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Fine-Scale Recombination Mapping of High-Throughput Sequence Data

Authors:

Catherine E. Welsh,

Fernando Pardo-Manuel de Villena,

Leonard McMillanAuthors Info & Claims

BCB'13: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics

Pages 585 - 594

https://doi.org/10.1145/2506583.2506642

Published: 22 September 2013 Publication History

Abstract

In this paper, we contrast the resolution and accuracy of determining recombination boundaries using genotyping arrays compared to high-throughput sequencing. In addition, we consider the impacts of sequence coverage and genetic diversity on localizing recombination boundaries. We developed a hidden Markov model for estimating recombination breakpoints based on variant observations seen in the read coverage spanning uniformly sized genomic windows. Our model includes 36 states representing all combinations of 8 genomes, and estimates a founder mosaic that is consistent with the variants observed in the aligned sequences. At HMM transition locations we consider the most likely founder-pair and refine the recombination breakpoints down to an interval spanning two informative variants. We compare this solution to alternate solutions based on microarrays that we have estimated. At 30x coverage the recombination mapping accuracy far exceeds the resolution attainable by any microarray. Even at coverages of 1x and below we are generally able to estimate recombination breakpoints with comparable accuracy.

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Cited By

Fu Cde Villena FMcMillan LBaldi PWang W(2014)Quantitative trait loci mapping with microarray marker intensitiesProceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/2649387.2649432(472-478)Online publication date: 20-Sep-2014
https://dl.acm.org/doi/10.1145/2649387.2649432
Kao CFu CMcMillan LBaldi PWang W(2014)InstantGenotypeProceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/2649387.2649422(147-154)Online publication date: 20-Sep-2014
https://dl.acm.org/doi/10.1145/2649387.2649422

Index Terms

Fine-Scale Recombination Mapping of High-Throughput Sequence Data
1. Applied computing
  1. Life and medical sciences

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cover image ACM Conferences

BCB'13: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics

September 2013

987 pages

ISBN:9781450324342

DOI:10.1145/2506583

Copyright © 2013 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 22 September 2013

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BCB'13

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SIGBio

BCB'13: ACM-BCB2013

September 22 - 25, 2013

Wshington DC, USA

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BCB'13 Paper Acceptance Rate 43 of 148 submissions, 29%;

Overall Acceptance Rate 254 of 885 submissions, 29%

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Cited By

Fu Cde Villena FMcMillan LBaldi PWang W(2014)Quantitative trait loci mapping with microarray marker intensitiesProceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/2649387.2649432(472-478)Online publication date: 20-Sep-2014
https://dl.acm.org/doi/10.1145/2649387.2649432
Kao CFu CMcMillan LBaldi PWang W(2014)InstantGenotypeProceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/2649387.2649422(147-154)Online publication date: 20-Sep-2014
https://dl.acm.org/doi/10.1145/2649387.2649422

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