RT Journal Article
SR Electronic
T1 Whole genome sequencing of 10K patients with acute ischaemic stroke or transient ischaemic attack: design, methods and baseline patient characteristics
JF Stroke and Vascular Neurology
JO Stroke Vasc Neurol
FD BMJ Publishing Group Ltd
SP 291
OP 297
DO 10.1136/svn-2020-000664
VO 6
IS 2
A1 Cheng, Si
A1 Xu, Zhe
A1 Liu, Yang
A1 Lin, Jinxi
A1 Jiang, Yong
A1 Wang, Yilong
A1 Meng, Xia
A1 Wang, Anxin
A1 Huang, Xinying
A1 Wang, Zhimin
A1 Chen, Guohua
A1 Wu, Songdi
A1 Jia, Zhengchang
A1 Chen, Yongming
A1 Qiu, Xuerong
A1 Wu, Jun
A1 Song, Binbin
A1 Ji, Weizhong
A1 An, Zhongping
A1 Xue, Wenjun
A1 Zhao, Lili
A1 Geng, Yu
A1 Li, Hongyan
A1 Li, Hao
A1 Wang, Yongjun
YR 2021
UL http://svn.bmj.com/content/6/2/291.abstract
AB Background and purpose Stroke is the second leading cause of death worldwide and the leading cause of mortality and long-term disability in China, but its underlying risk genes and pathways are far from being comprehensively understood. We here describe the design and methods of whole genome sequencing (WGS) for 10 914 patients with acute ischaemic stroke or transient ischaemic attack from the Third China National Stroke Registry (CNSR-III).Methods Baseline clinical characteristics of the included patients in this study were reported. DNA was extracted from white blood cells of participants. Libraries are constructed using qualified DNA, and WGS is conducted on BGISEQ-500 platform. The average depth is intended to be greater than 30× for each subject. Afterwards, Sentieon software is applied to process the sequencing data under the Genome Analysis Toolkit best practice guidance to call genotypes of single nucleotide variants (SNVs) and insertion-deletions. For each included subject, 21 fingerprint SNVs are genotyped by MassARRAY assays to verify that DNA sample and sequencing data originate from the same individual. The copy number variations and structural variations are also called for each patient. All of the genetic variants are annotated and predicted by bioinformatics software or by reviewing public databases.Results The average age of the included 10 914 patients was 62.2±11.3 years, and 31.4% patients were women. Most of the baseline clinical characteristics of the 10 914 and the excluded patients were balanced.Conclusions The WGS data together with abundant clinical and imaging data of CNSR-III could provide opportunity to elucidate the molecular mechanisms and discover novel therapeutic targets for stroke.Data are available upon reasonable request. Data in this article are available upon reasonable request.