Portability of tag SNPs across isolated population groups: an example from India.
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.
Sarkar Roy
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N
TCG-ISI Centre for Population Genomics, Bengal Intelligent Park Ltd., Salt Lake Electronics Complex, Kolkata 700091, India.
Farheen
S
S
Roy
N
N
Sengupta
S
S
Majumder
P P
PP
D044383:Black People; D041322:Chromosomes, Human, Y; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D005006:Ethnicity; D005260:Female; D005819:Genetic Markers; D005843:Geography; D006239:Haplotypes; D006801:Humans; D007194:India; D015810:Linkage Disequilibrium; D008297:Male; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D044382:Population Groups; D017422:Sequence Analysis, DNA; D044465:White People
D005819:Genetic Markers; D004247:DNA