Whole genome sequencing of 10K patients with acute ischaemic stroke or transient ischaemic attack: design, methods and baseline patient characteristics,Stroke and Vascular Neurology

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Whole genome sequencing of 10K patients with acute ischaemic stroke or transient ischaemic attack: design, methods and baseline patient characteristics
Stroke and Vascular Neurology ( IF 4.4 ) Pub Date : 2021-06-01 , DOI: 10.1136/svn-2020-000664
Si Cheng _{1,

2,

3} , Zhe Xu _{1,

2,

3} , Yang Liu _{1,

2,

3} , Jinxi Lin _{1,

2} , Yong Jiang _{1,

2} , Yilong Wang _{1,

2} , Xia Meng _{1,

2} , Anxin Wang _{1,

2} , Xinying Huang _{1,

2} , Zhimin Wang ₄ , Guohua Chen ₅ , Songdi Wu ₆ , Zhengchang Jia ₇ , Yongming Chen ₈ , Xuerong Qiu ₉ , Jun Wu ₁₀ , Binbin Song ₁₁ , Weizhong Ji ₁₂ , Zhongping An ₁₃ , Wenjun Xue ₁₄ , Lili Zhao ₁₅ , Yu Geng ₁₆ , Hongyan Li ₁₇ , Hao Li _{1,

2} , Yongjun Wang _{2,

3,

18}

Affiliation

Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
China National Clinical Research Center for Neurological Diseases, Beijing, China.
Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China.
Department of Neurology, The First people's Hospital of Taizhou, Taizhou, China.
Department of Neurology, Wuhan First Hospital, Wuhan, China.
Department of Neurology, The First People's Hospital of Xi'an, Xi'an, China.
Department of Neurology, The Second People's Hospital of Jinzhong, Jinzhong, China.
Department of Neurology, WuYuan County People's Hospital, Bayannur, China.
Department of Neurology, Qiqihar City Rongjian Stroke Prevention and Treatment Institute, Qiqihar, China.
Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China.
Department of Neurology, Luoyang Central Hospital, Luoyang, China.
Department of Neurology, Qinghai Provincial People's Hospital, Xining, China.
Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China.
Department of Neurology, Pingdingshan First People's Hospital, Pingdingshan, China.
Department of Neurology, Changzhi People's Hospital, Changzhi, China.
Department of Neurology, Zhejiang Provincial People's Hospital, Hangzhou, China.
Department of Neurology, Xinjiang Uygur Autonomous Region People's Hospital, Urumqi, China.
Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China

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.

更新日期：2021-06-29

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