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

• Published in: International journal of legal medicine 2013-05, Vol.127 (3), p.559-572
• Main Authors: Keating, Brendan, Bansal, Aruna T., Walsh, Susan, Millman, Jonathan, Newman, Jonathan, Kidd, Kenneth, Budowle, Bruce, Eisenberg, Arthur, Donfack, Joseph, Gasparini, Paolo, Budimlija, Zoran, Henders, Anjali K., Chandrupatla, Hareesh, Duffy, David L., Gordon, Scott D., Hysi, Pirro, Liu, Fan, Medland, Sarah E., Rubin, Laurence, Martin, Nicholas G., Spector, Timothy D., Kayser, Manfred
• Format: Article
• Language: English
• Subjects: Biogeography; Continental Population Groups; Criminal investigations; DNA Fingerprinting - methods; Eye Color; Feasibility Studies; Female; Forensic Genetics - methods; Forensic Medicine; Genetic testing; Genome-Wide Association Study; Genomes; Hair Color; Humans; Logistic Models; Male; Maternal & child health; Medical Law; Medicine; Medicine & Public Health; Missing persons; Mitochondrial DNA; Multivariate Analysis; Original; Original Article; Phenotype; Polymorphism, Single Nucleotide; Sensitivity and Specificity; Sex; Single-Blind Method
• ISSN: 0937-9827; 1437-1596
• DOI: 10.1007/s00414-012-0788-1

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