Genetic Epidemiology, Psychiatric Genetics, Asthma Genetics and Statistical Genetics Laboratories investigate the pattern of disease in families, particularly identical and non-identical twins, to assess the relative importance of genes and environment in a variety of important health problems.
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PMID
23149900
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.
DATE PUBLISHED
2013 May
HISTORY
PUBSTATUS PUBSTATUSDATE
received 2012/08/30
accepted 2012/10/17
aheadofprint 2012/11/13
entrez 2012/11/15 06:00
pubmed 2012/11/15 06:00
medline 2013/12/16 06:00
AUTHORS
NAME COLLECTIVENAME LASTNAME FORENAME INITIALS AFFILIATION AFFILIATIONINFO
Keating B Keating Brendan B The University of Pennsylvania, Office 1016, Abramson Building, 3615 Civic Center Bvld., Philadelphia, PA 19104-4399, USA. bkeating@mail.med.upenn.edu
Bansal AT Bansal Aruna T AT
Walsh S Walsh Susan S
Millman J Millman Jonathan J
Newman J Newman Jonathan J
Kidd K Kidd Kenneth K
Budowle B Budowle Bruce B
Eisenberg A Eisenberg Arthur A
Donfack J Donfack Joseph J
Gasparini P Gasparini Paolo P
Budimlija Z Budimlija Zoran Z
Henders AK Henders Anjali K AK
Chandrupatla H Chandrupatla Hareesh H
Duffy DL Duffy David L DL
Gordon SD Gordon Scott D SD
Hysi P Hysi Pirro P
Liu F Liu Fan F
Medland SE Medland Sarah E SE
Rubin L Rubin Laurence L
Martin NG Martin Nicholas G NG
Spector TD Spector Timothy D TD
Kayser M Kayser Manfred M
International Visible Trait Genetics (VisiGen) Consortium
INVESTIGATORS
JOURNAL
VOLUME: 127
ISSUE: 3
TITLE: International journal of legal medicine
ISOABBREVIATION: Int. J. Legal Med.
YEAR: 2013
MONTH: May
DAY:
MEDLINEDATE:
SEASON:
CITEDMEDIUM: Internet
ISSN: 1437-1596
ISSNTYPE: Electronic
MEDLINE JOURNAL
MEDLINETA: Int J Legal Med
COUNTRY: Germany
ISSNLINKING: 0937-9827
NLMUNIQUEID: 9101456
PUBLICATION TYPE
PUBLICATIONTYPE TEXT
Evaluation Studies
Journal Article
Research Support, Non-U.S. Gov't
COMMENTS AND CORRECTIONS
REFTYPE REFSOURCE REFPMID NOTE
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GRANTS
GRANTID AGENCY COUNTRY
Wellcome Trust United Kingdom
GENERAL NOTE
KEYWORDS
MESH HEADINGS
DESCRIPTORNAME QUALIFIERNAME
Continental Population Groups
DNA Fingerprinting methods
Eye Color methods
Feasibility Studies methods
Female methods
Forensic Genetics methods
Genome-Wide Association Study methods
Hair Color methods
Humans methods
Logistic Models methods
Male methods
Multivariate Analysis methods
Phenotype methods
Polymorphism, Single Nucleotide methods
Sensitivity and Specificity methods
Sex methods
Single-Blind Method methods
SUPPLEMENTARY MESH
GENE SYMBOLS
CHEMICALS
OTHER ID's
OTHERID SOURCE
PMC3631519 NLM