Evaluating HapMap SNP data transferability in a large-scale genotyping project involving 175 cancer-associated genes

Ribas, Gloría; González‐Neira, Anna; Salas, Antonio; Milne, Roger L.; Vega, Ana; Carracedo, Begoña; González, Emilio Esteban; Barroso, Eva; Fernández, Lilia; Yankilevich, Patricio; Robledo, Mercedes; Carracedo, Ángel; Benı́tez, Javier

doi:10.1007/s00439-005-0094-9

Cited by 91 publications

(51 citation statements)

References 45 publications

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“…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. A number of studies have also attempted to measure the transferability of tagging SNPs in nonHapMap populations, including Korean (Lim et al 2006;Yoo et al 2006), Spanish (Ribas et al 2006), Estonian (Montpetit et al 2006), and 12 population isolates from Europe (Service et al 2007). Together with the present study, we conclude that tagging SNPs selected from the HapMap populations are highly portable to other populations from the same continent.…”

Section: Discussionsupporting

confidence: 74%

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: 74%

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

et al. 2008

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“…Furthermore, results presented here confirm previous observations that the patterning of LD observed in the European HapMap population represents to a large degree that observed in other European populations. 4,6,8 Interestingly, among the populations we studied, the Irish population appeared the most highly correlated with European HapMap population in terms of LD (as measured by r 2 ), suggesting high portability of tSNPs, an observation confirmed by our tSNP transferability assessment. We note, however, that reported differences in correlations were not statistically significant.…”

Section: Discussionsupporting

confidence: 64%

An assessment of the Irish population for large-scale genetic mapping studies involving epilepsy and other complex diseases

et al. 2007

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The recent completion of the International HapMap Project has rapidly advanced our understanding of linkage disequilibrium (LD) in the human genome. Today, tagging SNPs (tSNPs) can be quickly and easily selected and consequently HapMap data are regularly applied to both small-and large-scale genetic mapping studies. However, to correctly interpret the application of HapMap-derived tSNPs in a genetic mapping study, an understanding of how well HapMap data represents LD in the study population is critical. The Irish population had not previously been characterised in this way. Here, we do so using a set of 4424 SNPs selected from 279 candidate genes for epilepsy genotyped across 1118 healthy individuals from the Irish, British, Finnish and Australian populations. By considering the Irish population alongside surrounding European populations, our results confirm that the HapMap European-derived population accurately estimates patterning of LD in European descent populations. The Irish population appears notably well matched to the European HapMap population, and is markedly similar to the neighbouring British population. Although we were unable to detect significant substructure within the Irish population (a favourable result for genetic mapping), methods for controlling stratification should always be incorporated. This analysis therefore confirms that the genetic architecture of the Irish population is well suited to the study of complex traits and that tSNPs selected using the HapMap data can be confidently applied to the Irish population.

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“…Genetic polymorphism in DNA repair genes is one of the major reasons introducing individual differences in DNA repair capacity. Hundreds of polymorphisms in DNA repair genes have been identified and some of them have been consistently associated with cancer susceptibility [Hung et al, 2005;Spitz et al, 2003;Ribas et al, 2006]. For example, the OGG1 p.S326C and the XRCC1 p.R194W have been shown to be associated with an increased risk of various types of human cancer; while the BRCA2 p.N372H was reported to be more specifically associated with an increased risk of breast cancer [Goode et al, 2002;Gu et al, 2005].…”

Section: Ercc6 (Also Known As Cockayne Syndrome [Cs] Complementation mentioning

confidence: 99%

A variant of the Cockayne syndrome B geneERCC6 confers risk of lung cancer

et al. 2007

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Cockayne syndrome B protein (ERCC6) plays an essential role in DNA repair. However, the Cockayne syndrome caused by the ERCC6 defect has not been linked to cancer predisposition; likely due to the fact that cells with severe disruption of the ERCC6 function are sensitive to lesion-induced apoptosis, thus reducing the chance of tumorigenesis. The biological function and cancer susceptibility of a common variant rs3793784:C>G (c.−6530C>G) in the ERCC6 was examined. We show that the c.−6530C allele has lower binding affinity of Sp1 by EMSA and displays a lower transcriptional activity in vitro and in vivo. We then examined the contribution of this polymorphism to the risk of lung cancer in a case-control study with 1,000 cases and 1,000 controls. The casecontrol analysis revealed a 1.76-fold (P = × 10 −9 ) excess risk of developing lung cancer for the c. −6530CC carriers compared with noncarriers. The c.−6530CC interacts with smoking to intensify lung cancer risk, with the odds ratio (OR) = 9 for developing lung cancer among heavy smokers. Our data constituted strong evidence that ERCC6 rs3793784:C>G alters its transcriptional activity and may confer personalized susceptibility to lung cancer.

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Evaluating HapMap SNP data transferability in a large-scale genotyping project involving 175 cancer-associated genes

Cited by 91 publications

References 45 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

An assessment of the Irish population for large-scale genetic mapping studies involving epilepsy and other complex diseases

A variant of the Cockayne syndrome B geneERCC6 confers risk of lung cancer

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