Testing optimally weighted combination of variants for hypertension

BMC Proceedings

Proceedings

Shuanglin Zhang¹  Qiuying Sha¹  Xingwang Zhao²  Xuexia Wang² 

[1] Department of Mathematical Sciences, Michigan Technological University, 1400 Townsend Drive, 49931, Houghton, MI, USA;Joseph J.Zilber School of Public Health, University of Wisconsin, P.O. Box 413, 53201, Milwaukee, WI, USA;

关键词: Rare Variant;    Unrelated Individual;    Genetic Analysis Workshop;    Slide Window Approach;    Genotypic Score;   

DOI  :  10.1186/1753-6561-8-S1-S59

来源: Springer

【 摘 要 】

Testing rare variants directly is possible with next-generation sequencing technology. In this article, we propose a sliding-window-based optimal-weighted approach to test for the effects of both rare and common variants across the whole genome. We measured the genetic association between a disease and a combination of variants of a single-nucleotide polymorphism window using the newly developed tests TOW and VW-TOW and performed a sliding-window technique to detect disease-susceptible windows. By applying the new approach to unrelated individuals of Genetic Analysis Workshop 18 on replicate 1 chromosome 3, we detected 3 highly susceptible windows across chromosome 3 for diastolic blood pressure and identified 10 of 48,176 windows as the most promising for both diastolic and systolic blood pressure. Seven of 9 top variants influencing diastolic blood pressure and 8 of 9 top variants influencing systolic blood pressure were found in or close to our top 10 windows.

【 授权许可】

Unknown   
© Zhao et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.