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

TitleTelomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.
Publication TypeJournal Article
Year of Publication2018
AuthorsFarmery, JHR, Smith, ML, Lynch, AG
Corporate Authors
JournalSci Rep
Volume8
Issue1
Pagination1300
Date Published2018 01 22
ISSN2045-2322
KeywordsAlgorithms, 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
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.

DOI10.1038/s41598-017-14403-y
Alternate JournalSci Rep
Citation Key10.1038/s41598-017-14403-y
PubMed ID29358629
PubMed Central IDPMC5778012
Grant List / / Wellcome Trust / United Kingdom
MR/K023489/1 / / Medical Research Council / United Kingdom
MR/L006197/1 / / Medical Research Council / United Kingdom