Genome-wide variants of Eurasian facial shape differentiation and a prospective model of DNA based face prediction

Lu Qiao^a,
Yajun Yang^{b, c},
Pengcheng Fu^d,
Sile Hu^a,
Hang Zhou^a,
Shouneng Peng^a,
Jingze Tan^{b, c},
Yan Lu^a,
Haiyi Lou^a,
Dongsheng Lu^a,
Sijie Wu^a,
Jing Guo^a,
Li Jin^{a, b, c, e},
Yaqun Guan^f,
Sijia Wang^{a, e, g
, ,},
Shuhua Xu^{a, e, g, h
, ,},
Kun Tang^{a
, ,}

a.
Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai 200031, China
b.
State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
c.
Fudan-Taizhou Institute of Health Sciences, Taizhou 225300, China
d.
Department of Neurology, The First People's Hospital of Chenzhou, Hunan 423000, China
e.
Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China
f.
Department of Biochemistry and Molecular Biology, Preclinical Medicine College, Xinjiang Medical University, Urumqi 830011, China
g.
Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
h.
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China

More Information

Corresponding author: E-mail address: wangsijia@picb.ac.cn (Sijia Wang); E-mail address: xushua@picb.ac.cn (Shuhua Xu); E-mail address: tangkun@picb.ac.cn (Kun Tang)

摘要

- /
- /
- /
- /
Abstract: It is a long-standing question as to which genes define the characteristic facial features among different ethnic groups. In this study, we use Uyghurs, an ancient admixed population to query the genetic bases why Europeans and Han Chinese look different. Facial traits were analyzed based on high-dense 3D facial images; numerous biometric spaces were examined for divergent facial features between European and Han Chinese, ranging from inter-landmark distances to dense shape geometrics. Genome-wide association studies (GWAS) were conducted on a discovery panel of Uyghurs. Six significant loci were identified, four of which, rs1868752, rs118078182, rs60159418 at or near UBASH3B, COL23A1, PCDH7 and rs17868256 were replicated in independent cohorts of Uyghurs or Southern Han Chinese. A prospective model was also developed to predict 3D faces based on top GWAS signals and tested in hypothetic forensic scenarios.
- Genome-wide association study /
- Dense 3D facial image /
- Ancestry-divergent phenotypes /
- Face prediction /
- Forensic scenario

HTML全文

参考文献(50)

