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.
QIMR Home Page
GenEpi Home Page
Publications
Contacts
Research
Staff Index
Collaborators
Software Tools
Computing Resources
Studies
Search
GenEpi Intranet
PMID
30268682
TITLE
Towards broadening Forensic DNA Phenotyping beyond pigmentation: Improving the prediction of head hair shape from DNA.
ABSTRACT
Human head hair shape, commonly classified as straight, wavy, curly or frizzy, is an attractive target for Forensic DNA Phenotyping and other applications of human appearance prediction from DNA such as in paleogenetics. The genetic knowledge underlying head hair shape variation was recently improved by the outcome of a series of genome-wide association and replication studies in a total of 26,964 subjects, highlighting 12 loci of which 8 were novel and introducing a prediction model for Europeans based on 14 SNPs. In the present study, we evaluated the capacity of DNA-based head hair shape prediction by investigating an extended set of candidate SNP predictors and by using an independent set of samples for model validation. Prediction model building was carried out in 9674 subjects (6068 from Europe, 2899 from Asia and 707 of admixed European and Asian ancestries), used previously, by considering a novel list of 90 candidate SNPs. For model validation, genotype and phenotype data were newly collected in 2415 independent subjects (2138 Europeans and 277 non-Europeans) by applying two targeted massively parallel sequencing platforms, Ion Torrent PGM and MiSeq, or the MassARRAY platform. A binomial model was developed to predict straight vs. non-straight hair based on 32 SNPs from 26 genetic loci we identified as significantly contributing to the model. This model achieved prediction accuracies, expressed as AUC, of 0.664 in Europeans and 0.789 in non-Europeans; the statistically significant difference was explained mostly by the effect of one EDAR SNP in non-Europeans. Considering sex and age, in addition to the SNPs, slightly and insignificantly increased the prediction accuracies (AUC of 0.680 and 0.800, respectively). Based on the sample size and candidate DNA markers investigated, this study provides the most robust, validated, and accurate statistical prediction models and SNP predictor marker sets currently available for predicting head hair shape from DNA, providing the next step towards broadening Forensic DNA Phenotyping beyond pigmentation traits.
Copyright 2018 Elsevier B.V. All rights reserved.
DATE PUBLISHED
2018 Aug 29
HISTORY
PUBSTATUS PUBSTATUSDATE
received 2018/02/26
revised 2018/07/18
accepted 2018/08/27
pubmed 2018/10/01 06:00
medline 2018/10/01 06:00
entrez 2018/10/01 06:00
AUTHORS
NAME COLLECTIVENAME LASTNAME FORENAME INITIALS AFFILIATION AFFILIATIONINFO
Pośpiech E Pośpiech Ewelina E Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa st. 9, 30-387, Kraków, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa st. 7A, 30-387, Kraków, Poland.
Chen Y Chen Yan Y Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beichen West Road 1-104, Chaoyang, Beijing, 100101, PR China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, PR China.
Kukla-Bartoszek M Kukla-Bartoszek Magdalena M Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa st. 7, 30-387, Kraków, Poland.
Breslin K Breslin Krystal K Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), IN, USA.
Aliferi A Aliferi Anastasia A King's Forensics, Faculty of Life Sciences and Medicine, King's College London, 150 Stamford Street, London, United Kingdom.
Andersen JD Andersen Jeppe D JD Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100, Copenhagen, Denmark.
Ballard D Ballard David D King's Forensics, Faculty of Life Sciences and Medicine, King's College London, 150 Stamford Street, London, United Kingdom.
Chaitanya L Chaitanya Lakshmi L Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, Netherlands.
Freire-Aradas A Freire-Aradas Ana A Institute of Legal Medicine, Medical Faculty, University of Cologne, Melatengürtel 60/62, D-50823, Cologne, Germany; Forensic Genetics Unit, Institute of Forensic Sciences, R/ San Francisco s/n, Faculty of Medicine, 15782, University of Santiago de Compostela, Santiago de Compostela, Spain.
van der Gaag KJ van der Gaag Kristiaan J KJ Division of Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA, The Hague, The Netherlands.
Girón-Santamaría L Girón-Santamaría Lorena L Forensic Genetics Unit, Institute of Forensic Sciences, R/ San Francisco s/n, Faculty of Medicine, 15782, University of Santiago de Compostela, Santiago de Compostela, Spain.
Gross TE Gross Theresa E TE Institute of Legal Medicine, Medical Faculty, University of Cologne, Melatengürtel 60/62, D-50823, Cologne, Germany.
