Chromosomal Haplotypes by Genetic Phasing of Human Families
Assignment of alleles to haplotypes for nearly all the variants on all chromosomes can be performed by genetic analysis of a nuclear family with three or more children. Whole-genome sequence data enable deterministic phasing of nearly all sequenced alleles by permitting assignment of recombinations...
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| Veröffentlicht in: | American journal of human genetics 2011-09, Vol.89 (3), p.382-397 |
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| creator | Roach, Jared C. Glusman, Gustavo Hubley, Robert Montsaroff, Stephen Z. Holloway, Alisha K. Mauldin, Denise E. Srivastava, Deepak Garg, Vidu Pollard, Katherine S. Galas, David J. Hood, Leroy Smit, Arian F.A. |
| description | Assignment of alleles to haplotypes for nearly all the variants on all chromosomes can be performed by genetic analysis of a nuclear family with three or more children. Whole-genome sequence data enable deterministic phasing of nearly all sequenced alleles by permitting assignment of recombinations to precise chromosomal positions and specific meioses. We demonstrate this process of genetic phasing on two families each with four children. We generate haplotypes for all of the children and their parents; these haplotypes span all genotyped positions, including rare variants. Misassignments of phase between variants (switch errors) are nearly absent. Our algorithm can also produce multimegabase haplotypes for nuclear families with just two children and can handle families with missing individuals. We implement our algorithm in a suite of software scripts (Haploscribe). Haplotypes and family genome sequences will become increasingly important for personalized medicine and for fundamental biology. |
| doi_str_mv | 10.1016/j.ajhg.2011.07.023 |
| format | Article |
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Whole-genome sequence data enable deterministic phasing of nearly all sequenced alleles by permitting assignment of recombinations to precise chromosomal positions and specific meioses. We demonstrate this process of genetic phasing on two families each with four children. We generate haplotypes for all of the children and their parents; these haplotypes span all genotyped positions, including rare variants. Misassignments of phase between variants (switch errors) are nearly absent. Our algorithm can also produce multimegabase haplotypes for nuclear families with just two children and can handle families with missing individuals. We implement our algorithm in a suite of software scripts (Haploscribe). Haplotypes and family genome sequences will become increasingly important for personalized medicine and for fundamental biology.</description><identifier>ISSN: 0002-9297</identifier><identifier>EISSN: 1537-6605</identifier><identifier>DOI: 10.1016/j.ajhg.2011.07.023</identifier><identifier>PMID: 21855840</identifier><identifier>CODEN: AJHGAG</identifier><language>eng</language><publisher>Cambridge, MA: Elsevier Inc</publisher><subject>Algorithms ; Biological and medical sciences ; Chromosomes ; Chromosomes, Human - genetics ; Families & family life ; Fundamental and applied biological sciences. Psychology ; General aspects. Genetic counseling ; Genetic algorithms ; Genetic Variation ; Genetics of eukaryotes. Biological and molecular evolution ; Genotype & phenotype ; Haplotypes ; Haplotypes - genetics ; Humans ; Inheritance Patterns - genetics ; Medical genetics ; Medical sciences ; Models, Genetic ; Molecular and cellular biology ; Mutation - genetics ; Pedigree ; Sequence Analysis, DNA - methods ; Software</subject><ispartof>American journal of human genetics, 2011-09, Vol.89 (3), p.382-397</ispartof><rights>2011 The American Society of Human Genetics</rights><rights>2015 INIST-CNRS</rights><rights>Copyright © 2011 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.</rights><rights>Copyright Cell Press Sep 9, 2011</rights><rights>2011 The American Society of Human Genetics. Published by Elsevier Ltd. All right reserved. 2011 The American Society of Human Genetics</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c543t-67a349220d4ba58c5ea1f0caeaf7e6197a215a33b213b9081b6b5503fe6298333</citedby><cites>FETCH-LOGICAL-c543t-67a349220d4ba58c5ea1f0caeaf7e6197a215a33b213b9081b6b5503fe6298333</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169815/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0002929711003181$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,3537,27901,27902,53766,53768,65306</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=24524140$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21855840$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Roach, Jared C.</creatorcontrib><creatorcontrib>Glusman, Gustavo</creatorcontrib><creatorcontrib>Hubley, Robert</creatorcontrib><creatorcontrib>Montsaroff, Stephen Z.</creatorcontrib><creatorcontrib>Holloway, Alisha K.</creatorcontrib><creatorcontrib>Mauldin, Denise E.</creatorcontrib><creatorcontrib>Srivastava, Deepak</creatorcontrib><creatorcontrib>Garg, Vidu</creatorcontrib><creatorcontrib>Pollard, Katherine S.</creatorcontrib><creatorcontrib>Galas, David J.