7Q11.23 Duplication Syndrome
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Analysis of Trans Esnps Infers Regulatory Network Architecture
Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Anat Kreimer All rights reserved ABSTRACT Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer eSNPs are genetic variants associated with transcript expression levels. The characteristics of such variants highlight their importance and present a unique opportunity for studying gene regulation. eSNPs affect most genes and their cell type specificity can shed light on different processes that are activated in each cell. They can identify functional variants by connecting SNPs that are implicated in disease to a molecular mechanism. Examining eSNPs that are associated with distal genes can provide insights regarding the inference of regulatory networks but also presents challenges due to the high statistical burden of multiple testing. Such association studies allow: simultaneous investigation of many gene expression phenotypes without assuming any prior knowledge and identification of unknown regulators of gene expression while uncovering directionality. This thesis will focus on such distal eSNPs to map regulatory interactions between different loci and expose the architecture of the regulatory network defined by such interactions. We develop novel computational approaches and apply them to genetics-genomics data in human. We go beyond pairwise interactions to define network motifs, including regulatory modules and bi-fan structures, showing them to be prevalent in real data and exposing distinct attributes of such arrangements. We project eSNP associations onto a protein-protein interaction network to expose topological properties of eSNPs and their targets and highlight different modes of distal regulation. -
Aneuploidy and Aneusomy of Chromosome 7 Detected by Fluorescence in Situ Hybridization Are Markers of Poor Prognosis in Prostate Cancer'
[CANCERRESEARCH54,3998-4002,August1, 19941 Advances in Brief Aneuploidy and Aneusomy of Chromosome 7 Detected by Fluorescence in Situ Hybridization Are Markers of Poor Prognosis in Prostate Cancer' Antonio Alcaraz, Satoru Takahashi, James A. Brown, John F. Herath, Erik J- Bergstralh, Jeffrey J. Larson-Keller, Michael M Lieber, and Robert B. Jenkins2 Depart,nent of Urology [A. A., S. T., J. A. B., M. M. U, Laboratory Medicine and Pathology (J. F. H., R. B. fl, and Section of Biostatistics (E. J. B., J. J. L-JCJ, Mayo Clinic and Foundation@ Rochester, Minnesota 55905 Abstract studies on prostate carcinoma samples. Interphase cytogenetic analy sis using FISH to enumerate chromosomes has the potential to over Fluorescence in situ hybridization is a new methodologj@which can be come many of the difficulties associated with traditional cytogenetic used to detect cytogenetic anomalies within interphase tumor cells. We studies. Previous studies from this institution have demonstrated that used this technique to identify nonrandom numeric chromosomal alter ations in tumor specimens from the poorest prognosis patients with path FISH analysis with chromosome enumeration probes is more sensitive ological stages T2N@M,Jand T3NOMOprostate carcinomas. Among 1368 than FCM for detecting aneuploid prostate cancers (4, 5, 7). patients treated by radical prostatectomy, 25 study patients were ascer We designed a case-control study to test the hypothesis that spe tamed who died most quickly from progressive prostate carcinoma within cific, nonrandom cytogenetic changes are present in tumors removed 3 years of diagnosis and surgery. Tumors from 25 control patients who from patients with prostate carcinomas with poorest prognoses . -
Williams Syndrome Specialized Health Needs Interagency Collaboration
