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A Class of Tests for Linkage Using Affected Pedigree Members
We describe a class of nonparametric tests for linkage between a marker and a gene assumed to exist and to govern susceptibility to a disease. The tests are formed by assigning a score to each possible pattern of marker allele sharing (identity-by-descent) among affected pedigree members, and then a...
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Published in: | Biometrics 1994-03, Vol.50 (1), p.118-127 |
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creator | Whittemore, Alice S. Halpern, Jerry |
description | We describe a class of nonparametric tests for linkage between a marker and a gene assumed to exist and to govern susceptibility to a disease. The tests are formed by assigning a score to each possible pattern of marker allele sharing (identity-by-descent) among affected pedigree members, and then averaging the scores over all patterns compatible with the observed marker genotype and genealogical relationship of the affected members. Different score functions give different tests. One function, which examines marker allele similarity across pairs of affected pedigree members, gives a test similar to that of Fimmers et al. (1989, in Multipoint Mapping and Linkage Based on Affected Pedigree Members: Genetic Analysis Workshop, R. C. Elston, M. A. Spence, S. E. Hodge, and J. W. MacCluer (eds), 123-128; City: Alan R. Liss). A second function examines allele similarity across arbitrary subsets, not just pairs, of affected members. The resulting test can be more powerful than the one based solely on pairs of affected members. The approach has several advantages: it does not require knowledge of the mode of disease inheritance; it does not require unambiguous determination of identity-by-descent at the marker; it does not suffer from variability due to chance allele similarity among affected members who are unrelated, such as spouses; it allows marker genotypes of unaffected members to contribute information on allele sharing among the affected; it permits calculation of exact P-values. Computational requirements limit the tests to many pedigrees with few ( |
doi_str_mv | 10.2307/2533202 |
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The tests are formed by assigning a score to each possible pattern of marker allele sharing (identity-by-descent) among affected pedigree members, and then averaging the scores over all patterns compatible with the observed marker genotype and genealogical relationship of the affected members. Different score functions give different tests. One function, which examines marker allele similarity across pairs of affected pedigree members, gives a test similar to that of Fimmers et al. (1989, in Multipoint Mapping and Linkage Based on Affected Pedigree Members: Genetic Analysis Workshop, R. C. Elston, M. A. Spence, S. E. Hodge, and J. W. MacCluer (eds), 123-128; City: Alan R. Liss). A second function examines allele similarity across arbitrary subsets, not just pairs, of affected members. The resulting test can be more powerful than the one based solely on pairs of affected members. The approach has several advantages: it does not require knowledge of the mode of disease inheritance; it does not require unambiguous determination of identity-by-descent at the marker; it does not suffer from variability due to chance allele similarity among affected members who are unrelated, such as spouses; it allows marker genotypes of unaffected members to contribute information on allele sharing among the affected; it permits calculation of exact P-values. Computational requirements limit the tests to many pedigrees with few (<16) affected members.</description><identifier>ISSN: 0006-341X</identifier><identifier>EISSN: 1541-0420</identifier><identifier>DOI: 10.2307/2533202</identifier><identifier>PMID: 8086596</identifier><identifier>CODEN: BIOMA5</identifier><language>eng</language><publisher>Malden, MA: International Biometric Society</publisher><subject>Alleles ; Biological and medical sciences ; Biometrics ; Biometry - methods ; Classical genetics, quantitative genetics, hybrids ; Disease susceptibility ; Female ; Fundamental and applied biological sciences. Psychology ; Genes, Dominant ; Genes, Recessive ; Genetic diseases ; Genetic inheritance ; Genetic Linkage ; Genetic loci ; Genetic Markers ; Genetic Techniques ; Genetics of eukaryotes. Biological and molecular evolution ; Genotypes ; Human genetics ; Humans ; Lod Score ; Male ; Medical genetics ; Methods, theories and miscellaneous ; Models, Genetic ; Models, Statistical ; Pedigree ; Recombination, Genetic ; Statistical discrepancies</subject><ispartof>Biometrics, 1994-03, Vol.50 (1), p.118-127</ispartof><rights>Copyright 1994 The International Biometric Society</rights><rights>1994 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c334t-9bb5bf28356921d5b02e7f8845a4d451c1b11adb431f1258fdcf9232173ccb973</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/2533202$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/2533202$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,58238,58471</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=4132498$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/8086596$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Whittemore, Alice S.</creatorcontrib><creatorcontrib>Halpern, Jerry</creatorcontrib><title>A Class of Tests for Linkage Using Affected Pedigree Members</title><title>Biometrics</title><addtitle>Biometrics</addtitle><description>We describe a class of nonparametric tests for linkage between a marker and a gene assumed to exist and to govern susceptibility to a disease. The tests are formed by assigning a score to each possible pattern of marker allele sharing (identity-by-descent) among affected pedigree members, and then averaging the scores over all patterns compatible with the observed marker genotype and genealogical relationship of the affected members. Different score functions give different tests. One function, which examines marker allele similarity across pairs of affected pedigree members, gives a test similar to that of Fimmers et al. (1989, in Multipoint Mapping and Linkage Based on Affected Pedigree Members: Genetic Analysis Workshop, R. C. Elston, M. A. Spence, S. E. Hodge, and J. W. MacCluer (eds), 123-128; City: Alan R. Liss). A second function examines allele similarity across arbitrary subsets, not just pairs, of affected members. The resulting test can be more powerful than the one based solely on pairs of affected members. The approach has several advantages: it does not require knowledge of the mode of disease inheritance; it does not require unambiguous determination of identity-by-descent at the marker; it does not suffer from variability due to chance allele similarity among affected members who are unrelated, such as spouses; it allows marker genotypes of unaffected members to contribute information on allele sharing among the affected; it permits calculation of exact P-values. Computational requirements limit the tests to many pedigrees with few (<16) affected members.</description><subject>Alleles</subject><subject>Biological and medical sciences</subject><subject>Biometrics</subject><subject>Biometry - methods</subject><subject>Classical genetics, quantitative genetics, hybrids</subject><subject>Disease susceptibility</subject><subject>Female</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes, Dominant</subject><subject>Genes, Recessive</subject><subject>Genetic diseases</subject><subject>Genetic inheritance</subject><subject>Genetic Linkage</subject><subject>Genetic loci</subject><subject>Genetic Markers</subject><subject>Genetic Techniques</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Genotypes</subject><subject>Human genetics</subject><subject>Humans</subject><subject>Lod Score</subject><subject>Male</subject><subject>Medical genetics</subject><subject>Methods, theories and miscellaneous</subject><subject>Models, Genetic</subject><subject>Models, Statistical</subject><subject>Pedigree</subject><subject>Recombination, Genetic</subject><subject>Statistical discrepancies</subject><issn>0006-341X</issn><issn>1541-0420</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1994</creationdate><recordtype>article</recordtype><recordid>eNp1kE1Lw0AQhhdRaq3iLxD2IHqK7uxHsgEvpfgFFT204C3sbnZLatLoTnrw3xtpqCdPw_A-vDM8hJwDu-GCZbdcCcEZPyBjUBISJjk7JGPGWJoICe_H5ARx3a-5YnxERprpVOXpmNxN6aw2iLQNdOGxQxraSOfV5sOsPF1itVnRaQjedb6kb76sVtF7-uIb6yOekqNgavRnw5yQ5cP9YvaUzF8fn2fTeeKEkF2SW6ts4FqoNOdQKsu4z4LWUhlZSgUOLIAprRQQgCsdShdyLjhkwjmbZ2JCrna9n7H92vZfFk2Fzte12fh2i0WWZqAFYz14vQNdbBGjD8VnrBoTvwtgxa-nYvDUkxdD5dY2vtxzg5g-vxxyg87UIZqNq3CPSRBc5voPW2PXxn-v_QBSQncq</recordid><startdate>19940301</startdate><enddate>19940301</enddate><creator>Whittemore, Alice S.