First all-in-one diagnostic tool for DNA intelligence: genome-wide inference of biogeographic ancestry, appearance, relatedness, and sex with the Identitas v1 Forensic Chip

Abstract

When a forensic DNA sample cannot be associated directly with a previously genotyped reference sample by standard short tandem repeat profiling, the investigation required for identifying perpetrators, victims, or missing persons can be both costly and time consuming. Here, we describe the outcome of a collaborative study using the Identitas Version 1 (v1) Forensic Chip, the first commercially available all-in-one tool dedicated to the concept of developing intelligence leads based on DNA. The chip allows parallel interrogation of 201,173 genome-wide autosomal, X-chromosomal, Y-chromosomal, and mitochondrial single nucleotide polymorphisms for inference of biogeographic ancestry, appearance, relatedness, and sex. The first assessment of the chip's performance was carried out on 3,196 blinded DNA samples of varying quantities and qualities, covering a wide range of biogeographic origin and eye/hair coloration as well as variation in relatedness and sex. Overall, 95 % of the samples (N = 3,034) passed quality checks with an overall genotype call rate >90 % on variable numbers of available recorded trait information. Predictions of sex, direct match, and first to third degree relatedness were highly accurate. Chip-based predictions of biparental continental ancestry were on average ~94 % correct (further support provided by separately inferred patrilineal and matrilineal ancestry). Predictions of eye color were 85 % correct for brown and 70 % correct for blue eyes, and predictions of hair color were 72 % for brown, 63 % for blond, 58 % for black, and 48 % for red hair. From the 5 % of samples (N = 162) with <90 % call rate, 56 % yielded correct continental ancestry predictions while 7 % yielded sufficient genotypes to allow hair and eye color prediction. Our results demonstrate that the Identitas v1 Forensic Chip holds great promise for a wide range of applications including criminal investigations, missing person investigations, and for national security purposes.

Fig. 1

Three-dimensional principal component analysis plot for a DNA sample from a European individual denoted by a black cross, together with reference data from HapMap v3 i.e., from individuals of European descent (CEU Utah residents with Northern and Western European ancestry from the CEPH collection; TSI Tuscans in Italy), African descent (ASW African ancestry in Southwest USA; LWK Luhya in Webuye, Kenya; MKK Maasai in Kinyawa, Kenya; YRI Yoruba in Ibadan, Nigeria), East Asian descent (CHB Han Chinese in Beijing, China; CHD Chinese in Metropolitan Denver, CO; JPT Japanese in Tokyo, Japan), South Asian descent (GIH Gujarati Indians in Houston, TX), and South American descent (MEX Mexican ancestry in Los Angeles, CA)

Fig. 2

Quantitative assessment of biogeographic ancestry from an individual whose father was of African origin and whose mother was of European origin

Fig. 3

Box plot for quantitative assessments of biogeographic ancestry for 24 Ethiopian individuals

Fig. 4

Box plot for quantitative assessments of biogeographic ancestry for 57 individuals from Kazakhstan