Genome-wide Variants of Eurasian Facial Shape Differentiation and a prospective model of DNA based Face Prediction

Prediction of human physical traits and demographic information from genomic data challenges privacy and data deidentification in personalized medicine. To explore the current capabilities of phenotype-based genomic identification, we applied whole-genome sequencing, detailed phenotyping, and statistical modeling to predict biometric traits in a cohort of 1,061 participants of diverse ancestry. Individually, for a large fraction of the traits, their predictive accuracy beyond ancestry and demographic information is limited. However, we have developed a maximum entropy algorithm that integrates multiple predictions to determine which genomic samples and phenotype measurements originate from the same person. Using this algorithm, we have reidentified an average of >8 of 10 held-out individuals in an ethnically mixed cohort and an average of 5 of either 10 African Americans or 10 Europeans. This work challenges current conceptions of personal privacy and may have far-reaching ethical and legal implications.

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“…Anc refers to 1,000 genomic PCs. SNPs refers to previously reported SNPs related to facial structure (5,14,27). …”

Section: Significancementioning

confidence: 99%

Identification of individuals by trait prediction using whole-genome sequencing data

Lippert

Sabatini

Maher

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

142

119

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“…In fact, racial factors are a major cause because the results come from different populations, such as Europeans, Americans, Africans and East Asians, etc. (Adhikari et al 2016 ; Cha et al 2018 ; Claes et al 2018 ; Cole et al 2016 ; Lee et al 2017 ; Liu et al 2012 ; Paternoster et al 2012 ; Qiao et al 2018 ; Shaffer et al 2016 ). Even in the same race, such as in Europeans, few of the genes or loci identified in each study have been replicated (Adhikari et al 2016 ; Lee et al 2017 ; Paternoster et al 2012 ).…”

Section: Discussionmentioning

confidence: 99%

“…The WinEDMA 1.0.1 software ( http://c.faculty.umkc.edu/colet ) was used to calculate the Euclidean distances between landmarks. The above-mentioned reports (Adhikari et al 2016 ; Cha et al 2018 ; Claes et al 2018 ; Cole et al 2016 ; Lee et al 2017 ; Liu et al 2012 ; Paternoster et al 2012 ; Qiao et al 2018 ; Shaffer et al 2016 ) concluded that gene loci of facial phenotypes were mostly associated with the shapes of the nose, mouth, and mandible, especially the nasal region. Therefore, this study selected phenotypes mostly from these regions.…”

Section: Methodsmentioning

confidence: 99%

“…To date, the published papers have shown whole-genome association analyses of human facial shapes (Adhikari et al 2016 ; Cha et al 2018 ; Claes et al 2018 ; Cole et al 2016 ; Lee et al 2017 ; Liu et al 2012 ; Paternoster et al 2012 ; Qiao et al 2018 ; Shaffer et al 2016 ). Researchers have successfully applied these results to human facial modeling predictions and achieved satisfactory results (Claes et al 2014 ).…”

Section: Introductionmentioning

confidence: 99%

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Whole-exome sequencing identified four loci influencing craniofacial morphology in northern Han Chinese

Zhai²,

Xu³

et al. 2019

Hum Genet

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Facial shape differences are one of the most significant phenotypes in humans. It is affected largely by skull shape. However, research into the genetic basis of the craniofacial morphology has rarely been reported. The present study aimed to identify genetic variants influencing craniofacial morphology in northern Han Chinese through whole-exome sequencing (WES). Phenotypic data of the volunteers’ faces and skulls were obtained through three-dimensional CT scan of the skull. A total of 48 phenotypes (35 facial and 13 cranial phenotypes) were used for the bioinformatics analysis. Four genetic loci were identified affecting the craniofacial shapes. The four candidate genes are RGPD3 , IGSF3 , SLC28A3, and USP40 . Four single-nucleotide polymorphism (SNP) site mutations in RGPD3 , IGSF3, and USP40 were significantly associated with the skull shape ( p < 1×10 −6 ), and three SNP site mutations in RGPD3 , IGSF3, and SLC28A3 were significantly associated with the facial shape ( p < 1×10 −6 ). The rs62152530 site mutation in the RGPD3 gene may be closely associated with the nasal length, ear length, and alar width. The rs647711 site mutation in the IGSF3 gene may be closely associated with the nasal length, mandibular width, and width between the mental foramina. The rs10868138 site mutation in the SLC28A3 gene may be associated with the nasal length, alar width, width between tragus, and width between the mental foramina. The rs1048603 and rs838543 site mutations in the USP40 gene may be closely associated with the pyriform aperture width. Our findings provide useful genetic information for the determination of face morphology.

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“…Due to their abundant distribution in both the nuclear and mitochondrial genome, SNPs increasingly can provide the genetic background for the prediction of physical characteristics [200,201], or geographical origin [202,203], and can also provide investigative tools to trace unknown individuals [204,205] even from historical remains [206][207][208]. Determination of ancestry [209,210] and externally visible characteristics, such as skin, eye and hair pigmentation [211,212], morphology [213,214], or age [215,216], is an ongoing research field of forensics, requiring both forensic validation of analytical platforms and computation data.…”

Section: Markers For Supplemental Informationmentioning

confidence: 99%

Forensic DNA Technological Advancements as an Emerging Perspective on Medico-Legal Autopsy: A Mini Review

Pádár¹,

Zenke²,

Kozma³

2018

Post Mortem Examination and Autopsy - Current Issues From Death to Laboratory Analysis

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The importance of biological traces and evidences related to a criminal matter has been recognized for a long time. The examination of the expression of genetic polymorphism has been an integral part of the multidisciplinary field of medico-legal autopsy for over a century. Since the initial application of blood group antigens for personalization of a putative perpetrator in a murder case, the discipline of forensic genetics has evolved as a standard of forensic sciences. The real breakthrough, the application of molecular tools and processes for the in-vitro replication of genetic substances, has increasingly allowed the exploitation of advances of molecular genetics for both forensic and criminal investigations. Although there are certainly many more applications and scientific fields in the medico-legal arena, the relatively fast progress of genetics, which has accelerated recently with state-of-art technologies, can provide ever more relevant information in relation to a corpse or the cause and manner that resulted in the corpse for autopsy. This topic concerns the currently accepted forensic DNA technology, and the last section reviews commonly used markers for nuclear and mitochondrial DNA analysis as well as ongoing research. This review also focuses on the increasingly important non-human sources of DNA, and shortly covers the main aspects of animal forensic DNA examination.

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Genome-wide Variants of Eurasian Facial Shape Differentiation and a prospective model of DNA based Face Prediction

Cited by 9 publications

References 66 publications

Identification of individuals by trait prediction using whole-genome sequencing data

Identification of individuals by trait prediction using whole-genome sequencing data

Whole-exome sequencing identified four loci influencing craniofacial morphology in northern Han Chinese

Forensic DNA Technological Advancements as an Emerging Perspective on Medico-Legal Autopsy: A Mini Review

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