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| PMID |
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| TITLE |
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| Towards broadening Forensic DNA Phenotyping beyond pigmentation: Improving the prediction of head hair shape from DNA. |
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| ABSTRACT |
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| 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. |
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| DATE PUBLISHED |
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| HISTORY |
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| PUBSTATUS |
PUBSTATUSDATE |
| received |
2018/02/26 |
| revised |
2018/07/18 |
| accepted |
2018/08/27 |
| pubmed |
2018/10/01 06:00 |
| medline |
2019/01/03 06:00 |
| entrez |
2018/10/01 06:00 |
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| AUTHORS |
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| 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 |
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Department of Dermatology, Collegium Medicum of the Jagiellonian University, Skawińska st. 8, 31-066, Kraków, Poland. |
| Carracedo Á |
|
Carracedo |
Ángel |
Á |
|
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 |
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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 |
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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 |
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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 |
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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 |
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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. |
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EUROFORGEN-NoE Consortium |
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| INVESTIGATORS |
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| JOURNAL |
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| VOLUME: 37 |
| ISSUE: |
| TITLE: Forensic science international. Genetics |
| ISOABBREVIATION: Forensic Sci Int Genet |
| YEAR: 2018 |
| MONTH: 11 |
| DAY: |
| MEDLINEDATE: |
| SEASON: |
| CITEDMEDIUM: Internet |
| ISSN: 1878-0326 |
| ISSNTYPE: Electronic |
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| MEDLINE JOURNAL |
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| MEDLINETA: Forensic Sci Int Genet |
| COUNTRY: Netherlands |
| ISSNLINKING: 1872-4973 |
| NLMUNIQUEID: 101317016 |
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| PUBLICATION TYPE |
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| PUBLICATIONTYPE TEXT |
| Journal Article |
| Research Support, Non-U.S. Gov't |
| Research Support, U.S. Gov't, Non-P.H.S. |
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| COMMENTS AND CORRECTIONS |
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| GRANTS |
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| GENERAL NOTE |
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| KEYWORDS |
|
| KEYWORD |
| DNA prediction |
| Externally visible characteristics |
| Forensic DNA Phenotyping |
| Hair shape |
| Head hair |
| Targeted massively parallel sequencing |
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| MESH HEADINGS |
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| DESCRIPTORNAME |
QUALIFIERNAME |
| Adult |
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| DNA |
genetics |
| Genome-Wide Association Study |
genetics |
| Genotyping Techniques |
instrumentation |
| Hair |
instrumentation |
| High-Throughput Nucleotide Sequencing |
instrumentation |
| Humans |
instrumentation |
| Logistic Models |
instrumentation |
| Models, Genetic |
instrumentation |
| Phenotype |
instrumentation |
| Polymorphism, Single Nucleotide |
instrumentation |
| Sequence Analysis, DNA |
instrumentation |
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| SUPPLEMENTARY MESH |
|
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| GENE SYMBOLS |
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| CHEMICALS |
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| REGISTRYNUMBER |
NAMEOFSUBSTANCE |
| 9007-49-2 |
DNA |
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| OTHER ID's |
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