Document Open Access Logo

Finding All Maximal Perfect Haplotype Blocks in Linear Time

Authors Jarno Alanko , Hideo Bannai , Bastien Cazaux , Pierre Peterlongo , Jens Stoye

PDF

File

Thumbnail PDF
PDF
LIPIcs.WABI.2019.8.pdf
  • Filesize: 434 kB
  • 9 pages

Document Identifiers

Subject Classification

ACM Subject Classification
  • Theory of computation → Pattern matching
  • Applied computing → Bioinformatics
  • Mathematics of computing → Combinatorial algorithms
  • Applied computing → Computational genomics
Keywords
  • Population genomics
  • selection coefficient
  • haplotype block
  • positional Burrows-Wheeler Transform

Metrics

  • Access Statistics
  • Total Accesses (updated on a weekly basis)
    0
    PDF Downloads
    0
    Metadata Views

Abstract

Recent large-scale community sequencing efforts allow at an unprecedented level of detail the identification of genomic regions that show signatures of natural selection. Traditional methods for identifying such regions from individuals' haplotype data, however, require excessive computing times and therefore are not applicable to current datasets. In 2019, Cunha et al. (Proceedings of BSB 2019) suggested the maximal perfect haplotype block as a very simple combinatorial pattern, forming the basis of a new method to perform rapid genome-wide selection scans. The algorithm they presented for identifying these blocks, however, had a worst-case running time quadratic in the genome length. It was posed as an open problem whether an optimal, linear-time algorithm exists. In this paper we give two algorithms that achieve this time bound, one conceptually very simple one using suffix trees and a second one using the positional Burrows-Wheeler Transform, that is very efficient also in practice.

Cite As Get BibTex

Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, and Jens Stoye. Finding All Maximal Perfect Haplotype Blocks in Linear Time. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 8:1-8:9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019) https://doi.org/10.4230/LIPIcs.WABI.2019.8

Author Details

Jarno Alanko
  • Department of Computer Science, University of Helsinki, Finland
Hideo Bannai
  • Department of Informatics, Kyushu University, Japan
Bastien Cazaux
  • Department of Computer Science, University of Helsinki, Finland
Pierre Peterlongo
  • Univ. Rennes, Inria, CNRS, Irisa, France
Jens Stoye
  • Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Germany

Funding

  • Bannai, Hideo: JSPS KAKENHI Grant Number JP16H02783
  • Peterlongo, Pierre: ANR Hydrogen ANR-14-CE23-0001

Acknowledgements

We thank the organizers of DSB 2019 (dsb2019.gitlab.io) for giving us the opportunity to present earlier work in this area and start a discussion from which the present results originated. We would also like to thank Michel T. Henrichs for providing a script to convert VCF files to haplotype matrices and for assisting with the production of Figure 3.

