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RETRACTED ARTICLE: EDAR, LYPLAL1, PRDM16, PAX3, DKK1, TNFSF12, CACNA2D3, and SUPT3H gene variants influence facial morphology in a Eurasian population

This article was retracted on 30 August 2021

This article has been updated

Abstract

In human society, the facial surface is visible and recognizable based on the facial shape variation which represents a set of highly polygenic and correlated complex traits. Understanding the genetic basis underlying facial shape traits has important implications in population genetics, developmental biology, and forensic science. A number of single nucleotide polymorphisms (SNPs) are associated with human facial shape variation, mostly in European populations. To bridge the gap between European and Asian populations in term of the genetic basis of facial shape variation, we examined the effect of these SNPs in a European–Asian admixed Eurasian population which included a total of 612 individuals. The coordinates of 17 facial landmarks were derived from high resolution 3dMD facial images, and 136 Euclidean distances between all pairs of landmarks were quantitatively derived. DNA samples were genotyped using the Illumina Infinium Global Screening Array and imputed using the 1000 Genomes reference panel. Genetic association between 125 previously reported facial shape-associated SNPs and 136 facial shape phenotypes was tested using linear regression. As a result, a total of eight SNPs from different loci demonstrated significant association with one or more facial shape traits after adjusting for multiple testing (significance threshold p < 1.28 × 10−3), together explaining up to 6.47% of sex-, age-, and BMI-adjusted facial phenotype variance. These included EDAR rs3827760, LYPLAL1 rs5781117, PRDM16 rs4648379, PAX3 rs7559271, DKK1 rs1194708, TNFSF12 rs80067372, CACNA2D3 rs56063440, and SUPT3H rs227833. Notably, the EDAR rs3827760 and LYPLAL1 rs5781117 SNPs displayed significant association with eight and seven facial phenotypes, respectively (2.39 × 10−5 < p < 1.28 × 10−3). The majority of these SNPs showed a distinct allele frequency between European and East Asian reference panels from the 1000 Genomes Project. These results showed the details of above eight genes influence facial shape variation in a Eurasian population.

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Acknowledgements

This project was supported by the National Key R&D Program of China (2017YFC0803501), National Natural Science Foundation of China (91651507), Fund from institute of forensic science (2018JB046), and open projects of the National Engineering Laboratory for Forensic Science (2017NELKFKT05). Biological samples were provided by the National Science and Technological Resources Platform (YCZYPT[2017]01-3 and 2017JB025). Author FL is supported by “The Thousand Talents Plan for Young Professionals”. Author CXL is supported by “The Beijing Leading Talent Program (Z18110006318006)”.

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Correspondence to Fan Liu or Caixia Li.

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The authors declare that they have no conflicts of interest regarding this work.

Data Availability Statement

The dataset analyzed during the current study is restricted due to participant confidentially. Restrictions apply to the availability of these data, which were used under license for the current study, and so are not entirely publicly available. However, the variation data reported in this paper have been deposited in the Genome Variation Map (Song et al. 2018) in the BIG Data Center (Members BIGDC 2018), Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under accession number GVM000031 and can be publicly accessed at http://bigd.big.ac.cn/gvm/getProjectDetail?project=GVM000031.

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This article has been retracted. Please see the retraction notice for more detail:https://doi.org/10.1007/s00439-021-02352-6

Electronic supplementary material

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Supplementary Figure 1: Distribution plots of 136 quantitative facial traits (TIFF 15662 kb)

439_2019_2023_MOESM2_ESM.tif

Supplementary Figure 2: (A) The relative proportion of variance of the first 20 PCs derived from genotyped data, including our 612 Eurasian samples and the EAS and EUR samples from the 1000 Genomes Project. (B) The PC1 and PC2 plots of genotyped data, including our 612 Eurasian samples and the EAS and EUR samples from the 1000 Genomes Project (TIFF 22719 kb)

Supplementary Figure 3: The hierarchical clustering results of 136 facial phenotypes (TIFF 13680 kb)

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Supplementary Figure 4: Worldwide allele-frequency distributions for the eight identified variants. Map displaying the geospatial distribution of the allele frequency of rs3827760 (EDAR), rs5781117 (LYPLAL1), rs4648379 (PRDM16), rs7559271 (PAX3), rs1194708 (DKK1), rs80067372 (TNFSF12), rs56063440 (CACNA2D3), and rs227833 (SUPT3H) across the world. The map is drawn based on allele frequencies of 2504 subjects obtained from 1000 Genome project datasets for each SNP. The pie denotes the sampling locations (TIFF 34735 kb)

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Li, Y., Zhao, W., Li, D. et al. RETRACTED ARTICLE: EDAR, LYPLAL1, PRDM16, PAX3, DKK1, TNFSF12, CACNA2D3, and SUPT3H gene variants influence facial morphology in a Eurasian population. Hum Genet 138, 681–689 (2019). https://doi.org/10.1007/s00439-019-02023-7

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  • DOI: https://doi.org/10.1007/s00439-019-02023-7