A Genetic Algorithm for Diploid Genome Reconstruction Using Paired-End Sequencing
The genome of many species in the biosphere is a diploid consisting of paternal and maternal haplotypes. The differences between these two haplotypes range from single nucleotide polymorphisms (SNPs) to large-scale structural variations (SVs). Existing genome assemblers for next-generation sequencin...
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| creator | Ting, Chuan-Kang Lin, Choun-Sea Chan, Ming-Tsai Chen, Jian-Wei Chuang, Sheng-Yu Huang, Yao-Ting |
| description | The genome of many species in the biosphere is a diploid consisting of paternal and maternal haplotypes. The differences between these two haplotypes range from single nucleotide polymorphisms (SNPs) to large-scale structural variations (SVs). Existing genome assemblers for next-generation sequencing platforms attempt to reconstruct one consensus sequence, which is a mosaic of two parental haplotypes. Reconstructing paternal and maternal haplotypes is an important task in linkage analysis and association studies. This study designs and implemented HapSVAssembler on the basis of Genetic Algorithm (GA) and paired-end sequencing. The proposed method builds a consensus sequence, identifies various types of heterozygous variants, and reconstructs the paternal and maternal haplotypes by solving an optimization problem with a GA algorithm. Experimental results indicate that the HapSVAssembler has high accuracy and contiguity under various sequencing coverage, error rates, and insert sizes. The program is tested on pilot sequencing of a highly heterozygous genome, and 12,781 heterozygous SNPs and 602 hemizygous SVs are identified. We observe that, although the number of SVs is much less than that of SNPs, the genomic regions occupied by SVs are much larger, implying the heterozygosity computed using SNPs or k-mer spectrum may be under-estimated. |
| doi_str_mv | 10.1371/journal.pone.0166721 |
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The differences between these two haplotypes range from single nucleotide polymorphisms (SNPs) to large-scale structural variations (SVs). Existing genome assemblers for next-generation sequencing platforms attempt to reconstruct one consensus sequence, which is a mosaic of two parental haplotypes. Reconstructing paternal and maternal haplotypes is an important task in linkage analysis and association studies. This study designs and implemented HapSVAssembler on the basis of Genetic Algorithm (GA) and paired-end sequencing. The proposed method builds a consensus sequence, identifies various types of heterozygous variants, and reconstructs the paternal and maternal haplotypes by solving an optimization problem with a GA algorithm. Experimental results indicate that the HapSVAssembler has high accuracy and contiguity under various sequencing coverage, error rates, and insert sizes. The program is tested on pilot sequencing of a highly heterozygous genome, and 12,781 heterozygous SNPs and 602 hemizygous SVs are identified. We observe that, although the number of SVs is much less than that of SNPs, the genomic regions occupied by SVs are much larger, implying the heterozygosity computed using SNPs or k-mer spectrum may be under-estimated.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0166721</identifier><identifier>PMID: 27861560</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Agricultural biotechnology ; Algorithms ; Analysis ; Bioinformatics ; Biology and Life Sciences ; Biosphere ; Chromosomes ; Computational Biology - methods ; Computer science ; Computer Simulation ; Conserved sequence ; Diploidy ; Error correction & detection ; Evolution, Molecular ; Gene sequencing ; Genetic algorithms ; Genetic aspects ; Genome ; Genomes ; Genomics ; Genomics - methods ; Haplotypes ; Heterozygosity ; Heterozygote ; High-Throughput Nucleotide Sequencing ; Linkage analysis ; Methods ; Mutation ; Nucleotide sequence ; Optimization ; Parenting ; Polymorphism, Single Nucleotide ; Problems ; Reproducibility of Results ; Research and analysis methods ; Researchers ; Sequence Analysis, DNA ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Software</subject><ispartof>PloS one, 2016-11, Vol.11 (11), p.e0166721-e0166721</ispartof><rights>COPYRIGHT 2016 Public Library of Science</rights><rights>2016 Ting et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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The differences between these two haplotypes range from single nucleotide polymorphisms (SNPs) to large-scale structural variations (SVs). Existing genome assemblers for next-generation sequencing platforms attempt to reconstruct one consensus sequence, which