Testing of relatives at risk...........................................................................761 Clinical diagnosis: MEN 2B ........................................................................756 -
A Germline Or De Novo Mutation in Two Families with Gaucher Disease: Implications for Recessive Disorders
European Journal of Human Genetics (2013) 21, 115–117 & 2013 Macmillan Publishers Limited All rights reserved 1018-4813/13 www.nature.com/ejhg SHORT REPORT A germline or de novo mutation in two families with Gaucher disease: implications for recessive disorders Hamid Saranjam1, Sameer S Chopra2,3, Harvey Levy3, Barbara K Stubblefield1, Emerson Maniwang1, Ian J Cohen4,5, Hagit Baris4,5, Ellen Sidransky*,1 and Nahid Tayebi1 Gaucher disease (GD) is an autosomal recessive storage disorder that most commonly results from the inheritance of one identifiable mutant glucocerebrosidase (GBA1) allele from each parent. Here, we report two cases of type 2 GD resulting from the inheritance of one identifiable paternal mutant allele and one allele that likely resulted from a maternal germline mutation. Germline mutations or mosiacism are not generally associated with autosomal recessive disorders. The probands from the two unrelated families had the same maternal mutation, leu444pro, that we propose resulted from a de novo maternal germline mutation occurring at this known ‘hotspot’ for mutation. This first report of a germline mutation for a common point mutation leu444pro (c.1448 T4C;p.leu483pro) in GD has significant implications for molecular diagnostics and genetic counseling in recessive disorders. European Journal of Human Genetics (2013) 21, 115–117; doi:10.1038/ejhg.2012.105; published online 20 June 2012 Keywords: acute neuronopathic Gaucher disease; glucocerebrosidase; germline mutation; DNA mutational analysis; molecular diagnostic INTRODUCTION However, in both cases, the second mutant allele, leu444pro, was Gaucher disease (GD), the most common lysosomal storage disorder, not detected in the mother. This prompted us to explore whether the results from the autosomal recessively inherited deficiency of gluco- leu444pro mutation might have resulted from a maternal germline cerebrosidase (GCase, EC 3.2.1.45).1,2 GD is subdivided into three mutation in these families.