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Sequence Variations of 31 Υ-Chromosomal Short Tandem Repeats Analyzed by Massively Parallel Sequencing in Three U.S. Population Groups and Korean Population.
J Korean Med Sci. 2022 Feb 14; 37(6):e40.JK

Abstract

BACKGROUND

Rapidly mutating (RM) Y-chromosomal short tandem repeats (Y-STRs) have been demonstrated to increase the possibility of distinguishing between male relatives due to a higher mutation rate than conventional Y-STRs. Massively parallel sequencing (MPS) can be useful for forensic DNA typing as it allows the detection of sequence variants of many forensic markers. Here, we present sequence variations of 31 Y-STRs including nine RM Y-STRs (DYF387S1, DYF399S1, DYF404S1, DYS449, DYS518, DYS570, DYS576, DYS612, and DYS627), their frequencies, distribution, and the gain in the number of alleles using MPS.

METHODS

We constructed a multiplex MPS assay capable of simultaneously amplifying 32 Y-chromosomal markers, producing amplicons ranging from 85-274 bp. Barcoded libraries from 220 unrelated males from four populations-African Americans, Caucasians, Hispanics, and Koreans-were generated via two-step polymerase chain reaction and sequenced on a MiSeq system. Genotype concordance between the capillary electrophoresis (CE) and MPS method and sequence variation of Y-STRs were investigated.

RESULTS

In total, 195 alleles were increased by MPS compared to CE-based alleles (261 to 456). The DYS518 marker showed the largest increase due to repeat region variation (a 3.69-fold increase). The highest increase in the number of alleles due to single nucleotide polymorphisms in the flanking region was found in DYF399S1. RM Y-STRs had more diverse sequences than conventional Y-STRs. Furthermore, null alleles were observed in DYS576 due to primer-binding site mutation, and allele drop-outs in DYS449 resulted from low marker coverage of less than the threshold.

CONCLUSION

The results suggest that the expanded and discriminative MPS assay could provide more genetic information for Y-STRs, especially for RM Y-STRs, and could advance male individualization. Compiling sequence-based Y-STR data for worldwide populations would facilitate the application of MPS in the field of forensic genetics and could be applicable in solving male-related forensic cases.

Authors+Show Affiliations

Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea. Graduate School of Medical Science and Brain Korea 21 Project, Yonsei University, Seoul, Korea.Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea.Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea. Graduate School of Medical Science and Brain Korea 21 Project, Yonsei University, Seoul, Korea. kjshin@yuhs.ac.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

35166077

Citation

Moon, Mi Hyeon, et al. "Sequence Variations of 31 Υ-Chromosomal Short Tandem Repeats Analyzed By Massively Parallel Sequencing in Three U.S. Population Groups and Korean Population." Journal of Korean Medical Science, vol. 37, no. 6, 2022, pp. e40.
Moon MH, Hong SR, Shin KJ. Sequence Variations of 31 Υ-Chromosomal Short Tandem Repeats Analyzed by Massively Parallel Sequencing in Three U.S. Population Groups and Korean Population. J Korean Med Sci. 2022;37(6):e40.
Moon, M. H., Hong, S. R., & Shin, K. J. (2022). Sequence Variations of 31 Υ-Chromosomal Short Tandem Repeats Analyzed by Massively Parallel Sequencing in Three U.S. Population Groups and Korean Population. Journal of Korean Medical Science, 37(6), e40. https://doi.org/10.3346/jkms.2022.37.e40
Moon MH, Hong SR, Shin KJ. Sequence Variations of 31 Υ-Chromosomal Short Tandem Repeats Analyzed By Massively Parallel Sequencing in Three U.S. Population Groups and Korean Population. J Korean Med Sci. 2022 Feb 14;37(6):e40. PubMed PMID: 35166077.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Sequence Variations of 31 Υ-Chromosomal Short Tandem Repeats Analyzed by Massively Parallel Sequencing in Three U.S. Population Groups and Korean Population. AU - Moon,Mi Hyeon, AU - Hong,Sae Rom, AU - Shin,Kyoung-Jin, Y1 - 2022/02/14/ PY - 2021/10/26/received PY - 2021/12/19/accepted PY - 2022/2/15/entrez PY - 2022/2/16/pubmed PY - 2022/3/22/medline KW - Massively Parallel Sequencing KW - RM Y-STR KW - Sequence Variation KW - Y-STR SP - e40 EP - e40 JF - Journal of Korean medical science JO - J Korean Med Sci VL - 37 IS - 6 N2 - BACKGROUND: Rapidly mutating (RM) Y-chromosomal short tandem repeats (Y-STRs) have been demonstrated to increase the possibility of distinguishing between male relatives due to a higher mutation rate than conventional Y-STRs. Massively parallel sequencing (MPS) can be useful for forensic DNA typing as it allows the detection of sequence variants of many forensic markers. Here, we present sequence variations of 31 Y-STRs including nine RM Y-STRs (DYF387S1, DYF399S1, DYF404S1, DYS449, DYS518, DYS570, DYS576, DYS612, and DYS627), their frequencies, distribution, and the gain in the number of alleles using MPS. METHODS: We constructed a multiplex MPS assay capable of simultaneously amplifying 32 Y-chromosomal markers, producing amplicons ranging from 85-274 bp. Barcoded libraries from 220 unrelated males from four populations-African Americans, Caucasians, Hispanics, and Koreans-were generated via two-step polymerase chain reaction and sequenced on a MiSeq system. Genotype concordance between the capillary electrophoresis (CE) and MPS method and sequence variation of Y-STRs were investigated. RESULTS: In total, 195 alleles were increased by MPS compared to CE-based alleles (261 to 456). The DYS518 marker showed the largest increase due to repeat region variation (a 3.69-fold increase). The highest increase in the number of alleles due to single nucleotide polymorphisms in the flanking region was found in DYF399S1. RM Y-STRs had more diverse sequences than conventional Y-STRs. Furthermore, null alleles were observed in DYS576 due to primer-binding site mutation, and allele drop-outs in DYS449 resulted from low marker coverage of less than the threshold. CONCLUSION: The results suggest that the expanded and discriminative MPS assay could provide more genetic information for Y-STRs, especially for RM Y-STRs, and could advance male individualization. Compiling sequence-based Y-STR data for worldwide populations would facilitate the application of MPS in the field of forensic genetics and could be applicable in solving male-related forensic cases. SN - 1598-6357 UR - https://www.unboundmedicine.com/medline/citation/35166077/Sequence_Variations_of_31_Υ_Chromosomal_Short_Tandem_Repeats_Analyzed_by_Massively_Parallel_Sequencing_in_Three_U_S__Population_Groups_and_Korean_Population_ DB - PRIME DP - Unbound Medicine ER -