Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data
Telomeres are the ends of eukaryotic chromosomes, consisting of consecutive short repeats that protect chromosome ends from degradation. Telomeres shorten with each cell division, leading to replicative cell senescence. Deregulation of telomere length homeostasis is associated with the development o...
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Public Library of Science
2015
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414351/ |
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pubmed-44143512015-05-07 Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data Nersisyan, Lilit Arakelyan, Arsen Research Article Telomeres are the ends of eukaryotic chromosomes, consisting of consecutive short repeats that protect chromosome ends from degradation. Telomeres shorten with each cell division, leading to replicative cell senescence. Deregulation of telomere length homeostasis is associated with the development of various age-related diseases and cancers. A number of experimental techniques exist for telomere length measurement; however, until recently, the absence of tools for extracting telomere lengths from high-throughput sequencing data has significantly obscured the association of telomere length with molecular processes in normal and diseased conditions. We have developed Computel, a program in R for computing mean telomere length from whole-genome next-generation sequencing data. Computel is open source, and is freely available at https://github.com/lilit-nersisyan/computel. It utilizes a short-read alignment-based approach and integrates various popular tools for sequencing data analysis. We validated it with synthetic and experimental data, and compared its performance with the previously available software. The results have shown that Computel outperforms existing software in accuracy, independence of results from sequencing conditions, stability against inherent sequencing errors, and better ability to distinguish pure telomeric sequences from interstitial telomeric repeats. By providing a highly reliable methodology for determining telomere lengths from whole-genome sequencing data, Computel should help to elucidate the role of telomeres in cellular health and disease. Public Library of Science 2015-04-29 /pmc/articles/PMC4414351/ /pubmed/25923330 http://dx.doi.org/10.1371/journal.pone.0125201 Text en © 2015 Nersisyan, Arakelyan http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Nersisyan, Lilit Arakelyan, Arsen |
| spellingShingle |
Nersisyan, Lilit Arakelyan, Arsen Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data |
| author_facet |
Nersisyan, Lilit Arakelyan, Arsen |
| author_sort |
Nersisyan, Lilit |
| title |
Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data |
| title_short |
Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data |
| title_full |
Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data |
| title_fullStr |
Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data |
| title_full_unstemmed |
Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data |
| title_sort |
computel: computation of mean telomere length from whole-genome next-generation sequencing data |
| description |
Telomeres are the ends of eukaryotic chromosomes, consisting of consecutive short repeats that protect chromosome ends from degradation. Telomeres shorten with each cell division, leading to replicative cell senescence. Deregulation of telomere length homeostasis is associated with the development of various age-related diseases and cancers. A number of experimental techniques exist for telomere length measurement; however, until recently, the absence of tools for extracting telomere lengths from high-throughput sequencing data has significantly obscured the association of telomere length with molecular processes in normal and diseased conditions. We have developed Computel, a program in R for computing mean telomere length from whole-genome next-generation sequencing data. Computel is open source, and is freely available at https://github.com/lilit-nersisyan/computel. It utilizes a short-read alignment-based approach and integrates various popular tools for sequencing data analysis. We validated it with synthetic and experimental data, and compared its performance with the previously available software. The results have shown that Computel outperforms existing software in accuracy, independence of results from sequencing conditions, stability against inherent sequencing errors, and better ability to distinguish pure telomeric sequences from interstitial telomeric repeats. By providing a highly reliable methodology for determining telomere lengths from whole-genome sequencing data, Computel should help to elucidate the role of telomeres in cellular health and disease. |
| publisher |
Public Library of Science |
| publishDate |
2015 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414351/ |
| _version_ |
1613217377550336000 |