Methods for scoring the collective effect of SNPs: Minor alleles of common SNPs quantitatively affect traits/diseases and are under both positive and negative selection
Sci China Life Sci. 57:876-888. (2014) Most common SNPs are popularly assumed to be neutral. We here developed novel methods to examine in animal models and humans whether extreme amount of minor alleles (MAs) carried by an individual may represent extreme trait values and common diseases. We analyz...
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| creator | Yuan, Dejian Zhu, Zuobin Tan, Xiaohua Liang, Jie Zeng, Ceng Zhang, Jiegen Chen, Jun Ma, Long Dogan, Ayca Brockmann, Gudrun Goldmann, Oliver Medina, Eva Rice, Amanda D Moyer, Richard W Man, Xian Yi, Ke Li, Yanke Lu, Qing Huang, Yimin Wang, Dapeng Yu, Jun Guo, Hui Xia, Kun Huang, Shi |
| description | Sci China Life Sci. 57:876-888. (2014) Most common SNPs are popularly assumed to be neutral. We here developed novel
methods to examine in animal models and humans whether extreme amount of minor
alleles (MAs) carried by an individual may represent extreme trait values and
common diseases. We analyzed panels of genetic reference populations and
identified the MAs in each panel and the MA content (MAC) that each strain
carried. We also analyzed 21 published GWAS datasets of human diseases and
identified the MAC of each case or control. MAC was nearly linearly linked to
quantitative variations in numerous traits in model organisms, including life
span, tumor susceptibility, learning and memory, sensitivity to alcohol and
anti-psychotic drugs, and two correlated traits poor reproductive fitness and
strong immunity. Similarly, in Europeans or European Americans, enrichment of
MAs of fast but not slow evolutionary rate was linked to autoimmune and
numerous other diseases, including type 2 diabetes, Parkinson's disease,
psychiatric disorders, alcohol and cocaine addictions, cancer, and less life
span. Therefore, both high and low MAC correlated with extreme values in many
traits, indicating stabilizing selection on most MAs. The methods here are
broadly applicable and may help solve the missing heritability problem in
complex traits and diseases. |
| doi_str_mv | 10.48550/arxiv.1209.2911 |
| format | Article |
| fullrecord | <record><control><sourceid>arxiv_GOX</sourceid><recordid>TN_cdi_arxiv_primary_1209_2911</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1209_2911</sourcerecordid><originalsourceid>FETCH-arxiv_primary_1209_29113</originalsourceid><addsrcrecordid>eNqFj7FuwkAMhm9hqKB7p8ovQEhokYC1ArFQVaJ75CY-YulypucDwRv1MZu7sney5f__bP_GPFVl8bpcLMoZhitfimperor5qqoezM-eYietgpUA2khgf4TYETTiHDWRLwRk7dCBWDi8f-ga9uwHMw66I03jRvpefFbh-4w-csREuhvgHxsDctRZy0qoA4S-BQwEZ99SgC-JHZxEOZ9Lmqdj3gBK-QvxEzOy6JQe73Vsnrebz7fdNEeqT4F7DLc6RatTtJd_Db8Ii1zx</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype></control><display><type>article</type><title>Methods for scoring the collective effect of SNPs: Minor alleles of common SNPs quantitatively affect traits/diseases and are under both positive and negative selection</title><source>arXiv.org</source><creator>Yuan, Dejian ; Zhu, Zuobin ; Tan, Xiaohua ; Liang, Jie ; Zeng, Ceng ; Zhang, Jiegen ; Chen, Jun ; Ma, Long ; Dogan, Ayca ; Brockmann, Gudrun ; Goldmann, Oliver ; Medina, Eva ; Rice, Amanda D ; Moyer, Richard W ; Man, Xian ; Yi, Ke ; Li, Yanke ; Lu, Qing ; Huang, Yimin ; Wang, Dapeng ; Yu, Jun ; Guo, Hui ; Xia, Kun ; Huang, Shi</creator><creatorcontrib>Yuan, Dejian ; Zhu, Zuobin ; Tan, Xiaohua ; Liang, Jie ; Zeng, Ceng ; Zhang, Jiegen ; Chen, Jun ; Ma, Long ; Dogan, Ayca ; Brockmann, Gudrun ; Goldmann, Oliver ; Medina, Eva ; Rice, Amanda D ; Moyer, Richard W ; Man, Xian ; Yi, Ke ; Li, Yanke ; Lu, Qing ; Huang, Yimin ; Wang, Dapeng ; Yu, Jun ; Guo, Hui ; Xia, Kun ; Huang, Shi</creatorcontrib><description>Sci China Life Sci. 57:876-888. (2014) Most common SNPs are popularly assumed to be neutral. We here developed novel
