In genetics, haplotype estimation (also known as "phasing") refers to the process of statistical estimation of haplotypes from genotype data. The most common situation arises when genotypes are collected at a set of polymorphic sites from a group of individuals. For example in human genetics, genome-wide association studies collect genotypes in thousands of individuals at between 200,000-5,000,000 SNPs using microarrays. Haplotype estimation methods are used in the analysis of these datasets and allow genotype imputation[1][2] of alleles from reference databases such as the HapMap Project and the 1000 Genomes Project.
^Marchini, J.; Howie, B. (2010). "Genotype imputation for genome-wide association studies". Nature Reviews Genetics. 11 (7): 499–511. doi:10.1038/nrg2796. PMID 20517342. S2CID 1465707.
^Howie, B.; Fuchsberger, C.; Stephens, M.; Marchini, J.; Abecasis, G. A. R. (2012). "Fast and accurate genotype imputation in genome-wide association studies through pre-phasing". Nature Genetics. 44 (8): 955–959. doi:10.1038/ng.2354. PMC 3696580. PMID 22820512.
and 23 Related for: Haplotype estimation information
In genetics, haplotypeestimation (also known as "phasing") refers to the process of statistical estimation of haplotypes from genotype data. The most...
A haplotype (haploid genotype) is a group of alleles in an organism that are inherited together from a single parent. Many organisms contain genetic material...
This is a list of notable software for haplotypeestimation and genotype imputation. Alphabetical order: AlphaImpute Beagle cnF2freq DAGPHASE Eagle fastPHASE...
group was responsible for the haplotypeestimation and genotype imputation for the UK Biobank dataset. He co-leads the Haplotype Reference Consortium. He has...
following functionalities: LD & haplotype block analysis Haplotype population frequency estimation Single SNP and haplotype association tests Permutation...
Browning, S. R. (2008). "Estimation of Pairwise Identity by Descent from Dense Genetic Marker Data in a Population Sample of Haplotypes". Genetics. 178 (4):...
referred to as its haplotype. In principle, since there are four base types, with 1000 base pairs, we could have 41000 distinct haplotypes. However, for organisms...
Frequencies, pg 294–295, S. Wright, Univ. of Chicago Press, Chicago, 1969 A haplotype map of the human genome, The International HapMap Consortium, Nature 2005...
Kamath, Govinda M.; Şaşoğlu, Eren; Tse, David (14–19 June 2015). Optimal haplotype assembly from high-throughput mate-pair reads. 2015 IEEE International...
manipulation allows exploration in the effects of missing populations on the estimation of population sizes and migration rates between two specific populations...
as Phylotree, feature internal nodes labeled with inferred ancestral haplotypes. The number of possible trees for a given number of leaf nodes depends...
A principal components analysis scatterplot of Y-STR haplotypes calculated from repeat-count values for 37 Y-chromosomal STR markers from 354 individuals...
2021-01-30. Excoffier, L.; Slatkin, M. (1995). "Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population". Molecular Biology and...
When an estimation was made using microsatellite loci, the Newfoundland was found to have high autosomal diversity and a high number of haplotypes, some...
markers which give a mitochondrial "DNA signature" or "haplotype" (e.g. the CRS is a haplotype). Each marker is a DNA base-pair that has resulted from...
PMC 5492993. PMID 28445722. Refer Figure 4 and Supplementary Table S2: "Mean Haplotype Sharing Totals that Reach the 95% Significance Level between All Pairs...
French-Acadian populations (Louisiana). Among Acadians, research into haplotype data is consistent with one single mutation being responsible for all...
reduction, and density estimation. Unsupervised learning algorithms also streamlined the process of identifying large indel based haplotypes of a gene of interest...
factor for the number of gene lineages, zygosity mutations, and founding haplotypes present in today's Indigenous peoples of the Americas populations. The...
(2016-12-01). "The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes". GigaScience. 5 (1): 42. doi:10.1186/s13742-016-0148-z...
worldwide revealed that one Kishu and one Siberian husky possessed the same haplotype as a Japanese wolf, indicating past cross-breeding. A more-refined study...
2023. Retrieved 13 April 2024. Karanth, K. U. & Nichols, J. D. (1998). "Estimation of tiger densities in India using photographic captures and recaptures"...
Institute of Anthropology in Paris, France, confirmed similarities in the Y-haplotype frequencies in Lebanese, Palestinian, and Sephardic Jewish men, identifying...
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