Systematic assessment of copy number variant detection via genome-wide SNP genotyping.
Systematic assessment of copy number variant detection via genome-wide SNP genotyping.
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DOI：
10.1038/ng.236
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发表时间：
2008-10
期刊：
影响因子：
30.8
通讯作者：
Nickerson, Deborah A.
中科院分区：
文献类型：
--
作者：
Cooper, Gregory M.;Zerr, Troy;Kidd, Jeffrey M.;Eichler, Evan E.;Nickerson, Deborah A.
单核苷酸多态性（SNP）基因分型已成为一种将拷贝数变异（CNVs）纳入人类性状遗传分析的技术。然而，SNP平台准确捕获CNVs的程度仍不清楚。使用独立的、基于序列的CNV图谱，我们发现常用的SNP平台对大部分CNV的探针覆盖有限或没有覆盖。尽管如此，在9个样本中，我们使用Illumina SNP基因分型数据推断出368个CNVs，并通过实验验证了其中三分之二以上。我们还开发了一种方法（SCIMM），使用少至两个SNP探针来稳健地进行基因型缺失。我们发现，HapMap SNP与82%的常见缺失密切相关，但最新的SNP平台有效标记了约50%。我们的结论是，目前可用的全基因组SNP检测可以准确地捕获CNVs，但是阵列设计的改进，特别是在重复序列中，需要促进更全面的基因组变异分析。
Single nucleotide polymorphism (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 nine samples we inferred 368 CNVs using Illumina SNP genotyping data and experimentally validated over two-thirds of these. We also developed a method (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.
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影响因子：
64.8
作者：
Eichler, Evan E.;Nickerson, Deborah A.;Altshuler, David;Bowcock, Anne M.;Brooks, Lisa D.;Carter, Nigel P.;Church, Deanna M.;Felsenfeld, Adam;Guyer, Mark;Lee, Charles;Lupski, James R.;Mullikin, James C.;Pritchard, Jonathan K.;Sebat, Jonathan;Sherry, Stephen T.;Smith, Douglas;Valle, David;Waterston, Robert H.
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通讯作者：
Gwinn-Hardy, K
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