SHNIC Factsheet: Williams Syndrome Specialized Health Needs Interagency Collaboration What is it? Williams syndrome (WS) is a random genetic mutation disorder that presents at birth, affecting both boys and girls equally. WS is caused by the deletion of genetic material from a specific region of chromosome 7. This disease is characterized by an array of medical problems that can range in severity and age of onset. However, all cases are characterized by dysmorphic facial features, cardiovascular disease, and developmental delay. These disabilities occur in conjunction with striking verbal abilities, highly social personalities, and an affinity for music. What are characteristics? Heart and blood vessel problems Low muscle tone and joint laxity Reflux Dental abnormalities Hypercalcemia Developmental Delays Hearing sensitivity Characteristic facial features: Kidney problems small upturned nose Hernias wide mouth Facial characteristics full lips Chronic ear infection small chin puffiness around the eyes Suggested school accommodations Most children with Williams Syndrome have some form of learning difficulties but they can significant- ly vary. As they age, you may notice the child struggling with concepts like spatial relations, numbers and abstract reasoning. Many children with WS appear scattered in their level of abilities across do- mains. Although a child with WS may be very social, remember to monitor their support systems and social interactions as they often have a difficult time understanding social cues. Physical/Medical -
7Q Deletions Proximal Interstitial FTNP
Support and Information Rare Chromosome Disorder Support Group, G1, The Stables, Station Road West, Oxted, Surrey RH8 9EE, United Kingdom Tel/Fax: +44(0)1883 723356 [email protected] III www.rarechromo.org Join Unique for family links, information and support. 7q deletions Unique is a charity without government funding, existing entirely on donations and grants. If you can, please make a donation via our website at www.rarechromo.org Please help us to help you! proximal interstitial Facebook group for 7q deletions and duplications: www.facebook.com/groups/493223084038489 Unique lists external message boards and websites in order to be helpful to families looking for information and support. This does not imply that we endorse their content or have any responsibility for it. This information guide is not a substitute for personal medical advice. Families should consult a medically qualified clinician in all matters relating to genetic diagnosis, management and health. Information on genetic changes is a very fast-moving field and while the information in this guide is believed to be the best available at the time of publication, some facts may later change. Unique does its best to keep abreast of changing information and to review its published guides as needed. The guide was compiled by Unique and reviewed by Dr Steve Scherer, Centre for Applied Genomics, Hospital for Sick Children, Toronto, Canada and by Professor Maj Hultén, BSc, PhD, MD, FRCPath, Professor of Medical Genetics, University of Warwick, 2009. Copyright © Unique 2009 Rare Chromosome Disorder Support Group Charity Number 1110661 Registered in England and Wales Company Number 5460413 rrraraaarrrreeeecccchhhhrrrroooommmmoooo....oooorrrrgggg 24 A 7q deletion the development of an embryo. -
The Contribution of CLIP2 Haploinsufficiency to the Clinical
REPORT The Contribution of CLIP2 Haploinsufficiency to the Clinical Manifestations of the Williams-Beuren Syndrome Geert Vandeweyer,1 Nathalie Van der Aa,1 Edwin Reyniers,1 and R. Frank Kooy1,* Williams-Beuren syndrome is a rare contiguous gene syndrome, characterized by intellectual disability, facial dysmorphisms, connec- tive-tissue abnormalities, cardiac defects, structural brain abnormalities, and transient infantile hypercalcemia. Genes lying telomeric to RFC2, including CLIP2, GTF2I and GTF2IRD1, are currently thought to be the most likely major contributors to the typical Williams syndrome cognitive profile, characterized by a better-than-expected auditory rote-memory ability, a relative sparing of language capa- bilities, and a severe visual-spatial constructive impairment. Atypical deletions in the region have helped to establish genotype-pheno- type correlations. So far, however, hardly any deletions affecting only a single gene in the disease region have been described. We present here two healthy siblings with a pure, hemizygous deletion of CLIP2. A putative role in the cognitive and behavioral abnormalities seen in Williams-Beuren patients has been suggested for this gene on the basis of observations in a knock-out mouse model. The presented siblings did not show any of the clinical features associated with the syndrome. Cognitive testing showed an average IQ for both and no indication of the Williams syndrome cognitive profile. This shows that CLIP2 haploinsufficiency by itself does not lead to the physical or cognitive characteristics of the Williams-Beuren syndrome, nor does it lead to the Williams syndrome cognitive profile. Although contri- bution of CLIP2 to the phenotype cannot be excluded when it is deleted in combination with other genes, our results support the hypothesis that GTF2IRD1 and GTF2I are the main genes causing the cognitive defects associated with Williams-Beuren syndrome. -
