Sentence examples for using the hapmap tag from inspiring English sources

Focusing solely on the genes located in the candidate region identified by the meta-analysis of the top candidate genes (PLINK filter from chromosome 6: 6–31 Mb), 2,730 SNPs remained, and among these only tag SNPs were selected using the HapMap tag SNP picking tool Tagger.

First using the HapMap data, we selected six tag SNPs (rs689466, rs2745557, rs2206593, rs4648307, rs4648261, and rs5272) to capture the common genetic variation across COX2 (mean r=1.0).

CANGES compensates the tag-SNP designs by using the HapMap database and producing a comprehensive list of SNPs in region pinpointed by the tag-SNPs.

The SNP module searches also allele frequencies and tag-SNPs for each annotated SNP, using the HapMap database version 3, draft 1 [10].

Furthermore, tagging SNPs in LARS2 were selected for genotyping in the NL1 sample using the HapMap database and Tagger software [ 20, 21] (selection criteria and SNPs shown in Electronic supplementary material [ESM] Table  1).

For the FGFR4 gene, based on the HapMap phase II SNP genotype data, we chose three tag-SNPs (rs1966265, rs376618, and rs351855) as surrogates for untyped polymorphisms in the FGFR4 gene using the HapMap Project 90 (30 trios) Caucasian samples from a US Utah population with Northern and Western European ancestry collected in 1980 by the Centre d'Etude du Polymorphisme Humain (CEPH) [ 39].

LSBL in HapMap was calculated using the HapMap database that considers all African, European and Asian populations together.

For each gene we used the HapMap browser release 20 (http://www.hapmap.org/cgi-perl/gbrowse/hapmap20_B35 .hapmap.org/cgi-perl/gbrowse/hapmap20_B35 of toe common (greater than 5%) variation within that gene.

We selected tagging single nucleotide polymorphisms (SNPs) with the criteria of R>0.8 and minor allele frequency (MAF)>0.05 across the region of the MTNR1B gene (include 3kb upstream and 3kb downstream of the gene) from the HapMap Phase II, using the pairwise tagging model.

Four tag SNPs for the 12.44 kb region encompassing the entire TF gene and eight tag SNPs for the 75.91 kb region encompassing the entire TFPI gene were identified by tagger within Haploview [ 24] using the following tagging criteria: pairwise tagging of the HapMap Han Chinese in Beijing population with r ≥ 0.8 and a minor allele frequency ≥5%.

In total, 12 tag SNPs in the five genes were selected by Tagger within Haploview using the following tagging criteria: pairwise tagging of the HapMap population with r 2 of at least 0.8 and a minor allele frequency (MAF) of at least 5%.