[1]	Adhikari, K., Fuentes-Guajardo, M., Quinto-Sanchez, M. et al. Nat. Commun., 7 (2016),p. 11616
[2]	Benjamini, Y., Hochberg, Y. Controlling the false discovery rate : a practical and powerful approach to multiple testing J. Roy. Stat. Soc. B, 57 (1995),pp. 289-300
[3]	Bulik-Sullivan, B., Finucane, H.K., Anttila, V. et al. An atlas of genetic correlations across human diseases and traits Nat. Genet., 47 (2015),pp. 1236-1241
[4]	Claes, P., Hill, H., Shriver, M.D. Toward DNA-based facial composites: preliminary results and validation Forensic. Sci. Int. Genet., 13 (2014),pp. 208-216
[5]	Cole, J.B., Manyama, M., Kimwaga, E. et al. PLoS Genet., 12 (2016),pp. 1-19
[6]	Delaneau, O., Marchini, J., McVeanh, G.A. et al. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel Nat. Commun., 5 (2014),p. 3934
[7]	Dick, K.J., Nelson, C.P., Tsaprouni, L. et al. DNA methylation and body-mass index: a genome-wide analysis Lancet, 383 (2014),pp. 1990-1998
[8]	Geiger, M., Li, R.H., Friess, W. Collagen sponges for bone regeneration with rhBMP-2 Adv. Drug Deliv. Rev., 55 (2003),pp. 1613-1629
[9]	Guo, J., Mei, X., Tang, K. Automatic landmark annotation and dense correspondence registration for 3D human facial images BMC Bioinf., 14 (2013),p. 232
[10]	Guo, J., Tan, J., Yang, Y. et al. Variation and signatures of selection on the human face J. Hum. Evol., 75 (2014),pp. 143-152
[11]	Hair, J.F., Hult, G.T.M., Ringle, C.M. et al.
[12]	Hoff-Olsen, P., Mevåg, B., Staalstrøm, E. et al. Extraction of DNA from decomposed human tissue: an evaluation of five extraction methods for short tandem repeat typing Forensic Sci. Int., 105 (1999),pp. 171-183
[13]	Hopman, S.M., Merks, J.H., Suttie, M. et al. Face shape differs in phylogenetically related populations Eur. J. Hum. Genet., 22 (2014),pp. 1268-1271
[14]	Howie, B.N., Donnelly, P., Marchini, J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies PLoS Genet., 5 (2009),pp. 1-15
[15]	Howie, B., Fuchsberger, C., Stephens, M. et al. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing Nat. Genet., 44 (2012),pp. 955-959
[16]	Hu, S., Xiong, J., Fu, P. et al. Signatures of personality on dense 3D facial images Sci. Rep., 7 (2017),p. 73
[17]	Indahl, U. A twist to partial least squares regression J. Chemom., 19 (2005),pp. 32-44
[18]	Indahl, U.G., Liland, K.H., Næs, T. Canonical partial least squares-a unified PLS approach to classification and regression problems J. Chemom., 23 (2009),pp. 495-504
[19]	Kamberov, Y.G., Wang, S., Tan, J. et al. Cell, 152 (2013),pp. 691-702
[20]	Kilpelainen, T.O., Carli, J.F., Skowronski, A.A. et al. Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels Nat. Commun., 7 (2016),p. 10494
[21]	Krishnan, A., Williams, L.J., McIntosh, A.R. et al. Partial Least Squares (PLS) methods for neuroimaging: a tutorial and review Neuroimage, 56 (2011),pp. 455-475
[22]	Liland, K.H., Indahl, U.G. Powered partial least squares discriminant analysis J. Chemom., 23 (2009),pp. 7-18
[23]	Liu, F., van der Lijn, F., Schurmann, C. et al. A genome-wide association study identifies five loci influencing facial morphology in Europeans PLoS Genet., 8 (2012),pp. 1-13
[24]	Liu, F., Hamer, M.A., Deelen, J. et al. Curr. Biol., 26 (2016),pp. 1213-1220
[25]	Loos, R.J. Nat. Genet., 48 (2016),pp. 976-978
[26]	Loos, R.J., Janssens, A.C. Predicting polygenic obesity using genetic information Cell Metabol., 25 (2017),pp. 535-543
[27]	Lu, Y., Day, F.R., Gustafsson, S. et al. New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk Nat. Commun., 7 (2016),p. 10495
[28]	Myles, S., Somel, M., Tang, K. et al. Identifying genes underlying skin pigmentation differences among human populations Hum. Genet., 120 (2007),pp. 613-621
[29]	Ng, M.C.Y., Graff, M., Lu, Y. et al. Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium PLoS Genet., 13 (2017),pp. 1-25
[30]	Paternoster, L., Zhurov, A.I., Toma, A.M. et al. Am. J. Hum. Genet., 90 (2012),pp. 478-485
