Pedigree- and SNP-Associated Genetics and Recent Environment are the Major Contributors to Anthropometric and Cardiometabolic Trait Variation.
Genome-wide association studies have successfully identified thousands of loci for a range of human complex traits and diseases. The proportion of phenotypic variance explained by significant associations is, however, limited. Given the same dense SNP panels, mixed model analyses capture a greater p...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2016-02-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC4737500?pdf=render |
| _version_ | 1818544182108618752 |
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| author | Charley Xia Carmen Amador Jennifer Huffman Holly Trochet Archie Campbell David Porteous Generation Scotland Nicholas D Hastie Caroline Hayward Veronique Vitart Pau Navarro Chris S Haley |
| author_facet | Charley Xia Carmen Amador Jennifer Huffman Holly Trochet Archie Campbell David Porteous Generation Scotland Nicholas D Hastie Caroline Hayward Veronique Vitart Pau Navarro Chris S Haley |
| author_sort | Charley Xia |
| collection | DOAJ |
| description | Genome-wide association studies have successfully identified thousands of loci for a range of human complex traits and diseases. The proportion of phenotypic variance explained by significant associations is, however, limited. Given the same dense SNP panels, mixed model analyses capture a greater proportion of phenotypic variance than single SNP analyses but the total is generally still less than the genetic variance estimated from pedigree studies. Combining information from pedigree relationships and SNPs, we examined 16 complex anthropometric and cardiometabolic traits in a Scottish family-based cohort comprising up to 20,000 individuals genotyped for ~520,000 common autosomal SNPs. The inclusion of related individuals provides the opportunity to also estimate the genetic variance associated with pedigree as well as the effects of common family environment. Trait variation was partitioned into SNP-associated and pedigree-associated genetic variation, shared nuclear family environment, shared couple (partner) environment and shared full-sibling environment. Results demonstrate that trait heritabilities vary widely but, on average across traits, SNP-associated and pedigree-associated genetic effects each explain around half the genetic variance. For most traits the recently-shared environment of couples is also significant, accounting for ~11% of the phenotypic variance on average. On the other hand, the environment shared largely in the past by members of a nuclear family or by full-siblings, has a more limited impact. Our findings point to appropriate models to use in future studies as pedigree-associated genetic effects and couple environmental effects have seldom been taken into account in genotype-based analyses. Appropriate description of the trait variation could help understand causes of intra-individual variation and in the detection of contributing loci and environmental factors. |
| first_indexed | 2024-12-11T22:45:07Z |
| format | Article |
| id | doaj.art-fcf6c56e90904ad59f7dd47c50ccb1d9 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-11T22:45:07Z |
| publishDate | 2016-02-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS Genetics |
| spelling | doaj.art-fcf6c56e90904ad59f7dd47c50ccb1d92022-12-22T00:47:39ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042016-02-01122e100580410.1371/journal.pgen.1005804Pedigree- and SNP-Associated Genetics and Recent Environment are the Major Contributors to Anthropometric and Cardiometabolic Trait Variation.Charley XiaCarmen AmadorJennifer HuffmanHolly TrochetArchie CampbellDavid PorteousGeneration ScotlandNicholas D HastieCaroline HaywardVeronique VitartPau NavarroChris S HaleyGenome-wide association studies have successfully identified thousands of loci for a range of human complex traits and diseases. The proportion of phenotypic variance explained by significant associations is, however, limited. Given the same dense SNP panels, mixed model analyses capture a greater proportion of phenotypic variance than single SNP analyses but the total is generally still less than the genetic variance estimated from pedigree studies. Combining information from pedigree relationships and SNPs, we examined 16 complex anthropometric and cardiometabolic traits in a Scottish family-based cohort comprising up to 20,000 individuals genotyped for ~520,000 common autosomal SNPs. The inclusion of related individuals provides the opportunity to also estimate the genetic variance associated with pedigree as well as the effects of common family environment. Trait variation was partitioned into SNP-associated and pedigree-associated genetic variation, shared nuclear family environment, shared couple (partner) environment and shared full-sibling environment. Results demonstrate that trait heritabilities vary widely but, on average across traits, SNP-associated and pedigree-associated genetic effects each explain around half the genetic variance. For most traits the recently-shared environment of couples is also significant, accounting for ~11% of the phenotypic variance on average. On the other hand, the environment shared largely in the past by members of a nuclear family or by full-siblings, has a more limited impact. Our findings point to appropriate models to use in future studies as pedigree-associated genetic effects and couple environmental effects have seldom been taken into account in genotype-based analyses. Appropriate description of the trait variation could help understand causes of intra-individual variation and in the detection of contributing loci and environmental factors.http://europepmc.org/articles/PMC4737500?pdf=render |
| spellingShingle | Charley Xia Carmen Amador Jennifer Huffman Holly Trochet Archie Campbell David Porteous Generation Scotland Nicholas D Hastie Caroline Hayward Veronique Vitart Pau Navarro Chris S Haley Pedigree- and SNP-Associated Genetics and Recent Environment are the Major Contributors to Anthropometric and Cardiometabolic Trait Variation. PLoS Genetics |
| title | Pedigree- and SNP-Associated Genetics and Recent Environment are the Major Contributors to Anthropometric and Cardiometabolic Trait Variation. |
| title_full | Pedigree- and SNP-Associated Genetics and Recent Environment are the Major Contributors to Anthropometric and Cardiometabolic Trait Variation. |
| title_fullStr | Pedigree- and SNP-Associated Genetics and Recent Environment are the Major Contributors to Anthropometric and Cardiometabolic Trait Variation. |
| title_full_unstemmed | Pedigree- and SNP-Associated Genetics and Recent Environment are the Major Contributors to Anthropometric and Cardiometabolic Trait Variation. |
| title_short | Pedigree- and SNP-Associated Genetics and Recent Environment are the Major Contributors to Anthropometric and Cardiometabolic Trait Variation. |
| title_sort | pedigree and snp associated genetics and recent environment are the major contributors to anthropometric and cardiometabolic trait variation |
| url | http://europepmc.org/articles/PMC4737500?pdf=render |
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