Tags

Type your tag names separated by a space and hit enter

Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons.
Forensic Sci Int Genet. 2016 May; 22:1-7.FS

Abstract

The next-generation sequencing (NGS) method has been utilized to analyze short tandem repeat (STR) markers, which are routinely used for human identification purposes in the forensic field. Some researchers have demonstrated the successful application of the NGS system to STR typing, suggesting that NGS technology may be an alternative or additional method to overcome limitations of capillary electrophoresis (CE)-based STR profiling. However, there has been no available multiplex PCR system that is optimized for NGS analysis of forensic STR markers. Thus, we constructed a multiplex PCR system for the NGS analysis of 18 markers (13CODIS STRs, D2S1338, D19S433, Penta D, Penta E and amelogenin) by designing amplicons in the size range of 77-210 base pairs. Then, PCR products were generated from two single-sources, mixed samples and artificially degraded DNA samples using a multiplex PCR system, and were prepared for sequencing on the MiSeq system through construction of a subsequent barcoded library. By performing NGS and analyzing the data, we confirmed that the resultant STR genotypes were consistent with those of CE-based typing. Moreover, sequence variations were detected in targeted STR regions. Through the use of small-sized amplicons, the developed multiplex PCR system enables researchers to obtain successful STR profiles even from artificially degraded DNA as well as STR loci which are analyzed with large-sized amplicons in the CE-based commercial kits. In addition, successful profiles can be obtained from mixtures up to a 1:19 ratio. Consequently, the developed multiplex PCR system, which produces small size amplicons, can be successfully applied to STR NGS analysis of forensic casework samples such as mixtures and degraded DNA samples.

Authors+Show Affiliations

Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea; Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea.Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea.Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea.Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea.Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea.Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea; Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea. Electronic address: kjshin@yuhs.ac.

Pub Type(s)

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

Language

eng

PubMed ID

26799314

Citation

Kim, Eun Hye, et al. "Massively Parallel Sequencing of 17 Commonly Used Forensic Autosomal STRs and Amelogenin With Small Amplicons." Forensic Science International. Genetics, vol. 22, 2016, pp. 1-7.
Kim EH, Lee HY, Yang IS, et al. Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons. Forensic Sci Int Genet. 2016;22:1-7.
Kim, E. H., Lee, H. Y., Yang, I. S., Jung, S. E., Yang, W. I., & Shin, K. J. (2016). Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons. Forensic Science International. Genetics, 22, 1-7. https://doi.org/10.1016/j.fsigen.2016.01.001
Kim EH, et al. Massively Parallel Sequencing of 17 Commonly Used Forensic Autosomal STRs and Amelogenin With Small Amplicons. Forensic Sci Int Genet. 2016;22:1-7. PubMed PMID: 26799314.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons. AU - Kim,Eun Hye, AU - Lee,Hwan Young, AU - Yang,In Seok, AU - Jung,Sang-Eun, AU - Yang,Woo Ick, AU - Shin,Kyoung-Jin, Y1 - 2016/01/08/ PY - 2015/03/06/received PY - 2015/12/09/revised PY - 2016/01/05/accepted PY - 2016/1/23/entrez PY - 2016/1/23/pubmed PY - 2017/1/28/medline KW - Autosomal STR KW - Degraded DNA KW - Mixture KW - Next-generation sequencing KW - Sequence variation KW - Small-sized amplicon SP - 1 EP - 7 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 22 N2 - The next-generation sequencing (NGS) method has been utilized to analyze short tandem repeat (STR) markers, which are routinely used for human identification purposes in the forensic field. Some researchers have demonstrated the successful application of the NGS system to STR typing, suggesting that NGS technology may be an alternative or additional method to overcome limitations of capillary electrophoresis (CE)-based STR profiling. However, there has been no available multiplex PCR system that is optimized for NGS analysis of forensic STR markers. Thus, we constructed a multiplex PCR system for the NGS analysis of 18 markers (13CODIS STRs, D2S1338, D19S433, Penta D, Penta E and amelogenin) by designing amplicons in the size range of 77-210 base pairs. Then, PCR products were generated from two single-sources, mixed samples and artificially degraded DNA samples using a multiplex PCR system, and were prepared for sequencing on the MiSeq system through construction of a subsequent barcoded library. By performing NGS and analyzing the data, we confirmed that the resultant STR genotypes were consistent with those of CE-based typing. Moreover, sequence variations were detected in targeted STR regions. Through the use of small-sized amplicons, the developed multiplex PCR system enables researchers to obtain successful STR profiles even from artificially degraded DNA as well as STR loci which are analyzed with large-sized amplicons in the CE-based commercial kits. In addition, successful profiles can be obtained from mixtures up to a 1:19 ratio. Consequently, the developed multiplex PCR system, which produces small size amplicons, can be successfully applied to STR NGS analysis of forensic casework samples such as mixtures and degraded DNA samples. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/26799314/Massively_parallel_sequencing_of_17_commonly_used_forensic_autosomal_STRs_and_amelogenin_with_small_amplicons_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(16)30001-1 DB - PRIME DP - Unbound Medicine ER -