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

Brendan Keating, Aruna T. Bansal, Susan Walsh, Jonathan Millman, Jonathan Newman, Kenneth Kidd, Bruce Budowle, Arthur Eisenberg, Joseph Donfack, Paolo Gasparini, Zoran Budimlija, Anjali K. Henders, Hareesh Chandrupatla, David L. Duffy, Scott D. Gordon, Pirro Hysi, Fan Liu, Sarah E. Medland, Laurence Rubin, Nicholas G. MartinTimothy D. Spector, Manfred Kayser

Research output: Contribution to journalArticlepeer-review

35 Scopus citations

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.

Original languageEnglish
Pages (from-to)559-572
Number of pages14
JournalInternational journal of legal medicine
Volume127
Issue number3
DOIs
StatePublished - May 2013

Keywords

  • Ancestry
  • DNA intelligence
  • Eye color
  • Forensic DNA phenotyping
  • Hair color
  • Kinship
  • Prediction
  • Relatedness
  • SNP
  • Sex

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