Mini-haplotypes as lineage informative SNPs and ancestry inference SNPs
We propose that haplotyped loci with high heterozygosity can be useful in human identification, especially within families, if recombination is very low among the sites. Three or more SNPs extending over small molecular intervals (
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| Veröffentlicht in: | European journal of human genetics : EJHG 2012-11, Vol.20 (11), p.1148-1154 |
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| container_title | European journal of human genetics : EJHG |
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| creator | PAKSTIS, Andrew J RIXUN FANG FURTADO, Manohar R KIDD, Judith R KIDD, Kenneth K |
| description | We propose that haplotyped loci with high heterozygosity can be useful in human identification, especially within families, if recombination is very low among the sites. Three or more SNPs extending over small molecular intervals ( |
| doi_str_mv | 10.1038/ejhg.2012.69 |
| format | Article |
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Three or more SNPs extending over small molecular intervals (<10 KB) can be identified in the human genome to define miniature haplotypes with moderate levels of linkage disequilibrium. Properly selected, these mini-haplotypes (or minihaps) consist of multiple haplotype lineages (alleles) that have evolved from the ancestral human haplotype but show no evidence of recurring recombination, allowing each distinct haplotype to be equated with an allele, all copies of which are essentially identical by descent. Historic recombinants, representing rare events that have drifted to common frequencies over many generations, can be identified in some cases, they do not equate to frequently recurring recombination. We have identified examples in our data collected on various projects and present eight such mini-haplotypes comprised of informative SNPs. We also discuss the ideal characteristics and advantages of minihaps for human familial identification and ancestry inference, and compare them to other types of forensic markers in use and/or that have been proposed. We expect that it is possible to carry out a systematic search and identify a useful panel of mini-haplotypes, with even better properties than the examples presented here.</description><identifier>ISSN: 1018-4813</identifier><identifier>EISSN: 1476-5438</identifier><identifier>DOI: 10.1038/ejhg.2012.69</identifier><identifier>PMID: 22535184</identifier><language>eng</language><publisher>Basingstoke: Nature Publishing Group</publisher><subject>Alleles ; Biological and medical sciences ; Deoxyribonucleic acid ; DNA ; Forensic science ; Forensic sciences ; Fundamental and applied biological sciences. Psychology ; Genealogy ; Genetics of eukaryotes. Biological and molecular evolution ; Genome, Human ; Genomes ; Haplotypes ; Heterozygosity ; Heterozygote ; Humans ; Indexing in process ; Internet resources ; Linkage Disequilibrium ; Medical genetics ; Medical sciences ; Medicine ; Molecular and cellular biology ; Mutation ; Polymorphism ; Polymorphism, Single Nucleotide ; Population ; Population Groups - genetics ; Recombinants ; Recombination ; Recombination, Genetic ; Single-nucleotide polymorphism</subject><ispartof>European journal of human genetics : EJHG, 2012-11, Vol.20 (11), p.1148-1154</ispartof><rights>2015 INIST-CNRS</rights><rights>Copyright Nature Publishing Group Nov 2012</rights><rights>Copyright © 2012 Macmillan Publishers Limited 2012 Macmillan Publishers Limited</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c475t-64675f6760cb000cb2faa8fc4fe90e7665a388c86b197c4db2552c13c660b0213</citedby><cites>FETCH-LOGICAL-c475t-64675f6760cb000cb2faa8fc4fe90e7665a388c86b197c4db2552c13c660b0213</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/PMC3476707/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3476707/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=26507369$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22535184$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>PAKSTIS, Andrew J</creatorcontrib><creatorcontrib>RIXUN FANG</creatorcontrib><creatorcontrib>FURTADO, Manohar R</creatorcontrib><creatorcontrib>KIDD, Judith R</creatorcontrib><creatorcontrib>KIDD, Kenneth K</creatorcontrib><title>Mini-haplotypes as lineage informative SNPs and ancestry inference SNPs</title><title>European journal of human genetics : EJHG</title><addtitle>Eur J Hum Genet</addtitle><description>We propose that haplotyped loci with high heterozygosity can be useful in human identification, especially within families, if recombination is very low among the sites. Three or more SNPs extending over small molecular intervals (<10 KB) can be identified in the human genome to define miniature haplotypes with moderate levels of linkage disequilibrium. Properly selected, these mini-haplotypes (or minihaps) consist of multiple haplotype lineages (alleles) that have evolved from the ancestral human haplotype but show no evidence of recurring recombination, allowing each distinct haplotype to be equated with an allele, all copies of which are essentially identical by descent. Historic recombinants, representing rare events that have drifted to common frequencies over many generations, can be identified in some cases, they do not equate to frequently recurring recombination. We have identified examples in our data collected on various projects and present eight such mini-haplotypes comprised of informative SNPs. We also discuss the ideal characteristics and advantages of minihaps for human familial identification and ancestry inference, and compare them to other types of forensic markers in use and/or that have been proposed. We expect that it is possible to carry out a systematic search and identify a useful panel of mini-haplotypes, with even better properties than the examples presented here.