methods to examine in animal models and humans whether extreme amount of minor
alleles (MAs) carried by an individual may represent extreme trait values and
common diseases. We analyzed panels of genetic reference populations and
identified the MAs in each panel and the MA content (MAC) that each strain
carried. We also analyzed 21 published GWAS datasets of human diseases and
identified the MAC of each case or control. MAC was nearly linearly linked to
quantitative variations in numerous traits in model organisms, including life
span, tumor susceptibility, learning and memory, sensitivity to alcohol and
anti-psychotic drugs, and two correlated traits poor reproductive fitness and
strong immunity. Similarly, in Europeans or European Americans, enrichment of
MAs of fast but not slow evolutionary rate was linked to autoimmune and
numerous other diseases, including type 2 diabetes, Parkinson's disease,
psychiatric disorders, alcohol and cocaine addictions, cancer, and less life
span. Therefore, both high and low MAC correlated with extreme values in many
traits, indicating stabilizing selection on most MAs. The methods here are
broadly applicable and may help solve the missing heritability problem in
complex traits and diseases.</description><identifier>DOI: 10.48550/arxiv.1209.2911</identifier><language>eng</language><subject>Quantitative Biology - Genomics ; Quantitative Biology - Populations and Evolution</subject><creationdate>2012-09</creationdate><rights>http://arxiv.org/licenses/nonexclusive-distrib/1.0</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>228,230,776,881</link.rule.ids><linktorsrc>$$Uhttps://arxiv.org/abs/1209.2911$$EView_record_in_Cornell_University$$FView_record_in_$$GCornell_University$$Hfree_for_read</linktorsrc><backlink>$$Uhttps://doi.org/10.48550/arXiv.1209.2911$$DView paper in arXiv$$Hfree_for_read</backlink><backlink>$$Uhttps://doi.org/10.1007/s11427-014-4704-4$$DView published paper (Access to full text may be restricted)$$Hfree_for_read</backlink></links><search><creatorcontrib>Yuan, Dejian</creatorcontrib><creatorcontrib>Zhu, Zuobin</creatorcontrib><creatorcontrib>Tan, Xiaohua</creatorcontrib><creatorcontrib>Liang, Jie</creatorcontrib><creatorcontrib>Zeng, Ceng</creatorcontrib><creatorcontrib>Zhang, Jiegen</creatorcontrib><creatorcontrib>Chen, Jun</creatorcontrib><creatorcontrib>Ma, Long</creatorcontrib><creatorcontrib>Dogan, Ayca</creatorcontrib><creatorcontrib>Brockmann, Gudrun</creatorcontrib><creatorcontrib>Goldmann, Oliver</creatorcontrib><creatorcontrib>Medina, Eva</creatorcontrib><creatorcontrib>Rice, Amanda D</creatorcontrib><creatorcontrib>Moyer, Richard W</creatorcontrib><creatorcontrib>Man, Xian</creatorcontrib><creatorcontrib>Yi, Ke</creatorcontrib><creatorcontrib>Li, Yanke</creatorcontrib><creatorcontrib>Lu, Qing</creatorcontrib><creatorcontrib>Huang, Yimin</creatorcontrib><creatorcontrib>Wang, Dapeng</creatorcontrib><creatorcontrib>Yu, Jun</creatorcontrib><creatorcontrib>Guo, Hui</creatorcontrib><creatorcontrib>Xia, Kun</creatorcontrib><creatorcontrib>Huang, Shi</creatorcontrib><title>Methods for scoring the collective effect of SNPs: Minor alleles of common SNPs quantitatively affect traits/diseases and are under both positive and negative selection</title><description>Sci China Life Sci. 57:876-888. (2014) Most common SNPs are popularly assumed to be neutral. We here developed novel
