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A novel forensic panel of 186-plex SNPs and 123-plex STR loci based on massively parallel sequencing.
Int J Legal Med. 2021 May; 135(3):709-718.IJ

Abstract

The MiSeq® FGX Forensic system and the HID-Ion AmpliSeq Panel were previously developed for massively parallel sequencing (MPS) for forensic casework. Among the three major sequencing platforms, BGISEQ-500TM, which is based on multiple PCRs, is still lacking in forensics. Here, a novel forensic panel was constructed to detect 186 single-nucleotide polymorphisms (SNPs) and 123 short tandem repeats (STRs) with MPS technology on the BGISEQ-500™ platform. First, the library preparation, sequencing process, and data analysis were performed, focusing on the average depth of coverage and heterozygote balance. We calculated the allelic frequencies and forensic parameters of STR and SNP loci in 73 unrelated Chinese Han individuals. In addition, performance was evaluated with accuracy, uniformity, sensitivity, PCR inhibitor, repeatability and reproducibility, mixtures, degraded samples, case-type samples, and pedigree analyses. The results showed that 100% accurate and concordant genotypes can be obtained, and the loci with an abundance in the interquartile range accounted for 92.90% of the total, suggesting reliable uniformity in this panel. We obtained a locus detection rate that was higher than 98.78% from 78 pg of input DNA, and the optimal amount was 1.25-10 ng. The maximum concentrations of hematin and humic acid were 200 and 100 μM, respectively (the ratios of detected loci were 96.52% and 92.41%), in this panel. As a mixture, compared with those of SNPs, minor-contributor alleles of STRs could be detected at higher levels. For the degraded sample, the ratio of detected loci was 98.41%, and most profiles from case-type samples were not significantly different in abundance in our studies. As a whole, this panel showed high-performance, reliable, robust, repeatable, and reproducible results, which are sufficient for paternity testing, individual identification, and use for potentially degraded samples in forensic science.

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Publisher Full Text (DOI)

Authors+Show Affiliations

Miao X
College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.
Shen Y
School of Life Science, Northwest A&F University, Yangling, People's Republic of China.
Gong X
College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China. School of Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.
Yu H
School of Life Science, Northwest A&F University, Yangling, People's Republic of China.
Li B
School of Life Science, Sichuan University, Chengdu, People's Republic of China.
Chang L
College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.
Wang Y
College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.
Fan J
College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.
Liang Z
Forensic Genomics International, The Beijing Genomics Institute (BGI), Shenzhen, People's Republic of China.
Tan B
School of Computer Science, City University of Hong Kong, Hong Kong, People's Republic of China.
Li S
College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.
Zhang B
College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China. zhangbao_814@mail.xjtu.edu.cn.

MeSH

AdultAsian PeopleChildFemaleHigh-Throughput Nucleotide SequencingHumansMaleMicrosatellite RepeatsMultiplex Polymerase Chain ReactionPolymorphism, Single NucleotidePregnancyReproducibility of ResultsSequence Analysis, DNA

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32851473

Citation

Miao, Xinyao, et al. "A Novel Forensic Panel of 186-plex SNPs and 123-plex STR Loci Based On Massively Parallel Sequencing." International Journal of Legal Medicine, vol. 135, no. 3, 2021, pp. 709-718.
Miao X, Shen Y, Gong X, et al. A novel forensic panel of 186-plex SNPs and 123-plex STR loci based on massively parallel sequencing. Int J Legal Med. 2021;135(3):709-718.
Miao, X., Shen, Y., Gong, X., Yu, H., Li, B., Chang, L., Wang, Y., Fan, J., Liang, Z., Tan, B., Li, S., & Zhang, B. (2021). A novel forensic panel of 186-plex SNPs and 123-plex STR loci based on massively parallel sequencing. International Journal of Legal Medicine, 135(3), 709-718. https://doi.org/10.1007/s00414-020-02403-z
Miao X, et al. A Novel Forensic Panel of 186-plex SNPs and 123-plex STR Loci Based On Massively Parallel Sequencing. Int J Legal Med. 2021;135(3):709-718. PubMed PMID: 32851473.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A novel forensic panel of 186-plex SNPs and 123-plex STR loci based on massively parallel sequencing. AU - Miao,Xinyao, AU - Shen,Yuesheng, AU - Gong,Xiaojuan, AU - Yu,Huiyun, AU - Li,Bowen, AU - Chang,Liao, AU - Wang,Yinan, AU - Fan,Jingna, AU - Liang,Zuhuan, AU - Tan,Bowen, AU - Li,Shengbin, AU - Zhang,Bao, Y1 - 2020/08/26/ PY - 2020/5/11/received PY - 2020/8/21/accepted PY - 2020/8/28/pubmed PY - 2021/6/29/medline PY - 2020/8/28/entrez KW - Forensic genomics system KW - Massively parallel sequencing (MPS) KW - Multiplex PCR KW - Short tandem repeat (STR) KW - Single-nucleotide polymorphism (SNP) SP - 709 EP - 718 JF - International journal of legal medicine JO - Int J Legal Med VL - 135 IS - 3 N2 - The MiSeq® FGX Forensic system and the HID-Ion AmpliSeq Panel were previously developed for massively parallel sequencing (MPS) for forensic casework. Among the three major sequencing platforms, BGISEQ-500TM, which is based on multiple PCRs, is still lacking in forensics. Here, a novel forensic panel was constructed to detect 186 single-nucleotide polymorphisms (SNPs) and 123 short tandem repeats (STRs) with MPS technology on the BGISEQ-500™ platform. First, the library preparation, sequencing process, and data analysis were performed, focusing on the average depth of coverage and heterozygote balance. We calculated the allelic frequencies and forensic parameters of STR and SNP loci in 73 unrelated Chinese Han individuals. In addition, performance was evaluated with accuracy, uniformity, sensitivity, PCR inhibitor, repeatability and reproducibility, mixtures, degraded samples, case-type samples, and pedigree analyses. The results showed that 100% accurate and concordant genotypes can be obtained, and the loci with an abundance in the interquartile range accounted for 92.90% of the total, suggesting reliable uniformity in this panel. We obtained a locus detection rate that was higher than 98.78% from 78 pg of input DNA, and the optimal amount was 1.25-10 ng. The maximum concentrations of hematin and humic acid were 200 and 100 μM, respectively (the ratios of detected loci were 96.52% and 92.41%), in this panel. As a mixture, compared with those of SNPs, minor-contributor alleles of STRs could be detected at higher levels. For the degraded sample, the ratio of detected loci was 98.41%, and most profiles from case-type samples were not significantly different in abundance in our studies. As a whole, this panel showed high-performance, reliable, robust, repeatable, and reproducible results, which are sufficient for paternity testing, individual identification, and use for potentially degraded samples in forensic science. SN - 1437-1596 UR - https://www.unboundmedicine.com/medline/citation/32851473/A_novel_forensic_panel_of_186_plex_SNPs_and_123_plex_STR_loci_based_on_massively_parallel_sequencing_ DB - PRIME DP - Unbound Medicine ER -