Database mining for selection of SNP markers useful in admixture mapping.
Database mining for selection of SNP markers useful in admixture mapping.
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DOI：
10.1186/1756-0381-2-1
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发表时间：
2009-02-14
期刊：
影响因子：
4.5
通讯作者：
Go RC
中科院分区：
文献类型：
--
作者：
Baye TM;Tiwari HK;Allison DB;Go RC
新技术首次使同时对数十万个snp进行基因分型成为可能。以公共可用数据库的形式提供的大量基因组信息作为揭示复杂人类特征的功能相关标记的潜在资源未得到充分利用。鉴于人类遗传变异注释中可获得的大量SNP数据，数据挖掘是一种合理的方法来调查对祖先信息有信息的SNP数量。通过使用HapMap、Affymetrix和Illumina SNP数据库，广泛研究了非洲和欧洲人群基因组中SNP的分布和密度。我们利用这些资源，从每个数据库中挖掘可用的数据，以优先考虑潜在的候选snp，这些snp对复杂的人类疾病和性状的混合定位有用。在预先指定的推荐等位基因频率差异（δ）值≥0.3的基础上，比较了非洲人和欧洲人之间超过400万个snp。该方法确定了15%的HapMap， 11%的Affymetrix和14%的Illumina SNP集作为候选SNP，称为祖先信息标记（AIMs）。这些带有指定的rs号、每个种族的等位基因频率、δ值和地图位置的AIM面板都发布在我们的网站上。本数据集中的所有标记信息均可免费公开获取，不受任何限制。所选择的SNP集代表了混合物作图研究的宝贵资源。讨论了在不同的平台上，通过这种单一的标记信息度量所选择的目标之间的重叠。
New technologies make it possible for the first time to genotype hundreds of thousands of SNPs simultaneously. A wealth of genomic information in the form of publicly available databases is underutilized as a potential resource for uncovering functionally relevant markers underlying complex human traits. Given the huge amount of SNP data available from the annotation of human genetic variation, data mining is a reasonable approach to investigating the number of SNPs that are informative for ancestry information. The distribution and density of SNPs across the genome of African and European populations were extensively investigated by using the HapMap, Affymetrix, and Illumina SNP databases. We exploited these resources by mining the data available from each of these databases to prioritize potential candidate SNPs useful for admixture mapping in complex human diseases and traits. Over 4 million SNPs were compared between Africans and Europeans on the basis of a pre-specified recommended allele frequency difference (delta) value of ≥ 0.3. The method identified 15% of HapMap, 11% of Affymetrix, and 14% of Illumina SNP sets as candidate SNPs, termed ancestry informative markers (AIMs). These AIM panels with assigned rs numbers, allele frequencies in each ethnic group, delta value, and map positions are all posted on our website . All marker information in this data set is freely and publicly available without restriction. The selected SNP sets represent valuable resources for admixture mapping studies. The overlap between selected AIMs by this single measure of marker informativeness in the different platforms is discussed.
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影响因子：
56.9
作者：
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Feldman, MW
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