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

Objectives The 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.Methods Unrelated 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.Results Among 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.Conclusions Our GS study suggests a role of rare genomic variants with various variant types contributing to the development of ICAD in Chinese patients.