Genome sequencing reveals the role of rare genomic variants in Chinese patients with symptomatic intracranial atherosclerotic disease

• Published in: Stroke and vascular neurology Vol. 7; no. 3; pp. 182 - 189
• Main Authors: Shi, Mengmeng, Leng, Xinyi, Li, Ying, Chen, Zihan, Cao, Ye, Chung, Tiffany, Ip, Bonaventure YM, Ip, Vincent HL, Soo, Yannie OY, Fan, Florence SY, Ma, Sze Ho, Ma, Karen, Chan, Anne Y Y, Au, Lisa WC, Leung, Howan, Lau, Alexander Y, Mok, Vincent CT, Choy, Kwong Wai, Dong, Zirui, Leung, Thomas W
• Format: Journal Article
• Language: English
• Published: London BMJ Publishing Group Ltd 01.06.2022; BMJ Publishing Group LTD; BMJ Publishing Group
• Subjects: Atherosclerosis; Chromosomes; Diabetes; Disease; Etiology; Genes; genetics; Genomes; Hypertension; Ischemia; Medical imaging; Mutation; Original Research; Patients; Risk factors; Stroke; Topography; Veins & arteries; Hong Kong China; United States > US; Massachusetts
• ISSN: 2059-8688; 2059-8696
• DOI: 10.1136/svn-2021-001157

ObjectivesThe predisposition of intracranial atherosclerotic disease (ICAD) to East Asians over Caucasians infers a genetic basis which, however, remains largely unknown. Higher prevalence of vascular risk factors (VRFs) in Chinese over Caucasian patients who had a stroke, and shared risk factors of ICAD with other stroke subtypes indicate genes related to VRFs and/or other stroke subtypes may also contribute to ICAD.MethodsUnrelated symptomatic patients with ICAD were recruited for genome sequencing (GS, 60-fold). Rare and potentially deleterious single-nucleotide variants (SNVs) and small insertions/deletions (InDels) were detected in genome-wide and correlated to genes related to VRFs and/or other stroke subtypes. Rare aneuploidies, copy number variants (CNVs) and chromosomal structural rearrangements were also investigated. Lastly, candidate genes were used for pathway and gene ontology enrichment analysis.ResultsAmong 92 patients (mean age at stroke onset 61.0±9.3 years), GS identified likely ICAD-associated rare genomic variants in 54.3% (50/92) of patients. Forty-eight patients (52.2%, 48/92) had 59 rare SNVs/InDels reported or predicted to be deleterious in genes related to VRFs and/or other stroke subtypes. None of the 59 rare variants were identified in local subjects without ICAD (n=126). 31 SNVs/InDels were related to conventional VRFs, and 28 were discovered in genes related to other stroke subtypes. Our study also showed that rare CNVs (n=7) and structural rearrangement (a balanced translocation) were potentially related to ICAD in 8.7% (8/92) of patients. Lastly, candidate genes were significantly enriched in pathways related to lipoprotein metabolism and cellular lipid catabolic process.ConclusionsOur GS study suggests a role of rare genomic variants with various variant types contributing to the development of ICAD in Chinese patients.