methods to examine in animal models and humans whether extreme amount of minor
alleles (MAs) carried by an individual may represent extreme trait values and
common diseases. We analyzed panels of genetic reference populations and
identified the MAs in each panel and the MA content (MAC) that each strain
carried. We also analyzed 21 published GWAS datasets of human diseases and
identified the MAC of each case or control. MAC was nearly linearly linked to
quantitative variations in numerous traits in model organisms, including life
span, tumor susceptibility, learning and memory, sensitivity to alcohol and
anti-psychotic drugs, and two correlated traits poor reproductive fitness and
strong immunity. Similarly, in Europeans or European Americans, enrichment of
MAs of fast but not slow evolutionary rate was linked to autoimmune and
numerous other diseases, including type 2 diabetes, Parkinson's disease,
psychiatric disorders, alcohol and cocaine addictions, cancer, and less life
span. Therefore, both high and low MAC correlated with extreme values in many
traits, indicating stabilizing selection on most MAs. The methods here are
broadly applicable and may help solve the missing heritability problem in
complex traits and diseases.</description><subject>Quantitative Biology - Genomics</subject><subject>Quantitative Biology - Populations and Evolution</subject><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>GOX</sourceid><recordid>eNqFj7FuwkAMhm9hqKB7p8ovQEhokYC1ArFQVaJ75CY-YulypucDwRv1MZu7sney5f__bP_GPFVl8bpcLMoZhitfimperor5qqoezM-eYietgpUA2khgf4TYETTiHDWRLwRk7dCBWDi8f-ga9uwHMw66I03jRvpefFbh-4w-csREuhvgHxsDctRZy0qoA4S-BQwEZ99SgC-JHZxEOZ9Lmqdj3gBK-QvxEzOy6JQe73Vsnrebz7fdNEeqT4F7DLc6RatTtJd_Db8Ii1zx</recordid><startdate>20120912</startdate><enddate>20120912</enddate><creator>Yuan, Dejian</creator><creator>Zhu, Zuobin</creator><creator>Tan, Xiaohua</creator><creator>Liang, Jie</creator><creator>Zeng, Ceng</creator><creator>Zhang, Jiegen</creator><creator>Chen, Jun</creator><creator>Ma, Long</creator><creator>Dogan, Ayca</creator><creator>Brockmann, Gudrun</creator><creator>Goldmann, Oliver</creator><creator>Medina, Eva</creator><creator>Rice, Amanda D</creator><creator>Moyer, Richard W</creator><creator>Man, Xian</creator><creator>Yi, Ke</creator><creator>Li, Yanke</creator><creator>Lu, Qing</creator><creator>Huang, Yimin</creator><creator>Wang, Dapeng</creator><creator>Yu, Jun</creator><creator>Guo, Hui</creator><creator>Xia, Kun</creator><creator>Huang, Shi</creator><scope>ALC</scope><scope>GOX</scope></search><sort><creationdate>20120912</creationdate><title>Methods for scoring the collective effect of SNPs: Minor alleles of common SNPs quantitatively affect traits/diseases and are under both positive and negative selection</title><author>Yuan, Dejian ; Zhu, Zuobin ; Tan, Xiaohua ; Liang, Jie ; Zeng, Ceng ; Zhang, Jiegen ; Chen, Jun ; Ma, Long ; Dogan, Ayca ; Brockmann, Gudrun ; Goldmann, Oliver ; Medina, Eva ; Rice, Amanda D ; Moyer, Richard W ; Man, Xian ; Yi, Ke ; Li, Yanke ; Lu, Qing ; Huang, Yimin ; Wang, Dapeng ; Yu, Jun ; Guo, Hui ; Xia, Kun ; Huang, Shi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-arxiv_primary_1209_29113</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Quantitative Biology - Genomics</topic><topic>Quantitative Biology - Populations and