ArticleAmerican journal of human genetics2009
Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies.
Article in American journal of human genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers, 3 of them syntheses that pooled it.
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Who cites it
139 citing papers in PubMed, 3 syntheses or guidelines pooled it.
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- Genome-wide meta-analysis of SNP-by9-ACEI/ARB and SNP-by-thiazide diuretic and effect on serum potassium in cohorts of European and African ancestry.The pharmacogenomics journal · 2019Pooled it
- Discovery of common and rare genetic risk variants for colorectal cancer.Nature genetics · 2019Pooled it
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- Integrative genome-wide association and haplotype-based analyses reveal genetic structure and local adaptation in Korean landrace soybeans.BMC plant biology · 2025Article
- Sex-Biased Admixture Followed by Isolation and Adaptive Evolution Shaped the Genomic and Blood Pressure Diversity of the LopNur People.Molecular biology and evolution · 2025Article
- Enabling efficient analysis of biobank-scale data with genotype representation graphs.Nature computational science · 2025Article
- GWAS for identification of genomic regions and candidate genes in vegetable crops.Functional & integrative genomics · 2024Review
- Segregation GWAS to linearize a non-additive locus with incomplete penetrance: an example of horn status in sheep.Genetics, selection, evolution : GSE · 2024Article
- Genotype Representation Graphs: Enabling Efficient Analysis of Biobank-Scale Data.bioRxiv : the preprint server for biology · 2024Article
- Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations.Nature communications · 2024Article
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- Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients.GigaByte (Hong Kong, China) · 2024Article
- Sequenced-based GWAS for linear classification traits in Belgian Blue beef cattle reveals new coding variants in genes regulating body size in mammals.Genetics, selection, evolution : GSE · 2023Article
- QTLs and Candidate Genes Associated with Semen Traits in Merino Sheep.Animals : an open access journal from MDPI · 2023Article
- PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data.BMC bioinformatics · 2022Article
- A Fast and Robust Strategy to Remove Variant-Level Artifacts in Alzheimer Disease Sequencing Project Data.Neurology. Genetics · 2022Article
- Population genomic monitoring provides insight into conservation status but no correlation with demographic estimates of extinction risk in a threatened trout.Evolutionary applications · 2022Article
79 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
We present a novel method for simultaneous genotype calling and haplotype-phase inference. Our method employs the computationally efficient BEAGLE haplotype-frequency model, which can be applied to large-scale studies with millions of markers and thousands of samples. We compare genotype calls made with our method to genotype calls made with the BIRDSEED, CHIAMO, GenCall, and ILLUMINUS genotype-calling methods, using genotype data from the Illumina 550K and Affymetrix 500K arrays. We show that our method has higher genotype-call accuracy and yields fewer uncalled genotypes than competing methods. We perform single-marker analysis of data from the Wellcome Trust Case Control Consortium bipolar disorder and type 2 diabetes studies. For bipolar disorder, the genotype calls in the original study yield 25 markers with apparent false-positive association with bipolar disorder at a p < 10(-7) significance level, whereas genotype calls made with our method yield no associated markers at this significance threshold. Conversely, for markers with replicated association with type 2 diabetes, there is good concordance between genotype calls used in the original study and calls made by our method. Results from single-marker and haplotypic analysis of our method's genotype calls for the bipolar disorder study indicate that our method is highly effective at eliminating genotyping artifacts that cause false-positive associations in genome-wide association studies. Our new genotype-calling methods are implemented in the BEAGLE and BEAGLECALL software packages.
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