Construction of two fluorescence‐labeled non‐combined DNA index system miniSTR multiplex systems to analyze degraded DNA samples in the Chinese Han Population

Abstract

MiniSTR loci have been demonstrated to be an effective approach in recovering genetic information from degraded specimens, because of the reduced PCR amplicon sizes which improved the PCR efficiency. Eight non-combined DNA index system miniSTR loci suitable for the Chinese Han Population were analyzed in 300 unrelated Chinese Han individuals using two novel five fluorescence-labeled miniSTR multiplex systems(multiplex I: D10S1248, D2S441, D1S1677 and D9S2157; multiplex II: D9S1122, D10S1435, D12ATA63, D2S1776 and Amelogenin). The allele frequency distribution and forensic parameters in the Chinese Han Population were reported in this article. The Exact Test demonstrated that all loci surveyed here were found to be no deviation from Hardy-Weinberg equilibrium. The accumulated power of discrimination and power of exclusion for the eight loci were 0.999999992 and 0.98, respectively. The highly degraded DNA from artificially degraded samples and the degraded forensic case work samples was assessed with the two miniSTR multiplex systems, and the results showed that the systems were quite effective.

Non-invasive prenatal paternity testing by analysis of Y-chromosome mini-STR haplotype using next-generation sequencing

“…As a result, numerous loci and multiple samples can be simultaneously analyzed in a single reaction. The mini-STRs were redesigned with primers flanking the repeat region to reduce the amplicon size for small DNA fragment detection [17]. Compared to the commercial kits using CE with amplicon length of 79-430 bp, the mini-STR amplicon lengths analyzed by NGS in our study were all less than 150 bp (Fig 4).…”

“…Since Y-specific cffDNA can be easily distinguished from the abundant maternal DNA signals in the maternal plasma, detection of Ychromosome markers can be used to assess the paternity of male fetuses by capillary electrophoresis (CE) or SNP-based next-generation sequencing (NGS) [15,16]. In addition, mini-STR loci detection is an effective strategy for recovering genetic information from highly degraded DNA samples, and was solely used to fingerprint 20% of the degraded DNA samples from the aftermath of the 9/11 World Trade Centre terrorist attacks with reduced PCR amplicon sizes [17,18]. The aim of our study was to evaluate the efficacy of Y-chromosome mini-STR-based NGS for NIPPT, and quantify the extent of match using paternity testing parameters.…”

Universal fluorescent labeling of amplification products using locked nucleic acids

“…We selected eight non‐CODIS STRs (D3S1744, D4S2366, D9S1122, D10S1435, D11S4463, D14S1434, D17S1301, and D20S470), which are highly polymorphic in Asian populations . Sequences flanking these STRs were obtained using the University of California Santa Cruz Genome Browser (Human February 2009 Assembly) at http://genome.ucsc.edu/.…”

Allelic ladder production for a 10 locus Y‐chromosome DNA profiling system

“…Although this approach is less labor intensive and provides faster turnover, it demands frequent utilization of genomic DNA especially for the rare alleles that may become depleted. The cloning of each allele presents a promising alternative as the massive allele enrichment is suitable for large productions and long‐term storage [9,12,13]. The major advantage of the cloning method is that recombinant bacterial colonies can be stored in glycerol for long term [14] and plated for outgrowth when required.…”

“…In this report, we make technical recommendations for producing a balanced allelic ladder using the allele cloning approach. Although this approach has been previously recommended [9,12,13], the current study identified various technical challenges that can impact the balance of the ladder, the quality, and the production throughput. We propose a simplified workflow with quality control steps to address these challenges and yield a multilocus ladder applicable for forensic applications.…”