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High-Performance Haplotype Assembly
"... 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 ..."
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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
, 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 ..."
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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
TUMOR HAPLOTYPE ASSEMBLY ALGORITHMS FOR CANCER GENOMICS
"... 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 ..."
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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
Haplotype assembly from aligned weighted SNP fragments �
"... 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 ..."
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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
A Markov Chain Model for Haplotype Assembly from SNP Fragments
- GENOME INFORMATICS 17(2): 162{171 (2006)
, 2006
"... Single nucleotide polymorphism (SNP) is the most frequent form of human genetic variations and of importance for medical diagnosis and tracking disease genes. A haplotype is a sequence of SNPs from a single copy of a chromosome, and haplotype assembly from SNP fragments is based on DNA fragments wit ..."
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Single nucleotide polymorphism (SNP) is the most frequent form of human genetic variations and of importance for medical diagnosis and tracking disease genes. A haplotype is a sequence of SNPs from a single copy of a chromosome, and haplotype assembly from SNP fragments is based on DNA fragments
RESEARCH Open Access Strobe sequence design for haplotype assembly
"... Background: Humans are diploid, carrying two copies of each chromosome, one from each parent. Separating the paternal and maternal chromosomes is an important component of genetic analyses such as determining genetic association, inferring evolutionary scenarios, computing recombination rates, and d ..."
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, and detecting cis-regulatory events. As the pair of chromosomes are mostly identical to each other, linking together of alleles at heterozygous sites is sufficient to phase, or separate the two chromosomes. In Haplotype Assembly, the linking is done by sequenced fragments that overlap two heterozygous sites
An MCMC algorithm for haplotype assembly from whole genome sequence data
- Genome Res
, 2008
"... sequence data ..."
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