is a mosaic of two parental haplotypes. Reconstructing paternal and maternal haplotypes is an important task in linkage analysis and association studies. This study designs and implemented HapSVAssembler on the basis of Genetic Algorithm (GA) and paired-end sequencing. The proposed method builds a consensus sequence, identifies various types of heterozygous variants, and reconstructs the paternal and maternal haplotypes by solving an optimization problem with a GA algorithm. Experimental results indicate that the HapSVAssembler has high accuracy and contiguity under various sequencing coverage, error rates, and insert sizes. The program is tested on pilot sequencing of a highly heterozygous genome, and 12,781 heterozygous SNPs and 602 hemizygous SVs are identified. 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Genetic Algorithm for Diploid Genome Reconstruction Using Paired-End Sequencing</title><author>Ting, Chuan-Kang ; Lin, Choun-Sea ; Chan, Ming-Tsai ; Chen, Jian-Wei ; Chuang, Sheng-Yu ; Huang, Yao-Ting</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c725t-9af425e8abe237f28f7b1516c05375436cf3821e4172018f1a1c3c993cdd6f523</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Agricultural biotechnology</topic><topic>Algorithms</topic><topic>Analysis</topic><topic>Bioinformatics</topic><topic>Biology and Life Sciences</topic><topic>Biosphere</topic><topic>Chromosomes</topic><topic>Computational Biology - methods</topic><topic>Computer science</topic><topic>Computer Simulation</topic><topic>Conserved sequence</topic><topic>Diploidy</topic><topic>Error correction & detection</topic><topic>Evolution, Molecular</topic><topic>Gene sequencing</topic><topic>Genetic 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Jian-Wei</au><au>Chuang, Sheng-Yu</au><au>Huang, Yao-Ting</au><au>Xu, Peng</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A Genetic Algorithm for Diploid Genome Reconstruction Using Paired-End Sequencing</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2016-11-18</date><risdate>2016</risdate><volume>11</volume><issue>11</issue><spage>e0166721</spage><epage>e0166721</epage><pages>e0166721-e0166721</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The genome of many species in the biosphere is a diploid consisting of paternal and maternal haplotypes. The differences between these two haplotypes range from single nucleotide polymorphisms (SNPs) to large-scale structural variations (SVs). Existing genome assemblers for next-generation sequencing platforms attempt to reconstruct one consensus sequence, which is a mosaic of two parental haplotypes. Reconstructing paternal and maternal haplotypes is an important task in linkage analysis and association studies. This study designs and implemented HapSVAssembler on the basis of Genetic Algorithm (GA) and paired-end sequencing. The proposed method builds a consensus sequence, identifies various types of heterozygous variants, and reconstructs the paternal and maternal haplotypes by solving an optimization problem with a GA algorithm. Experimental results indicate that the HapSVAssembler has high accuracy and contiguity under various sequencing coverage, error rates, and insert sizes. The program is tested on pilot sequencing of a highly heterozygous genome, and 12,781 heterozygous SNPs and 602 hemizygous SVs are identified. We observe that, although the number of SVs is much less than that of SNPs, the genomic regions occupied by SVs are much larger, implying the heterozygosity computed using SNPs or k-mer spectrum may be under-estimated.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>27861560</pmid><doi>10.1371/journal.pone.0166721</doi><tpages>e0166721</tpages><oa>free_for_read</oa></addata></record> |
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| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Agricultural biotechnology Algorithms Analysis Bioinformatics Biology and Life Sciences Biosphere Chromosomes Computational Biology - methods Computer science Computer Simulation Conserved sequence Diploidy Error correction & detection Evolution, Molecular Gene sequencing Genetic algorithms Genetic aspects Genome Genomes Genomics Genomics - methods Haplotypes Heterozygosity Heterozygote High-Throughput Nucleotide Sequencing Linkage analysis Methods Mutation Nucleotide sequence Optimization Parenting Polymorphism, Single Nucleotide Problems Reproducibility of Results Research and analysis methods Researchers Sequence Analysis, DNA Single nucleotide polymorphisms Single-nucleotide polymorphism Software |
| title | A Genetic Algorithm for Diploid Genome Reconstruction Using Paired-End Sequencing |
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