ArticleGenome medicine2017
Exploration of haplotype research consortium imputation for genome-wide association studies in 20,032 Generation Scotland participants.
Article in Genome medicine, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers, 8 of them syntheses that pooled it.
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Who cites it
66 citing papers in PubMed, 8 syntheses or guidelines pooled it, 136 citations in OpenAlex.
- Genetic insights into resting heart rate and its role in cardiovascular disease.Nature communications · 2023Pooled it
- Twenty-Five Novel Loci for Carotid Intima-Media Thickness: A Genome-Wide Association Study in >45 000 Individuals and Meta-Analysis of >100 000 Individuals.Arteriosclerosis, thrombosis, and vascular biology · 2022Pooled it
- Association of Genetic Variant at Chromosome 12q23.1 With Neuropathic Pain Susceptibility.JAMA network open · 2021Pooled it
- Multi-omics analysis identifies CpGs near G6PC2 mediating the effects of genetic variants on fasting glucose.Diabetologia · 2021Pooled it
- Mendelian pathway analysis of laboratory traits reveals distinct roles for ciliary subcompartments in common disease pathogenesis.American journal of human genetics · 2021Pooled it
- Genome-wide association study of antidepressant treatment resistance in a population-based cohort using health service prescription data and meta-analysis with GENDEP.The pharmacogenomics journal · 2020Pooled it
- Genome-wide meta-analysis of depression identifies 102 independent variants and highlights the importance of the prefrontal brain regions.Nature neuroscience · 2019Pooled it
- Genome-wide meta-analyses of stratified depression in Generation Scotland and UK Biobank.Translational psychiatry · 2018Pooled it
- Integrative exome sequencing and multi-omics analysis elucidates the regulatory role of rare variants in metabolic syndrome.Functional & integrative genomics · 2026Article
- The non-linear and linear effects of CYP2C19 metaboliser status on DNA methylation: a methylome-wide association study.Clinical epigenetics · 2026Article
- A genetic study of immunity in depression and interactions with childhood maltreatment.Translational psychiatry · 2026Article
- Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants.Genome biology · 2025Article
- The causal effects of remnant cholesterol on increased risk of cardiovascular diseases in East Asians.BMC medicine · 2025Observational
- Epigenome-wide association study of objectively measured physical activity in peripheral blood leukocytes.BMC genomics · 2025Article
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- Whole genome sequence association analysis of fasting glucose and fasting insulin levels in diverse cohorts from the NHLBI TOPMed program.Communications biology · 2022Article
- Comparing personalized brain-based and genetic risk scores for major depressive disorder in large population samples of adults and adolescents.European psychiatry : the journal of the Association of European Psychiatrists · 2022Article
- The Arg82Cys Polymorphism of the Protein Nepmucin Implies a Role in HDL Metabolism.Journal of the Endocrine Society · 2022Article
- Genome-wide association study identifies genetic risk loci for adiposity in a Taiwanese population.PLoS genetics · 2022Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
25 authors at 7 institutions in 1 country.
Funding
Abstract
backgroundThe Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based population cohort with DNA, biological samples, socio-demographic, psychological and clinical data from approximately 24,000 adult volunteers across Scotland. Although data collection was cross-sectional, GS:SFHS became a prospective cohort due to of the ability to link to routine Electronic Health Record (EHR) data. Over 20,000 participants were selected for genotyping using a large genome-wide array.
methodsGS:SFHS was analysed using genome-wide association studies (GWAS) to test the effects of a large spectrum of variants, imputed using the Haplotype Research Consortium (HRC) dataset, on medically relevant traits measured directly or obtained from EHRs. The HRC dataset is the largest available haplotype reference panel for imputation of variants in populations of European ancestry and allows investigation of variants with low minor allele frequencies within the entire GS:SFHS genotyped cohort.
resultsGenome-wide associations were run on 20,032 individuals using both genotyped and HRC imputed data. We present results for a range of well-studied quantitative traits obtained from clinic visits and for serum urate measures obtained from data linkage to EHRs collected by the Scottish National Health Service. Results replicated known associations and additionally reveal novel findings, mainly with rare variants, validating the use of the HRC imputation panel. For example, we identified two new associations with fasting glucose at variants near to Y_RNA and WDR4 and four new associations with heart rate at SNPs within CSMD1 and ASPH, upstream of HTR1F and between PROKR2 and GPCPD1. All were driven by rare variants (minor allele frequencies in the range of 0.08-1%). Proof of principle for use of EHRs was verification of the highly significant association of urate levels with the well-established urate transporter SLC2A9.
conclusionsGS:SFHS provides genetic data on over 20,000 participants alongside a range of phenotypes as well as linkage to National Health Service laboratory and clinical records. We have shown that the combination of deeper genotype imputation and extended phenotype availability make GS:SFHS an attractive resource to carry out association studies to gain insight into the genetic architecture of complex traits.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.