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- Analysis of paterniy cases with a single exclusion in a genetic marker using precision ID GLOBALFILER™ NGS STR PANEL v2Publication . Gouveia, Nair; Lopes, Virginia; Porto, Maria João; Bento, Ana; Andrade Sampaio, Lisa; Serra, Armando; Balsa, Filipa; Bogas, Vanessa; São Bento, Marta; Amorim, AntónioPaternity test results can sometimes evidence incompatibilities in the allelic transmission from parents to children, such as the presence of a single exclusion in one specific genetic marker, revealing a mismatch between the genetic profiles of the biological parent and the offspring. In these cases, it is important to determine whether the exclusion could be the result of a mutation or other factors as null or silent alleles. Capillary electrophoresis (CE) is the traditional method used in forensic genetics to analyze STRs (Short Tandem Repeats), however it is not possible to know the exact allele number variation due to the lack of sequence data. The application of Next-Generation Sequencing (NGS) technology may provide additional information, since it allows to detect and sequence simultaneously SNPs (Single Nucleotide Polymorphisms) present in the flanking regions and also distinguish isometric alleles with the same length but different sequences, that were misinterpreted as homozygous. In this study, a set of reference samples (buccal swabs and blood stains), previously amplified with the GlobalFiler™ PCR Amplification Kit and sequenced by CE on the 3500 Genetic Analyzer, were selected from paternity cases with a single exclusion, reported after GeneMapper ID-X Software analysis. All samples were automatically prepared with the Precision ID GlobalFiler™ NGS STR Panel v2 on the Ion Chef™ System, followed by sequencing on the Ion S5™ System and finally Converge™ Software analysis, according to the manufacturer’s instructions. The aim was to verify if the NGS methodology provides valuable information in these paternity cases and to identify the parental origin of a mutant allele. The NGS results were in concordance with those obtained by CE. In addition, this methodology demonstrated to be useful to clarify the paternity cases, because it enables a higher power of discrimination through 9 additional multi-allelic STRs, in a total of 35 markers instead of 24 markers of the GlobalFiler™ PCR Amplification Kit used in the traditional method. Therefore, the Precision ID GlobalFiler™ NGS STR Panel v2 shows to be a powerful method for kinship analyses and typing reference samples.
- Internal Validation of the Investigator 26Plex QS Amplification Kit: a high-throughput multiplex assay for reference and low copy number DNA samplesPublication . Cardoso, Paula; Serra, Armando; Bogas, Vanessa; Balsa, Filipa; Lopes, Virginia; Dario, Rita; Porto, Maria João; Amorim, António; Corte Real, F.; Brito, PedroThe Investigator® 26plex QS Amplification Kit, from QIAGEN, provides reliable and rapid DNA profiles while enabling the multiplex amplification of 24 STRs, 2 Quality Sensors and a gender-determining marker, Amelogenin. The Quality Sensors incorporated in this kit provide insight into the sample quality and the PCR's success while alerting to the presence of inhibitors. Through an extensive internal validation study, this research sought to implement the Investigator® 26plex QS in the laboratory routine of the Forensic Genetic and Biology Service, Central branch (SGBF-C) of the Portuguese National Institute of Legal Medicine and Forensic Sciences. Here we detail the procedures and parameters applied which followed the SWGDAM guidelines, as well as report the results obtained throughout. Firstly, it was crucial to establish unique analytical criteria that would be the baseline for the interpretation of the results obtained. To accomplish such, analytical, stochastic, heterozygous balance and stutter thresholds were defined. Thereupon, this study intended to gauge the kit’s performance, by evaluating its concordance with normalized methodologies while assessing its sensitivity, specificity, robustness, and precision, besides its efficiency in the presence of degraded and/or inhibited samples. Lastly, in favour of optimizing the laboratory workflow, an assay was carried out to test half volume reactions and direct amplification on reference samples. In this study a wide range of sample types were analysed, which made it possible to acquire robust data pertaining to the performance of the assay. The laboratory methodology applied comprehended: DNA extraction using Prep-n-Go™ Buffer and PrepFiler Express™ Forensic DNA Extraction Kit, quantification with the Quantifiler™ Trio Quantification Kit, followed by the amplification with the Investigator® 26plex QS. Capillary electrophoresis was performed in the Applied Biosystems™ 3500 Genetic Analyzer, and the electropherograms’ were analysed using the GeneMapper™ ID-X Software v1.6. Through this work, it was possible to characterize the main advantages of the Investigator® 26plex QS kit, as well as its limitations. The validation data demonstrated that this system produces reliable profiles in the presence of minute DNA quantities and identifies the minor contributor in a mixture up to a 1:50 ratio. The results inferred a high human specificity, robustness, and sensitivity, while producing concordant and reproducible results with optimized protocols for both reference and low copy number DNA samples. Through concordance studies it was further shown that there is a high consistency between this novel amplification kit and those currently implemented in the SGBF-C, thus proving its suitability for the analysis of forensic samples.