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ACEseq – allele specific copy number estimation from whole genome sequencing
Kortine Kleinheinz, Isabell Bludau, Daniel Hübschmann, Michael Heinold, Philip Kensche, Zuguang Gu, Cristina López, Michael Hummel, Wolfram Klapper, Peter Möller, Inga Vater, Rabea Wagener, ICGC MMML-Seq project, Benedikt Brors, Reiner Siebert, Roland Eils, Matthias Schlesner
doi: https://doi.org/10.1101/210807
Kortine Kleinheinz
1Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Germany
2Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
Isabell Bludau
2Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
3Present address: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
Daniel Hübschmann
1Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Germany
2Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
4Department of Pediatric Immunology, Hematology and Oncology, University Hospital Heidelberg, Germany
Michael Heinold
1Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Germany
2Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
Philip Kensche
2Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
Zuguang Gu
2Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
5Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany.
Cristina López
6Institute of Human Genetics, University of Ulm and University Hospital of Ulm, Ulm, Germany
Michael Hummel
7Institute of Pathology, Charité - University Medicine Berlin, Berlin, Germany.
Wolfram Klapper
8Pathology, Haematopathology Section and Lymph Node Registry, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
Peter Möller
9Institute of Pathology, University of Ulm and University Hospital of Ulm, Ulm, Ulm, Germany.
Inga Vater
10Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
Rabea Wagener
6Institute of Human Genetics, University of Ulm and University Hospital of Ulm, Ulm, Germany
Benedikt Brors
11Division of Applied Bioinformatics (G200), German Cancer Research Center (DKFZ), Heidelberg, Germany.
Reiner Siebert
6Institute of Human Genetics, University of Ulm and University Hospital of Ulm, Ulm, Germany
Roland Eils
1Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Germany
2Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
5Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany.
Matthias Schlesner
2Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
12Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany
Abstract
ACEseq is a computational tool for allele-specific copy number estimation in tumor genomes based on whole genome sequencing. In contrast to other tools it features GC-bias correction, unique replication timing-bias correction and integration of structural variant (SV) breakpoints for improved genome segmentation. ACEseq clearly outperforms widely used state-of-the art methods, provides a fully automated estimation of tumor cell content and ploidy, and additionally computes homologous recombination deficiency scores.
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 4.0 International license.
Posted October 29, 2017.
ACEseq – allele specific copy number estimation from whole genome sequencing
Kortine Kleinheinz, Isabell Bludau, Daniel Hübschmann, Michael Heinold, Philip Kensche, Zuguang Gu, Cristina López, Michael Hummel, Wolfram Klapper, Peter Möller, Inga Vater, Rabea Wagener, ICGC MMML-Seq project, Benedikt Brors, Reiner Siebert, Roland Eils, Matthias Schlesner
bioRxiv 210807; doi: https://doi.org/10.1101/210807
ACEseq – allele specific copy number estimation from whole genome sequencing
Kortine Kleinheinz, Isabell Bludau, Daniel Hübschmann, Michael Heinold, Philip Kensche, Zuguang Gu, Cristina López, Michael Hummel, Wolfram Klapper, Peter Möller, Inga Vater, Rabea Wagener, ICGC MMML-Seq project, Benedikt Brors, Reiner Siebert, Roland Eils, Matthias Schlesner
bioRxiv 210807; doi: https://doi.org/10.1101/210807
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