Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Export

@article{citeulike:3225800, abstract = {SNP genotyping has emerged as a technology to incorporate copy number variants (CNVs) into genetic analyses of human traits. However, the extent to which SNP platforms accurately capture CNVs remains unclear. Using independent, sequence-based CNV maps, we find that commonly used SNP platforms have limited or no probe coverage for a large fraction of CNVs. Despite this, in 9 samples we inferred 368 CNVs using Illumina SNP genotyping data and experimentally validated over two-thirds of these. We also developed a method (SNP-Conditional Mixture Modeling, SCIMM) to robustly genotype deletions using as few as two SNP probes. We find that HapMap SNPs are strongly correlated with 82\% of common deletions, but the newest SNP platforms effectively tag about 50\%. We conclude that currently available genome-wide SNP assays can capture CNVs accurately, but improvements in array designs, particularly in duplicated sequences, are necessary to facilitate more comprehensive analyses of genomic variation.}, address = {[1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. [2] These authors contributed equally to this work.}, author = {Cooper, Gregory M. and Zerr, Troy and Kidd, Jeffrey M. and Eichler, Evan E. and Nickerson, Deborah A.}, citeulike-article-id = {3225800}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/ng.236}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/ng.236}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18776910}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18776910}, day = {7}, doi = {10.1038/ng.236}, issn = {1546-1718}, journal = {Nature genetics}, keywords = {cnv, genome, snp}, month = {October}, number = {10}, pages = {1199--1203}, posted-at = {2008-10-19 11:04:49}, priority = {2}, publisher = {Nature Publishing Group}, title = {Systematic assessment of copy number variant detection via genome-wide SNP genotyping.}, url = {http://dx.doi.org/10.1038/ng.236}, volume = {40}, year = {2008} }

TY - JOUR ID - citeulike:3225800 L3 - citeulike-article-id:3225800 N2 - SNP genotyping has emerged as a technology to incorporate copy number variants (CNVs) into genetic analyses of human traits. However, the extent to which SNP platforms accurately capture CNVs remains unclear. Using independent, sequence-based CNV maps, we find that commonly used SNP platforms have limited or no probe coverage for a large fraction of CNVs. Despite this, in 9 samples we inferred 368 CNVs using Illumina SNP genotyping data and experimentally validated over two-thirds of these. We also developed a method (SNP-Conditional Mixture Modeling, SCIMM) to robustly genotype deletions using as few as two SNP probes. We find that HapMap SNPs are strongly correlated with 82% of common deletions, but the newest SNP platforms effectively tag about 50%. We conclude that currently available genome-wide SNP assays can capture CNVs accurately, but improvements in array designs, particularly in duplicated sequences, are necessary to facilitate more comprehensive analyses of genomic variation. IS - 10 JF - Nature genetics SN - 1546-1718 AD - [1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. [2] These authors contributed equally to this work. EP - 1203 TI - Systematic assessment of copy number variant detection via genome-wide SNP genotyping. PB - Nature Publishing Group VL - 40 SP - 1199 KW - cnv KW - genome KW - snp AU - Cooper, Gregory AU - Zerr, Troy AU - Kidd, Jeffrey AU - Eichler, Evan AU - Nickerson, Deborah PY - 2008/10/07/ UR - http://dx.doi.org/10.1038/ng.236 ER -