Evolution</topic><toplevel>online_resources</toplevel><creatorcontrib>Yuan, Dejian</creatorcontrib><creatorcontrib>Zhu, Zuobin</creatorcontrib><creatorcontrib>Tan, Xiaohua</creatorcontrib><creatorcontrib>Liang, Jie</creatorcontrib><creatorcontrib>Zeng, Ceng</creatorcontrib><creatorcontrib>Zhang, Jiegen</creatorcontrib><creatorcontrib>Chen, Jun</creatorcontrib><creatorcontrib>Ma, Long</creatorcontrib><creatorcontrib>Dogan, Ayca</creatorcontrib><creatorcontrib>Brockmann, Gudrun</creatorcontrib><creatorcontrib>Goldmann, Oliver</creatorcontrib><creatorcontrib>Medina, Eva</creatorcontrib><creatorcontrib>Rice, Amanda D</creatorcontrib><creatorcontrib>Moyer, Richard W</creatorcontrib><creatorcontrib>Man, Xian</creatorcontrib><creatorcontrib>Yi, Ke</creatorcontrib><creatorcontrib>Li, Yanke</creatorcontrib><creatorcontrib>Lu, Qing</creatorcontrib><creatorcontrib>Huang, Yimin</creatorcontrib><creatorcontrib>Wang, Dapeng</creatorcontrib><creatorcontrib>Yu, Jun</creatorcontrib><creatorcontrib>Guo, Hui</creatorcontrib><creatorcontrib>Xia, Kun</creatorcontrib><creatorcontrib>Huang, Shi</creatorcontrib><collection>arXiv Quantitative Biology</collection><collection>arXiv.org</collection></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Yuan, Dejian</au><au>Zhu, Zuobin</au><au>Tan, Xiaohua</au><au>Liang, Jie</au><au>Zeng, Ceng</au><au>Zhang, Jiegen</au><au>Chen, Jun</au><au>Ma, Long</au><au>Dogan, Ayca</au><au>Brockmann, Gudrun</au><au>Goldmann, Oliver</au><au>Medina, Eva</au><au>Rice, Amanda D</au><au>Moyer, Richard W</au><au>Man, Xian</au><au>Yi, Ke</au><au>Li, Yanke</au><au>Lu, Qing</au><au>Huang, Yimin</au><au>Wang, Dapeng</au><au>Yu, Jun</au><au>Guo, Hui</au><au>Xia, Kun</au><au>Huang, Shi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Methods for scoring the collective effect of SNPs: Minor alleles of common SNPs quantitatively affect traits/diseases and are under both positive and negative selection</atitle><date>2012-09-12</date><risdate>2012</risdate><abstract>Sci China Life Sci. 57:876-888. (2014) Most common SNPs are popularly assumed to be neutral. We here developed novel
methods to examine in animal models and humans whether extreme amount of minor
alleles (MAs) carried by an individual may represent extreme trait values and
common diseases. We analyzed panels of genetic reference populations and
identified the MAs in each panel and the MA content (MAC) that each strain
carried. We also analyzed 21 published GWAS datasets of human diseases and
identified the MAC of each case or control. MAC was nearly linearly linked to
quantitative variations in numerous traits in model organisms, including life
span, tumor susceptibility, learning and memory, sensitivity to alcohol and
anti-psychotic drugs, and two correlated traits poor reproductive fitness and
strong immunity. Similarly, in Europeans or European Americans, enrichment of
MAs of fast but not slow evolutionary rate was linked to autoimmune and
numerous other diseases, including type 2 diabetes, Parkinson's disease,
psychiatric disorders, alcohol and cocaine addictions, cancer, and less life
span. Therefore, both high and low MAC correlated with extreme values in many
traits, indicating stabilizing selection on most MAs. The methods here are
broadly applicable and may help solve the missing heritability problem in
complex traits and diseases.</abstract><doi>10.48550/arxiv.1209.2911</doi><oa>free_for_read</oa></addata></record> |
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| title | Methods for scoring the collective effect of SNPs: Minor alleles of common SNPs quantitatively affect traits/diseases and are under both positive and negative selection |
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