References

  1. 1000 Genomes Project Consortium, Adam Auton, Lisa D Brooks, Richard M Durbin, Erik P Garrison, Hyun Min Kang, Jan O Korbel, Jonathan L Marchini, Shane McCarthy, Gil A McVean, and Gonçalo R Abecasis. A global reference for human genetic variation. Nature, 526(7571):68-74, 2015. URL: https://doi.org/10.1038/nature15393.
  2. Mohamed Ibrahim Abouelhoda, Stefan Kurtz, and Enno Ohlebusch. Replacing suffix trees with enhanced suffix arrays. Journal of Discrete Algorithms, 2(1):53-86, 2004. URL: https://doi.org/10.1016/S1570-8667(03)00065-0.
  3. Annalisa Buniello, Jacqueline A L MacArthur, Maria Cerezo, Laura W Harris, James Hayhurst, Cinzia Malangone, Aoife McMahon, Joannella Morales, Edward Mountjoy, Elliot Sollis, Daniel Suveges, Olga Vrousgou, Patricia L Whetzel, Ridwan Amode, Jose A Guillen, Harpreet S Riat, Stephen J Trevanion, Peggy Hall, Heather Junkins, Paul Flicek, Tony Burdett, Lucia A Hindorff, Fiona Cunningham, and Helen Parkinson. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Research, 47(D1):D1005–D1012, 2018. URL: https://doi.org/10.1093/nar/gky1120.
  4. Luís Cunha, Yoan Diekmann, Luis Antonio Brasil Kowada, and Jens Stoye. Identifying Maximal Perfect Haplotype Blocks. In Advances in Bioinformatics and Computational Biology - 11th Brazilian Symposium on Bioinformatics, BSB 2018, Niterói, Brazil, October 30 - November 1, 2018, Proceedings, pages 26-37, 2018. URL: https://doi.org/10.1007/978-3-030-01722-4_3.
  5. Richard Durbin. Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT). Bioinformatics, 30(9):1266-1272, 2014. URL: https://doi.org/10.1093/bioinformatics/btu014.
  6. Martin Farach. Optimal suffix tree construction with large alphabets. In Proceedings 38th Annual Symposium on Foundations of Computer Science, pages 137-143. IEEE, 1997. Google Scholar
  7. John H. Gillespie. Population Genetics - A Concise Guide. The Johns Hopkins University Press, Baltimore and London, 1998. Google Scholar
  8. Daniel F Gudbjartsson, Hannes Helgason, Sigurjon A Gudjonsson, Florian Zink, Asmundur Oddson, Arnaldur Gylfason, Søren Besenbacher, Gisli Magnusson, Bjarni V Halldorsson, Eirikur Hjartarson, Gunnar Th Sigurdsson, Simon N Stacey, Michael L Frigge, Hilma Holm, Jona Saemundsdottir, Hafdis Th Helgadottir, Hrefna Johannsdottir, Gunnlaugur Sigfusson, Gudmundur Thorgeirsson, Jon Th Sverrisson, Solveig Gretarsdottir, G Bragi Walters, Thorunn Rafnar, Bjarni Thjodleifsson, Einar S Bjornsson, Sigurdur Olafsson, Hildur Thorarinsdottir, Thora Steingrimsdottir, Thora S Gudmundsdottir, Asgeir Theodors, Jon G Jonasson, Asgeir Sigurdsson, Gyda Bjornsdottir, Jon J Jonsson, Olafur Thorarensen, Petur Ludvigsson, Hakon Gudbjartsson, Gudmundur I Eyjolfsson, Olof Sigurdardottir, Isleifur Olafsson, David O Arnar, Olafur Th Magnusson, Augustine Kong, Gisli Masson, Unnur Thorsteinsdottir, Agnar Helgason, Patrick Sulem, and Kari Stefansson. Large-scale whole-genome sequencing of the Icelandic population. Nature Genetics, 47:435-444, 2015. URL: https://doi.org/10.1038/ng.3247.
  9. Dan Gusfield. Algorithms on strings, trees, and sequences: computer science and computational biology. Cambridge University Press, Cambridge, 1997. Google Scholar
