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Development of new PCR multiplex system by the simultaneous detection of 10 miniSTRs, SE33, Penta E, Penta D, and four Y-STRs

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Abstract

The 18 loci multiplex system has been instigated for co-amplification and fluorescent detection of Amelogenin and 17 STRs, including 10 MiniSTRs (CSF1PO, D18S51, D7S820, D2S1338, TPOX, D13S317, FGA, D5S818, D21S11, D16S539), SE33, Penta E, Penta D, and four Y-STRs (DYS385a/b, DYS438, DYS392). This multiplex system was developed for the simultaneous analysis of compromised DNA samples, Y-amelogenin marker mutation, motherless paternity issues where single allele sharing occurs at autosomal STRs in unrelated individuals, and other complex forensic cases. Selection of loci, primers, and allelic ladders were designed and created in-house with a design strategy to work in this multiplex. The multiplex system was evaluated by sensitivity, specificity, stability, precision and accuracy, case-type samples, mixture studies, PCR-based and population distribution studies to establish the robustness and reliability of the system as the current requirements of the forensic case work. Among all the markers evaluated for this study, 209 alleles including 44 variants were observed with combined power of discrimination, combined power of exclusion, and the combined probability of matching calculated as 0.999999999999999999893916339344, 0.999993816173890, and 5.90019 × 10−19, respectively. Due to highly polymorphic characteristics of these loci particularly SE33 and Penta E which are most discriminatory (PD = 0.991 and 0.983, respectively) in the Pakistani population, this multiplex would be highly valuable for individual identification in complex forensic cases and paternity issues as well as population database.

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Authors and Affiliations

  1. Forensic DNA Typing Laboratory, National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan

    Muhammad Shafique, Ziaur Rahman, Ahmad Ali Shahid & Tayyab Husnain

  2. Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan

    Muhammad Saqib Shahzad

  3. Forensic Services Laboratory, Centre for Applied Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan

    Muhammad Adnan Shan, Rukhsana Perveen, Muhammad Shahzad & Manzoor Hussain

Authors
  1. Muhammad Shafique
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  2. Muhammad Saqib Shahzad
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  4. Muhammad Adnan Shan
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  9. Tayyab Husnain
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Correspondence to Muhammad Shafique.

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Shafique, M., Shahzad, M.S., Rahman, Z. et al. Development of new PCR multiplex system by the simultaneous detection of 10 miniSTRs, SE33, Penta E, Penta D, and four Y-STRs. Int J Legal Med 130, 1409–1419 (2016). https://doi.org/10.1007/s00414-016-1372-x

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  • DOI: https://doi.org/10.1007/s00414-016-1372-x

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