Iam hiQ-a novel pair of accuracy indices for imputed genotypes.
Iam hiQ-a novel pair of accuracy indices for imputed genotypes.
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DOI：
10.1186/s12859-022-04568-3
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发表时间：
2022-01-24
影响因子：
3
通讯作者：
INTEGRAL-ILCCO consortium
中科院分区：
文献类型：
--
作者：
Rosenberger A;Tozzi V;Bickeböller H;INTEGRAL-ILCCO consortium
在全基因组关联研究中，非分型标记的插入是一种标准工具，可以缩小直接基因分型与其他已知DNA变异之间的差距。然而，基因型输入的准确性是至关重要的。已经提出了几种精度措施，其中一些是在插补软件中实现的，不幸的是跨平台的差异。在本文中，我们介绍了Iam hiQ，一个独立的精度测量对，可以应用于剂量文件，所有的输入软件的输出。Iam（归算精度测量）以线性方式量化个体特异性与群体特异性基因型信息的平均数量。hiQ（剂量数量的异质性）解决了手头样品中标记物剂量之间的个体间异质性。将这两种测量方法应用于国际肺癌协会（ILCCO）的大型病例对照样本，包括27,065名个体，我们发现Iam和hiQ的有意义阈值适用于对准确性较差的标记物进行分类。我们展示了Iam和hiQ的类曼哈顿图和移动平均线如何用于识别含有较不准确的输入标记的区域，而这些区域在应用精度测量信息（在IMPUTE2中实现）时可能会被遗漏。我们建议在分析输入的GWAS数据之前，除了使用其他精度分数外，还使用Iam hiQ进行变量过滤。在线版本包含补充材料，可在10.1186/s12859-022-04568-3获得。
Imputation of untyped markers is a standard tool in genome-wide association studies to close the gap between directly genotyped and other known DNA variants. However, high accuracy with which genotypes are imputed is fundamental. Several accuracy measures have been proposed and some are implemented in imputation software, unfortunately diversely across platforms. In the present paper, we introduce Iam hiQ, an independent pair of accuracy measures that can be applied to dosage files, the output of all imputation software. Iam (imputation accuracy measure) quantifies the average amount of individual-specific versus population-specific genotype information in a linear manner. hiQ (heterogeneity in quantities of dosages) addresses the inter-individual heterogeneity between dosages of a marker across the sample at hand. Applying both measures to a large case–control sample of the International Lung Cancer Consortium (ILCCO), comprising 27,065 individuals, we found meaningful thresholds for Iam and hiQ suitable to classify markers of poor accuracy. We demonstrate how Manhattan-like plots and moving averages of Iam and hiQ can be useful to identify regions enriched with less accurate imputed markers, whereas these regions would by missed when applying the accuracy measure info (implemented in IMPUTE2). We recommend using Iam hiQ additional to other accuracy scores for variant filtering before stepping into the analysis of imputed GWAS data. The online version contains supplementary material available at 10.1186/s12859-022-04568-3.
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影响因子：
30.8
作者：
Marchini, Jonathan;Howie, Bryan;Donnelly, Peter
通讯作者：
Donnelly, Peter
DOI：
10.1038/ejhg.2017.51
发表时间：
2017-06
期刊：
European journal of human genetics : EJHG
影响因子：
--
作者：
Mitt M;Kals M;Pärn K;Gabriel SB;Lander ES;Palotie A;Ripatti S;Morris AP;Metspalu A;Esko T;Mägi R;Palta P
通讯作者：
Palta P
影响因子：
64.8
作者：
Bycroft C;Freeman C;Petkova D;Band G;Elliott LT;Sharp K;Motyer A;Vukcevic D;Delaneau O;O'Connell J;Cortes A;Welsh S;Young A;Effingham M;McVean G;Leslie S;Allen N;Donnelly P;Marchini J
通讯作者：
Marchini J
影响因子：
2.7
作者：
Krithika S;Valladares-Salgado A;Peralta J;Escobedo-de La Peña J;Kumate-Rodríguez J;Cruz M;Parra EJ
通讯作者：
Parra EJ
影响因子：
2.1
作者：
Li, Yun;Willer, Cristen J.;Ding, Jun;Scheet, Paul;Abecasis, Goncalo R.
通讯作者：
Abecasis, Goncalo R.