  10. Jayne Y Hehir-Kwa, Tobias Marschall, Wigard P Kloosterman, Laurent C Francioli, Jasmijn A Baaijens, Louis J Dijkstra, Abdel Abdellaoui, Vyacheslav Koval, Djie Tjwan Thung, René Wardenaar, Ivo Renkens, Bradley P Coe, Patrick Deelen, Joep de Ligt, Eric-Wubbo Lameijer, Freerk van Dijk, Fereydoun Hormozdiari, The Genome of the Netherlands Consortium, Jasper A Bovenberg, Anton J M de Craen, Marian Beekman, Albert Hofman, Gonneke Willemsen, Bruce Wolffenbuttel, Mathieu Platteel, Yuanping Du, Ruoyan Chen, Hongzhi Cao, Rui Cao, Yushen Sun, Jeremy Sujie Cao, Pieter B T Neerincx, Martijn Dijkstra, George Byelas, Alexandros Kanterakis, Jan Bot, Martijn Vermaat, Jeroen F J Laros, Johan T den Dunnen, Peter de Knijff, Lennart C Karssen, Elisa M van Leeuwen, Najaf Amin, Fernando Rivadeneira, Karol Estrada, Jouke-Jan Hottenga, V Mathijs Kattenberg, David van Enckevort, Hailiang Mei, Mark Santcroos, Barbera D C van Schaik, Robert E Handsaker, Steven A McCarroll, Arthur Ko, Peter Sudmant, Isaac J Nijman, André G Uitterlinden, Cornelia M van Duijn, Evan E Eichler, Paul I W de Bakker, Morris A Swertz, Cisca Wijmenga, Gert-Jan B van Ommen, P Eline Slagboom, Dorret I Boomsma, Alexander Schönhuth, Kai Ye, and Victor Guryev. A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nature Communications, 7:12989, 2016. URL: https://doi.org/10.1038/ncomms12989.
  11. Motoo Kimura. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics, 61(4):893, 1969. Google Scholar
  12. Peter H Sudmant, Tobias Rausch, Eugene J Gardner, Robert E Handsaker, Alexej Abyzov, John Huddleston, Yan Zhang, Kai Ye, Goo Jun, Markus Hsi-Yang Fritz, Miriam K Konkel, Ankit Malhotra, Adrian M Stütz, Xinghua Shi, Francesco Paolo Casale, Jieming Chen, Fereydoun Hormozdiari, Gargi Dayama, Ken Chen, Maika Malig, Mark J P Chaisson, Klaudia Walter, Sascha Meiers, Seva Kashin, Erik Garrison, Adam Auton, Hugo Y K Lam, Xinmeng Jasmine Mu, Can Alkan, Danny Antaki, Taejeong Bae, Eliza Cerveira, Peter Chines, Zechen Chong, Laura Clarke, Elif Dal, Li Ding, Sarah Emery, Xian Fan, Madhusudan Gujral, Fatma Kahveci, Jeffrey M Kidd, Yu Kong, Eric-Wubbo Lameijer, Shane McCarthy, Paul Flicek, Richard A Gibbs, Gabor Marth, Christopher E Mason, Androniki Menelaou, Donna M Muzny, Bradley J Nelson, Amina Noor, Nicholas F Parrish, Matthew Pendleton, Andrew Quitadamo, Benjamin Raeder, Eric E Schadt, Mallory Romanovitch, Andreas Schlattl, Robert Sebra, Andrey A Shabalin, Andreas Untergasser, Jerilyn A Walker, Min Wang, Fuli Yu, Chengsheng Zhang, Jing Zhang, Xiangqun Zheng-Bradley, Wanding Zhou, Thomas Zichner, Jonathan Sebat, Mark A Batzer, Steven A McCarroll, The 1000 Genomes Project Consortium, Ryan E Mills, Mark B Gerstein, Ali Bashir, Oliver Stegle, Scott E Devine, Charles Lee, Evan E Eichler, and Jan O Korbel. An integrated map of structural variation in 2,504 human genomes. Nature, 526(7571):75-81, 2015. URL: https://doi.org/10.1038/nature15394.
  13. Clare Turnbull, Richard H Scott, Ellen Thomas, Louise Jones, Nirupa Murugaesu, Freya Boardman Pretty, Dina Halai, Emma Baple, Clare Craig, Angela Hamblin, Shirley Henderson, Christine Patch, Amanda O'Neill, Andrew Devereau, Katherine Smith, Antonio Rueda Martin, Alona Sosinsky, Ellen M McDonagh, Razvan Sultana, Michael Mueller, Damian Smedley, Adam Toms, Lisa Dinh, Tom Fowler, Mark Bale, Tim J P Hubbard, Augusto Rendon, Sue Hill, Mark J Caulfield, and 100 000 Genomes Project. The 100 000 Genomes Project: bringing whole genome sequencing to the NHS. BMJ, 361:k1687, 2018. URL: https://doi.org/10.1136/bmj.k1687.
Questions / Remarks / Feedback
X

Feedback for Dagstuhl Publishing


Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail
© 2023-2025 Schloss Dagstuhl – LZI GmbH About DROPS Imprint Privacy Contact