Results 1 - 10 of 108

Bayesian Haplotype Inference for Multiple Linked Single-Nucleotide Polymorphisms .American

by Tianhua Niu, Zhaohui S. Qin, Xiping Xu, Jun S. Liu - Journal of Human Genetics , 2002
"... Haplotypes have gained increasing attention in the mapping of complex-disease genes, because of the abundance of single-nucleotide polymorphisms (SNPs) and the limited power of conventional single-locus analyses. It has been shown that haplotype-inference methods such as Clark’s algorithm, the expec ..."
Abstract - Cited by 230 (6 self) - Add to MetaCart
the whole haplotype into smaller segments. Then, we use the Gibbs sampler both to construct the partial haplotypes of each segment and to assemble all the segments together. Our algorithm can accurately and rapidly infer haplotypes for a large number of linked SNPs. By using a wide variety of real

The diploid genome sequence of an individual human

by Samuel Levy, Granger Sutton, Pauline C. Ng, Lars Feuk, Aaron L. Halpern, Brian P. Walenz, Nelson Axelrod, Jiaqi Huang, Ewen F. Kirkness, Gennady Denisov, Yuan Lin, Jeffrey R. Macdonald, Andy Wing, Chun Pang, Mary Shago, Timothy B. Stockwell, Alexia Tsiamouri, Vineet Bafna, Vikas Bansal, Saul A. Kravitz, Dana A. Busam, Karen Y. Beeson, Tina C. Mcintosh, Karin A. Remington, Josep F. Abril, John Gill, Jon Borman, Yu-hui Rogers, Marvin E. Frazier, Stephen W. Scherer, Robert L. Strausberg, J. Craig Venter - PLoS Biol
"... Presented here is a genome sequence of an individual human. It was produced from;32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb) of contiguous sequence with approximately 7.5-fold coverage for any given r ..."
Abstract - Cited by 293 (6 self) - Add to MetaCart
genome structure. Moreover, 44 % of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of

High-Performance Haplotype Assembly

by Marco Aldinucci, Andrea Bracciali, Tobias Marschall, Murray Patterson, Nadia Pisanti, Massimo Torquati
"... Abstract. The problem of Haplotype Assembly is an essential step in human genome analysis. It is typically formalised as the Minimum Error Correction (MEC) problem which is NP-hard. MEC has been approached using heuristics, integer linear programming, and fixed-parameter tractability (FPT), includin ..."
Abstract - Add to MetaCart
Abstract. The problem of Haplotype Assembly is an essential step in human genome analysis. It is typically formalised as the Minimum Error Correction (MEC) problem which is NP-hard. MEC has been approached using heuristics, integer linear programming, and fixed-parameter tractability (FPT

THEORY AND ALGORITHMS FOR THE HAPLOTYPE ASSEMBLY PROBLEM

by Russell Schwartz , 2010
"... Genome sequencing studies to date have generally sought to assemble consensus genomes by merging sequence contributions from multiple homologous copies of each chromosome. With growing interest in genetic variations, however, there is a need for methods to separate these distinct contributions and ..."
Abstract - Cited by 7 (0 self) - Add to MetaCart
as the “haplotype assembly ” problem. This review paper surveys results on the theory and algorithms for haplotype assembly. It first describes common abstractions of the problem. It then discusses some notable intractibility results for different problem variants. It next examines a variety of combinatorial

RESEARCH Open Access On the design of clone-based haplotyping

by Christine Lo, Rui Liu, Jehyuk Lee, Kimberly Robasky, Susan Byrne, Carolina Lucchesi, John Aach, George Church, Vineet Bafna, Kun Zhang
"... Background: Haplotypes are important for assessing genealogy and disease susceptibility of individual genomes, but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on assembling fragments of individual chromosomes is promising, but with variable ..."
Abstract - Add to MetaCart
Background: Haplotypes are important for assessing genealogy and disease susceptibility of individual genomes, but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on assembling fragments of individual chromosomes is promising

Haplotype assembly from aligned weighted SNP fragments �

by Yu-ying Zhao, Ling-yun Wu, Ji-hong Zhang, Rui-sheng Wang, Xiang-sun Zhang
"... Given an assembled genome of a diploid organism the haplotype assembly problem can be formulated as retrieval of a pair of haplotypes from a set of aligned weighted SNP fragments. Known computational formulations (models) of this problem are minimum letter flips (MLF) and the weighted minimum letter ..."
Abstract - Cited by 9 (0 self) - Add to MetaCart
Given an assembled genome of a diploid organism the haplotype assembly problem can be formulated as retrieval of a pair of haplotypes from a set of aligned weighted SNP fragments. Known computational formulations (models) of this problem are minimum letter flips (MLF) and the weighted minimum

TUMOR HAPLOTYPE ASSEMBLY ALGORITHMS FOR CANCER GENOMICS

by Derek Aguiar , Wendy S W Wong , Sorin Istrail
"... The growing availability of inexpensive high-throughput sequence data is enabling researchers to sequence tumor populations within a single individual at high coverage. But, cancer genome sequence evolution and mutational phenomena like driver mutations and gene fusions are difficult to investigate ..."
Abstract - Add to MetaCart
to investigate without first reconstructing tumor haplotype sequences. Haplotype assembly of single individual tumor populations is an exceedingly difficult task complicated by tumor haplotype heterogeneity, tumor or normal cell sequence contamination, polyploidy, and complex patterns of variation. While

An MCMC algorithm for haplotype assembly from whole genome sequence data

by Vikas Bansal, Aaron L. Halpern, Nelson Axelrod, Vineet Bafna - Genome Res , 2008
"... sequence data ..."
Abstract - Cited by 31 (1 self) - Add to MetaCart
sequence data

On the design of clone-based haplotyping

by Christine Lo , Rui Liu , Jehyuk Lee , Kimberly Robasky , Susan Byrne , Carolina Lucchesi , John Aach , George Church , Vineet Bafna , Kun Zhang - Genome Biol , 2013
"... Abstract Background: Haplotypes are important for assessing genealogy and disease susceptibility of individual genomes, but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on assembling fragments of individual chromosomes is promising, but wit ..."
Abstract - Cited by 2 (0 self) - Add to MetaCart
Abstract Background: Haplotypes are important for assessing genealogy and disease susceptibility of individual genomes, but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on assembling fragments of individual chromosomes is promising

Haplotype reconstruction from SNP alignment

by Lei M. Li, Jonghyun Kim, Michael S. Waterman - J. Comput. Biol , 2004
"... In this paper, we describe a method for statistical reconstruction of haplotypes from a set of aligned SNP fragments. We consider the case of a pair of homologous human chromosomes, one from the mother and the other from the father. After fragment assembly, we wish to reconstruct the two haplotypes ..."
Abstract - Cited by 25 (1 self) - Add to MetaCart
In this paper, we describe a method for statistical reconstruction of haplotypes from a set of aligned SNP fragments. We consider the case of a pair of homologous human chromosomes, one from the mother and the other from the father. After fragment assembly, we wish to reconstruct the two haplotypes
Results 1 - 10 of 108