Sentences with phrase «using haplotype»

On detecting incomplete soft or hard selective sweeps using haplotype structure Ferrer - Admetlla, A., M. Liang, T. Korneliussen, and R. Nielsen.

On detecting incomplete soft or hard selective sweeps using haplotype structure.

Not exact matches

Genetic tools still under construction, such as a haplotype map that will be used to discern genetic variation behind common diseases, could further accelerate the search for disease genes.

We also performed the first example of cross validation using complementary CC resources to verify the effect of sperm curvilinear velocity from the PWK / PhJ haplotype on chromosome 2 in an independent population across multiple generations.

While the new Y haplotype does increase the diversity, and thus the TMRCA, the TMRCA calculation is extremely sensitive to the mutation rate used.

Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species Hey, J., Y. Won, A. Sivasundar, R. Nielsen, et al. 2004.

These were error - corrected and utilized to infer haplotypes using HASH and HAPCUT, yielding 269,392 phased haplotype blocks.

Here we report the assembly of a haplotype - resolved diploid genome without using a reference genome.

Haplotype mapping of a diploid non-meiotic organism using existing and induced aneuploidies.

Because the polyT repeat is reported as the key variant to define TOMM40 clades A and B, 12 we used this marker and APOE isoform information to perform analyses based on phylogenetic groups as described by Roses et al. 12 Haplotype phase was estimated using PHASE software.22 The phylogeny, which represents the evolutionary relatedness of the haploytpes, was estimated using neighbor - joining with 10 000 bootstrapping replicates in the CLC DNA workbench (CLC bio, Aarhus, Denmark)(Supplemental Figure 3; http://neuroscienceresearch.wustl.edu/Pages/cruchaga2011.aspx).

Remarkably, through iterative use of two online archives, FamilySearch and Sorenson Molecular Genetic Foundation, I was able to infer the Y chromosome STR haplotypes of these two founders.

Association of APOE 3 — TOMM40 clade A and B haplotypes with case - control status was performed using a Fisher exact test.

We estimate that with the gPBWT of the order of 100,000 diploid genomes, including all forms structural variation, could be stored and made searchable for haplotype queries using a single large compute node.

We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues.

By using the recent haplotype - based methods ChromoPainter (CP) and FineSTRUCTURE (FS) we reveal a highly geographically clustered genetic structure in Finland and report its connections to the settlement history as well as to the current dialectal regions of the Finnish language.

9,961 individuals from the UK Household Longitudinal Study were genotyped using the Illumina HumanCoreExome array and variants imputed to the 1000 Genomes Project and UK10K haplotypes.

As a demonstration, we use the gPBWT to quickly count the number of haplotypes consistent with random walks in a genome graph, and with the paths taken by mapped reads; results suggest that haplotype consistency information can be practically incorporated into graph - based read mappers.

164/5: 15 A novel algorithm for estimating shared haplotype segments using rare genetic variants.

To summarize haplotype diversity within each dog breed, we used the number of distinct haplotypes within each window in windows across the genome.

The role of HLA haplotypes in celiac disease will be used to show the role of deamidation in celiac disease and how this is not a process that happens with the non-celiac gluten sensitivity form.

In this project, we proposed to characterize haplotypes, in over 1200 dogs from 50 pure AKC breeds using DNA sequencing.

Four paternal haplotypes, with one occurring in 93 % of dogs, were identified using six Y - short tandem repeat (STR) markers.

Thirty - three STR loci across 25 chromosomes were used to assess genomic diversity, while four STR loci were used to determine DLA class I haplotypes and three STR loci were used for DLA class II haplotypes.

This study examines genetic diversity among 102 registered English Bulldogs used for breeding based on maternal and paternal haplotypes, allele frequencies in 33 highly polymorphic short tandem repeat (STR) lo...

Independent analyses of two of the most widely used mtDNA genes in mammalian phylogeography, cytochrome b and D - loop, recovered only 15 and 20 haplotypes, respectively, instead of the 35 haplotypes recovered by sequencing whole mitogenomes (S2 Table).

Bayesian phylogenetic analysis in BEAST [36] of all unique mainland and island haplotypes (Fig. 3) used the earliest island fox radiocarbon date as a prior estimate for the coalescence of all island fox lineages.

Previous analyses using mtDNA RFLP's identified more mtDNA haplotypes than detected by our whole mitogenome (WMG) sequencing analysis on San Miguel (2 RFLP: 1 WMG genotypes) and Santa Catalina (3 RFLP: 2 WMG genotypes), suggesting a possible loss of mtDNA diversity on these islands as a result of population bottlenecks over the past 25 years [15].

From this minimum census, Branch and Jackson [17] used a rarefaction approach to predict that a total of only 51 haplotypes (i.e., haplotype richness) survive in the contemporary population.

This prediction is of interest because haplotype richness can be used in population dynamic modeling to inform a lower boundary on the minimum number of whales (Nmin) that survived the exploitation bottleneck caused by commercial whaling [18].

Haplotype analyses were conducted using PHASE software for SNPs from the 1b receptor gene, TPH1 and TPH2.