</creatorcontrib><creatorcontrib>Hood, Leroy</creatorcontrib><creatorcontrib>Smit, Arian F.A.</creatorcontrib><title>Chromosomal Haplotypes by Genetic Phasing of Human Families</title><title>American journal of human genetics</title><addtitle>Am J Hum Genet</addtitle><description>Assignment of alleles to haplotypes for nearly all the variants on all chromosomes can be performed by genetic analysis of a nuclear family with three or more children. Whole-genome sequence data enable deterministic phasing of nearly all sequenced alleles by permitting assignment of recombinations to precise chromosomal positions and specific meioses. We demonstrate this process of genetic phasing on two families each with four children. We generate haplotypes for all of the children and their parents; these haplotypes span all genotyped positions, including rare variants. Misassignments of phase between variants (switch errors) are nearly absent. Our algorithm can also produce multimegabase haplotypes for nuclear families with just two children and can handle families with missing individuals. We implement our algorithm in a suite of software scripts (Haploscribe). Haplotypes and family genome sequences will become increasingly important for personalized medicine and for fundamental biology.</description><subject>Algorithms</subject><subject>Biological and medical sciences</subject><subject>Chromosomes</subject><subject>Chromosomes, Human - genetics</subject><subject>Families & family life</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>General aspects. Genetic counseling</subject><subject>Genetic algorithms</subject><subject>Genetic Variation</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Genotype & phenotype</subject><subject>Haplotypes</subject><subject>Haplotypes - genetics</subject><subject>Humans</subject><subject>Inheritance Patterns - genetics</subject><subject>Medical genetics</subject><subject>Medical sciences</subject><subject>Models, Genetic</subject><subject>Molecular and cellular biology</subject><subject>Mutation - genetics</subject><subject>Pedigree</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Software</subject><issn>0002-9297</issn><issn>1537-6605</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkU2P0zAQhi0EYruFP8ABRUhoTwljO05ssUJCFbtFWgkOcLYmrtM6SuJiJyv13-PSsnwc4OTDPPNq_D6EvKBQUKDVm67AbrctGFBaQF0A44_Iggpe51UF4jFZAADLFVP1BbmMsYMESuBPyQWjUghZwoK8Xe2CH3z0A_bZGve9nw57G7PmkN3a0U7OZJ93GN24zXybrecBx-wGB9c7G5-RJy320T4_v0vy9ebDl9U6v_t0-3H1_i43ouRTXtXIS8UYbMoGhTTCIm3BoMW2thVVNTIqkPOGUd4okLSpGiGAt7ZiSnLOl-TdKXc_N4PdGDtOAXu9D27AcNAenf5zMrqd3vp7zWmlZCpkSa7OAcF_m22c9OCisX2Po_Vz1IpCrUAw9V9SSpUqTCUm8tVfZOfnMKYetFQMhKrKYxw7QSb4GINtH46moI8OdaePDvXRoYZaJ4dp6eXv331Y-SktAa_PAEaDfRtwNC7-4krBSvqDuz5xNsm5dzboaJwdjd24YM2kN979647vwOy4sw</recordid><startdate>20110909</startdate><enddate>20110909</enddate><creator>Roach, Jared C.</creator><creator>Glusman, Gustavo</creator><creator>Hubley, Robert</creator><creator>Montsaroff, Stephen Z.</creator><creator>Holloway, Alisha K.</creator><creator>Mauldin, Denise E.</creator><creator>Srivastava, Deepak</creator><creator>Garg, Vidu</creator><creator>Pollard, Katherine S.</creator><creator>Galas, David J.</creator><creator>Hood, Leroy</creator><creator>Smit, Arian F.A.</creator><general>Elsevier Inc</general><general>Cell Press</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QP</scope><scope>7TK</scope><scope>7TM</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>K9.</scope><scope>NAPCQ</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20110909</creationdate><title>Chromosomal Haplotypes by Genetic Phasing of Human Families</title><author>Roach, Jared C. ; Glusman, Gustavo ; Hubley, Robert ; Montsaroff, Stephen Z. ; Holloway, Alisha K. ; Mauldin, Denise E. ; Srivastava, Deepak ; Garg, Vidu ; Pollard, Katherine S. ; Galas, David J. ; Hood, Leroy ; Smit, Arian F.A.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c543t-67a349220d4ba58c5ea1f0caeaf7e6197a215a33b213b9081b6b5503fe6298333</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Algorithms</topic><topic>Biological and medical sciences</topic><topic>Chromosomes</topic><topic>Chromosomes, Human - genetics</topic><topic>Families & family life</topic><topic>Fundamental and applied biological sciences. 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| source | MEDLINE; ScienceDirect Journals (5 years ago - present); Cell Press Free Archives; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central |
| subjects | Algorithms Biological and medical sciences Chromosomes Chromosomes, Human - genetics Families & family life Fundamental and applied biological sciences. Psychology General aspects. Genetic counseling Genetic algorithms Genetic Variation Genetics of eukaryotes. Biological and molecular evolution Genotype & phenotype Haplotypes Haplotypes - genetics Humans Inheritance Patterns - genetics Medical genetics Medical sciences Models, Genetic Molecular and cellular biology Mutation - genetics Pedigree Sequence Analysis, DNA - methods Software |
| title | Chromosomal Haplotypes by Genetic Phasing of Human Families |
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