ArticleBMC bioinformatics2019
Exploring effective approaches for haplotype block phasing.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- HPTAS: An Alignment-Free Haplotype Phasing Algorithm Focused on Allele-Specific Studies Using Transcriptome Data.International journal of molecular sciences · 2025Article
- A genotype imputation reference panel specific for native Southeast Asian populations.NPJ genomic medicine · 2024Article
- haploMAGIC: accurate phasing and detection of recombination in multiparental populations despite genotyping errors.G3 (Bethesda, Md.) · 2024Article
- A cautionary tale of low-pass sequencing and imputation with respect to haplotype accuracy.Genetics, selection, evolution : GSE · 2024Article
- How local reference panels improve imputation in French populations.Scientific reports · 2024Article
- Two germline mutations can serve as genetic susceptibility screening makers for a lung adenocarcinoma family.Journal of cancer research and clinical oncology · 2023Article
- New insights into trait introgression with the look-ahead intercrossing strategy.G3 (Bethesda, Md.) · 2023Article
- On the origin and structure of haplotype blocks.Molecular ecology · 2023Article
- Haplotyping-Assisted Diploid Assembly and Variant Detection with Linked Reads.Methods in molecular biology (Clifton, N.J.) · 2023Review
- Assessing Human Genome-wide Variation in the Massim Region of Papua New Guinea and Implications for the Kula Trading Tradition.Molecular biology and evolution · 2022Article
- Features and applications of haplotypes in crop breeding.Communications biology · 2021Review
- Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database.BMC bioinformatics · 2021Article
- A SNaPshot Assay for Determination of the Mannose-Binding Lectin Gene Variants and an Algorithm for Calculation of Haplogenotype Combinations.Diagnostics (Basel, Switzerland) · 2021Article
- Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region.Frontiers in genetics · 2021Article
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Authors and funding
5 authors.
Funding
Abstract
backgroundKnowledge of phase, the specific allele sequence on each copy of homologous chromosomes, is increasingly recognized as critical for detecting certain classes of disease-associated mutations. One approach for detecting such mutations is through phased haplotype association analysis. While the accuracy of methods for phasing genotype data has been widely explored, there has been little attention given to phasing accuracy at haplotype block scale. Understanding the combined impact of the accuracy of phasing tool and the method used to determine haplotype blocks on the error rate within the determined blocks is essential to conduct accurate haplotype analyses.
resultsWe present a systematic study exploring the relationship between seven widely used phasing methods and two common methods for determining haplotype blocks. The evaluation focuses on the number of haplotype blocks that are incorrectly phased. Insights from these results are used to develop a haplotype estimator based on a consensus of three tools. The consensus estimator achieved the most accurate phasing in all applied tests. Individually, EAGLE2, BEAGLE and SHAPEIT2 alternate in being the best performing tool in different scenarios. Determining haplotype blocks based on linkage disequilibrium leads to more correctly phased blocks compared to a sliding window approach. We find that there is little difference between phasing sections of a genome (e.g. a gene) compared to phasing entire chromosomes. Finally, we show that the location of phasing error varies when the tools are applied to the same data several times, a finding that could be important for downstream analyses.
conclusionsThe choice of phasing and block determination algorithms and their interaction impacts the accuracy of phased haplotype blocks. This work provides guidance and evidence for the different design choices needed for analyses using haplotype blocks. The study highlights a number of issues that may have limited the replicability of previous haplotype analysis.
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