title: 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.
authors.affiliation: The University of Pennsylvania, Office 1016, Abramson Building, 3615 Civic Center Bvld., Philadelphia, PA 19104-4399, USA. bkeating@mail.med.upenn.edu
authors.forename: Brendan
authors.initials: B
authors.lastname: Keating
authors.forename: Aruna T
authors.initials: AT
authors.lastname: Bansal
authors.forename: Susan
authors.initials: S
authors.lastname: Walsh
authors.forename: Jonathan
authors.initials: J
authors.lastname: Millman
authors.forename: Jonathan
authors.initials: J
authors.lastname: Newman
authors.forename: Kenneth
authors.initials: K
authors.lastname: Kidd
authors.forename: Bruce
authors.initials: B
authors.lastname: Budowle
authors.forename: Arthur
authors.initials: A
authors.lastname: Eisenberg
authors.forename: Joseph
authors.initials: J
authors.lastname: Donfack
authors.forename: Paolo
authors.initials: P
authors.lastname: Gasparini
authors.forename: Zoran
authors.initials: Z
authors.lastname: Budimlija
authors.forename: Anjali K
authors.initials: AK
authors.lastname: Henders
authors.forename: Hareesh
authors.initials: H
authors.lastname: Chandrupatla
authors.forename: David L
authors.initials: DL
authors.lastname: Duffy
authors.forename: Scott D
authors.initials: SD
authors.lastname: Gordon
authors.forename: Pirro
authors.initials: P
authors.lastname: Hysi
authors.forename: Fan
authors.initials: F
authors.lastname: Liu
authors.forename: Sarah E
authors.initials: SE
authors.lastname: Medland
authors.forename: Laurence
authors.initials: L
authors.lastname: Rubin
authors.forename: Nicholas G
authors.initials: NG
authors.lastname: Martin
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Spector
authors.forename: Manfred
authors.initials: M
authors.lastname: Kayser
mesh_terms: D016172:DNA Fingerprinting / Q000379:methods*; D005127:Eye Color; D005240:Feasibility Studies; D005260:Female; D053803:Forensic Genetics / Q000379:methods*; D055106:Genome-Wide Association Study; D006200:Hair Color; D006801:Humans; D016015:Logistic Models; D008297:Male; D015999:Multivariate Analysis; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D044469:Racial Groups; D012680:Sensitivity and Specificity; D012723:Sex; D016037:Single-Blind Method