Similarity of the allele frequency and linkage disequilibrium pattern of single nucleotide polymorphisms in drug-related gene loci between Thai and northern East Asian populations: implications for tagging SNP selection in Thais

Mahasirimongkol, Surakameth; Chantratita, Wasun; Promso, Somying; Pasomsab, Ekawat; Jinawath, Natini; Jongjaroenprasert, Wallaya; Lulitanond, Viraphong; Krittayapoositpot, Phanida; Tongsima, Sissades; Sawanpanyalert, Pathom; Kamatani, Naoyuki; Nakamura, Yusuke; Sura, Thanyachai

doi:10.1007/s10038-006-0041-1

Cited by 22 publications

(21 citation statements)

References 29 publications

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“…High transferability has also been reported for drug-related genes (Mahasirimongkol et al 2006). We therefore conclude that tagging SNPs selected from CHB + JPT captures common variants well, at least in Thais and probably in Southeast Asians as a whole, and that the genotype information of CHB + JPT is very useful for association studies in Southeast Asians.…”

Section: Discussionsupporting

confidence: 56%

Linkage disequilibrium structure of the 5q31-33 region in a Thai population

et al. 2008

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A number of loci related to the immune response are located on human chromosomal region 5q31-33, and polymorphisms in this region have been reported to be associated with autoimmune and infectious diseases. In Southeast Asian populations, no systematic survey with dense SNP markers has been performed for the 5q31-33 region. In this study, the LD and haplotype structures for a 472-kb region on 5q31 were investigated in a Thai population to provide useful information for association studies. In addition, the LD structure in Thais was compared with that of the CHB and JPT HapMap populations (CHB + JPT) to evaluate the transferability of tagging SNPs from CHB + JPT for Thais. We show that the minor allele frequency, pattern of LD block, and genetic structure in the 5q31-33 region were highly concordant between Thais and CHB + JPT. A high transferability of tagging SNPs from CHB + JPT for Thais was observed. Our results suggest that tagging SNPs from CHB + JPT (Northeast Asians) can efficiently capture common variants in Southeast Asians, and that the HapMap data are useful for association studies in Southeast Asian populations.

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Section: Discussionsupporting

confidence: 56%

Linkage disequilibrium structure of the 5q31-33 region in a Thai population

et al. 2008

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“…The strong correlations observed between Cebu Filipino samples and HapMap Asian panels are broadly consistent with other assessments of tagging transferability outside the HapMap ENCODE regions (Weale et al 2003;Nejentsev et al 2004;Ke et al 2005;Mueller et al 2005;Ramirez-Soriano et al 2005;Evans and Cardon 2005;Gonzalez-Neira et al 2006;Huang et al 2006;Mahasirimongkol et al 2006;Montpetit et al 2006;Ribas et al 2006;Willer et al 2006).…”

Section: Discussionsupporting

confidence: 85%

“…Studies that examined many populations worldwide found Asian and Oceania populations to be most similar to the Asian HapMap panel tested (Conrad et al 2006 andGonzalez-Neira et al 2006). Two studies have investigated the tagging transferability between the HapMap CHB, JPT, and CHB + JPT with sample sets from Thailand and from Korea (Mahasirimongkol et al 2006;Yoo et al 2006). A combination of tag SNPs from CHB + JPT best captured the LD structure of the Thais, while SNP selection based on JPT was most transferable to the Korean samples.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, for populations similar to those genotyped in the HapMap project, HapMap data may be used to directly predict genotypes of non-tag SNPs for analysis in association studies (Eyheramendy et al 2007;Paschou et al 2007). Previous studies observed that the HapMap CHB and JPT panels have very similar patterns of LD and could act as a proxy for other geographically related populations (Beaty et al 2005;Lim et al 2006;de Bakker et al 2006;Conrad et al 2006;Mahasirimongkol et al 2006;Yoo et al 2006). However, data are currently unavailable to assess the effectiveness of using the existing HapMap data to guide SNP selection and interpretation for samples from the Cebu Longitudinal Health and Nutrition Survey (CLHNS) cohort from metro Cebu in the central Philippines (Cebu Study Team 1991;Adair 2004).…”

