Ion AmpliSeq Community Panels for Human Identification

Ion AmpliSeq VISAGE-Basic Tool Research Panel
Ion AmpliSeq DNA Phenotyping Panel
Ion AmpliSeq PhenoTrivium Panel

Ion AmpliSeq HID Y-SNP Research Panel v1
Ion AmpliSeq MH-74 Plex Research Panel

Forensic DNA phenotyping can provide investigative leads on externally visible characteristics (EVCs) and biogeographical ancestry (BGA) to assist in investigations where there is no database hit or CE-STR analysis fails. The Ion AmpliSeq VISAGE (Visible Attributes through Genomics)-Basic Tool Research Panel consists of 153 SNPs, allowing prediction of EVCs and biogeographical ancestry, and incorporating 41 SNPs of the HIrisPlex-S assay¹ and 115 BGA markers chosen for differentiation of seven continental populations. The assay design is beneficial for degraded samples with an average amplicon size of 175 bp. Preliminary validation of the assay shows high sensitivity with full profiles down to 100 pg of genomic DNA (gDNA) and 240 minutes of sonication.

DNA phenotyping can be useful for generating investigative leads in cases where STR profiles have not resulted in a database match. The Ion AmpliSeq DNA Phenotyping Panel is used to predict hair and eye color using 24 phenotype SNPs from the HIrisPlex system. This panel targets 23 SNPs and one indel from the following genes: MC1R, SLC45A2, ASIP/PIGU, EXOC2, HERC2, IRF4, KITLG, OCA2, TYR, SLC24A4, and TRYP1. Results suggesting probability of blue, intermediate, or brown eye color along with shade of black, brown, red, or blond hair are provided by the HIrisPlex prediction model (http://hirisplex.erasmusmc.nl/). For further details see Walsh et. al., Forensic Science International: Genetics 2013.

Growing research on the application of alternative markers in the field of forensic genetics has aided in identifying methods to obtain more genetic information from challenging samples. The use of biogeographical ancestry, DNA phenotyping, and lineage markers can provide investigative leads in cold cases and cases where there are no suspects. The Ion AmpliSeq PhenoTrivium Panel contains ancestry, DNA phenotyping, and male lineage markers for a total of 200 autosomal SNPs and 120 Y chromosomal SNPs in a single panel. Diepenbroek et. al. show show that reliable ancestry and phenotype predictions can be obtained with the panel down to 125 pg of genomic DNA (gDNA) and the added benefits of combining ancestry, phenotype, and male lineage predictions on casework samples.

The analysis of alternative marker types can complement CE-STR results for challenging samples, such as complex mixtures or degraded samples, to generate investigative leads. Microhaplotypes have arisen as an alternative marker to traditional STR-CE typing due to the additive enhanced mixture analysis and biogeographical ancestry prediction capabilities that favor its use for forensic samples. The Ion AmpliSeq MH-74 Plex Research Panel is a 157–325 bp assay covering 74 microhaplotypes (230 SNPs) selected from a set of 130 microhaplotypes previously characterized by the Kidd Laboratory. Microhaplotypes were selected based on high Ae (effective number of alleles) and In (informativeness) values to enhance mixture deconvolution and biogeographic ancestry prediction capabilities. Oldoni et. al. demonstrate sensitivity down to 50 pg of genomic DNA (gDNA) and the utility of the assay in analyzing complex mixtures to complement CE-STR typing results.