TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population.
BACKGROUND
The application of a subset of single nucleotide polymorphisms, the tagSNPs, can be useful in capturing untyped SNPs information in a genomic region. TagSNP transferability from the HapMap dataset to admixed populations is of uncertain value due population structure, admixture, drift and recombination effects. In this work an empirical dataset from a Brazilian admixed sample was evaluated against the HapMap population to measure tagSNP transferability and the relative loss of variability prediction.


METHODS
The transferability study was carried out using SNPs dispersed over four genomic regions: the PTPN22, HMGCR, VDR and CETP genes. Variability coverage and the prediction accuracy for tagSNPs in the selected genomic regions of HapMap phase II were computed using a prediction accuracy algorithm. Transferability of tagSNPs and relative loss of prediction were evaluated according to the difference between the Brazilian sample and the pooled and single HapMap population estimates.


RESULTS
Each population presented different levels of prediction per gene. On average, the Brazilian (BRA) sample displayed a lower power of prediction when compared to HapMap and the pooled sample. There was a relative loss of prediction for BRA when using single HapMap populations, but a pooled HapMap dataset generated minor loss of variability prediction and lower standard deviations, except at the VDR locus at which loss was minor using CEU tagSNPs.


CONCLUSIONS
Studies that involve tagSNP selection for an admixed population should not be generally correlated with any specific HapMap population and can be better represented with a pooled dataset in most cases.
Lins
Tulio C
TC
Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil. lins.tulio@gmail.com
Abreu
Breno S
BS
Pereira
Rinaldo W
RW
D000349:Africa / Q000208:ethnology; D000465:Algorithms; D001938:Brazil; D053480:Cholesterol Ester Transfer Proteins / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D005006:Ethnicity / Q000235:genetics*; D005060:Europe / Q000208:ethnology; D005202:Asia, Eastern / Q000208:ethnology; D014644:Genetic Variation / Q000235:genetics*; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D006903:Hydroxymethylglutaryl CoA Reductases / Q000235:genetics; D015810:Linkage Disequilibrium; D008393:Marriage / Q000208:ethnology; D056186:Metagenomics / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D054596:Protein Tyrosine Phosphatase, Non-Receptor Type 22 / Q000235:genetics; D018167:Receptors, Calcitriol / Q000235:genetics; D012494:Sampling Studies; D013020:South America / Q000208:ethnology
C506642:CETP protein, human; D053480:Cholesterol Ester Transfer Proteins; D018167:Receptors, Calcitriol; D006903:Hydroxymethylglutaryl CoA Reductases; C516765:PTPN22 protein, human; D054596:Protein Tyrosine Phosphatase, Non-Receptor Type 22
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