TY - JOUR
T1 - First all-in-one diagnostic tool for DNA intelligence
T2 - Genome-wide inference of biogeographic ancestry, appearance, relatedness, and sex with the Identitas v1 Forensic Chip
AU - Keating, Brendan
AU - Bansal, Aruna T.
AU - Walsh, Susan
AU - Millman, Jonathan
AU - Newman, Jonathan
AU - Kidd, Kenneth
AU - Budowle, Bruce
AU - Eisenberg, Arthur
AU - Donfack, Joseph
AU - Gasparini, Paolo
AU - Budimlija, Zoran
AU - Henders, Anjali K.
AU - Chandrupatla, Hareesh
AU - Duffy, David L.
AU - Gordon, Scott D.
AU - Hysi, Pirro
AU - Liu, Fan
AU - Medland, Sarah E.
AU - Rubin, Laurence
AU - Martin, Nicholas G.
AU - Spector, Timothy D.
AU - Kayser, Manfred
N1 - Funding Information:
The International VisiGen Consortium wishes to acknowledge the contributions of their research institutions, study investigators, field staff, and the study participants, in creating the scientific resources accessed. We also would like to thank the scientists at Illumina for the help with assay scoring, assay selection, and genotyping. TwinsUK is supported by the Wellcome Trust and the NHS NIHR Biomedical resource grant to Guys and St. Thomas’ foundation hospitals and KCL. Identitas Inc. sponsors VisiGen via a research grant to a number of the respective academic institutions.
Funding Information:
SNP genotyping was supported in part by the FBI Laboratory Division. Names of commercial manufacturers are provided for identification only and inclusion does not imply endorsement of the manufacturer or its products or services by the FBI. The views expressed are those of the authors and do not necessarily reflect the official policy or position of the FBI or the US Government. This manuscript was filed under the number 12-18 at the Counterterrorism and Forensic Science Research Unit, Federal Bureau of Investigation Laboratory Division.
PY - 2013/5
Y1 - 2013/5
N2 - 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.
AB - 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.
KW - Ancestry
KW - DNA intelligence
KW - Eye color
KW - Forensic DNA phenotyping
KW - Hair color
KW - Kinship
KW - Prediction
KW - Relatedness
KW - SNP
KW - Sex
UR - http://www.scopus.com/inward/record.url?scp=84877873104&partnerID=8YFLogxK
U2 - 10.1007/s00414-012-0788-1
DO - 10.1007/s00414-012-0788-1
M3 - Article
C2 - 23149900
AN - SCOPUS:84877873104
SN - 0937-9827
VL - 127
SP - 559
EP - 572
JO - International Journal of Legal Medicine
JF - International Journal of Legal Medicine
IS - 3
ER -