Section: Introductionmentioning

confidence: 99%

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Comparison of ENCODE region SNPs between Cebu Filipino and Asian HapMap samples

Marvelle

Lange

et al. 2007

J Hum Genet

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Patterns of linkage disequilibrium (LD) act as the framework for designing efficient association studies; these patterns are being studied and catalogued by The International HapMap Project. The current study assessed the transferability of tag SNPs chosen from HapMap panels to a cohort of 80 individuals from metro Cebu, Philippines, who participated in the Cebu Longitudinal Health and Nutrition Survey (CLHNS). The analyses focused on 627 single nucleotide polymorphisms (SNPs) in the central 40 kb within each of the 10 HapMap ENCODE regions. The similarity between the genetic variants in Cebu Filipino samples and HapMap panels was examined using allele frequency estimates, measures of pairwise linkage disequilibrium (LD), and haplotype frequency estimates. For these measures, strong correlations were observed between the Cebu Filipino samples and the Asian panels from HapMap, with the strongest correlations observed with the Han Chinese from Beijing (CHB) panel. Tag SNPs selected using the HapMap CHB panel were particularly effective at representing the genetic variation in Cebu Filipino samples. These results suggest that the HapMap data will be an effective resource for future studies in Cebu Filipino samples.

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“…Populations in these regions were highly similar to each other and also close to the HapMap Chinese population. 13 All cases were human immunodeficiency virus-seronegative when TB was diagnosed, and the diagnosis of TB was confirmed by microscopic identification or mycobacterial culture.…”

Section: Japanese and Thai Genome-wide Association Samplesmentioning

confidence: 99%

Genome-wide association studies of tuberculosis in Asians identify distinct at-risk locus for young tuberculosis

et al. 2012

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Tuberculosis (TB) is one of the most devastating chronic infectious diseases, but the role of host genetics in disease development after infection in this disease remains unidentified. Genome-wide association studies (GWASs) in Thais and Japanese were carried out and separately analyzed, attempted replication, then, combined by meta-analysis were not yielding any convincing association evidences; these results suggested that moderate to high effect-size genetic risks are not existed for TB per se. Because of failure in replication attempt of the top 50 single-nucleotide polymorphisms (SNPs) identified form meta-analysis data, we empirically split TB cases into young TB case/control data sets (GWAS-T young ¼ 137/295 and GWAS-J young ¼ 60/249) and old TB case/control data sets (GWAS-T old ¼ 300/295 and GWAS-J old ¼ 123/685), re-analyzed GWAS based on age-stratified data and replicated the significant findings in two independent replication samples (young TB; Rep-T young ¼ 155/249, Rep-J young ¼ 41/462 and old TB; Rep-T old ¼ 212/187, Rep-J old ¼ 71/619). GWAS and replication studies conducted in young TB identified at-risk locus in 20q12. Although the locus is located in inter-genic region, the nearest genes (HSPEP1-MAFB) from this locus are promising candidates for TB susceptibility. This locus was also associated with anti-TNF responsiveness, drug with increased susceptibility for TB. Moreover, eight SNPs in an old TB meta-analysis and six SNPs in young TB meta-analysis provided replication evidences but did not survive genome-wide significance.These findings suggest that host genetic risks for TB are affected by age at onset of TB, and this approach may accelerate the identification of the major host factors that affect TB in human populations.

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Similarity of the allele frequency and linkage disequilibrium pattern of single nucleotide polymorphisms in drug-related gene loci between Thai and northern East Asian populations: implications for tagging SNP selection in Thais

Cited by 22 publications

References 29 publications

Linkage disequilibrium structure of the 5q31-33 region in a Thai population

Linkage disequilibrium structure of the 5q31-33 region in a Thai population

Comparison of ENCODE region SNPs between Cebu Filipino and Asian HapMap samples

Genome-wide association studies of tuberculosis in Asians identify distinct at-risk locus for young tuberculosis

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