Portability of tag SNPs across isolated population groups: an example from India.

Abstract:

:Isolated population groups are useful in conducting association studies of complex diseases to avoid various pitfalls, including those arising from population stratification. Since DNA resequencing is expensive, it is recommended that genotyping be carried out at tagSNP (tSNP) loci. For this, tSNPs identified in one isolated population need to be used in another. Unless tSNPs are highly portable across populations this strategy may result in loss of information in association studies. We examined the issue of tSNP portability by sampling individuals from 10 isolated ethnic groups from India. We generated DNA resequencing data pertaining to 3 genomic regions and identified tSNPs in each population. We defined an index of tSNP portability and showed that portability is low across isolated Indian ethnic groups. The extent of portability did not significantly correlate with genetic similarity among the populations studied here. We also analyzed our data with sequence data from individuals of African and European descent. Our results indicated that it may be necessary to carry out resequencing in a small number of individuals to discover SNPs and identify tSNPs in the specific isolated population in which a disease association study is to be conducted.

journal_name

Ann Hum Genet

journal_title

Annals of human genetics

authors

Sarkar Roy N,Farheen S,Roy N,Sengupta S,Majumder PP

doi

10.1111/j.1469-1809.2006.00383.x

subject

Has Abstract

pub_date

2008-01-01 00:00:00

pages

82-9

issue

Pt 1

eissn

0003-4800

issn

1469-1809

pii

AHG383

journal_volume

72

pub_type

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