Gysi M Gysi Mario M Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
Huber G Huber Gabriela G Institute of Legal Medicine, Medical University of Innsbruck, Müllerstrasse 44, 6020, Innsbruck, Austria.
Mosquera-Miguel A Mosquera-Miguel Ana A Forensic Genetics Unit, Institute of Forensic Sciences, R/ San Francisco s/n, Faculty of Medicine, 15782, University of Santiago de Compostela, Santiago de Compostela, Spain.
Muralidharan C Muralidharan Charanya C Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), IN, USA.
Skowron M Skowron Małgorzata M Department of Dermatology, Collegium Medicum of the Jagiellonian University, Skawińska st. 8, 31-066, Kraków, Poland.
Carracedo Á Carracedo Ángel Forensic Genetics Unit, Institute of Forensic Sciences, R/ San Francisco s/n, Faculty of Medicine, 15782, University of Santiago de Compostela, Santiago de Compostela, Spain; Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, KSA, Saudi Arabia.
Haas C Haas Cordula C Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
Morling N Morling Niels N Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100, Copenhagen, Denmark.
Parson W Parson Walther W Institute of Legal Medicine, Medical University of Innsbruck, Müllerstrasse 44, 6020, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, 13 Thomas Building, University Park, PA, 16802, USA.
Phillips C Phillips Christopher C Forensic Genetics Unit, Institute of Forensic Sciences, R/ San Francisco s/n, Faculty of Medicine, 15782, University of Santiago de Compostela, Santiago de Compostela, Spain.
Schneider PM Schneider Peter M PM Institute of Legal Medicine, Medical Faculty, University of Cologne, Melatengürtel 60/62, D-50823, Cologne, Germany.
Sijen T Sijen Titia T Division of Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA, The Hague, The Netherlands.
Syndercombe-Court D Syndercombe-Court Denise D King's Forensics, Faculty of Life Sciences and Medicine, King's College London, 150 Stamford Street, London, United Kingdom.
Vennemann M Vennemann Marielle M Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany.
Wu S Wu Sijie S University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, PR China; Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road Shanghai, 200031, PR China.
Xu S Xu Shuhua S University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, PR China; Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road Shanghai, 200031, PR China; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, 2005 Song Hu Road Shanghai, 200438, PR China; School of Life Science and Technology, Shanghai-Tech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, PR China.
Jin L Jin Li L Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road Shanghai, 200031, PR China; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, 2005 Song Hu Road Shanghai, 200438, PR China.
Wang S Wang Sijia S University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, PR China; Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road Shanghai, 200031, PR China; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, 2005 Song Hu Road Shanghai, 200438, PR China.
Zhu G Zhu Ghu G Queensland Institute of Medical Research, Royal Brisbane Hospital, QLD 4029, Brisbane, Australia.
Martin NG Martin Nick G NG Queensland Institute of Medical Research, Royal Brisbane Hospital, QLD 4029, Brisbane, Australia.
Medland SE Medland Sarah E SE Queensland Institute of Medical Research, Royal Brisbane Hospital, QLD 4029, Brisbane, Australia.
Branicki W Branicki Wojciech W Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa st. 7A, 30-387, Kraków, Poland.
Walsh S Walsh Susan S Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), IN, USA.
Liu F Liu Fan F Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beichen West Road 1-104, Chaoyang, Beijing, 100101, PR China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, PR China; Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, Netherlands.
Kayser M Kayser Manfred M Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, Netherlands. Electronic address: m.kayser@erasmusmc.nl.
EUROFORGEN-NoE Consortium
INVESTIGATORS
JOURNAL
VOLUME: 37
ISSUE:
TITLE: Forensic science international. Genetics
ISOABBREVIATION: Forensic Sci Int Genet
YEAR: 2018
MONTH: Aug
DAY: 29
MEDLINEDATE:
SEASON:
CITEDMEDIUM: Internet
ISSN: 1878-0326
ISSNTYPE: Electronic
MEDLINE JOURNAL
MEDLINETA: Forensic Sci Int Genet
COUNTRY: Netherlands
ISSNLINKING: 1872-4973
NLMUNIQUEID: 101317016
PUBLICATION TYPE
PUBLICATIONTYPE TEXT
Journal Article
COMMENTS AND CORRECTIONS
GRANTS
GENERAL NOTE
KEYWORDS
KEYWORD
DNA prediction
Externally visible characteristics
Forensic DNA Phenotyping
Hair shape
Head hair
Targeted massively parallel sequencing
MESH HEADINGS
SUPPLEMENTARY MESH
GENE SYMBOLS
CHEMICALS
OTHER ID's