In This Table Protein Name, Uniprot Code, Gene Name P-Value
Supplementary Table S1: In this table protein name, uniprot code, gene name p-value and Fold change (FC) for each comparison are shown, for 299 of the 301 significantly regulated proteins found in both comparisons (p-value<0.01, fold change (FC) >+/-0.37) ALS versus control and FTLD-U versus control. Two uncharacterized proteins have been excluded from this list Protein name Uniprot Gene name p value FC FTLD-U p value FC ALS FTLD-U ALS Cytochrome b-c1 complex P14927 UQCRB 1.534E-03 -1.591E+00 6.005E-04 -1.639E+00 subunit 7 NADH dehydrogenase O95182 NDUFA7 4.127E-04 -9.471E-01 3.467E-05 -1.643E+00 [ubiquinone] 1 alpha subcomplex subunit 7 NADH dehydrogenase O43678 NDUFA2 3.230E-04 -9.145E-01 2.113E-04 -1.450E+00 [ubiquinone] 1 alpha subcomplex subunit 2 NADH dehydrogenase O43920 NDUFS5 1.769E-04 -8.829E-01 3.235E-05 -1.007E+00 [ubiquinone] iron-sulfur protein 5 ARF GTPase-activating A0A0C4DGN6 GIT1 1.306E-03 -8.810E-01 1.115E-03 -7.228E-01 protein GIT1 Methylglutaconyl-CoA Q13825 AUH 6.097E-04 -7.666E-01 5.619E-06 -1.178E+00 hydratase, mitochondrial ADP/ATP translocase 1 P12235 SLC25A4 6.068E-03 -6.095E-01 3.595E-04 -1.011E+00 MIC J3QTA6 CHCHD6 1.090E-04 -5.913E-01 2.124E-03 -5.948E-01 MIC J3QTA6 CHCHD6 1.090E-04 -5.913E-01 2.124E-03 -5.948E-01 Protein kinase C and casein Q9BY11 PACSIN1 3.837E-03 -5.863E-01 3.680E-06 -1.824E+00 kinase substrate in neurons protein 1 Tubulin polymerization- O94811 TPPP 6.466E-03 -5.755E-01 6.943E-06 -1.169E+00 promoting protein MIC C9JRZ6 CHCHD3 2.912E-02 -6.187E-01 2.195E-03 -9.781E-01 Mitochondrial 2- -
Ongoing Human Chromosome End Extension Revealed by Analysis of Bionano and Nanopore Data Received: 4 May 2018 Haojing Shao , Chenxi Zhou , Minh Duc Cao & Lachlan J
www.nature.com/scientificreports OPEN Ongoing human chromosome end extension revealed by analysis of BioNano and nanopore data Received: 4 May 2018 Haojing Shao , Chenxi Zhou , Minh Duc Cao & Lachlan J. M. Coin Accepted: 22 October 2018 The majority of human chromosome ends remain incompletely assembled due to their highly repetitive Published: xx xx xxxx structure. In this study, we use BioNano data to anchor and extend chromosome ends from two European trios as well as two unrelated Asian genomes. At least 11 BioNano assembled chromosome ends are structurally divergent from the reference genome, including both missing sequence and extensions. These extensions are heritable and in some cases divergent between Asian and European samples. Six out of nine predicted extension sequences from NA12878 can be confrmed and flled by nanopore data. We identify two multi-kilobase sequence families both enriched more than 100- fold in extension sequence (p-values < 1e-5) whose origins can be traced to interstitial sequence on ancestral primate chromosome 7. Extensive sub-telomeric duplication of these families has occurred in the human lineage subsequent to divergence from chimpanzees. Te genome sequence of chromosome ends in the reference human genome remains incompletely assembled. In the latest draf of the human genome1 21 out of 48 chromosome ends were incomplete; amongst which fve chromosome ends (13p, 14p, 15p, 21p, 22p) are completely unknown and the remaining chromosome ends are capped with 10–110 kb of unknown sequence. Tere are many interesting observations in the chromosome end regions which remain unexplained, such as the observed increase in genetic divergence between Chimpanzee and Humans towards the chromosome ends2. -
Familial Bone Marrow Monosomy 7 Evidence That the Predisposing Locus Is Not on the Long Arm of Chromosome 7 Kevin M
