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Massively parallel sequencing of 25 autosomal STRs including SE33 in four population groups for forensic applications.
Sci Rep. 2021 02 25; 11(1):4701.SR

Abstract

The introduction of massively parallel sequencing (MPS) in forensic investigation enables sequence-based large-scale multiplexing beyond size-based analysis using capillary electrophoresis (CE). For the practical application of MPS to forensic casework, many population studies have provided sequence data for autosomal short tandem repeats (STRs). However, SE33, a highly polymorphic STR marker, has little sequence-based data because of difficulties in analysis. In this study, 25 autosomal STRs were analyzed, including SE33, using an in-house MPS panel for 350 samples from four populations (African-American, Caucasian, Hispanic, and Korean). The barcoded MPS library was generated using a two-step PCR method and sequenced using a MiSeq System. As a result, 99.88% genotype concordance was obtained between length- and sequence-based analyses. In SE33, the most discordances (eight samples, 0.08%) were observed because of the 4 bp deletion between the CE and MPS primer binding sites. Compared with the length-based CE method, the number of alleles increased from 332 to 725 (2.18-fold) for 25 autosomal STRs in the sequence-based MPS method. Notably, additional 129 unique alleles, a 4.15-fold increase, were detected in SE33 by identifying sequence variations. This population data set provides sequence variations and sequence-based allele frequencies for 25 autosomal STRs.

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Authors+Show Affiliations

Kwon YL
Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea. Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
Kim BM
Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea. Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
Lee EY
Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
Shin KJ
Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea. KJSHIN@yuhs.ac. Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea. KJSHIN@yuhs.ac.

MeSH

Electrophoresis, CapillaryForensic GeneticsGene FrequencyHigh-Throughput Nucleotide SequencingHumansMicrosatellite RepeatsPolymerase Chain ReactionPolymorphism, Single NucleotidePopulation Groups

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

33633141

Citation

Kwon, Ye-Lim, et al. "Massively Parallel Sequencing of 25 Autosomal STRs Including SE33 in Four Population Groups for Forensic Applications." Scientific Reports, vol. 11, no. 1, 2021, p. 4701.
Kwon YL, Kim BM, Lee EY, et al. Massively parallel sequencing of 25 autosomal STRs including SE33 in four population groups for forensic applications. Sci Rep. 2021;11(1):4701.
Kwon, Y. L., Kim, B. M., Lee, E. Y., & Shin, K. J. (2021). Massively parallel sequencing of 25 autosomal STRs including SE33 in four population groups for forensic applications. Scientific Reports, 11(1), 4701. https://doi.org/10.1038/s41598-021-82814-z
Kwon YL, et al. Massively Parallel Sequencing of 25 Autosomal STRs Including SE33 in Four Population Groups for Forensic Applications. Sci Rep. 2021 02 25;11(1):4701. PubMed PMID: 33633141.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Massively parallel sequencing of 25 autosomal STRs including SE33 in four population groups for forensic applications. AU - Kwon,Ye-Lim, AU - Kim,Bo Min, AU - Lee,Eun Young, AU - Shin,Kyoung-Jin, Y1 - 2021/02/25/ PY - 2020/09/04/received PY - 2021/01/25/accepted PY - 2021/2/26/entrez PY - 2021/2/27/pubmed PY - 2021/12/21/medline SP - 4701 EP - 4701 JF - Scientific reports JO - Sci Rep VL - 11 IS - 1 N2 - The introduction of massively parallel sequencing (MPS) in forensic investigation enables sequence-based large-scale multiplexing beyond size-based analysis using capillary electrophoresis (CE). For the practical application of MPS to forensic casework, many population studies have provided sequence data for autosomal short tandem repeats (STRs). However, SE33, a highly polymorphic STR marker, has little sequence-based data because of difficulties in analysis. In this study, 25 autosomal STRs were analyzed, including SE33, using an in-house MPS panel for 350 samples from four populations (African-American, Caucasian, Hispanic, and Korean). The barcoded MPS library was generated using a two-step PCR method and sequenced using a MiSeq System. As a result, 99.88% genotype concordance was obtained between length- and sequence-based analyses. In SE33, the most discordances (eight samples, 0.08%) were observed because of the 4 bp deletion between the CE and MPS primer binding sites. Compared with the length-based CE method, the number of alleles increased from 332 to 725 (2.18-fold) for 25 autosomal STRs in the sequence-based MPS method. Notably, additional 129 unique alleles, a 4.15-fold increase, were detected in SE33 by identifying sequence variations. This population data set provides sequence variations and sequence-based allele frequencies for 25 autosomal STRs. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/33633141/Massively_parallel_sequencing_of_25_autosomal_STRs_including_SE33_in_four_population_groups_for_forensic_applications_ DB - PRIME DP - Unbound Medicine ER -