Sentence examples for using the hapmap phase from inspiring English sources
In order to verify this finding using data from a larger genomic region, we repeated the same analysis using the HapMap Phase II data for more than 200 SNPs spanning approximately 100 kb centered on the NAT2 coding region [23].
We restricted this evaluation to the two-step protocol using the HapMap phase II combined sample.
Population stratification was assessed with Eigenstrat and SmartPCA (both available from http://genepath.med.harvard.edu/∼reich/Software.htm) using the HapMap phase 3 Release 27 data (Price et al. 2006).
Genome-wide imputation was done using the HapMap phase I-II CEU data (release 22, NCBI build 36) as the reference sample and MACH software.
We calculated genetic distance to the centromere for all SNPs using the HapMap phase II genetic map (Frazer et al. 2007) and gaps in the assembly annotated as centromeres by the UCSC Genome Browser (http://genome.ucsc.edu/), using build HG18.
The INFO scores based on the two-step imputation method using the HapMap phase II combined and the 1000 Genomes (June 2011 release) reference panels were compared for different allele frequency categories, grouping markers in 5% bins.
We used the HapMap phase 3 European population (CEU) chromosome 12 [ 18] phase-known dataset that has been created for each family trio in the database.
To estimate the power for predicting deletions, we use the HapMap Phase 1 CEU, Phase2+3 CEU and AGRE autism data; this selection fixes the allele frequencies.
SNPs in regions of interest were imputed with MACH v1.0 [ 30] using the HapMap Release 22 (Phase II) phased haplotype data as the reference.
SNPs from these genes were identified using the HapMap Genome Browser (Phase 1 and 2, release 24; http://hapmap.ncbi.nlm.nih.gov/), among the CEPH (Caucasian) population.
DNA samples used in the HapMap Phase 1 project (CEU, European Americans from Utah; YRI, Yoruba from Ibadan, Nigeria; CHB, Chinese from Beijing; JPT, Japanese from Tokyo) were obtained from Coriell Cell Repositories.
