Center for Toxicoinformatics, Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
Adv Exp Med Biol. 2010;680:355-60. doi: 10.1007/978-1-4419-5913-3_40.
Highly accurate and reproducible genotype calling is a key to success of genome-wide association studies (GWAS) since errors introduced by calling algorithms can lead to inflation of false associations between genotype and phenotype. The Affymetrix Genome-Wide Human SNP Array 6.0 is widely utilized and was used in the current GWAS. Birdseed, a genotype-calling algorithm for this chip, is available in two versions. It is important to know the reproducibility between the two versions. We assessed the inconsistency in genotypes called by the two versions of Birdseed and examined the propagation of the genotype inconsistency to the downstream association analysis by using the 270 HapMap samples. Our results revealed that genotypes called from version-1 and version-2 of Birdseed were slightly different and the inconsistency in genotypes propagated to the downstream association analysis.
高度准确且可重复的基因型调用是全基因组关联研究 (GWAS) 成功的关键，因为调用算法引入的错误可能导致基因型和表型之间的虚假关联膨胀。Affymetrix 全基因组人类 SNP 阵列 6.0 被广泛应用，并用于当前的 GWAS。Birdseed 是这款芯片的一种基因型调用算法，有两个版本。了解这两个版本之间的可重复性非常重要。我们评估了两个版本的 Birdseed 调用的基因型之间的不一致性，并使用 270 个 HapMap 样本检查了基因型不一致性向下游关联分析的传播。我们的结果表明，来自 Birdseed 的版本 1 和版本 2 的基因型略有不同，并且基因型的不一致性传播到下游的关联分析中。
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