</description><subject>Alleles</subject><subject>Biological and medical sciences</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Forensic science</subject><subject>Forensic sciences</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genealogy</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Genome, Human</subject><subject>Genomes</subject><subject>Haplotypes</subject><subject>Heterozygosity</subject><subject>Heterozygote</subject><subject>Humans</subject><subject>Indexing in process</subject><subject>Internet resources</subject><subject>Linkage Disequilibrium</subject><subject>Medical genetics</subject><subject>Medical sciences</subject><subject>Medicine</subject><subject>Molecular and cellular biology</subject><subject>Mutation</subject><subject>Polymorphism</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population</subject><subject>Population Groups - genetics</subject><subject>Recombinants</subject><subject>Recombination</subject><subject>Recombination, Genetic</subject><subject>Single-nucleotide polymorphism</subject><issn>1018-4813</issn><issn>1476-5438</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkUtLAzEUhYMotlZ3rqUgggun5p3MRpCiVagPUNchk2balOlMTaaF_nszttbHykWSG87H4d57ADhGsIcgkZd2Ohn3MES4x9Md0EZU8IRRIndjDZFMqESkBQ5CmEIYRYH2QQtjRhiStA0GD650yUTPi6pezW3o6tAtXGn12HZdmVd-pmu3tN2Xx-eolaN4jA21XzWq9Tb-PrVDsJfrItijzdsBb7c3r_27ZPg0uO9fDxNDBasTTrlgORccmgzCeOFca5kbmtsUWsE500RKI3mGUmHoKMOMYYOI4RxmECPSAVdr3_kim9mRsWXtdaHm3s20X6lKO_VbKd1EjaulInEvAopocL4x8NX7Io6iZi4YWxS6tNUiKIQwwwRzSf6BIpJKjGTT1ukfdFotfBk30VBYUCxgQ12sKeOrELzNt30jqJowVROmasJUPI34yc9Zt_BXehE42wA6GF3kPobjwjfHWRw4Gn0A0rOmfg</recordid><startdate>20121101</startdate><enddate>20121101</enddate><creator>PAKSTIS, Andrew J</creator><creator>RIXUN FANG</creator><creator>FURTADO, Manohar R</creator><creator>KIDD, Judith R</creator><creator>KIDD, Kenneth K</creator><general>Nature Publishing Group</general><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>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20121101</creationdate><title>Mini-haplotypes as lineage informative SNPs and ancestry inference SNPs</title><author>PAKSTIS, Andrew J ; RIXUN FANG ; FURTADO, Manohar R ; KIDD, Judith R ; KIDD, Kenneth K</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c475t-64675f6760cb000cb2faa8fc4fe90e7665a388c86b197c4db2552c13c660b0213</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Alleles</topic><topic>Biological and medical sciences</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Forensic science</topic><topic>Forensic sciences</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genealogy</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Genome, Human</topic><topic>Genomes</topic><topic>Haplotypes</topic><topic>Heterozygosity</topic><topic>Heterozygote</topic><topic>Humans</topic><topic>Indexing in process</topic><topic>Internet resources</topic><topic>Linkage Disequilibrium</topic><topic>Medical genetics</topic><topic>Medical sciences</topic><topic>Medicine</topic><topic>Molecular and cellular biology</topic><topic>Mutation</topic><topic>Polymorphism</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Population</topic><topic>Population Groups - genetics</topic><topic>Recombinants</topic><topic>Recombination</topic><topic>Recombination, Genetic</topic><topic>Single-nucleotide polymorphism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>PAKSTIS, Andrew J</creatorcontrib><creatorcontrib>RIXUN FANG</creatorcontrib><creatorcontrib>FURTADO, Manohar R</creatorcontrib><creatorcontrib>KIDD, Judith R</creatorcontrib><creatorcontrib>KIDD, Kenneth K</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>European journal of human genetics : EJHG</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>PAKSTIS, Andrew J</au><au>RIXUN FANG</au><au>FURTADO, Manohar R</au><au>KIDD, Judith R</au><au>KIDD, Kenneth K</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Mini-haplotypes as lineage informative SNPs and ancestry inference SNPs</atitle><jtitle>European journal of human genetics : EJHG</jtitle><addtitle>Eur J Hum Genet</addtitle><date>2012-11-01</date><risdate>2012</risdate><volume>20</volume><issue>11</issue><spage>1148</spage><epage>1154</epage><pages>1148-1154</pages><issn>1018-4813</issn><eissn>1476-5438</eissn><abstract>We propose that haplotyped loci with high heterozygosity can be useful in human identification, especially within families, if recombination is very low among the sites. Three or more SNPs extending over small molecular intervals (<10 KB) can be identified in the human genome to define miniature haplotypes with moderate levels of linkage disequilibrium. Properly selected, these mini-haplotypes (or minihaps) consist of multiple haplotype lineages (alleles) that have evolved from the ancestral human haplotype but show no evidence of recurring recombination, allowing each distinct haplotype to be equated with an allele, all copies of which are essentially identical by descent. Historic recombinants, representing rare events that have drifted to common frequencies over many generations, can be identified in some cases, they do not equate to frequently recurring recombination. We have identified examples in our data collected on various projects and present eight such mini-haplotypes comprised of informative SNPs. We also discuss the ideal characteristics and advantages of minihaps for human familial identification and ancestry inference, and compare them to other types of forensic markers in use and/or that have been proposed. We expect that it is possible to carry out a systematic search and identify a useful panel of mini-haplotypes, with even better properties than the examples presented here.</abstract><cop>Basingstoke</cop><pub>Nature Publishing Group</pub><pmid>22535184</pmid><doi>10.1038/ejhg.2012.69</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Alleles Biological and medical sciences Deoxyribonucleic acid DNA Forensic science Forensic sciences Fundamental and applied biological sciences. Psychology Genealogy Genetics of eukaryotes. Biological and molecular evolution Genome, Human Genomes Haplotypes Heterozygosity Heterozygote Humans Indexing in process Internet resources Linkage Disequilibrium Medical genetics Medical sciences Medicine Molecular and cellular biology Mutation Polymorphism Polymorphism, Single Nucleotide Population Population Groups - genetics Recombinants Recombination Recombination, Genetic Single-nucleotide polymorphism |
| title | Mini-haplotypes as lineage informative SNPs and ancestry inference SNPs |
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