[31]	Patterson, N., Price, A.L., Reich, D. Population structure and eigenanalysis PLoS Genet., 2 (2006),pp. 2074-2093
[32]	Peng, S., Tan, J., Hu, S. et al. Detecting genetic association of common human facial morphological variation using high density 3D image registration PLoS Comput. Biol., 9 (2013),pp. 1-11
[33]	Price, A.L., Patterson, N.J., Plenge, R.M. et al. Principal components analysis corrects for stratification in genome-wide association studies Nat. Genet., 38 (2006),pp. 904-909
[34]	Pruim, R.J., Welch, R.P., Sanna, S. et al. LocusZoom: regional visualization of genome-wide association scan results Bioinformatics, 26 (2010),pp. 2336-2337
[35]	Purcell, S., Neale, B., Todd-Brown, K. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses Am. J. Hum. Genet., 81 (2007),pp. 559-575
[36]	Rahimov, F., Marazita, M.L., Visel, A. et al. Nat. Genet., 40 (2008),pp. 1341-1347
[37]	Relethford, J.H. Apportionment of global human genetic diversity based on craniometrics and skin color Am. J. Phys. Anthropol., 118 (2002),pp. 393-398
[38]	Relethford, J. Global patterns of isolation by distance based on genetic and morphological data Hum. Biol., 76 (2004),pp. 499-513
[39]	Ried, J.S., Jeff, M.J., Chu, A.Y. et al. A principal component meta-analysis on multiple anthropometric traits identifies novel loci for body shape Nat. Commun., 7 (2016),p. 13357
[40]	Shaffer, J.R., Orlova, E., Lee, M.K. et al. Genome-wide association study reveals multiple loci influencing normal human facial morphology PLoS Genet., 12 (2016),pp. 1-21
[41]	Smeets, D., Claes, P., Vandermeulen, D. et al. Objective 3D face recognition: evolution, approaches and challenges Forensic Sci. Int., 201 (2010),pp. 125-132
[42]	Talbert, L., Kau, C.H., Christou, T. et al. A 3D analysis of Caucasian and African American facial morphologies in a US population J. Orthod., 41 (2014),pp. 19-29
[43]	Turner, D., S qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots J. Open Source Softw., 3 (2018),p. 731
[44]	Weinberg, S.M., Parsons, T.E., Marazita, M.L. et al. Heritability of face shape in twins: a preliminary study using 3D stereophotogrammetry and geometric morphometrics Inside Dent., 3000 (2013)
[45]	Wood, A.R., Esko, T., Yang, J. et al. Defining the role of common variation in the genomic and biological architecture of adult human height Nat. Genet., 46 (2014),pp. 1173-1186
[46]	Xu, S., Jin, L. A genome-wide analysis of admixture in Uyghurs and a high-density admixture map for disease-gene discovery Am. J. Hum. Genet., 83 (2008),pp. 322-336
[47]	Xu, S., Huang, W., Qian, J. et al. Analysis of genomic admixture in Uyghur and its implication in mapping strategy Am. J. Hum. Genet., 82 (2008),pp. 883-894
[48]	Xu, S., Jin, W., Jin, L. Haplotype-sharing analysis showing Uyghurs are unlikely genetic donors Mol. Biol. Evol., 26 (2009),pp. 2197-2206
[49]	Yang, J., Benyamin, B., McEvoy, B.P. et al. Common SNPs explain a large proportion of the heritability for human height Nat. Genet., 42 (2010),pp. 565-569
[50]	Yang, J., Manolio, T.A., Pasquale, L.R. et al. Genome partitioning of genetic variation for complex traits using common SNPs Nat. Genet., 43 (2011),pp. 519-525

施引文献

资源附件(0)

访问统计

点击查看大图

计量

文章访问数: 116
HTML全文浏览量: 60
PDF下载量: 4
被引次数: 0

姓名
邮箱
手机号码
标题
留言内容
验证码

留言板

doi: 10.1016/j.jgg.2018.07.009

计量

Genome-wide variants of Eurasian facial shape differentiation and a prospective model of DNA based face prediction

Corresponding author: E-mail address: wangsijia@picb.ac.cn (Sijia Wang); E-mail address: xushua@picb.ac.cn (Shuhua Xu); E-mail address: tangkun@picb.ac.cn (Kun Tang)

计量

目录

留言板

doi: 10.1016/j.jgg.2018.07.009

计量

出版历程

Genome-wide variants of Eurasian facial shape differentiation and a prospective model of DNA based face prediction

Corresponding author: E-mail address: wangsijia@picb.ac.cn (Sijia Wang); E-mail address: xushua@picb.ac.cn (Shuhua Xu); E-mail address: tangkun@picb.ac.cn (Kun Tang)

计量

出版历程

目录