Comparison of ENCODE region SNPs between Cebu Filipino and Asian HapMap samples.
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.
Marvelle
Amanda F
AF
Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, 4109-F Neuroscience Research Building, 103 Mason Farm Road, Chapel Hill, NC, 27599-7264, USA.
Lange
Leslie A
LA
Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, 4109-F Neuroscience Research Building, 103 Mason Farm Road, Chapel Hill, NC, 27599-7264, USA.
Qin
Li
L
Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, 4109-F Neuroscience Research Building, 103 Mason Farm Road, Chapel Hill, NC, 27599-7264, USA.
Wang
Yunfei
Y
Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, 4109-F Neuroscience Research Building, 103 Mason Farm Road, Chapel Hill, NC, 27599-7264, USA.
Lange
Ethan M
EM
Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, 4109-F Neuroscience Research Building, 103 Mason Farm Road, Chapel Hill, NC, 27599-7264, USA.|Department of Biostatistics, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
Adair
Linda S
LS
Department of Nutrition, Schools of Medicine and Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
Mohlke
Karen L
KL
Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, 4109-F Neuroscience Research Building, 103 Mason Farm Road, Chapel Hill, NC, 27599-7264, USA. mohlke@med.unc.edu.
D044466:Asian People / Q000235:genetics*; D005787:Gene Frequency; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D010679:Philippines; D020641:Polymorphism, Single Nucleotide