A novel forensic panel of 186-plex SNPs and 123-plex STR loci based on massively parallel sequencing
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ORIGINAL ARTICLE
A novel forensic panel of 186-plex SNPs and 123-plex STR loci based on massively parallel sequencing Bao Zhang 1 & Xinyao Miao 1 & Yuesheng Shen 2 & Xiaojuan Gong 1,3 & Huiyun Yu 2 & Bowen Li 4 & Liao Chang 1 & Yinan Wang 1 & Jingna Fan 1 & Zuhuan Liang 5 & Bowen Tan 6 & Shengbin Li 1 Received: 11 May 2020 / Accepted: 21 August 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
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, minorcontributor 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. Keywords Multiplex PCR . Forensic genomics system . Massively parallel sequencing (MPS) . Single-nucleotide polymorphism (SNP) . Short tandem repeat (STR)
Xinyao Miao, Yuesheng Shen and Xiaojuan Gong contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00414-020-02403-z) contains supplementary material, which is available to authorized users. * Bao Zhang [email protected] 1
2
College of Forensic Medicine, Health Science Center, Xi’an Jiaotong University, Xi’an, People’s Republic of China School of Life Science, Northwest A&F University, Yangling, People’s Republic of China
3
School of Health Scie
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