Utilizing linkage disequilibrium information from Indian Genome Variation Database for mapping mutations: SCA12 case study

Journal of genetics

Mitali Mukerji1¹  The Indian Genome Variation Consortium²  Ikhlak Ahmed³  Samira Bahl¹ 

[1] Functional Genomics Unit, Institute of Genomics and Integrative Biology (CSIR), Mall Road, New Delhi, 110 007, India$$;Composition first described in Hum. Genet. 2005, 118, 1–11$$;G. N. Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology (CSIR), Mall Road, New Delhi, 110 007, India$$

关键词: Indian genome variation;    SNP;    linkage disequilibrium;    mutation mapping;    SCA12;    HapMap.;   

DOI  :  

学科分类：生物科学（综合）

来源: Indian Academy of Sciences

【 摘 要 】

Stratification in heterogeneous populations poses an enormous challenge in linkage disequilibrium (LD) based identification of causal loci using surrogate markers. In this study, we demonstrate the enormous potential of endogamous Indian populations for mapping mutations in candidate genes using minimal SNPs, mainly due to larger regions of LD. We show this by a case study of the PPP2R2B gene (∼400 kb) that harbours a CAG repeat, expansion of which has been implicated in spinocerebellar ataxia type 12 (SCA12). Using LD information derived from Indian Genome Variation database (IGVdb) on populations which share similar ethnic and linguistic backgrounds as the SCA12 study population, we could map the causal loci using a minimal set of three SNPs, without the generation of additional basal data from the ethnically matched population. We could also demonstrate transferability of tagSNPs from a related HapMap population for mapping the mutation.

【 授权许可】

Unknown