Equine population genomics
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB52367 | ENA |
REPOSITORIES: ENA
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Project description:The common genetic variants associated with complex traits typically lie in non-coding DNA and may alter gene regulation in a cell-type specific manner. Consequently, the choice of tissue or cell model in the dissection of disease associations is important. We carried out an eQTL study of primary human osteoblasts (HOb) derived from unrelated donors of Swedish origin, each represented by two independently derived primary lines to provide biological replication. We combined our data with publicly available information from a genome-wide association study (GWAS) of bone mineral density (BMD). The top BMD-associated SNPs were tested for cis-association of gene expression in HObs and in lymphoblastoid cell lines (LCLs) using publicly available data and showed that HObs have a significantly greater enrichment of converging cis-eQTLs as compared to LCLs. The top BMD loci with SNPs showing strong cis-effects on gene expression in HObs were selected for further validation using a staged design in two cohorts of Caucasian male subjects. All variants were tested in the Swedish MrOs Cohort (n=3014), providing evidence for two novel BMD loci. These variants were then tested in the Rotterdam Study (n=2100), yielding converging evidence for BMD association at one locus. The cis-regulatory effect was further fine-mapped to the proximal promoter of the gene. Our results suggest that primary cells relevant to disease phenotypes complement traditional approaches for prioritization and validation of GWAS hits for follow-up studies.
2009-04-16 | GSE15678 | GEO
Project description:A substantial proportion of disease variants reside in non-coding RNAs (ncRNAs), which serve as important regulatory elements. However, most ncRNA targets remain unknown, hindering our understanding of complex diseases. We found allele-specific ncRNAs enriched near allelic protein-coding genes, suggesting that allele-specific expression could be used to predict ncRNA-targets. We applied this concept to mouse organs, revealing 397 enhancing or repressive ncRNA-to-target associations. Next, we applied this strategy to tissues from nearly 1,000 individuals (GTEx). Given the outbred nature of humans, each individual harbors a unique allele-specific landscape, allowing novel ncRNA-to-target discovery with each individual. We uncovered 2,291 ncRNA-to-targets along with their mechanisms, which we benchmarked against sample-matched eQTLs. Further GWAS integration assigned 30.59% of variants overlapping informative ncRNA to their protein-coding targets. As more sequencing data and risk variants become available, this strategy will continue to elucidate targets and mechanisms, ultimately decoding the entire cis-acting landscape of the non-coding genome.
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Project description:Obsessive-compulsive disorder (OCD), a severe mental disease manifested in time-consuming repetition of behaviors, affects 1-3% of the human population. While highly heritable, complex genetics has hampered attempts to elucidate OCD etiology. Dogs suffer from naturally occurring compulsive disorders that closely model human OCD, manifested as an excessive repetition of normal canine behaviors that only partially responds to drug therapy. The limited diversity within dog breeds makes identifying underlying genetic factors easier. We use genome wide association of 87 Doberman Pinscher cases and 63 controls to identify genomic loci associated with OCD and sequence these regions in 8 affected dogs from high-risk breeds and 8 breed-matched controls. We find 119 variants in evolutionarily conserved sites that are specific to dogs with OCD. These case-only variants are significantly more common in high OCD risk breeds compared to breeds with no known psychiatric problems. Four genes, all with synaptic function, have the most case-only variation: neuronal cadherin (CDH2), catenin alpha2 (CTNNA2), ataxin-1 (ATXN1), and plasma glutamate carboxypeptidase (PGCP). Two different case-only variants targeted the same approximately 500-bp highly conserved regulatory element between the cadherin genes CDH2 and DSC3. We functionally test these variants in a human neuroblastoma cell line and show that they cause significant changes in gene expression, likely due to disrupted transcription factor binding. This work demonstrates how we can use the unique genetics of dog breeds, and mechanistic similarities between human and dog diseases, to find genes and regulatory pathways underlying complex psychiatric disorders. Affymetrix SNP arrays were performed according to the manufacturer's directions. Genome wide association analysis was performed for 87 doberman pinshcers OCD cases and 63 breed-matched controls.
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Project description:Obsessive-compulsive disorder (OCD), a severe mental disease manifested in time-consuming repetition of behaviors, affects 1-3% of the human population. While highly heritable, complex genetics has hampered attempts to elucidate OCD etiology. Dogs suffer from naturally occurring compulsive disorders that closely model human OCD, manifested as an excessive repetition of normal canine behaviors that only partially responds to drug therapy. The limited diversity within dog breeds makes identifying underlying genetic factors easier. We use genome wide association of 87 Doberman Pinscher cases and 63 controls to identify genomic loci associated with OCD and sequence these regions in 8 affected dogs from high-risk breeds and 8 breed-matched controls. We find 119 variants in evolutionarily conserved sites that are specific to dogs with OCD. These case-only variants are significantly more common in high OCD risk breeds compared to breeds with no known psychiatric problems. Four genes, all with synaptic function, have the most case-only variation: neuronal cadherin (CDH2), catenin alpha2 (CTNNA2), ataxin-1 (ATXN1), and plasma glutamate carboxypeptidase (PGCP). Two different case-only variants targeted the same approximately 500-bp highly conserved regulatory element between the cadherin genes CDH2 and DSC3. We functionally test these variants in a human neuroblastoma cell line and show that they cause significant changes in gene expression, likely due to disrupted transcription factor binding. This work demonstrates how we can use the unique genetics of dog breeds, and mechanistic similarities between human and dog diseases, to find genes and regulatory pathways underlying complex psychiatric disorders.
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Project description:Population genomic of Rhynchosporium commune
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2017-06-12 | GSE73593 | GEO
Project description:The development of whole genome association studies from the general population has lead to the robust identification of several loci involved in different common human diseases. Interestingly, most of the strongest signals of association observed in these studies arise from non-coding regions, raising the possibility that these regions are involved in the etiology of the disease through regulatory mechanisms. These findings highlight the importance of better understanding the inter-individual differences in gene expression in humans. Aim of the study was to search for biomarker, to identify eQTLs and to elucidate whether whole-blood eQTLs allow to identify putative functional variants involved in the etiology of complex traits. For more information about the KORA F4 study, please see http://www.helmholtz-muenchen.de/en/kora-en/information-for-scientists/current-kora-studies/f4-study/index.html .
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