Familial Bone Marrow Monosomy 7 Evidence That the Predisposing Locus Is Not on the Long Arm of Chromosome 7 Kevin M. Shannon,* All G. Turhan,*$ Sharon S. Y. Chang,"1 Anne M. Bowcock,' Paul C. J. Rogers,** William L. Carroll,# Morton J. Cowan,* Bertil E. Glader,* Connie J. Eaves, *1111 Allen C. Eaves,t1111 and Yuet Wai Kan1ltl Departments of*Pediatrics and "'Medicine and 1lHoward Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94143; Departments of Pathology, **Pediatrics, and 111IMedicine, University ofBritish Columbia, and the §Terry Fox Laboratory, British Columbia Cancer Centre, Vancouver, British Columbia, Canada; Departments of'Genetics and "Pediatrics, Stanford University Medical School, Stanford, California 94303; and t*Department ofPediatrics, Washington University School of Medicine, St. Louis, Missouri 63110 Abstract cinogen exposure (3, 6). The age distribution of these de novo cases shows peaks in the first and fifth decades (6). Overall, Loss of expression of a tumor-suppressing gene is an attractive monosomy 7 or 7q- is identified in - 5% of de novo and in model to explain the cytogenetic and epidemiologic features of 40% of secondary cases of AML (1, 3-5). Although childhood cases of myelodysplasia and acute myelogenous leukemia bone marrow monosomy 7 is an uncommon disorder, it has (AML) associated with bone marrow monosomy 7 or partial been observed in two or more siblings at least seven times deletion of the long arm (7q-). We used probes from within the (7-10, Lange, B. J., personal communication, and our unpub- breakpoint region on 7q- chromosomes (7q22-34) that detect lished data). -
Transcriptome Network of the Papillary Thyroid Carcinoma Radiation Marker
Selmansberger et al. Radiation Oncology (2020) 15:182 https://doi.org/10.1186/s13014-020-01620-5 RESEARCH Open Access Transcriptome network of the papillary thyroid carcinoma radiation marker CLIP2 Martin Selmansberger1, Agata Michna1, Herbert Braselmann1, Ines Höfig2, Kenji Schorpp3, Peter Weber1, Natasa Anastasov2, Horst Zitzelsberger1,4,5, Julia Hess1,4,5 and Kristian Unger1,4,5* Abstract Background: We present a functional gene association network of the CLIP2 gene, generated by de-novo reconstruction from transcriptomic microarray data. CLIP2 was previously identified as a potential marker for radiation induced papillary thyroid carcinoma (PTC) of young patients in the aftermath of the Chernobyl reactor accident. Considering the rising thyroid cancer incidence rates in western societies, potentially related to medical radiation exposure, the functional characterization of CLIP2 is of relevance and contributes to the knowledge about radiation-induced thyroid malignancies. Methods: We generated a transcriptomic mRNA expression data set from a CLIP2-perturbed thyroid cancer cell line (TPC-1) with induced CLIP2 mRNA overexpression and siRNA knockdown, respectively, followed by gene-association network reconstruction using the partial correlation-based approach GeneNet. Furthermore, we investigated different approaches for prioritizing differentially expressed genes for network reconstruction and compared the resulting networks with existing functional interaction networks from the Reactome, Biogrid and STRING databases. The derived CLIP2 interaction partners were validated on transcript and protein level. Results: The best reconstructed network with regard to selection parameters contained a set of 20 genes in the 1st neighborhood of CLIP2 and suggests involvement of CLIP2 in the biological processes DNA repair/maintenance, chromosomal instability, promotion of proliferation and metastasis. -
Williams Syndrome (WS): Recent Research on Music and Sound
American Music Therapy Association 8455 Colesville Rd., Ste. 1000 • Silver Spring, Maryland 20910 Tel. (301) 589-3300 • Fax (301) 589-5175 • www.musictherapy.org Williams Syndrome (WS): Recent Research on Music and Sound STATEMENT OF PURPOSE Description: Music Therapy (MT) is the clinical and evidence-based use of music interventions to accomplish individualized goals within a therapeutic relationship by a credentialed professional who has completed an approved music therapy program. Although WS is a rare disease, MTs may have more contact with these clients since many people with WS have a strong affinity for music, melody and song. Parents of children with WS express a strong interest in adaptive music programs for their children. The aim of therapy is to help people with WS to optimize their talents and musical affinity in order to address multiple potential outcomes. MT sessions may include the use