TY - JOUR
T1 - Human short tandem repeat identification using a nanopore-based DNA sequencer
T2 - a pilot study
AU - Asogawa, Minoru
AU - Ohno, Ayumu
AU - Nakagawa, So
AU - Ochiai, Eriko
AU - Katahira, Yasuhiro
AU - Sudo, Megumi
AU - Osawa, Motoki
AU - Sugisawa, Masatoshi
AU - Imanishi, Tadashi
N1 - Funding Information:
Funding This research was supported in part by joint-research funds from Tokai University provided by NEC Corporation.
Funding Information:
Conflict of interest This study was a joint-research project of NEC Corporation and Tokai University, which was financially supported by NEC Corporation.
Publisher Copyright:
© 2019, The Author(s), under exclusive licence to The Japan Society of Human Genetics.
PY - 2020/1/1
Y1 - 2020/1/1
N2 - Short tandem repeats (STRs) are repetitive DNA sequences that are highly polymorphic and widely used for personal identification in the field of forensic medicine. The standard method for determining the repeat number of STRs is capillary electrophoresis of PCR products; however, the use of DNA sequencing has increased because it can identify same-sized alleles with nucleotide substitutions (iso-alleles). In this study, we performed human STR genotyping using a portable nanopore-based DNA sequencer, the MinION, and evaluated its performance. Because the sequence quality obtained by MinION is considerably lower than those obtained with other DNA sequencers, we developed an original scoring scheme for judging the genotypes from MinION reads. Analysis of seven human samples for 21–45 STR loci yielded an average of 857 thousand reads per sample, and the accuracy of genotyping and iso-allele identification reached 75.7% and 82%, respectively. Although the accuracy is higher than that reported previously, further improvements are required before this method can be practically applied.
AB - Short tandem repeats (STRs) are repetitive DNA sequences that are highly polymorphic and widely used for personal identification in the field of forensic medicine. The standard method for determining the repeat number of STRs is capillary electrophoresis of PCR products; however, the use of DNA sequencing has increased because it can identify same-sized alleles with nucleotide substitutions (iso-alleles). In this study, we performed human STR genotyping using a portable nanopore-based DNA sequencer, the MinION, and evaluated its performance. Because the sequence quality obtained by MinION is considerably lower than those obtained with other DNA sequencers, we developed an original scoring scheme for judging the genotypes from MinION reads. Analysis of seven human samples for 21–45 STR loci yielded an average of 857 thousand reads per sample, and the accuracy of genotyping and iso-allele identification reached 75.7% and 82%, respectively. Although the accuracy is higher than that reported previously, further improvements are required before this method can be practically applied.
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U2 - 10.1038/s10038-019-0688-z
DO - 10.1038/s10038-019-0688-z
M3 - Review article
C2 - 31649301
AN - SCOPUS:85074796037
SN - 1434-5161
VL - 65
SP - 21
EP - 24
JO - Jinrui idengaku zasshi. The Japanese journal of human genetics
JF - Jinrui idengaku zasshi. The Japanese journal of human genetics
IS - 1
ER -
