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Computel: computation of mean telomere length from whole-genome next-generation sequencing data.

Nersisyan L, Arakelyan A - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Group of Bioinformatics of the Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia.

ABSTRACT
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.

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Related in: MedlinePlus

Mean telomere length estimates for osteosarcoma and matched normal tissues by qPCR, Computel and TelSeq.SJOS002_D, SJOS004_D—osteosarcoma tissue samples; SJOS002_N, SJOS004_N—paired healthy tissue samples.
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pone.0125201.g004: Mean telomere length estimates for osteosarcoma and matched normal tissues by qPCR, Computel and TelSeq.SJOS002_D, SJOS004_D—osteosarcoma tissue samples; SJOS002_N, SJOS004_N—paired healthy tissue samples.

Mentions: Next we used Computel to estimate telomere lengths for two osteosarcoma samples (SJOS002 and SJOS004) and compared the estimates with absolute qPCR and mTRF values [21]. Computel length estimates were partially consistent with TelSeq estimates and qPCR results, with some differences for each technique (Fig 4). In two out of the four cases, Computel estimates were closer to qPCR values than TelSeq estimates, with TelSeq estimates being closer in the other two cases.


Computel: computation of mean telomere length from whole-genome next-generation sequencing data.

Nersisyan L, Arakelyan A - PLoS ONE (2015)

Mean telomere length estimates for osteosarcoma and matched normal tissues by qPCR, Computel and TelSeq.SJOS002_D, SJOS004_D—osteosarcoma tissue samples; SJOS002_N, SJOS004_N—paired healthy tissue samples.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4414351&req=5

pone.0125201.g004: Mean telomere length estimates for osteosarcoma and matched normal tissues by qPCR, Computel and TelSeq.SJOS002_D, SJOS004_D—osteosarcoma tissue samples; SJOS002_N, SJOS004_N—paired healthy tissue samples.
Mentions: Next we used Computel to estimate telomere lengths for two osteosarcoma samples (SJOS002 and SJOS004) and compared the estimates with absolute qPCR and mTRF values [21]. Computel length estimates were partially consistent with TelSeq estimates and qPCR results, with some differences for each technique (Fig 4). In two out of the four cases, Computel estimates were closer to qPCR values than TelSeq estimates, with TelSeq estimates being closer in the other two cases.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Group of Bioinformatics of the Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus