Comparison of mitochondrial DNA variants detection using short- and long-read sequencing View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2019-08-13

AUTHORS

Ahmed N. Alkanaq, Kohei Hamanaka, Futoshi Sekiguchi, Masataka Taguri, Atsushi Takata, Noriko Miyake, Satoko Miyatake, Takeshi Mizuguchi, Naomichi Matsumoto

ABSTRACT

The recent advent of long-read sequencing technologies is expected to provide reasonable answers to genetic challenges unresolvable by short-read sequencing, primarily the inability to accurately study structural variations, copy number variations, and homologous repeats in complex parts of the genome. However, long-read sequencing comes along with higher rates of random short deletions and insertions, and single nucleotide errors. The relatively higher sequencing accuracy of short-read sequencing has kept it as the first choice of screening for single nucleotide variants and short deletions and insertions. Albeit, short-read sequencing still suffers from systematic errors that tend to occur at specific positions where a high depth of reads is not always capable to correct for these errors. In this study, we compared the genotyping of mitochondrial DNA variants in three samples using PacBio’s Sequel (Pacific Biosciences Inc., Menlo Park, CA, USA) long-read sequencing and illumina’s HiSeqX10 (illumine Inc., San Diego, CA, USA) short-read sequencing data. We concluded that, despite the differences in the type and frequency of errors in the long-reads sequencing, its accuracy is still comparable to that of short-reads for genotyping short nuclear variants; due to the randomness of errors in long reads, a lower coverage, around 37 reads, can be sufficient to correct for these random errors. More... »

PAGES

1107-1116

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s10038-019-0654-9

DOI

http://dx.doi.org/10.1038/s10038-019-0654-9

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1120282551

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/31409854


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