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TelomereHunter – in silico estimation of telomere content and composition from cancer genomes

Feuerbach, Lars ; Sieverling, Lina ; Deeg, Katharina I. ; Ginsbach, Philip ; Hutter, Barbara ; Buchhalter, Ivo ; Northcott, Paul A. ; Mughal, Sadaf S. ; Chudasama, Priya ; Glimm, Hanno ; Scholl, Claudia ; Lichter, Peter ; Fröhling, Stefan ; Pfister, Stefan M. ; Jones, David T. W. ; Rippe, Karsten ; Brors, Benedikt

In: BMC Bioinformatics, 20 (2019), Nr. 272. pp. 1-11. ISSN 1471-2105

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Download (900kB) | Lizenz: Creative Commons LizenzvertragTelomereHunter – in silico estimation of telomere content and composition from cancer genomes by Feuerbach, Lars ; Sieverling, Lina ; Deeg, Katharina I. ; Ginsbach, Philip ; Hutter, Barbara ; Buchhalter, Ivo ; Northcott, Paul A. ; Mughal, Sadaf S. ; Chudasama, Priya ; Glimm, Hanno ; Scholl, Claudia ; Lichter, Peter ; Fröhling, Stefan ; Pfister, Stefan M. ; Jones, David T. W. ; Rippe, Karsten ; Brors, Benedikt underlies the terms of Creative Commons Attribution 4.0

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Abstract

Background: Establishment of telomere maintenance mechanisms is a universal step in tumor development to achieve replicative immortality. These processes leave molecular footprints in cancer genomes in the form of altered telomere content and aberrations in telomere composition. To retrieve these telomere characteristics from high-throughput sequencing data the available computational approaches need to be extended and optimized to fully exploit the information provided by large scale cancer genome data sets.

Results: We here present TelomereHunter, a software for the detailed characterization of telomere maintenance mechanism footprints in the genome. The tool is implemented for the analysis of large cancer genome cohorts and provides a variety of diagnostic diagrams as well as machine-readable output for subsequent analysis. A novel key feature is the extraction of singleton telomere variant repeats, which improves the identification and subclassification of the alternative lengthening of telomeres phenotype. We find that whole genome sequencing-derived telomere content estimates strongly correlate with telomere qPCR measurements (r = 0.94). For the first time, we determine the correlation of in silico telomere content quantification from whole genome sequencing and whole genome bisulfite sequencing data derived from the same tumor sample (r = 0.78). An analogous comparison of whole exome sequencing data and whole genome sequencing data measured slightly lower correlation (r = 0.79). However, this is considerably improved by normalization with matched controls (r = 0.91).

Conclusions: TelomereHunter provides new functionality for the analysis of the footprints of telomere maintenance mechanisms in cancer genomes. Besides whole genome sequencing, whole exome sequencing and whole genome bisulfite sequencing are suited for in silico telomere content quantification, especially if matched control samples are available. The software runs under a GPL license and is available at https://www.dkfz.de/en/applied-bioinformatics/telomerehunter/telomerehunter.html.

Item Type: Article
Journal or Publication Title: BMC Bioinformatics
Volume: 20
Number: 272
Publisher: BioMed Central ; Springer
Place of Publication: London ; Berlin, Heidelberg
Date Deposited: 06 Aug 2019 12:10
Date: 2019
ISSN: 1471-2105
Page Range: pp. 1-11
Faculties / Institutes: Service facilities > German Cancer Research Center (DKFZ)
Subjects: 610 Medical sciences Medicine
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