Markowski, Julia and Kempfer, Rieke and Kukalev, Alexander and Irastorza-Azcarate, Ibai and Loof, Gesa and Kehr, Birte and Pombo, Ana and Rahmann, Sven and Schwarz, Roland F. (2021) GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data. BIOINFORMATICS, 37 (19). pp. 3128-3135. ISSN 1367-4803, 1460-2059
Full text not available from this repository. (Request a copy)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 optimize 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.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | CHROMOSOME; |
| Subjects: | 600 Technology > 610 Medical sciences Medicine |
| Divisions: | Medicine > Zentren des Universitätsklinikums Regensburg > Regensburger Centrum für Interventionelle Immunologie (RCI) |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 13 Sep 2022 08:22 |
| Last Modified: | 13 Sep 2022 08:22 |
| URI: | https://pred.uni-regensburg.de/id/eprint/47280 |
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