Your browser doesn't support javascript.
loading
Telogator: a method for reporting chromosome-specific telomere lengths from long reads.
Stephens, Zachary; Ferrer, Alejandro; Boardman, Lisa; Iyer, Ravishankar K; Kocher, Jean-Pierre A.
Afiliação
  • Stephens Z; Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
  • Ferrer A; Division of Hematology, Mayo Clinic, Rochester, MN 55902, USA.
  • Boardman L; Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55902, USA.
  • Iyer RK; Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
  • Kocher JA; Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55902, USA.
Bioinformatics ; 38(7): 1788-1793, 2022 03 28.
Article em En | MEDLINE | ID: mdl-35022670
MOTIVATION: Telomeres are the repetitive sequences found at the ends of eukaryotic chromosomes and are often thought of as a 'biological clock,' with their average length shortening during division in most cells. In addition to their association with senescence, abnormal telomere lengths are well known to be associated with multiple cancers, short telomere syndromes and as risk factors for a broad range of diseases. While a majority of methods for measuring telomere length will report average lengths across all chromosomes, it is known that aberrations in specific chromosome arms are biomarkers for certain diseases. Due to their repetitive nature, characterizing telomeres at this resolution is prohibitive for short read sequencing approaches, and is challenging still even with longer reads. RESULTS: We present Telogator: a method for reporting chromosome-specific telomere length from long read sequencing data. We demonstrate Telogator's sensitivity in detecting chromosome-specific telomere length in simulated data across a range of read lengths and error rates. Telogator is then applied to 10 germline samples, yielding a high correlation with short read methods in reporting average telomere length. In addition, we investigate common subtelomere rearrangements and identify the minimum read length required to anchor telomere/subtelomere boundaries in samples with these haplotypes. AVAILABILITY AND IMPLEMENTATION: Telogator is written in Python3 and is available at github.com/zstephens/telogator. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Sequências Repetitivas de Ácido Nucleico / Telômero Tipo de estudo: Prognostic_studies / Risk_factors_studies Idioma: En Revista: Bioinformatics Assunto da revista: INFORMATICA MEDICA Ano de publicação: 2022 Tipo de documento: Article País de afiliação: Estados Unidos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Sequências Repetitivas de Ácido Nucleico / Telômero Tipo de estudo: Prognostic_studies / Risk_factors_studies Idioma: En Revista: Bioinformatics Assunto da revista: INFORMATICA MEDICA Ano de publicação: 2022 Tipo de documento: Article País de afiliação: Estados Unidos