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GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data

View ORCID ProfileJulia Markowski, View ORCID ProfileRieke Kempfer, View ORCID ProfileAlexander Kukalev, View ORCID ProfileIbai Irastorza-Azcarate, View ORCID ProfileGesa Loof, Birte Kehr, View ORCID ProfileAna Pombo, View ORCID ProfileSven Rahmann, View ORCID ProfileRoland F Schwarz
doi: https://doi.org/10.1101/2020.01.30.927061
Julia Markowski
1Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany
2Department of Biology, Humboldt University of Berlin, Unter den Linden 6, 10099 Berlin, Germany
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Rieke Kempfer
1Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany
2Department of Biology, Humboldt University of Berlin, Unter den Linden 6, 10099 Berlin, Germany
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Alexander Kukalev
1Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany
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Ibai Irastorza-Azcarate
1Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany
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Gesa Loof
1Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany
2Department of Biology, Humboldt University of Berlin, Unter den Linden 6, 10099 Berlin, Germany
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Birte Kehr
3Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany
4Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
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Ana Pombo
1Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany
2Department of Biology, Humboldt University of Berlin, Unter den Linden 6, 10099 Berlin, Germany
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Sven Rahmann
5Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
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Roland F Schwarz
1Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany
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  • For correspondence: roland.schwarz@mdc-berlin.de
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Abstract

Motivation Genome Architecture Mapping (GAM) was recently introduced as a digestion- and ligation-free method to detect chromatin conformation. Orthogonal to existing approaches based on chromatin conformation capture (3C), GAM’s ability to capture both inter- and intra-chromosomal contacts from low amounts of input data makes it particularly well suited for allele-specific analyses in a clinical setting. Allele-specific analyses are powerful tools to investigate the effects of genetic variants on many cellular phenotypes including chromatin conformation, but require the haplotypes of the individuals under study to be known a-priori. So far however, no algorithm exists for haplotype reconstruction and phasing of genetic variants from GAM data, hindering the allele-specific analysis of chromatin contact points in non-model organisms or individuals with unknown haplotypes.

Results We present GAMIBHEAR, a tool for accurate haplotype reconstruction from GAM data. GAMIBHEAR aggregates allelic co-observation frequencies from GAM data and employs a GAM-specific probabilistic model of haplotype capture to optimise phasing accuracy. Using a hybrid mouse embryonic stem cell line with known haplotype structure as a benchmark dataset, we assess correctness and completeness of the reconstructed haplotypes, and demonstrate the power of GAMIBHEAR to infer accurate genome-wide haplotypes from GAM data.

Availability GAMIBHEAR is available as an R package under the open source GPL-2 license at https://bitbucket.org/schwarzlab/gamibhear

Maintainer: julia.markowski{at}mdc-berlin.de

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 21, 2021.
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GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data
Julia Markowski, Rieke Kempfer, Alexander Kukalev, Ibai Irastorza-Azcarate, Gesa Loof, Birte Kehr, Ana Pombo, Sven Rahmann, Roland F Schwarz
bioRxiv 2020.01.30.927061; doi: https://doi.org/10.1101/2020.01.30.927061
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GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data
Julia Markowski, Rieke Kempfer, Alexander Kukalev, Ibai Irastorza-Azcarate, Gesa Loof, Birte Kehr, Ana Pombo, Sven Rahmann, Roland F Schwarz
bioRxiv 2020.01.30.927061; doi: https://doi.org/10.1101/2020.01.30.927061

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