Constructing an initial map of transmission distortion based on high density HapMap SNPs across the human autosomes
Transmission distortion （TD） is a significant departure from Mendelian predictions of genes or chromosomes to offspring. While many biological processes have been implicated, there is still much to be understood about TD in humans. Here we present our findings from a genome-wide scan for evidence of...
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| Veröffentlicht in: | Journal of genetics and genomics 2009-12, Vol.36 (12), p.703-709 |
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| creator | Deng, Libin Zhang, Dake Richards, Elliott Tang, Xiaoli Fang, Jin Long, Fei Wang, Yan |
| description | Transmission distortion （TD） is a significant departure from Mendelian predictions of genes or chromosomes to offspring. While many biological processes have been implicated, there is still much to be understood about TD in humans. Here we present our findings from a genome-wide scan for evidence of TD using haplotype data of 60 trio families from the International HapMap Project. Fisher＇s exact test was applied to assess the extent of TD in 629,958 SNPs across the autosomes. Based on the empirical distribution of PFisher and further permutation tests, we identified 1,205 outlier loci and 224 candidate genes with TD. Using the PANTHER gene ontology database, we found 19 categories of biological processes with an enrichment of candidate genes. In particular, the “protein phosphorylation” category contained the largest number of candidates in both HapMap samples. Further analysis uncovered an intriguing non-synonymous change in PPPIR12B, a gene related to protein phosphorylation, which appears to influence the allele transmission from male parents in the YRI （Yoruba from Ibadan, Nigeria） population. Our findings also indicate an ethnicity-related property of TD signatures in HapMap samples and provide new clues for our understanding of TD in humans. |
| doi_str_mv | 10.1016/S1673-8527(08)60163-0 |
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While many biological processes have been implicated, there is still much to be understood about TD in humans. Here we present our findings from a genome-wide scan for evidence of TD using haplotype data of 60 trio families from the International HapMap Project. Fisher＇s exact test was applied to assess the extent of TD in 629,958 SNPs across the autosomes. Based on the empirical distribution of PFisher and further permutation tests, we identified 1,205 outlier loci and 224 candidate genes with TD. Using the PANTHER gene ontology database, we found 19 categories of biological processes with an enrichment of candidate genes. In particular, the “protein phosphorylation” category contained the largest number of candidates in both HapMap samples. Further analysis uncovered an intriguing non-synonymous change in PPPIR12B, a gene related to protein phosphorylation, which appears to influence the allele transmission from male parents in the YRI （Yoruba from Ibadan, Nigeria） population. Our findings also indicate an ethnicity-related property of TD signatures in HapMap samples and provide new clues for our understanding of TD in humans.</description><identifier>ISSN: 1673-8527</identifier><identifier>DOI: 10.1016/S1673-8527(08)60163-0</identifier><identifier>PMID: 20129397</identifier><language>eng</language><publisher>China: Elsevier Ltd</publisher><subject>gene ontology ; Genetic Variation ; Genome, Human - genetics ; Genome-Wide Association Study - methods ; Genome-Wide Association Study - standards ; Genomics - methods ; Genotype ; Haplotypes ; HapMap Project ; Humans ; Male ; Oligonucleotide Array Sequence Analysis - methods ; Polymorphism, Single Nucleotide - genetics ; SNP ; transmission distortion ; 人类染色体 ; 传输 ; 单核苷酸多态性 ; 地图 ; 失真 ; 蛋白磷酸化 ; 高密度</subject><ispartof>Journal of genetics and genomics, 2009-12, Vol.36 (12), p.703-709</ispartof><rights>2009 Institute of Genetics and Developmental Biology and the Genetics Society of China</rights><rights>2009 Institute of Genetics and Developmental Biology and the Genetics Society of China. 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All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c453t-65afd76accb42711c76c05fc6c04cc3cb28d930529977c8236027f55bfe9e0ee3</citedby><cites>FETCH-LOGICAL-c453t-65afd76accb42711c76c05fc6c04cc3cb28d930529977c8236027f55bfe9e0ee3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://image.cqvip.com/vip1000/qk/95085X/95085X.jpg</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S1673852708601630$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3536,27903,27904,65309</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20129397$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Deng, Libin</creatorcontrib><creatorcontrib>Zhang, Dake</creatorcontrib><creatorcontrib>Richards, Elliott</creatorcontrib><creatorcontrib>Tang, Xiaoli</creatorcontrib><creatorcontrib>Fang, Jin</creatorcontrib><creatorcontrib>Long, Fei</creatorcontrib><creatorcontrib>Wang, Yan</creatorcontrib><title>Constructing an initial map of transmission distortion based on high density HapMap SNPs across the human autosomes</title><title>Journal of genetics and genomics</title><addtitle>Journal of Genetics and Genomics</addtitle><description>Transmission distortion （TD） is a significant departure from Mendelian predictions of genes or chromosomes to offspring. 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Our findings also indicate an ethnicity-related property of TD signatures in HapMap samples and provide new clues for our understanding of TD in humans.