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 svn-2020-000664 DO 10.1136/svn-2020-000664 A1 Si Cheng A1 Zhe Xu A1 Yang Liu A1 Jinxi Lin A1 Yong Jiang A1 Yilong Wang A1 Xia Meng A1 Anxin Wang A1 Xinying Huang A1 Zhimin Wang A1 Guohua Chen A1 Songdi Wu A1 Zhengchang Jia A1 Yongming Chen A1 Xuerong Qiu A1 Jun Wu A1 Binbin Song A1 Weizhong Ji A1 Zhongping An A1 Wenjun Xue A1 Lili Zhao A1 Yu Geng A1 Hongyan Li A1 Hao Li A1 Yongjun Wang YR 2020 UL http://svn.bmj.com/content/early/2020/12/17/svn-2020-000664.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.