Validation of genotype imputation in Southeast Asian populations and the effect of single nucleotide polymorphism annotation on imputation outcome

Worachart Lert-Itthiporn (1) , Bhoom Suktitipat (1) , Harald Grove (1) , Anavaj Sakuntabhai (2, 1) , Prida Malasit (1) , Nattaya Tangthawornchaikul (1) , Fumihiko Matsuda (3) , Prapat Suriyaphol (1)

1 Mahidol University [Bangkok]
2 Génétique fonctionnelle des Maladies infectieuses - Functional Genetics of Infectious Diseases
3 Kyoto University

Background: Imputation involves the inference of untyped single nucleotide polymorphisms (SNPs) in genome-wide association studies. The haplotypic reference of choice for imputation in Southeast Asian populations is unclear. Moreover, the influence of SNP annotation on imputation results has not been examined.

Keywords: Genotype; Imputation; Pan-Asian SNP; Reference; SNP annotation

Domains: Computer Science [cs]; Bioinformatics [q-bio.QM]; Life Sciences [q-bio]; Quantitative Methods [q-bio.QM]; Life Sciences [q-bio]; Genetics; Human genetics; Life Sciences [q-bio]; Genetics; Populations and Evolution [q-bio.PE]; Life Sciences [q-bio]; Microbiology and Parasitology; Virology; Life Sciences [q-bio]; Microbiology and Parasitology; Parasitology; Life Sciences [q-bio]; Santé publique et épidémiologie

Worachart Lert-Itthiporn, Bhoom Suktitipat, Harald Grove, Anavaj Sakuntabhai, Prida Malasit, et al.. Validation of genotype imputation in Southeast Asian populations and the effect of single nucleotide polymorphism annotation on imputation outcome. BMC Medical Genetics, 2018, 19 (1), pp.23. ⟨10.1186/s12881-018-0534-8⟩. ⟨pasteur-02003873⟩