期刊
BRIEFINGS IN BIOINFORMATICS
卷 21, 期 6, 页码 1971-1986出版社
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbz099
关键词
trinucleotide repeat disorders; Oxford Nanopore Technologies; Pacific Bioscience SMRT sequencing; long-read sequencing; single-molecule sequencing
资金
- Italian Ministero dell' Istruzione, Universita e Ricerca: PRIN 2017, Consiglio Nazionale delle Ricerche: Flagship Projects Epigen and Interomics
- H2020 Project ELIXIR-EXCELERATE
- Elixir-IIB
A number of studies have reported the successful application of single-molecule sequencing technologies to the determination of the size and sequence of pathological expanded microsatellite repeats over the last 5 years. However, different custom bioinformatics pipelines were employed in each study, preventing meaningful comparisons and somewhat limiting the reproducibility of the results. In this review, we provide a brief summary of state-of-the-art methods for the characterization of expanded repeats alleles, along with a detailed comparison of bioinformatics tools for the determination of repeat length and sequence, using both real and simulated data. Our reanalysis of publicly available human genome sequencing data suggests a modest, but statistically significant, increase of the error rate of single-molecule sequencing technologies at genomic regions containing short tandem repeats. However, we observe that all the methods herein tested, irrespective of the strategy used for the analysis of the data (either based on the alignment or assembly of the reads), show high levels of sensitivity in both the detection of expanded tandem repeats and the estimation of the expansion size, suggesting that approaches based on single-molecule sequencing technologies are highly effective for the detection and quantification of tandem repeat expansions and contractions.
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