SG-ADVISER CNV: Copy-number variant annotation and interpretation

Genetics in Medicine

Volumn 17, Issue 9, 2015, Pages 714-718

  Erikson, Galina A ^a,b   Deshpande, Neha ^a,b   Kesavan, Balachandar G ^a,b   Torkamani, Ali ^a,b,c,d  

^a SCRIPPS HEALTH   (United States)

^b SCRIPPS TRANSLATIONAL SCIENCE INSTITUTE   (United States)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

^d Cypher Genomics   (United States)

Author keywords

copy number variant; copy number variant interpretation; genome interpretation; genome sequencing; structural variant interpretation

Indexed keywords

ALGORITHM; ALLELE; ARTICLE; AUTISM; BIOINFORMATICS; CALCULATION; COMPARATIVE STUDY; COMPUTER INTERFACE; CONTROLLED STUDY; COPY NUMBER VARIATION; GENE FREQUENCY; GENOMICS; HUMAN; MEDICAL GENETICS; NEOPLASM; PHENOTYPE; PRACTICE GUIDELINE; PREDICTION; SCHIZOPHRENIA; BIOLOGY; GENETIC DATABASE; GENETIC VARIATION; HUMAN GENOME; INTERNET; MOLECULAR GENETICS; PROCEDURES; SOFTWARE;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA COPY NUMBER VARIATIONS; GENOME, HUMAN; GENOMIC STRUCTURAL VARIATION; HUMANS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; SOFTWARE;

EID: 84940922955     PISSN: 10983600     EISSN: 15300366     Source Type: Journal    
DOI: 10.1038/gim.2014.180     Document Type: Article

References (23)

1. Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet 2006;7:85-97.
2. Zhang F, Gu W, Hurles ME, Lupski JR. Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 2009;10:451-481.
3. Sebat J, Lakshmi B, Malhotra D, et al. Strong association of de novo copy number mutations with autism. Science 2007;316:445-449.
4. Xu B, Roos JL, Levy S, van Rensburg EJ, Gogos JA, Karayiorgou M. Strong association of de novo copy number mutations with sporadic schizophrenia. Nat Genet 2008;40:880-885.
5. Cooper GM, Coe BP, Girirajan S, et al. A copy number variation morbidity map of developmental delay. Nat Genet 2011;43:838-846.
6. Itsara A, Wu H, Smith JD, et al. De novo rates and selection of large copy number variation. Genome Res 2010;20:1469-1481.
7. Pinto D, Darvishi K, Shi X, et al. Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol 2011;29:512-520.
8. Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 2011;21:974-984.
9. Handsaker RE, Korn JM, Nemesh J, McCarroll SA. Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat Genet 2011;43:269-276.
10. Krumm N, O'Roak BJ, Karakoc E, et al. Transmission disequilibrium of small CNVs in simplex autism. Am J Hum Genet 2013;93:595-606.
11. Ching MS, Shen Y, Tan WH, et al.; Children's Hospital Boston Genotype Phenotype Study Group. Deletions of NRXN1 (neurexin-1) predispose to a wide spectrum of developmental disorders. Am J Med Genet B Neuropsychiatr Genet 2010;153B:937-947.
12. Wang K, Li M, Hadley D, et al. PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 2007;17:1665-1674.
13. Abecasis GR, Auton A, Brooks LD, et al.; 1000 Genomes Project Consortium. An integrated map of genetic variation from 1, 092 human genomes. Nature 2012;491:56-65.
14. Stenson PD, Ball E, Howells K, Phillips A, Mort M, Cooper DN. Human Gene Mutation Database: towards a comprehensive central mutation database. J Med Genet 2008;45:124-126.
15. Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005;33(Database issue):D514-D517.
16. Swaminathan GJ, Bragin E, Chatzimichali EA, et al. DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders. Hum Mol Genet 2012;21(R1):R37-R44.
17. Mitelman F, Johansson B, Mertens F. The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 2007;7:233-245.
18. Landrum MJ, Lee JM, Riley GR, et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res 2014;42(Database issue):D980-D985.
19. Forbes SA, Bindal N, Bamford S, et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 2011;39(Database issue):D945-D950.
20. Mills RE, Walter K, Stewart C, et al.; 1000 Genomes Project. Mapping copy number variation by population-scale genome sequencing. Nature 2011;470:59-65.
21. Gai X, Perin JC, Murphy K, et al. CNV Workshop: An integrated platform for high-throughput copy number variation discovery and clinical diagnostics. BMC Bioinformatics 2010;11:74.
22. Zhao M, Zhao Z. CNVannotator: A comprehensive annotation server for copy number variation in the human genome. PLoS One 2013;8:e80170.
23. CNVAnalysisToolkit 1. 3 [computer program]. 2014. http://statgen. org/.