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mcPBWT: Space-Efficient Multi-column PBWT Scanning Algorithm for Composite Haplotype Matching

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Computational Advances in Bio and Medical Sciences (ICCABS 2021)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 13254))

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Abstract

Positional Burrows-Wheeler Transform (PBWT) is a data structure that supports efficient algorithms for finding matching segments in a panel of haplotypes. It is of interest to study the composite patterns of multiple matching segments or blocks arranged contiguously along a same haplotype as they can indicate recombination crossover events, gene-conversion tracts, or, sometimes, errors of phasing algorithms. However, current PBWT algorithms do not support search of such composite patterns efficiently. Here, we present our algorithm, mcPBWT (multi-column PBWT), that uses multiple synchronized runs of PBWT at different variant sites providing a “look-ahead" information of matches at those variant sites. Such “look-ahead” information allows us to analyze multiple contiguous matching pairs in a single pass. We present two specific cases of mcPBWT, namely double-PBWT and triple-PBWT which utilize two and three columns of PBWT respectively. double-PBWT finds two matching pairs’ combinations representative of crossover event or phasing error while triple-PBWT finds three matching pairs’ combinations representative of gene-conversion tract.

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Acknowledgments

PS, AN, DZ and SZ were supported by the National Institutes of Health grant R01 HG010086. AN, DZ and SZ were also supported by the National Institutes of Health grants R56 HG011509. AN and DZ were also supported by the National Institutes of Health grant OT2-OD002751.

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Authors and Affiliations

  1. Department of Computer Science, University of Central Florida, Orlando, FL, USA

    Pramesh Shakya & Shaojie Zhang

  2. School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA

    Ardalan Naseri & Degui Zhi

Authors
  1. Pramesh Shakya
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  2. Ardalan Naseri
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  3. Degui Zhi
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  4. Shaojie Zhang
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Corresponding author

Correspondence to Shaojie Zhang .

Editor information

Editors and Affiliations

  1. University of Connecticut, Storrs, CT, USA

    Mukul S. Bansal

  2. University of Connecticut, Storrs, CT, USA

    Ion Măndoiu

  3. University of Connecticut Health Center, Farmington, CT, USA

    Marmar Moussa

  4. Georgia State University, Atlanta, GA, USA

    Murray Patterson

  5. University of Connecticut, Storrs, CT, USA

    Sanguthevar Rajasekaran

  6. Georgia State University, Atlanta, GA, USA

    Pavel Skums

  7. Georgia State University, Atlanta, GA, USA

    Alexander Zelikovsky

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Shakya, P., Naseri, A., Zhi, D., Zhang, S. (2022). mcPBWT: Space-Efficient Multi-column PBWT Scanning Algorithm for Composite Haplotype Matching. In: Bansal, M.S., et al. Computational Advances in Bio and Medical Sciences. ICCABS 2021. Lecture Notes in Computer Science(), vol 13254. Springer, Cham. https://doi.org/10.1007/978-3-031-17531-2_10

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  • DOI: https://doi.org/10.1007/978-3-031-17531-2_10

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-031-17530-5

  • Online ISBN: 978-3-031-17531-2

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