ArticleBriefings in functional genomics2016
Quality control, imputation and analysis of genome-wide genotyping data from the Illumina HumanCoreExome microarray.
Article in Briefings in functional genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers, 2 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
42 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A systematic review of neuroimaging epigenetic research: calling for an increased focus on development.Molecular psychiatry · 2023Pooled it
- A genome-wide association meta-analysis of prognostic outcomes following cognitive behavioural therapy in individuals with anxiety and depressive disorders.Translational psychiatry · 2019Pooled it
- Summer Rainfall Drives Adaptation with Gene Flow in a Widespread Butterfly.Molecular ecology · 2026Article
- Sharing approaches in predictive genomics across animals, plants and humans.Nature genetics · 2026Review
- Analysis of Genome-Wide Association Studies.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Rivaroxaban for Thromboembolism Prophylaxis in Patients with Nephrotic Syndrome: A Single-Arm, Prospective Study.Kidney diseases (Basel, Switzerland) · 2024Article
- GRIEVOUS: your command-line general for resolving cross-dataset genotype inconsistencies.Bioinformatics (Oxford, England) · 2024Article
- Ensuring Trust in Genomics Research.... IEEE International Conference on Trust, Privacy and Security in Intelligent Systems and Applications : (TPS-ISA ...). IEEE International Conference on Trust, Privacy and Security in Intelligent Systems and Applications · 2023Article
- Brain structure, phenotypic and genetic correlates of reading performance.Nature human behaviour · 2023Article
- A likelihood ratio approach for utilizing case-control data in the clinical classification of rare sequence variants: application toHuman mutation · 2023Article
- The RNA editing landscape in acute myeloid leukemia reveals associations with disease mutations and clinical outcome.iScience · 2022Article
- Polygenic risk scores for schizophrenia and major depression are associated with socio-economic indicators of adversity in two British community samples.Translational psychiatry · 2022Article
- MagicalRsq: Machine-learning-based genotype imputation quality calibration.American journal of human genetics · 2022Article
- Polygenic scores for schizophrenia and major depression are associated with psychosocial risk factors in children: evidence of gene-environment correlation.Journal of child psychology and psychiatry, and allied disciplines · 2022Article
- Article
- Localized variation in ancestral admixture identifies pilocytic astrocytoma risk loci among Latino children.PLoS genetics · 2022Article
- Exploring polygenic-environment and residual-environment interactions for depressive symptoms within the UK Biobank.Genetic epidemiology · 2022Article
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- Recombination landscape divergence between populations is marked by larger low-recombining regions in domesticated rye.Molecular biology and evolution · 2022Article
- Genetic effects on educational attainment in Hungary.Brain and behavior · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The decreasing cost of performing genome-wide association studies has made genomics widely accessible. However, there is a paucity of guidance for best practice in conducting such analyses. For the results of a study to be valid and replicable, multiple biases must be addressed in the course of data preparation and analysis. In addition, standardizing methods across small, independent studies would increase comparability and the potential for effective meta-analysis. This article provides a discussion of important aspects of quality control, imputation and analysis of genome-wide data from a low-coverage microarray, as well as a straight-forward guide to performing a genome-wide association study. A detailed protocol is provided online, with example scripts available at https://github.com/JoniColeman/gwas_scripts.
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Registered trials
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.