Publications by authors named "Gesa Loof"

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

Bioinformatics 2021 Apr 8. Epub 2021 Apr 8.

Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany.

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@mdc-berlin.de.

Supplementary Information: Supplementary information is available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btab238DOI Listing
April 2021