ReviewHuman genetics2006
Evaluating HapMap SNP data transferability in a large-scale genotyping project involving 175 cancer-associated genes.
Review in Human genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Malaria-Related Host Genetic Variation in an Endemic Population of Southern Senegal.International journal of molecular sciences · 2026Article
- Association of NDRG4 gene methylation in peripheral blood leukocytes with gastric cancer risk, chemotherapy efficacy and prognosis.Frontiers in oncology · 2026Article
- Genetic Variations in Prostaglandin EInternational journal of molecular sciences · 2021Article
- Association betweenRadiology and oncology · 2017Article
- Are polymorphisms of the immunoregulatory factor CD40LG implicated in acute transfusion reactions?Scientific reports · 2014Article
- Evaluating the accuracy of AIM panels at quantifying genome ancestry.BMC genomics · 2014Article
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- Using haplotype analysis to elucidate significant associations between genes and Hodgkin lymphoma.Leukemia research · 2012Article
- Hodgkin lymphoma risk: role of genetic polymorphisms and gene-gene interactions in DNA repair pathways.Molecular carcinogenesis · 2011Article
- Identifying highly conserved and highly differentiated gene ontology categories in human populations.PloS one · 2011Article
- APC Yin-Yang haplotype associated with colorectal cancer risk.Experimental and therapeutic medicine · 2010Article
- Comparison of genome-wide variation between Malawians and African ancestry HapMap populations.Journal of human genetics · 2010Article
- Global similarity with local differences in linkage disequilibrium between the Dutch and HapMap-CEU populations.European journal of human genetics : EJHG · 2009Article
- Article
- Article
- Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India.Annals of human genetics · 2008Article
- Article
- A variant of the Cockayne syndrome B gene ERCC6 confers risk of lung cancer.Human mutation · 2008Article
- Linkage disequilibrium structure of the 5q31-33 region in a Thai population.Journal of human genetics · 2008Article
- Comprehensive testing of positionally cloned asthma genes in two populations.American journal of respiratory and critical care medicine · 2007Article
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One of the many potential uses of the HapMap project is its application to the investigation of complex disease aetiology among a wide range of populations. This study aims to assess the transferability of HapMap SNP data to the Spanish population in the context of cancer research. We have carried out a genotyping study in Spanish subjects involving 175 candidate cancer genes using an indirect gene-based approach and compared results with those for HapMap CEU subjects. Allele frequencies were very consistent between the two samples, with a high positive correlation (R) of 0.91 (P<<1x10(-6)). Linkage disequilibrium patterns and block structures across each gene were also very similar, with disequilibrium coefficient (r (2)) highly correlated (R=0.95, P<<1x10(-6)). We found that of the 21 genes that contained at least one block larger than 60 kb, nine (ATM, ATR, BRCA1, ERCC6, FANCC, RAD17, RAD50, RAD54B and XRCC4) belonged to the GO category "DNA repair". Haplotype frequencies per gene were also highly correlated (mean R=0.93), as was haplotype diversity (R=0.91, P<<1x10(-6)). "Yin yang" haplotypes were observed for 43% of the genes analysed and 18% of those were identical to the ancestral haplotype (identified in Chimpazee). Finally, the portability of tagSNPs identified in the HapMap CEU data using pairwise r (2) thresholds of 0.8 and 0.5 was assessed by applying these to the Spanish and current HapMap data for 66 genes. In general, the HapMap tagSNPs performed very well. Our results show generally high concordance with HapMap data in allele frequencies and haplotype distributions and confirm the applicability of HapMap SNP data to the study of complex diseases among the Spanish population.
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