NDLI: Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays

Content Provider	PubMed Central
Author	Komura, Daisuke Shen, Fan Ishikawa, Shumpei Fitch, Karen R. Chen, Wenwei Zhang, Jane Liu, Guoying Ihara, Sigeo Nakamura, Hiroshi Hurles, Matthew E. Lee, Charles Scherer, Stephen W. Jones, Keith W. Shapero, Michael H. Huang, Jing Hiroyuki, Aburatani
Copyright Year	2006
Abstract	Recent reports indicate that copy number variations (CNVs) within the human genome contribute to nucleotide diversity to a larger extent than single nucleotide polymorphisms (SNPs). In addition, the contribution of CNVs to human disease susceptibility may be greater than previously expected, although a complete understanding of the phenotypic consequences of CNVs is incomplete. We have recently reported a comprehensive view of CNVs among 270 HapMap samples using high-density SNP genotyping arrays and BAC array CGH. In this report, we describe a novel algorithm using Affymetrix GeneChip Human Mapping 500K Early Access (500K EA) arrays that identified 1203 CNVs ranging in size from 960 bp to 3.4 Mb. The algorithm consists of three steps: (1) Intensity pre-processing to improve the resolution between pairwise comparisons by directly estimating the allele-specific affinity as well as to reduce signal noise by incorporating probe and target sequence characteristics via an improved version of the Genomic Imbalance Map (GIM) algorithm; (2) CNV extraction using an adapted SW-ARRAY procedure to automatically and robustly detect candidate CNV regions; and (3) copy number inference in which all pairwise comparisons are summarized to more precisely define CNV boundaries and accurately estimate CNV copy number. Independent testing of a subset of CNVs by quantitative PCR and mass spectrometry demonstrated a >90% verification rate. The use of high-resolution oligonucleotide arrays relative to other methods may allow more precise boundary information to be extracted, thereby enabling a more accurate analysis of the relationship between CNVs and other genomic features.
Related Links	http://dx.doi.org/10.1101/gr.5629106
Ending Page	1584
Page Count	10
Starting Page	1575
File Format	PDF
ISSN	10889051
e-ISSN	15495477
Journal	Genome Research
Issue Number	12
Volume Number	16
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2006-10-01
Access Restriction	Open
Rights Holder	Cold Spring Harbor Laboratory Press
Subject Keyword	Genetics(clinical) Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

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