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A novel forensic panel of 186-plex SNPs and 123-plex STR loci based on massively parallel sequencing

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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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Acknowledgments

The acquisition of the study was inseparable from the efforts of volunteers and laboratory staff.

Funding

This study was funded by China Postdoctoral Science Foundation (Grant No. 2018M633526 and 2019M663745).

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Author notes

  1. Xinyao Miao, Yuesheng Shen and Xiaojuan Gong contributed equally to this work.

Authors and Affiliations

  1. College of Forensic Medicine, Health Science Center, Xi’an Jiaotong University, Xi’an, People’s Republic of China

    Xinyao Miao, Xiaojuan Gong, Liao Chang, Yinan Wang, Jingna Fan, Shengbin Li & Bao Zhang

  2. School of Life Science, Northwest A&F University, Yangling, People’s Republic of China

    Yuesheng Shen & Huiyun Yu

  3. School of Health Science Center, Xi’an Jiaotong University, Xi’an, People’s Republic of China

    Xiaojuan Gong

  4. School of Life Science, Sichuan University, Chengdu, People’s Republic of China

    Bowen Li

  5. Forensic Genomics International, The Beijing Genomics Institute (BGI), Shenzhen, People’s Republic of China

    Zuhuan Liang

  6. School of Computer Science, City University of Hong Kong, Hong Kong, People’s Republic of China

    Bowen Tan

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Contributions

BZ designed experiment and reviewed the manuscript. HYY, BL, and LC collected and prepared the samples. ZHL and BT developed the methods and protocols. YSS, YNW, and JNF performed the experiments. XYM, YSS, and XJG analyzed the data and prepared the original manuscript. XYM and YSS prepared the figures and tables. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Bao Zhang.

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Ethics statement

All works were approved by the Institutional Review 98 Board Administration in BGI (No. BGI-IRB 16036, voted at April 29, 2016). All human samples and experiments involved were in line with the ethical standards of the institutional and national research committees and the Helsinki Declaration.

We certify that this manuscript is original and has not been published and will not be submitted elsewhere for publication while being considered by IJLM. And the study is not split up into several parts to increase the quantity of submissions and submitted to various journals or to one journal over time. No data have been fabricated or manipulated (including images) to support your conclusions. No data, text, or theories by others are presented as if they were our own.

The submission has been received explicitly from all co-authors. And authors whose names appear on the submission have contributed sufficiently to the scientific work and therefore share collective responsibility and accountability for the results.

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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 135, 709–718 (2021). https://doi.org/10.1007/s00414-020-02403-z

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