</creator><creator>Halpern, Jerry</creator><general>International Biometric Society</general><general>Blackwell</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>7X8</scope></search><sort><creationdate>19940301</creationdate><title>A Class of Tests for Linkage Using Affected Pedigree Members</title><author>Whittemore, Alice S. ; Halpern, Jerry</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c334t-9bb5bf28356921d5b02e7f8845a4d451c1b11adb431f1258fdcf9232173ccb973</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1994</creationdate><topic>Alleles</topic><topic>Biological and medical sciences</topic><topic>Biometrics</topic><topic>Biometry - methods</topic><topic>Classical genetics, quantitative genetics, hybrids</topic><topic>Disease susceptibility</topic><topic>Female</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes, Dominant</topic><topic>Genes, Recessive</topic><topic>Genetic diseases</topic><topic>Genetic inheritance</topic><topic>Genetic Linkage</topic><topic>Genetic loci</topic><topic>Genetic Markers</topic><topic>Genetic Techniques</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Genotypes</topic><topic>Human genetics</topic><topic>Humans</topic><topic>Lod Score</topic><topic>Male</topic><topic>Medical genetics</topic><topic>Methods, theories and miscellaneous</topic><topic>Models, Genetic</topic><topic>Models, Statistical</topic><topic>Pedigree</topic><topic>Recombination, Genetic</topic><topic>Statistical discrepancies</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Whittemore, Alice S.</creatorcontrib><creatorcontrib>Halpern, Jerry</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>MEDLINE - Academic</collection><jtitle>Biometrics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Whittemore, Alice S.</au><au>Halpern, Jerry</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A Class of Tests for Linkage Using Affected Pedigree Members</atitle><jtitle>Biometrics</jtitle><addtitle>Biometrics</addtitle><date>1994-03-01</date><risdate>1994</risdate><volume>50</volume><issue>1</issue><spage>118</spage><epage>127</epage><pages>118-127</pages><issn>0006-341X</issn><eissn>1541-0420</eissn><coden>BIOMA5</coden><abstract>We describe a class of nonparametric tests for linkage between a marker and a gene assumed to exist and to govern susceptibility to a disease. The tests are formed by assigning a score to each possible pattern of marker allele sharing (identity-by-descent) among affected pedigree members, and then averaging the scores over all patterns compatible with the observed marker genotype and genealogical relationship of the affected members. Different score functions give different tests. One function, which examines marker allele similarity across pairs of affected pedigree members, gives a test similar to that of Fimmers et al. (1989, in Multipoint Mapping and Linkage Based on Affected Pedigree Members: Genetic Analysis Workshop, R. C. Elston, M. A. Spence, S. E. Hodge, and J. W. MacCluer (eds), 123-128; City: Alan R. Liss). A second function examines allele similarity across arbitrary subsets, not just pairs, of affected members. The resulting test can be more powerful than the one based solely on pairs of affected members. The approach has several advantages: it does not require knowledge of the mode of disease inheritance; it does not require unambiguous determination of identity-by-descent at the marker; it does not suffer from variability due to chance allele similarity among affected members who are unrelated, such as spouses; it allows marker genotypes of unaffected members to contribute information on allele sharing among the affected; it permits calculation of exact P-values. Computational requirements limit the tests to many pedigrees with few (<16) affected members.</abstract><cop>Malden, MA</cop><pub>International Biometric Society</pub><pmid>8086596</pmid><doi>10.2307/2533202</doi><tpages>10</tpages></addata></record> |
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subjects | Alleles Biological and medical sciences Biometrics Biometry - methods Classical genetics, quantitative genetics, hybrids Disease susceptibility Female Fundamental and applied biological sciences. Psychology Genes, Dominant Genes, Recessive Genetic diseases Genetic inheritance Genetic Linkage Genetic loci Genetic Markers Genetic Techniques Genetics of eukaryotes. Biological and molecular evolution Genotypes Human genetics Humans Lod Score Male Medical genetics Methods, theories and miscellaneous Models, Genetic Models, Statistical Pedigree Recombination, Genetic Statistical discrepancies |
title | A Class of Tests for Linkage Using Affected Pedigree Members |
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