Comparative high-resolution analysis of linkage disequilibrium and tag single nucleotide polymorphisms between populations in the vitamin D receptor gene

Nejentsev, Sergey; Godfrey, Lisa; Snook, Hywel; Rance, Helene; Nutland, Sarah; Walker, Neil M.; Lam, Adam; Guja, C; Ionescu-Tîrgovişte, C; Undlien, Dag E.; Rønningen, Kjersti S.; Tuomilehto‐Wolf, Eva; Tuomilehto, Jaakko; Newport, Melanie J.; Clayton, David; Todd, John A.

doi:10.1093/hmg/ddh169

Cited by 173 publications

(169 citation statements)

References 28 publications

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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%

“…However, worldwide population variation is not completely characterized, and an essential question is whether tag SNPs chosen using HapMap panels will adequately capture patterns of genetic variation in other populations (Weale et al 2003;Nejentsev et al 2004;Evans and Cardon 2005;Ke et al 2005;Mueller et al 2005;Ramirez-Soriano et al 2005;Gonzalez-Neira et al 2006;Huang et al 2006;Montpetit et al 2006;Ribas et al 2006;Willer et al 2006). 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).…”

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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Section: Discussionsupporting

confidence: 85%

Section: Introductionmentioning

confidence: 99%

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

Marvelle

Lange

et al. 2007

J Hum Genet

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“…All of the European populations showed dramatically similar LD properties in the gene, and that tags generated from the CEPH sample performed reasonably well. The authors conclude that the similarity of LD is consistent with the model predicting no major founder effect for the Europeans [Nejentsev et al, 2004]. Recently, Ribas et al published an examination of population differences between a Spanish sample and the CEPH sample.…”

Section: Introductionsupporting

confidence: 59%

“…Accordingly, the Belgian, English, German, Dutch, Irish, and to a lesser extent Swiss appear similar for pairwise tagging, with the Spanish, and Israelis more distinct. Other work in this vein indicates that the CEPH sample, which is of Northern European ancestry, provides a good tagging set [de Bakker et al, 2006;Gonzalez-Neira et al, 2006;Nejentsev et al, 2004]. However, the sample size appears to be the distinguishing factor in terms of performance when using aggressive tagging.…”

Section: Discussionmentioning

confidence: 99%

Population differences in the International Multi‐Centre ADHD Gene Project

Neale

Sham

Purcell

et al. 2007

Genetic Epidemiology

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) ascertained from clinics for combined-type attention definity hyperactivity disorder in an offspring. 863 SNPs were successfully genotyped across 47 autosomal genes implicated in psychiatric disorders yielding a single nucleotide polymorphism (SNP) density of approximately one SNP per 2.5 kb. A global test of heterogeneity showed 269 SNPs nominally significant (expected 43). Inclusion of the Israeli population accounted for approximately 70% of these nominally significant tests. Hardy-Weinberg equilibrium tests suggest that combining all these populations would induce stratification, but that the Northern European populations (Belgium, England, Germany, Holland, and Ireland) could be appropriate. Tag SNPs were generated using pair-wise and aggressive tagging from Carlson et al. [2004] and de Bakker et al. [2005], respectively, in each population and applied to the other populations. Cross-population performance across Northern Europe was consistent with within population comparisons. Smaller sample size for each population tended to yield more problems for the generation of aggressive tags and the application of pair-wise tags. Any case-control sample employing an Israeli sample with Northern Europeans must consider stratification. A Northern European tag set, however, appears to be appropriate for capturing the variation across populations. Genet. Epidemiol. 32:98-107, 2008. r 2007 Wiley-Liss, Inc.

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“…Moreover, the Cdx2 and GATA polymorphisms have been described to show a linkage disequilibrium describing three haplotypes (7). In case of linkage disequilibrium it is more appropriate to study the associations for haplotypes instead of separate polymorphisms (7,19,20). In Fig.…”

Section: Dna Isolation and Genotypingmentioning

confidence: 99%

Associations between vitamin D receptor genotypes and mortality in a cohort of older Dutch individuals

Jongh

Lips

Rijs

et al. 2011

European Journal of Endocrinology

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Context: Vitamin D receptor (VDR) polymorphisms are associated with a variety of diseases, which may translate into an effect on mortality. Objective: To investigate the associations between VDR gene variants and mortality among older people. Design: The analyses were conducted in a population-based, prospective cohort of the Longitudinal Aging Study Amsterdam. Adequate DNA analysis was performed in 923 men and women (R65 years). We aimed to assess the associations between mortality and the VDR polymorphism FokI, three haplotypes of the Cdx2 and GATA polymorphisms, and three haplotypes of the BsmI, ApaI, and TaqI polymorphisms. Results: During the median follow-up of 10.7 years, 480 participants deceased (51%). Homozygosity for the Cdx2-GATA haplotype 1 allele was associated with a 30% higher mortality risk compared to the absence of alleles (hazard ratios (HR) 1.30, 95% confidence intervals (CI) 1.01-1.68). Adjustment for cardiovascular risk factors and 25-hydroxyvitamin D levels did not affect this HR. The number of copies of the Cdx2-GATA haplotype 1 allele was associated, although not significantly, with an increased risk of osteoporotic fractures (0 copiesZreference, HR, 95% CI: 1 copy 2.01, 0.99-4.07 and 2 copies 1.81, 0.87-4.18). After adjustment for osteoporotic fractures, homozygosity for the Cdx2-GATA haplotype 1 allele was no longer associated with higher mortality risk (HR 1.08, 95% CI 0.83-1.41).

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Comparative high-resolution analysis of linkage disequilibrium and tag single nucleotide polymorphisms between populations in the vitamin D receptor gene

Cited by 173 publications

References 28 publications

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

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

Population differences in the International Multi‐Centre ADHD Gene Project

Associations between vitamin D receptor genotypes and mortality in a cohort of older Dutch individuals

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