ArticleGenome research2006
The portability of tagSNPs across populations: a worldwide survey.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Reflections on the Human Genome Diversity Project: a conversation with Marcus W. Feldman, Henry T. Greely, and Mary-Claire King.Genetics · 2026Article
- Exome-Wide Association Analysis of Coronary Artery Disease in the Kingdom of Saudi Arabia Population.PloS one · 2016Article
- Population and genomic lessons from genetic analysis of two Indian populations.Human genetics · 2014Article
- The Genetic Diversity and Structure of Linkage Disequilibrium of the MTHFR Gene in Populations of Northern Eurasia.Acta naturae · 2012Article
- Genome-wide association studies of hypertension: light at the end of the tunnel.International journal of hypertension · 2010Article
- Isolated populations as treasure troves in genetic epidemiology: the case of the Basques.European journal of human genetics : EJHG · 2009Article
- Looking for race in all the wrong places: analyzing the lack of productivity in the ongoing debate about race and genetics.Human genetics · 2009Review
- TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population.Journal of biomedical science · 2009Article
- Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD.BMC genomics · 2009Article
- Global similarity with local differences in linkage disequilibrium between the Dutch and HapMap-CEU populations.European journal of human genetics : EJHG · 2009Article
- Use of weighted reference panels based on empirical estimates of ancestry for capturing untyped variation.Human genetics · 2009Article
- Genotype-imputation accuracy across worldwide human populations.American journal of human genetics · 2009Article
- High-throughput SNP genotyping: combining tag SNPs and molecular beacons.Methods in molecular biology (Clifton, N.J.) · 2009Article
- Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India.Annals of human genetics · 2008Article
- Article
- Calibrating the performance of SNP arrays for whole-genome association studies.PLoS genetics · 2008Article
- Evaluating linkage disequilibrium and recombination provides a haplotype-tagging SNP panel of the major histocompatibility complex in African Americans.Genes and immunity · 2008Article
- Article
- Genetic variation and population structure in native Americans.PLoS genetics · 2007Article
- 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
14 authors.
Funding
Abstract
In the search for common genetic variants that contribute to prevalent human diseases, patterns of linkage disequilibrium (LD) among linked markers should be considered when selecting SNPs. Genotyping efficiency can be increased by choosing tagging SNPs (tagSNPs) in LD with other SNPs. However, it remains to be seen whether tagSNPs defined in one population efficiently capture LD in other populations; that is, how portable tagSNPs are. Indeed, tagSNP portability is a challenge for the applicability of HapMap results. We analyzed 144 SNPs in a 1-Mb region of chromosome 22 in 1055 individuals from 38 worldwide populations, classified into seven continental groups. We measured tagSNP portability by choosing three reference populations (to approximate the three HapMap populations), defining tagSNPs, and applying them to other populations independently on the availability of information on the tagSNPs in the compared population. We found that tagSNPs are highly informative in other populations within each continental group. Moreover, tagSNPs defined in Europeans are often efficient for Middle Eastern and Central/South Asian populations. TagSNPs defined in the three reference populations are also efficient for more distant and differentiated populations (Oceania, Americas), in which the impact of their special demographic history on the genetic structure does not interfere with successfully detecting the most common haplotype variation. This high degree of portability lends promise to the search for disease association in different populations, once tagSNPs are defined in a few reference populations like those analyzed in the HapMap initiative.
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