</description><subject>gene ontology</subject><subject>Genetic Variation</subject><subject>Genome, Human - genetics</subject><subject>Genome-Wide Association Study - methods</subject><subject>Genome-Wide Association Study - standards</subject><subject>Genomics - methods</subject><subject>Genotype</subject><subject>Haplotypes</subject><subject>HapMap Project</subject><subject>Humans</subject><subject>Male</subject><subject>Oligonucleotide Array Sequence Analysis - methods</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>SNP</subject><subject>transmission distortion</subject><subject>人类染色体</subject><subject>传输</subject><subject>单核苷酸多态性</subject><subject>地图</subject><subject>失真</subject><subject>蛋白磷酸化</subject><subject>高密度</subject><issn>1673-8527</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkctu1TAQhr0A0ar0EUAWCy6LgC_HcbJC6AgoUluQCmvLmUxOLBL71HaQ-vb1udAlZWOPR9_845mfkBecveeM1x9ueK1l1Sih37LmXV1SsmJPyOlD-oScp-Q6xgSTrdb6GTkRjIu2PE5JWgefclwgO7-h1lPnXXZ2orPd0jDQHK1PsysCwdPepRxi3oWdTdjTEoxuM9IefXL5jl7Y7VWpu7n-kaiFGFKieUQ6LnNRtksOKcyYnpOng50Snh_vM_Lry-ef64vq8vvXb-tPlxWslMxVrezQ69oCdCuhOQddA1MDlHMFIKETTd9KpkRbpoJGyJoJPSjVDdgiQ5Rn5M1BdxvD7YIpmzII4DRZj2FJRkvZMq1FU8jX_yQFl1Krlv8HKJQUjSqgOoD7LUQczDa62cY7w5nZ-Wb2vpmdQYY1Zu-bYaXu5bHB0s3YP1T9dawAHw8Als39cRhNAocesHcRIZs-uEdbvDp-bQx-c1t8N52F34Ob0EixqhupuLwHb122EQ</recordid><startdate>20091201</startdate><enddate>20091201</enddate><creator>Deng, Libin</creator><creator>Zhang, Dake</creator><creator>Richards, Elliott</creator><creator>Tang, Xiaoli</creator><creator>Fang, Jin</creator><creator>Long, Fei</creator><creator>Wang, Yan</creator><general>Elsevier Ltd</general><scope>2RA</scope><scope>92L</scope><scope>CQIGP</scope><scope>W94</scope><scope>WU4</scope><scope>~WA</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>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20091201</creationdate><title>Constructing an initial map of transmission distortion based on high density HapMap SNPs across the human autosomes</title><author>Deng, Libin ; Zhang, Dake ; Richards, Elliott ; Tang, Xiaoli ; Fang, Jin ; Long, Fei ; Wang, Yan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c453t-65afd76accb42711c76c05fc6c04cc3cb28d930529977c8236027f55bfe9e0ee3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>gene ontology</topic><topic>Genetic Variation</topic><topic>Genome, Human - genetics</topic><topic>Genome-Wide Association Study - methods</topic><topic>Genome-Wide Association Study - standards</topic><topic>Genomics - methods</topic><topic>Genotype</topic><topic>Haplotypes</topic><topic>HapMap Project</topic><topic>Humans</topic><topic>Male</topic><topic>Oligonucleotide Array Sequence Analysis - methods</topic><topic>Polymorphism, Single Nucleotide - genetics</topic><topic>SNP</topic><topic>transmission distortion</topic><topic>人类染色体</topic><topic>传输</topic><topic>单核苷酸多态性</topic><topic>地图</topic><topic>失真</topic><topic>蛋白磷酸化</topic><topic>高密度</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Deng, Libin</creatorcontrib><creatorcontrib>Zhang, Dake</creatorcontrib><creatorcontrib>Richards, Elliott</creatorcontrib><creatorcontrib>Tang, Xiaoli</creatorcontrib><creatorcontrib>Fang, Jin</creatorcontrib><creatorcontrib>Long, Fei</creatorcontrib><creatorcontrib>Wang, Yan</creatorcontrib><collection>中文科技期刊数据库</collection><collection>中文科技期刊数据库-CALIS站点</collection><collection>中文科技期刊数据库-7.0平台</collection><collection>中文科技期刊数据库-自然科学</collection><collection>中文科技期刊数据库-自然科学-生物科学</collection><collection>中文科技期刊数据库- 镜像站点</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of genetics and genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Deng, Libin</au><au>Zhang, Dake</au><au>Richards, Elliott</au><au>Tang, Xiaoli</au><au>Fang, Jin</au><au>Long, Fei</au><au>Wang, Yan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Constructing an initial map of transmission distortion based on high density HapMap SNPs across the human autosomes</atitle><jtitle>Journal of genetics and genomics</jtitle><addtitle>Journal of Genetics and Genomics</addtitle><date>2009-12-01</date><risdate>2009</risdate><volume>36</volume><issue>12</issue><spage>703</spage><epage>709</epage><pages>703-709</pages><issn>1673-8527</issn><abstract>Transmission distortion （TD） is a significant departure from Mendelian predictions of genes or chromosomes to offspring. While many biological processes have been implicated, there is still much to be understood about TD in humans. Here we present our findings from a genome-wide scan for evidence of TD using haplotype data of 60 trio families from the International HapMap Project. Fisher＇s exact test was applied to assess the extent of TD in 629,958 SNPs across the autosomes. Based on the empirical distribution of PFisher and further permutation tests, we identified 1,205 outlier loci and 224 candidate genes with TD. Using the PANTHER gene ontology database, we found 19 categories of biological processes with an enrichment of candidate genes. In particular, the “protein phosphorylation” category contained the largest number of candidates in both HapMap samples. Further analysis uncovered an intriguing non-synonymous change in PPPIR12B, a gene related to protein phosphorylation, which appears to influence the allele transmission from male parents in the YRI （Yoruba from Ibadan, Nigeria） population. 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| subjects | gene ontology Genetic Variation Genome, Human - genetics Genome-Wide Association Study - methods Genome-Wide Association Study - standards Genomics - methods Genotype Haplotypes HapMap Project Humans Male Oligonucleotide Array Sequence Analysis - methods Polymorphism, Single Nucleotide - genetics SNP transmission distortion 人类染色体 传输 单核苷酸多态性 地图 失真 蛋白磷酸化 高密度 |
| title | Constructing an initial map of transmission distortion based on high density HapMap SNPs across the human autosomes |
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