Development and validation of a multiplex insertion/deletion marker panel, SifaInDel 45plex system. (July 2019)

• Record Type: Journal Article
• Authors: Tao, Ruiyang; Zhang, Jingyi; Sheng, Xiang; Zhang, Jiashuo; Yang, Zihao; Chen, Chong; Bian, Yingnan; Liu, Xiling; Zhang, Suhua; Li, Chengtao
• Is Part Of: Forensic science international. Volume 41(2019)
• Page Start: 128
• Page End: 136
• Publication Date: 2019-07
• Subjects: Forensic science -- Capillary electrophoresis (CE) -- DNA genotyping -- Insertion and deletion polymorphisms (InDels); Forensic genetics -- Periodicals; Génétique légale -- Périodiques; Forensic genetics; Electronic journals; Periodicals; 614.1
• DOI: 10.1016/j.fsigen.2019.04.008
• Languages: English
• ISSNs: 1872-4973

Abstract

Highlights: A InDel multiplex system was developed, including 27 A-InDels, 16 X-InDels and two Y-InDels. This system was validated to be accurate, sensitive, reliable and human-specific. This system could be a powerful complementary tool in human identification and kinship analysis. Abstract: In addition to commonly used short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), insertion and deletion polymorphisms (InDels) have considerable potential in the field of forensic genetics because they combine desirable characteristics of both STRs and SNPs. In the present study, the SifaInDel 45plex system was designed to amplify 45 InDel markers, including 27 autosomal InDels (A-InDels), 16 X chromosome InDels (X-InDels) and two Y chromosome InDels (Y-InDels), simultaneously in a single PCR procedure and then detect products by capillary electrophoresis (CE). We also optimized the PCR conditions for the novel panel and performed several validation studies including repeatability/reproducibility, concordance, accuracy, sensitivity, stability, species specificity and population genetics. The results confirmed that full profiles could be obtained from ≥62.5 pg of input DNA and from a series of challenging samples encountered in routine casework. The SifaInDel 45plex panel could tolerate different concentrations of inhibitors, such as ≤50 μM hematin, ≤20 ng/μL nigrosine and ≤8000 ng/μL urea. In a population investigation, for the 27 A-InDels, the combined power of discrimination (CPD) exceeded 0.999999, and the combined power of exclusion in duos (CPED ) and trios (CPET ) was 0.955118 and 0.997754, respectively. For the 16 X-InDels, the combined PDMale and PDFemale was computed as 0.999845 and 0.999998, respectively, and the combined mean exclusion chance in father/daughter or mother/son duos (MECDuo ) and mean exclusion chance in standard trios involving daughters (MECTrio ) was 0.976220 and 0.998163, respectively. In addition, the two Y-InDels could play a role in correctly determining gender. Overall, the established SifaInDel 45plex panel is a well-performing, reliable and robust multiplex system that stands out for combining a considerable number of A-indels, X-indels and Y-indels based on a CE platform. The population study results also demonstrated that the SifaInDel 45plex panel could be a valid complementary approach for human identification and complex kinship analysis.