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使用稀疏数据方法鉴定高血压的低频和罕见变异体。

Identification of low frequency and rare variants for hypertension using sparse-data methods.

作者信息

Shin Ji-Hyung, Yi Ruiyang, Bull Shelley B

机构信息

Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, ON M5T 3L9 Canada.

出版信息

BMC Proc. 2016 Oct 11;10(Suppl 7):389-395. doi: 10.1186/s12919-016-0061-6. eCollection 2016.

DOI:10.1186/s12919-016-0061-6
PMID:27980667
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5133522/
Abstract

Availability of genomic sequence data provides opportunities to study the role of low-frequency and rare variants in the etiology of complex disease. In this study, we conduct association analyses of hypertension status in the cohort of 1943 unrelated Mexican Americans provided by Genetic Analysis Workshop 19, focusing on exonic variants in on chromosome 3. Our primary interest is to compare the performance of standard and sparse-data approaches for single-variant tests and variant-collapsing tests for sets of rare and low-frequency variants. We analyze both the real and the simulated phenotypes.

摘要

基因组序列数据的可获得性为研究低频和罕见变异在复杂疾病病因学中的作用提供了机会。在本研究中，我们对遗传分析研讨会19提供的1943名无亲缘关系的墨西哥裔美国人队列中的高血压状况进行了关联分析，重点关注3号染色体上的外显子变异。我们主要感兴趣的是比较单变异检测的标准方法和稀疏数据方法以及罕见和低频变异集的变异合并检测的性能。我们分析了真实和模拟的表型。

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本文引用的文献

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Omics-squared: human genomic, transcriptomic and phenotypic data for genetic analysis workshop 19.组学平方：用于遗传分析研讨会19的人类基因组、转录组和表型数据
BMC Proc. 2016 Oct 18;10(Suppl 7):71-77. doi: 10.1186/s12919-016-0008-y. eCollection 2016.
2
Above and beyond state-of-the-art approaches to investigate sequence data: summary of methods and results from the population-based association group at the Genetic Analysis Workshop 19.
BMC Genet. 2016 Feb 3;17 Suppl 2(Suppl 2):2. doi: 10.1186/s12863-015-0310-0.
3
Fine-scale patterns of population stratification confound rare variant association tests.人群分层的精细模式使稀有变异关联测试产生混淆。
PLoS One. 2013 Jul 4;8(7):e65834. doi: 10.1371/journal.pone.0065834. Print 2013.
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Recommended joint and meta-analysis strategies for case-control association testing of single low-count variants.推荐用于单低计数变异体病例对照关联检验的联合和荟萃分析策略。
Genet Epidemiol. 2013 Sep;37(6):539-50. doi: 10.1002/gepi.21742. Epub 2013 Jun 20.
5
Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies.最优统一方法用于罕见变异关联测试及其在小样本病例对照全外显子测序研究中的应用。
Am J Hum Genet. 2012 Aug 10;91(2):224-37. doi: 10.1016/j.ajhg.2012.06.007. Epub 2012 Aug 2.
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Reconsidering association testing methods using single-variant test statistics as alternatives to pooling tests for sequence data with rare variants.重新考虑使用单变量检验统计量作为合并检验的替代方法，用于具有罕见变异的序列数据的关联检验方法。
PLoS One. 2012;7(2):e30238. doi: 10.1371/journal.pone.0030238. Epub 2012 Feb 17.
7
A groupwise association test for rare mutations using a weighted sum statistic.使用加权和统计量对罕见突变进行分组关联测试。
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