of active music making, singing, interactive music play, and improvisational techniques. MT may include both individual and group therapy. STANDARDIZATION: MT sessions are documented in a treatment plan and delivered in accordance with standards of practice. Music selections and certain active music making activities are modified for client preferences and individualized needs (i.e., song selection, musical instruments, and music may vary). REPLICATION: Yes; MT and music special education has been used with different settings, providers, and populations. Research replication in the area of music response and WS is growing. OUTCOMES: Improved global state, enhanced learning, general functioning, improved social functioning, and enhanced leisure time. OVERVIEW OF RESEARCH The prevalence rate for WS is estimated at 0.01% or about 36,266 people in the United States. -
Preimplantation Genetic Screening and Diagnosis
Lab Management Guidelines v2.0.2019 Preimplantation Genetic Screening and Diagnosis MOL.CU.119.P v2.0.2019 Description Preimplantation Genetic Diagnosis (PGD) and Preimplantation Genetic Screening (PGS) are used to detect genetic conditions, chromosome abnormalities, and fetal sex during assisted reproduction with in vitro fertilization (IVF). PGD refers to embryo testing that is performed when one or both parents have a known genetic abnormality. This includes single-gene mutations and chromosome rearrangements. PGS refers to screening an embryo for aneuploidy when both parents are chromosomally normal. Genetic testing is performed on cells from the developing embryo prior to implantation. Only those embryos not affected with a genetic condition are implanted. PGD may allow at-risk couples to avoid a pregnancy affected with a genetic condition. The Society for Assisted Reproductive Technology and the American Society for Reproductive Medicine have published joint practice committee opinions to address the safety, accuracy, and overall efficacy of PGD and PGS.1,2 This guideline does not include prenatal or preconception carrier screening. Please refer to Genetic Testing for Carrier Status for that purpose. This guideline does not include prenatal genetic testing. Please see Genetic Testing for Prenatal Screening and Diagnostic Testing for genetic testing done during pregnancy. Criteria Criteria: General coverage guidance Preimplantation genetic diagnosis may be considered when ALL of the following conditions are met: Technical and clinical validity: The test must be accurate, sensitive and specific, based on sufficient, quality scientific evidence to support the claims of the test. In the case of PGD, the mutation(s) or translocation(s) to be tested in the embryo should first be well-characterized in the parent(s) AND the embryonic test results must be demonstrated to be highly accurate. -
The Behavioural Phenotype of Angelman Syndrome
The behavioural phenotype of Angelman syndrome. Horsler, K. and Oliver, C. Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham Please use this reference when citing this work: Horsler, K. and Oliver, C. (2006). The behavioural phenotype of Angelman syndrome. Journal of Intellectual Disability Research , 50 , 33-53. The Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Edgbaston, Birmingham, B15 2TT Website: www.cndd.Bham.ac.uk E-mail : [email protected] 1 ABSTRACT Background. The purpose of this review is to examine the notion of a behavioural phenotype for Angelman syndrome and identify methodological and conceptual influences on the accepted presentation. Method. Studies examining the behavioural characteristics associated with Angelman syndrome are reviewed and methodology is described. Results. Potential bias in the description of the phenotype emerges with the use of case and cohort studies with the absence of comparison groups. A trend in the literature from a direct gene effect to a socially mediated effect on laughter is evident. Conclusion. Evidence for a behavioural phenotype of Angelman syndrome has begun to emerge. However, by adopting the concept of a ‘behavioural phenotype’, attention may become biased towards the underlying biological basis of the syndrome, with developmental and environmental factors being overlooked. 2 INTRODUCTION Angelman described three children in 1965 who all presented with intellectual disability