Sentence examples for genome phasing from inspiring English sources

A combination of genetic, physical and population-based approaches in a quartet yielded complete genome phasing, including phasing of 99.8% of fully heterozygous variants [ 53].

Here, we present a tool, variant analysis of sequenced pedigrees (VASP), a flexible data integration environment capable of producing a summary of pedigree variation, providing relevant information such as compound heterozygosity, genome phasing and disease inheritance patterns.

Despite the fact that differences between these copies play an important biological role, until recently, decoding these differences (a process known as haplotyping or genome phasing) has been a major technological challenge.

Honey Bee Genome Phase II White Paper Authors: JDE, MB, CGE1, 2, RM, HMR, GER, DBW, CWW.

The GTEx project used the Illumina Omni5 array for direct sample genotyping and subsequently imputed with IMPUTE2 [ 25] using the 1000 Genome phase 1 release reference panel.

After excluding common variants (≥5% minor allele frequency represented in the NHLBI exome server or the 1000 genome phase 1 data set, or ∼2000 internal exomes), two shared homozygous missense variants were identified in the genes PPP1R15B and AQR.

We imputed all 44 621 samples genotyped in the iCOGS PRACTICAL (http://ccge.medschl.cam.ac.uk/consortia/practical) sample set for variants in the 1000 Genome Phase 1 integrated variant set (March 2012) for the interval Chr5:1227693-1361669 using IMPUTE v2.2.2.

Before imputation, individuals were recorded for 299 735 autosomal SNPs with minor allele frequency >0.01; after imputation against the 1000 Genome Phase I June 2011 (interim) reference panel using IMPUTE2 (The 1000 Genomes Project Consortium, 2010; Howie et al., 2011), this number increased to 4 238 038.

Conserved regions longer then the average fragment length (450 bp) may introduce ambiguity in the assembly process due to a lack of direct evidence of sub-genomes phasing across the conserved region.

Linked SNPs were identified using PLINK and 1000 Genomes (phase 1) variant call format files [29,57].

Sequencing data was obtained from the 1000 Genomes Phase 1 exome project [ 12].