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Large-scale East-Asian eQTL mapping reveals novel candidate genes for LD mapping and the genomic landscape of transcriptional effects of sequence variants.

ABSTRACT: Profiles of sequence variants that influence gene transcription are very important for understanding mechanisms that affect phenotypic variation and disease susceptibility. Using genotypes at 1.4 million SNPs and a comprehensive transcriptional profile of 15,454 coding genes and 6,113 lincRNA genes obtained from peripheral blood cells of 298 Japanese individuals, we mapped expression quantitative trait loci (eQTLs). We identified 3,804 cis-eQTLs (within 500 kb from target genes) and 165 trans-eQTLs (>500 kb away or on different chromosomes). Cis-eQTLs were often located in transcribed or adjacent regions of genes; among these regions, 5' untranslated regions and 5' flanking regions had the largest effects. Epigenetic evidence for regulatory potential accumulated in public databases explained the magnitude of the effects of our eQTLs. Cis-eQTLs were often located near the respective target genes, if not within genes. Large effect sizes were observed with eQTLs near target genes, and effect sizes were obviously attenuated as the eQTL distance from the gene increased. Using a very stringent significance threshold, we identified 165 large-effect trans-eQTLs. We used our eQTL map to assess 8,069 disease-associated SNPs identified in 1,436 genome-wide association studies (GWAS). We identified genes that might be truly causative, but GWAS might have failed to identify for 148 out of the GWAS-identified SNPs; for example, TUFM (P?=?3.3E-48) was identified for inflammatory bowel disease (early onset); ZFP90 (P?=?4.4E-34) for ulcerative colitis; and IDUA (P?=?2.2E-11) for Parkinson's disease. We identified four genes (P<2.0E-14) that might be related to three diseases and two hematological traits; each expression is regulated by trans-eQTLs on a different chromosome than the gene.

SUBMITTER: Narahara M

PROVIDER: S-EPMC4067418 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Large-scale East-Asian eQTL mapping reveals novel candidate genes for LD mapping and the genomic landscape of transcriptional effects of sequence variants.

Narahara Maiko M Higasa Koichiro K Nakamura Seiji S Tabara Yasuharu Y Kawaguchi Takahisa T Ishii Miho M Matsubara Kenichi K Matsuda Fumihiko F Yamada Ryo R

PloS one 20140623 6

Profiles of sequence variants that influence gene transcription are very important for understanding mechanisms that affect phenotypic variation and disease susceptibility. Using genotypes at 1.4 million SNPs and a comprehensive transcriptional profile of 15,454 coding genes and 6,113 lincRNA genes obtained from peripheral blood cells of 298 Japanese individuals, we mapped expression quantitative trait loci (eQTLs). We identified 3,804 cis-eQTLs (within 500 kb from target genes) and 165 trans-eQ ...[more]

PMID: 24956270

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Project description:BACKGROUND AND GOAL:The study is conducted to facilitate conservation of migratory wader species along the East Asian-Australasian Flyway, particularly to 1) Identify hotspots of wader species richness along the flyway and effectively map how these might change between breeding, non-breeding and migratory phases; 2) Determine if the existing network of protected areas (PA) is sufficient to effectively conserve wader biodiversity hotspots along the EAAF; 3) Assess how species distribution models can provide complementary distribution estimates to existing BirdLife range maps. METHODS:We use a species distribution modelling (SDM) approach (MaxEnt) to develop temporally explicit individual range maps of 57 migratory wader species across their annual cycle, including breeding, non-breeding and migratory phases, which in turn provide the first biodiversity hotspot map of migratory waders along the EAAF for each of these phases. We assess the protected area coverage during each migration period, and analyse the dominant environmental drivers of distributions for each period. Additionally, we compare model hotspots to those existing range maps of the same species obtained from the BirdLife Internationals' database. RESULTS:Our model results indicate an overall higher and a spatially different species richness pattern compared to that derived from a wader biodiversity hotspot map based on BirdLife range maps. Field observation records from the eBird database for our 57 study species confirm many of the hotspots revealed by model outputs (especially within the Yellow Sea coastal region), suggesting that current richness of the EAAF may have been underestimated and certain hotspots overlooked. Less than 10% of the terrestrial zones area (inland and coastal) which support waders are protected and, only 5% of areas with the highest 10% species richness is protected. MAIN CONCLUSIONS:The study results suggest the need for new areas for migratory wader research and conservation priorities including Yellow Sea region and Russian far-East. It also suggests a need to increase the coverage and percentage of current PA network to achieve Aichi Target 11 for Flyway countries, including giving stronger consideration to the temporal dynamics of wader migration.

Dataset Information

Large-scale East-Asian eQTL mapping reveals novel candidate genes for LD mapping and the genomic landscape of transcriptional effects of sequence variants.

Publications

Large-scale East-Asian eQTL mapping reveals novel candidate genes for LD mapping and the genomic landscape of transcriptional effects of sequence variants.

Similar Datasets

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