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Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Farmery, JHR; Smith, ML; NIHR BioResource - Rare Diseases; Lynch, AG (2018) Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data. Sci Rep, 8 (1). p. 1300. ISSN 2045-2322 https://doi.org/10.1038/s41598-017-14403-y
SGUL Authors: Southgate, Laura

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Abstract

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype.

Item Type: Article
Additional Information: Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. © The Author(s) 2018
Keywords: Algorithms, Carcinoma, Hepatocellular, Gene Expression, Genotype, Humans, Induced Pluripotent Stem Cells, Liver Neoplasms, Mesenchymal Stem Cells, Ploidies, Primary Cell Culture, Telomerase, Telomere, Telomere Homeostasis, Whole Genome Sequencing, NIHR BioResource - Rare Diseases, Telomere, Humans, Carcinoma, Hepatocellular, Liver Neoplasms, Telomerase, Gene Expression, Genotype, Ploidies, Algorithms, Induced Pluripotent Stem Cells, Primary Cell Culture, Mesenchymal Stromal Cells, Telomere Homeostasis, Whole Genome Sequencing
SGUL Research Institute / Research Centre: Academic Structure > Molecular and Clinical Sciences Research Institute (MCS)
Journal or Publication Title: Sci Rep
ISSN: 2045-2322
Language: eng
Dates:
DateEvent
22 January 2018Published
22 September 2017Accepted
Publisher License: Creative Commons: Attribution 4.0
Projects:
Project IDFunderFunder ID
UNSPECIFIEDWellcome Trusthttp://dx.doi.org/10.13039/100004440
MR/K023489/1Medical Research Councilhttp://dx.doi.org/10.13039/501100000265
MR/L006197/1Medical Research Councilhttp://dx.doi.org/10.13039/501100000265
C14303/A17197Cancer Research UKhttp://dx.doi.org/10.13039/501100000289
305626Seventh Framework Programmehttp://dx.doi.org/10.13039/501100004963
633974Horizon 2020UNSPECIFIED
PubMed ID: 29358629
Go to PubMed abstract
URI: https://openaccess.sgul.ac.uk/id/eprint/110461
Publisher's version: https://doi.org/10.1038/s41598-017-14403-y

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