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.
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Acknowledgements
This work was supported by AMED under the grant numbers JP19ek0109280, JP19dm0107090, JP19ek0109301, JP19ek0109348, and JP18kk020501; JSPS KAKENHI grant numbers JP17H01539, JP16H05357, JP16H06254, JP17K10080, and JP 17K15630; the Takeda Science Foundation; and the Ichiro Kanehara Foundation for the Promotion of Medical Science and Medical Care. We also thank T. Miyama for their technical assistance.
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Alkanaq, A.N., Hamanaka, K., Sekiguchi, F. et al. Comparison of mitochondrial DNA variants detection using short- and long-read sequencing. J Hum Genet 64, 1107–1116 (2019). https://doi.org/10.1038/s10038-019-0654-9
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DOI: https://doi.org/10.1038/s10038-019-0654-9
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