Evaluation of the VISAGE basic tool for appearance and ancestry inference using ForenSeq® chemistry on the MiSeq FGx® system

Abstract

The possibility of providing investigative leads when conventional DNA identification methods fail to solve a case can be of extreme relevance to law enforcement. Therefore, the forensic genetics community has focused research towards the broadened use of DNA, particularly for prediction of appearance traits, bio-geographical ancestry and age. The VISible Attributes through GEnomics (VISAGE) Consortium expanded the use of DNA phenotyping by developing new molecular and statistical tools for appearance, age and ancestry prediction. The VISAGE basic tool for appearance (EVC) and ancestry (BGA) prediction was initially developed using Ampliseq chemistry, but here is being evaluated using ForenSeq chemistry. The VISAGE basic tool offers a total of 41 EVC and 115 BGA SNPs and thus provides more predictions, i.e., skin color, than achieved with the ForenSeq DNA Signature Prep kit that is based on 24 EVC and 56 BGA SNPs. Five VISAGE laboratories participated in collaborative experiments to provide foreground for developmental validation of the assay. Assessment of assay performance and quality metrics, reproducibility, sensitivity, inhibitor tolerance and species specificity are described. Furthermore, the assay was tested using challenging samples such as mock casework samples and artificially degraded DNA. Two different analysis strategies were applied for this study and output on genotype calls and read depth was compared. Overall, interlaboratory, inter-method and concordance with publicly available data were analysed and compared. Finally, the results showed a reliable and robust tool, which can be easily applied for laboratories already using a MiSeq FGx with ForenSeq reagents.

Applying Unique Molecular Indices with an Extensive All-in-One Forensic SNP Panel for Improved Genotype Accuracy and Sensitivity

“…Different strategies can be applied for mixture detection with MPS-based biallelic SNP assays. Mixtures can be identified by observing variation in the allele read frequency or by detecting an increase in heterozygotes [ 40 ]. We could successfully distinguish mixtures from single-source samples down to 1:10 mixtures by applying either of the proposed detection methods.…”

“…All mixtures were analyzed in duplicate, with 10 ng DNA as input amount. The ability to detect a mixture was evaluated by investigating the allele read frequency (ARF) distribution and by calculating the heterozygosity rate [ 40 ]. The ARF for each locus was calculated by dividing the read depth of the allele with the most reads with the total number of reads.…”

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019–2022

“…The VISAGE ( Vis ible A ttributes Through Ge nomics) Consortium, which consists of 13 partners from academic, police, and justice institutions in 8 European countries, has established new scientific knowledge and developed and tested prototype tools for DNA analysis and statistical interpretation as well as conducted education for stakeholders. In the 2019 to 2022 time window of this review, this concerted effort produced 45 one review article [ 417 ], 22 original research publications [ 337 , [420] , [421] , [422] , [423] , [424] , [425] , [426] , [427] , [428] , [429] , [430] , [431] , [432] , [433] , [434] , [435] , [436] , [437] , [438] , [439] , [440] ], and three reports [ [441] , [442] , [443] ].…”

Development and Validation of MPS-Based System for Human Appearance Prediction in Challenging Forensic Samples

“…Recently, more researchers have started to apply massively parallel sequencing technologies for ECVs application for both commercial [ 7 , 8 , 9 ] and non-commercial developments [ 10 ]. However, only a few MPS studies concerning forensic DNA phenotyping focused on degraded DNA samples, i.e., DNA samples with poor quality or low quantity of DNA [ 9 , 10 , 11 , 12 , 13 , 14 ] whose analysis often shows partial or inconclusive genetic results.…”

“…Most of these studies [ 9 , 10 , 11 , 12 , 14 ] reported the performance of the MPS assay on a set of forensic samples, different for biological tissue, and artificially degraded samples obtained with sonication treatment. The results showed well-balanced tests suitable for forensic casework by their high sensitivity with full SNP profiles obtained down to 100 pg of DNA input.…”