Development of an NGS panel containing 42 autosomal STR loci and the evaluation focusing on secondary kinship analysis
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ORIGINAL ARTICLE
Development of an NGS panel containing 42 autosomal STR loci and the evaluation focusing on secondary kinship analysis Qingxia Liu 1 & Guanju Ma 1 & Qingqing Du 1 & Chaolong Lu 1 & Lihong Fu 1 & Qian Wang 1 & Guangping Fu 1 & Shujin Li 1 & Bin Cong 1 Received: 4 September 2019 / Accepted: 3 April 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract High-throughput next-generation sequencing (NGS) is a feasible technique to detect considerably more markers and simultaneously obtain length and sequence information in a single reaction. In this study, we developed an NGS panel including 42 commonly used autosomal short tandem repeats (STRs) and amelogenin on the Illumina MiSeq FGx™. Sequencing accuracy was validated by the consistency of 2800M Control DNA detected using the ForenSeq™ DNA Signature Prep Kit and Sanger sequencing. Nomenclature incompatibility was found between NGS-STR and CE-STR typing at 9 loci (D3S3045, D6S477, D7S3048, D9S925, D14S608, D17S1290, D18S535, D21S1270, GATA198B05), despite the correct sequence. The difference was caused by the two different methods of identifying motif sequence and a one-to-one correspondence can be found. We evaluated the panel by investigating consistency, sequencing sensitivity and the effectiveness of the 2nd-degree relationship identification. Herein, we present sequencing results from 58 unrelated individuals of the Hebei Han population. The total discrimination power (TDP) and cumulative probability of exclusion for trio paternity testing (CPEtrio) of the 42 NGS-STR panels reached 1–2.84 × 10−57 and 1–9.87 × 10−21, respectively. By family simulation and likelihood ratio (LR) calculation, this panel was shown to have effectiveness for the 2nd-degree kinship identification similar to the ForenSeq™ DNA Signature Prep Kit and certain advantages compared with it due to the relatively small number of loci. As expected, it provides new data for the development of NGS-STR typing technology. Keywords Next-generation sequencing . Short tandem repeats . MiSeq FGx™ . Second kinship analysis . Chinese Han
Introduction Short tandem repeats (STRs) play an important role in human forensic identification and parentage testing because of its high polymorphism [1]. The traditional STR detection method is based on capillary electrophoresis Qingxia Liu and Guanju Ma contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00414-020-02295-z) contains supplementary material, which is available to authorized users. * Shujin Li [email protected]; [email protected] * Bin Cong [email protected] 1
College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang 050017, People’s Republic of China
(CE) technology, which can co-amplify 20~30 STR loci in a single multiplex reaction [2, 3]. However, this number of STR loci is not sufficient for some forensic cases, such as complicated kinship testing. Therefore, it is necessary to d
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