ArticleBioinformatics (Oxford, England)2019
Efficient haplotype matching between a query and a panel for genealogical search.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 21 citations in OpenAlex.
- An Efficient Dynamic Data Structure for Haplotype Matching and Compression on Biobank-Scale Data.Journal of computational biology : a journal of computational molecular cell biology · 2026Article
- DynamicbioRxiv : the preprint server for biology · 2025Article
- Haplotype Matching with GBWT for Pangenome Graphs.bioRxiv : the preprint server for biology · 2025Article
- An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025Article
- Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in UK Biobank.eLife · 2024Article
- RaPID-Query for fast identity by descent search and genealogical analysis.Bioinformatics (Oxford, England) · 2023Article
- Syllable-PBWT for space-efficient haplotype long-match query.Bioinformatics (Oxford, England) · 2023Article
- Haplotype Threading Using the Positional Burrows-Wheeler Transform.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2022Article
- GRAPE: genomic relatedness detection pipeline.F1000Research · 2022Article
- d-PBWT: dynamic positional Burrows-Wheeler transform.Bioinformatics (Oxford, England) · 2021Article
- Fast and Robust Identity-by-Descent Inference with the Templated Positional Burrows-Wheeler Transform.Molecular biology and evolution · 2021Article
- Personalized genealogical history of UK individuals inferred from biobank-scale IBD segments.BMC biology · 2021Article
- Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in UK Biobank.medRxiv : the preprint server for health sciences · 2020Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
motivationWith the wide availability of whole-genome genotype data, there is an increasing need for conducting genetic genealogical searches efficiently. Computationally, this task amounts to identifying shared DNA segments between a query individual and a very large panel containing millions of haplotypes. The celebrated Positional Burrows-Wheeler Transform (PBWT) data structure is a pre-computed index of the panel that enables constant time matching at each position between one haplotype and an arbitrarily large panel. However, the existing algorithm (Durbin's Algorithm 5) can only identify set-maximal matches, the longest matches ending at any location in a panel, while in real genealogical search scenarios, multiple 'good enough' matches are desired.
resultsIn this work, we developed two algorithmic extensions of Durbin's Algorithm 5, that can find all L-long matches, matches longer than or equal to a given length L, between a query and a panel. In the first algorithm, PBWT-Query, we introduce 'virtual insertion' of the query into the PBWT matrix of the panel, and then scanning up and down for the PBWT match blocks with length greater than L. In our second algorithm, L-PBWT-Query, we further speed up PBWT-Query by introducing additional data structures that allow us to avoid iterating through blocks of incomplete matches. The efficiency of PBWT-Query and L-PBWT-Query is demonstrated using the simulated data and the UK Biobank data. Our results show that our proposed algorithms can detect related individuals for a given query efficiently in very large cohorts which enables a fast on-line query search. AVAILABILITY AND IMPLEMENTATION: genome.ucf.edu/pbwt-query. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.