Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise

Abstract

(C. Phillips).• Nineteen laboratories completed a collaborative EDNAP exercise to evaluate two forensic ancestry informative marker (AIM) assays and accompanying statistical tools to infer ancestry from the genotype data.• Laboratories were sent primers, reference data and five test DNAs of undisclosed origin plus an unmarked DNA mixture (but reported to be one of the samples).• Fourteen laboratories successfully genotyped the DNAs with a 34-plex SNP assay using SNaPshot, achieving 96.1% profile completeness and 93.5% genotype concordance.• All laboratories successfully genotyped the DNAs with a 46-plex Indel assay using dye-labelled PCR primers, achieving 99.8% profile completeness and genotype concordance.• All laboratories identified the mixed DNA sample, indicated by disrupted peak height ratios in the Indel profile and three-allele patterns in SNP rs5030240. 18/19 laboratories assigned the correct ancestry to each of the test DNAs of unknown origin, obtaining likelihood ratios from 80 markers in the range: 1.25E+07 to 1.78E+41. 25This exercise demonstrates that ancestry inference tests based on binary marker sets can be readily 26 adopted by laboratories that already have well-established CE regimes in place. The Indel test proved to 27 be easy to use and allowed all exercise participants to detect the DNA mixture as well as achieving 28 complete and concordant profiles in nearly all cases. Lastly, two participants successfully ran parallel next-29 generation sequencing analyses (each using different systems) and achieved high levels of genotyping 30 concordance using the exercise PCR primer mixes unmodified. 31 32

A GHEP-ISFG collaborative study on the genetic variation of 38 autosomal indels for human identification in different continental populations

“…From these, 47 obtained identical results for all samples and markers. The results of this phase showed a good performance of the indel multiplex, similar to what was observed in a previous collaborative inter-laboratory exercise organized by the European DNA Profiling group (EDNAP) involving indel-and SNP-based ancestry informative marker panels [12]. In fact, the genotyping completeness and concordance was even higher in the present study, with only six laboratories out of 53 presenting incomplete profiles and/or genotyping errors.…”

“…5,6,7]. Indel multiplexes are advantageous over SNPs in regard to easier genotyping with conventional automated fragment size analysis, which is common technique available in most forensic laboratories worldwide [8][9][10][11][12].…”

A panel of 74 AISNPs: Improved ancestry inference within Eastern Asia

“…Until now, the most common method of multiplexing a forensic assay has been primer extension reaction followed by capillary electrophoresis. However, while that procedure is easily implemented in most forensic laboratories [19,20], the size of such a panel is limited to a few dozen SNPs because of dye and size constraints. Modern massively parallel sequencing (MPS) and DNA array-based technologies provide good alternative typing methods without the limitation in the number of SNPs that can be simultaneously assayed [21,22].…”

A review of the method and validation of the MiSeq FGx™ Forensic Genomics Solution

“…Additional forensic DNA methods have developed as important investigative tools enabling the inference of biogeographical ancestry (BGA) (J. R. Kidd et al, ; Phillips et al, ) and externally visible characteristics (EVCs) (Allwood & Harbison, ; Chaitanya et al, ; Ruiz et al, ; S. Walsh et al, , ). These markers are generally single nucleotide polymorphisms (SNPs), but can be microhaplotypes (Bulbul et al, ; K. K. Kidd & Pakstis et al, ), nucleotide insertions or deletions (Moriot, Santos, Freire‐Aradas, Phillips, & Hall, ; Santos et al, ), mitochondrial haplotypes, or STRs (Messina et al, ; Moriot et al, ; Phillips et al, ).…”