Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs.
Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs.
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DOI：
10.1038/ng.237
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发表时间：
2008-10
期刊：
影响因子：
30.8
通讯作者：
Altshuler, David
中科院分区：
文献类型：
--
作者：
Korn, Joshua M.;Kuruvilla, Finny G.;McCarroll, Steven A.;Wysoker, Alec;Nemesh, James;Cawley, Simon;Hubbell, Earl;Veitch, Jim;Collins, Patrick J.;Darvishi, Katayoon;Lee, Charles;Nizzari, Marcia M.;Gabriel, Stacey B.;Purcell, Shaun;Daly, Mark J.;Altshuler, David
准确和完整的测量单核苷酸（SNP）和拷贝数（CNV）变异，无论是常见的还是罕见的，都需要了解遗传变异在疾病中的作用。我们提出了Birdsuite，一个四阶段的分析框架，在软件中实例化，用于获得集成和相互一致的拷贝数和SNP基因型。所述方法顺序地在常见拷贝数多态性（CNP）的区域之间分配拷贝数，调用SNP的基因型，经由隐马尔可夫模型（HMM）鉴定罕见CNV，并在每个基因座处生成整合的序列和拷贝数基因型（例如，除了AA、AB和BB调用之外，还包括基因型如A-null、AAB和BBB）。这样的基因型更准确地描述了每个个体的潜在序列，减少了明显的孟德尔不一致的比率。在此将Birdsuite软件应用于来自Affyssite SNP 6.0阵列的数据。此外，我们描述了一种方法，在PLINK中实现，利用这些组合的SNP和CNV基因型与表型的关联测试。
Accurate and complete measurement of single nucleotide (SNP) and copy number (CNV) variants, both common and rare, will be required to understand the role of genetic variation in disease. We present Birdsuite, a four-stage analytical framework instantiated in software for deriving integrated and mutually consistent copy number and SNP genotypes. The method sequentially assigns copy number across regions of common copy number polymorphisms (CNPs), calls genotypes of SNPs, identifies rare CNVs via a hidden Markov model (HMM), and generates an integrated sequence and copy number genotype at every locus (for example, including genotypes such as A-null, AAB and BBB in addition to AA, AB and BB calls). Such genotypes more accurately depict the underlying sequence of each individual, reducing the rate of apparent mendelian inconsistencies. The Birdsuite software is applied here to data from the Affymetrix SNP 6.0 array. Additionally, we describe a method, implemented in PLINK, to utilize these combined SNP and CNV genotypes for association testing with a phenotype.
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