Evaluation of DNA Polymorphisms for Kinship Testing in the Population of Saudi Arabia

Abstract

Short Tandem Repeats (STRs) have been the standard DNA marker employed in forensic laboratories for more than two decades. Due to the advances in the kit chemistries and separation technologies (capillary electrophoresis (CE) systems), the number of STRs that can be simultaneously typed has grown to 21-26; this provides sufficient confidence in the conclusions of
most kinship cases. However, more complex cases (e.g. testing distant relatives, potential mutations, deficient cases or incest cases) or when the target population shows an increased level of consanguinity, the genetic evidence may prove inconclusive. This necessitates testing additional STRs included in supplementary STR kits. Another option is by using Massively Parallel
Sequencing (MPS) systems that allow simultaneous sequencing of additional DNA markers.
A total 500 samples from the population of Saudi Arabia were collected. Two CE-based STR kits were used: Globalfiler™ PCR amplification kit (AB, USA) and SureID® 23 comp Human Identification kit (Health Gene Technologies, China) that together allowed 38 aSTRs to be analysed.
In addition, as the SureID® 23 comp kit has not been validated either by an independent laboratory or by the manufacturer, the kit was validated following the minimum criteria of the European Network of Forensic Science Institutes (ENFSI) and the Scientific Working Group on DNA Analysis Methods (SWGDAM). Moreover, the ForenSeq™ DNA Signature Prep Kit
(Verogen) was used to sequence 87 samples and to generate sequence-based data for 122 autosomal markers included in the kit. The project allowed, in total, obtaining size-based data for 136 autosomal markers (42 aSTRs and 94 iiSNPs) and sequence-based data for 122 autosomal markers (28 aSTRs including
SE33 and 94 iiSNPs). The data were evaluated for human identification and kinship testing in Saudi Arabia Although Globalfiler™ kit provided combined match probability (CMP) of 1.42E-26 that is much higher than the kit currently used in Saudi Arabia that has a CMP of 2.23E-18 (Identifiler plus kit), the availability of data for 42 aSTRs allowed other commercially available kits to be evaluated (based on the loci they contain). The study suggests adopting VeriFilerTM Plus (AB) or
PowerPlex Fusion 6C system (Promega Corporation, USA) as a standard STR kit that would provide the lowest CMPs (9.26E-29 and 1.03E-29, respectively).
Adopting any of the three kits would provide sufficient confidence in most parent-child cases (trio or duo). The validation of the SureID® 23 comp has shown that the kit met the criteria commonly used in forensic genetics laboratories. In addition, the kit can benefit from some developments that were identified by the validation, in particular the addition of extra alleles in
the allelic ladder and also to increase the amount of input DNA that can be added to an amplification. The kit can be used if any kinship cases showed inconclusive results with GlobalFilerTM, VeriFilerTM Plus or PowerPlex Fusion 6C allowing 38-40 aSTRs to be analysed.
The ForenSeq™ DNA Signature Prep Kit provided CMP of 1.97E-68 and 3.65E-77 for the size and sequencebased data respectively, where 1.24E-37 (size-based data) and 5.6E-41 (sequence-based data) were provided from the iiSNPs alone. The kit can be used when two or three mismatches were suspected to be mutations or when testing distant relationships.
The study highlighted 220 syntenic pairs, 46 of which would have significant impact on LR estimation due to lower RFs (< 0.12). The case-specific impact of linkage should be included in the estimation of LRs by using the RFs values estimated in this project.