ArticleAmerican journal of human genetics2022
Genotype error biases trio-based estimates of haplotype phase accuracy.
Article in American journal of human genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 29 citations in OpenAlex.
- Direct probabilistic quantification of mosaic loss of chromosome Y from sequencing data.bioRxiv : the preprint server for biology · 2026Article
- A Benchmark of Modern Statistical Phasing Methods.bioRxiv : the preprint server for biology · 2026Article
- Biallelic variants in RNU2-2 cause a remarkably frequent developmental and epileptic encephalopathy.Nature genetics · 2026Article
- Fine-scale recombination rates inferred using the canFam4 assembly are strongly correlated with previous maps of dog recombination.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Genotype imputation from low-coverage WGS using haplotype reference panels in cultivated strawberry.BMC genomics · 2025Article
- Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin analyses.HGG advances · 2025Article
- High-resolution detection of copy number alterations in single cells with HiScanner.Nature communications · 2025Article
- Identifying individuals with rare disease variants by inferring shared ancestral haplotypes from SNP array data.NAR genomics and bioinformatics · 2025Article
- High-resolution detection of copy number alterations in single cells with HiScanner.bioRxiv : the preprint server for biology · 2025Article
- A T2T-CHM13 recombination map and globally diverse haplotype reference panel improves phasing and imputation.bioRxiv : the preprint server for biology · 2025Article
- How to handle high subgenome sequence similarity in allopolyploid Fragaria x ananassa: linkage disequilibrium based variant filtering.BMC genomics · 2024Article
- Dissecting the genetic basis of resistance to Soil-borne cereal mosaic virus (SBCMV) in durum wheat by bi-parental mapping and GWAS.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Reconstructing parent genomes using siblings and other relatives.bioRxiv : the preprint server for biology · 2024Article
- Simultaneous estimation of genotype error and uncalled deletion rates in whole genome sequence data.PLoS genetics · 2024Article
- Statistical phasing of 150,119 sequenced genomes in the UK Biobank.American journal of human genetics · 2023Article
- A Pipeline for Phasing and Genotype Imputation on Mixed Human Data (Parents-Offspring Trios and Unrelated Subjects) by Reviewing Current Methods and Software.Life (Basel, Switzerland) · 2022Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Haplotypes can be estimated from unphased genotype data via statistical methods. When parent-offspring trios are available for inferring the true phase from Mendelian inheritance rules, the accuracy of statistical phasing is usually measured by the switch error rate, which is the proportion of pairs of consecutive heterozygotes that are incorrectly phased. We present a method for estimating the genotype error rate from parent-offspring trios and a method for estimating the bias that occurs in the observed switch error rate as a result of genotype error. We apply these methods to 485,301 genotyped UK Biobank samples that include 898 White British trios and to 38,387 sequenced TOPMed samples that include 217 African Caribbean trios and 669 European American trios. We show that genotype error inflates the observed switch error rate and that the relative bias increases with sample size. For the UK Biobank White British trios, the observed switch error rate in the trio offspring is 2.4 times larger than the estimated true switch error rate (1.4 × 10
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