The remaining 15 samples were negative controls, which included 13 DNA specimens that tested negative for mutations in selected genes and 2
HapMap samples (NA12878 and NA19240).
MAFs for all five tagSNPs in our controls were similar to those for Chinese subjects in
HapMap database (Table 2).
On the other hand, the "C" allele frequency of rs2070744 was significantly higher than those displayed among Chinese, Japanese and other
HapMap populations (for all comparisons, p=0.
Among the GIH population (Gujarati Indians in Houston, Texas) in the
Hapmap 3 SNP data set, ICAM1 rs28l432 was not found, and no proxy SNPs were identified for VCAM1 rs3176867 (SNAP; Johnson et al.
Since the CEPH
HapMap data included trio data on proband and parents, calculation of 0-, 1-, and 2-copy genotype frequencies was performed using only parental data to minimize overestimation.
Concurrently with the HGP, the International
HapMap (52) Consortium
Location of each SNP was identified through the
HapMap project Database.
3m variants per sample selected from the International
HapMap Project and the 1000 Genomes Project, offers flexibility to include up to 500,000 custom markers.
Comparison with
HapMap database: SNP data obtained on control samples from the north Indian subpopulations were compared with the data available on the other world populations available through the
HapMap Genome Browser (
HapMap Public Release #27) of
Hapmap database (24).
To design the array, researchers at the Bio-X Center of Shanghai Jiao Tong University and Beijing's Fuwai Hospital took advantage of more than 10 million validated markers in the Axiom Genomic Database, including content drawn from the 1000 Genomes Project and the International
HapMap Project.
gov/snp/]) and International
HapMap Project (Rel 28 PhasesII+III, on NCBI B36 assembly, dbSNP b126 [http://
hapmap.
The University of Pennsylvania genotyped 98 samples using the IBCvl microarray; and the MAF for each of the TMCC SNPs was compared with the
HapMap prevalence in the Caucasian population (5).
