Interpretation of Genomic Copy Number Variants Using DECIPHER

Manuel Corpas1, Eugene Bragin1, Stephen Clayton1, Paul Bevan1, Helen V. Firth2

1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom, 2 Cambridge University Hospitals Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 8.14
DOI:  10.1002/0471142905.hg0814s72
Online Posting Date:  January, 2012
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Abstract

Many patients suffering from developmental disorders have submicroscopic deletions or duplications affecting the copy number of dosage‐sensitive genes or disrupting normal gene expression. Many of these changes are novel or extremely rare, making clinical interpretation problematic and genotype/phenotype correlations difficult. Identification of patients sharing a genomic rearrangement and having phenotypes in common increases certainty in the diagnosis and allows characterization of new syndromes. The DECIPHER database is an online repository of genotype and phenotype data whose chief objective is to facilitate the association of genomic variation with phenotype to enable the clinical interpretation of copy number variation (CNV). This unit shows how DECIPHER can be used to (1) search for consented patients sharing a defined chromosomal location, (2) navigate regions of interest using in‐house visualization tools and the Ensembl genome browser, (3) analyze affected genes and prioritize them according to their likelihood of haploinsufficiency, (4) upload patient aberrations and phenotypes, and (5) create printouts at different levels of detail. By following this protocol, clinicians and researchers alike will be able to learn how to characterize their patients' chromosomal imbalances using DECIPHER. Curr. Protoc. Hum. Genet. 72:8.14.1‐8.14.17 © 2012 by John Wiley & Sons, Inc.

Keywords: copy number variation; clinical genetics; array CGH; genotype; phenotype; developmental disorders; bioinformatics

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Searching DECIPHER by Location as a Public User
  • Basic Protocol 2: Searching DECIPHER for a Phenotype as a Public User
  • Basic Protocol 3: Adding a Patient to DECIPHER as a Registered Member
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Literature Cited

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