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Algorithms for Haplotype Phasing

by Christine Lo
"... A haplotype is the sequence of nucleotides along a single chromosome. As humans, we have 23 pairs of chromosomes. However, with current technology, it is dicult to separate the two chromosomes of a pair and we often get combined haplotype, or genotype, information. The objective of haplotype phasing ..."
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phasing is to resolve (phase) the haplotypes given genotype information. Knowing the haplotypes not only gives us a complete picture of an individual’s genome, but also has other significant biological motivations. Here we study how the haplotype phasing problem has been reformulated as technology to read

A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotype phase

by Paul Scheet, Matthew Stephens - American Journal of Human Genetics , 2005
"... We present a statistical model for patterns of genetic variation in samples of unrelated individuals from natural populations. This model is based on the idea that, over short regions, haplotypes in a population tend to cluster into groups of similar haplotypes. To capture the fact that, because of ..."
Abstract - Cited by 408 (10 self) - Add to MetaCart
missing genotypes and estimating haplotypic phase. For imputing missing genotypes, methods based on this model are as accurate or more accurate than existing methods. For haplotype estimation, the point estimates are slightly less accurate than those from the best existing methods (e.g., for unrelated

Haplotype phasing using semidefinite programming

by Konstantinos Kalpakis, Parag Namjoshi - In BIBE , 2005
"... Diploid organisms, such as humans, inherit one copy of each chromosome (haplotype) from each parent. The conflation of inherited haplotypes is called the genotype of the organism. In many disease association studies, the haplotype data is more informative than the genotype data. Unfortunately, getti ..."
Abstract - Cited by 14 (1 self) - Add to MetaCart
Diploid organisms, such as humans, inherit one copy of each chromosome (haplotype) from each parent. The conflation of inherited haplotypes is called the genotype of the organism. In many disease association studies, the haplotype data is more informative than the genotype data. Unfortunately

A comparison of bayesian methods for haplotype reconstruction from population genotype data.

by Matthew Stephens , Peter Donnelly , Dr Matthew Stephens - Am J Hum Genet , 2003
"... In this report, we compare and contrast three previously published Bayesian methods for inferring haplotypes from genotype data in a population sample. We review the methods, emphasizing the differences between them in terms of both the models ("priors") they use and the computational str ..."
Abstract - Cited by 557 (7 self) - Add to MetaCart
PHASE, version 2.0, available online (http://www.stat.washington.edu/stephens/ software.html). Current high-throughput genotyping technologies, when applied to DNA from a diploid individual, are able to determine which two alleles are present at each locus but not the haplotype information (that is

HAPLOTYPE PHASING BY MULTI-ASSEMBLY OF SHARED HAPLOTYPES: PHASE-DEPENDENT INTERACTIONS BETWEEN RARE VARIANTS ∗

by Bjarni V. Halld Órsson, Derek Aguiar, Sorin Istrail
"... In this paper we propose algorithmic strategies, Lander-Waterman-like statistical estimates, and genome-wide software for haplotype phasing by multi-assembly of shared haplotypes. Specifically, we consider four types of results which together provide a comprehensive workflow of GWAS data sets: (1) s ..."
Abstract - Cited by 2 (2 self) - Add to MetaCart
In this paper we propose algorithmic strategies, Lander-Waterman-like statistical estimates, and genome-wide software for haplotype phasing by multi-assembly of shared haplotypes. Specifically, we consider four types of results which together provide a comprehensive workflow of GWAS data sets: (1

HAPLOTYPE PHASING BY MULTI-ASSEMBLY OF SHARED HAPLOTYPES: PHASE-DEPENDENT INTERACTIONS BETWEEN RARE VARIANTS∗

by Bjarni V. Halldórsson, Derek Aguiar, Sorin Istrail , 2010
"... In this paper we propose algorithmic strategies, Lander-Waterman-like statistical estimates, and genome-wide software for haplotype phasing by multi-assembly of shared haplotypes. Specifically, we consider four types of results which together provide a comprehensive workflow of GWAS data sets: (1) s ..."
Abstract - Cited by 1 (0 self) - Add to MetaCart
In this paper we propose algorithmic strategies, Lander-Waterman-like statistical estimates, and genome-wide software for haplotype phasing by multi-assembly of shared haplotypes. Specifically, we consider four types of results which together provide a comprehensive workflow of GWAS data sets: (1

WinHAP: An Efficient Haplotype Phasing Algorithm Based on Scalable Sliding Windows

by Yun Xu, Wenhua Cheng, Pengyu Nie, Fengfeng Zhou , 2012
"... Haplotype phasing represents an essential step in studying the association of genomic polymorphisms with complex genetic diseases, and in determining targets for drug designing. In recent years, huge amounts of genotype data are produced from the rapidly evolving high-throughput sequencing technolog ..."
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Haplotype phasing represents an essential step in studying the association of genomic polymorphisms with complex genetic diseases, and in determining targets for drug designing. In recent years, huge amounts of genotype data are produced from the rapidly evolving high-throughput sequencing

A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness

by Deepti Gurdasani, Olivier Delaneau, Nicola Pirastu, Sheila Ulivi, Massimiliano Cocca, Michela Traglia, Jie Huang, Jennifer E. Huffman, Igor Rudan, Ruth Mcquillan, Ross M. Fraser, Harry Campbell, Ozren Polasek, Gershim Asiki, Kenneth Ekoru, Caroline Hayward, Alan F. Wright, Veronique Vitart, Pau Navarro, Jean-francois Zagury, James F. Wilson, Daniela Toniolo, Paolo Gasparini, Nicole Soranzo, Manjinder S. S, Jonathan Marchini
"... Many existing cohorts contain a range of relatedness between genotyped individuals, either by design or by chance. Haplotype estimation in such cohorts is a central step in many downstream analyses. Using genotypes from six cohorts from isolated populations and two cohorts from non-isolated populati ..."
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Many existing cohorts contain a range of relatedness between genotyped individuals, either by design or by chance. Haplotype estimation in such cohorts is a central step in many downstream analyses. Using genotypes from six cohorts from isolated populations and two cohorts from non

RESEARCH ARTICLE Haplotype Phasing and Inheritance of Copy Number Variants in Nuclear Families

by Priit Palta, Lauris Kaplinski, Liina Nagirnaja, Andres Veidenberg, Märt Möls, Mari Nelis, Tõnu Esko, Andres Metspalu, Maris Laan, Maido Remm
"... ..."
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ARTICLE Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering

by Sharon R. Browning, Brian L. Browning
"... Whole-genome association studies present many new statistical and computational challenges due to the large quantity of data obtained. One of these challenges is haplotype inference; methods for haplotype inference designed for small data sets from candidate-gene studies do not scale well to the lar ..."
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to the large number of individuals genotyped in whole-genome association studies. We present a new method and software for inference of haplotype phase and missing data that can accurately phase data from whole-genome association studies, and we present the first comparison of haplotype-inference methods
Results 1 - 10 of 310