3D Facial Phenotyping by Biometric Sibling Matching Used in Contemporary Genomic Methodologies

Overview

Journal PLoS Genet

Specialty Genetics

Date 2021 May 13

PMID 33983923

Citations 11

Authors

Hanne Hoskens

Dongjing Liu

Sahin Naqvi

Myoung Keun Lee

Ryan J Eller

Karlijne Indencleef

Julie D White

Jiarui Li

Maarten H D Larmuseau

Greet Hens

Joanna Wysocka

Susan Walsh

Stephen Richmond

Mark D Shriver

John R Shaffer

Hilde Peeters

Seth M Weinberg

Peter Claes

Affiliations

Soon will be listed here.

Abstract

The analysis of contemporary genomic data typically operates on one-dimensional phenotypic measurements (e.g. standing height). Here we report on a data-driven, family-informed strategy to facial phenotyping that searches for biologically relevant traits and reduces multivariate 3D facial shape variability into amendable univariate measurements, while preserving its structurally complex nature. We performed a biometric identification of siblings in a sample of 424 children, defining 1,048 sib-shared facial traits. Subsequent quantification and analyses in an independent European cohort (n = 8,246) demonstrated significant heritability for a subset of traits (0.17-0.53) and highlighted 218 genome-wide significant loci (38 also study-wide) associated with facial variation shared by siblings. These loci showed preferential enrichment for active chromatin marks in cranial neural crest cells and embryonic craniofacial tissues and several regions harbor putative craniofacial genes, thereby enhancing our knowledge on the genetic architecture of normal-range facial variation.

Citing Articles

Enhanced insights into the genetic architecture of 3D cranial vault shape using pleiotropy-informed GWAS.

Goovaerts S, Naqvi S, Hoskens H, Herrick N, Yuan M, Shriver M Commun Biol. 2025; 8(1):439.

PMID: 40087503 DOI: 10.1038/s42003-025-07875-6.

Optimized phenotyping of complex morphological traits: enhancing discovery of common and rare genetic variants.

Yuan M, Goovaerts S, Lee M, Devine J, Richmond S, Walsh S Brief Bioinform. 2025; 26(2).

PMID: 40062617 PMC: 11891655. DOI: 10.1093/bib/bbaf090.

Syndrome-informed phenotyping identifies a polygenic background for achondroplasia-like facial variation in the general population.

Vanneste M, Hoskens H, Goovaerts S, Matthews H, Devine J, Aponte J Nat Commun. 2024; 15(1):10458.

PMID: 39622794 PMC: 11612227. DOI: 10.1038/s41467-024-54839-1.

Mapping genes for human face shape: Exploration of univariate phenotyping strategies.

Yuan M, Goovaerts S, Vanneste M, Matthews H, Hoskens H, Richmond S PLoS Comput Biol. 2024; 20(12):e1012617.

PMID: 39621772 PMC: 11661606. DOI: 10.1371/journal.pcbi.1012617.

A comprehensive evaluation of the phenotype-first and data-driven approaches in analyzing facial morphological traits.

Qiao H, Tan J, Yan J, Sun C, Yin X, Li Z iScience. 2024; 27(3):109325.

PMID: 38487017 PMC: 10937830. DOI: 10.1016/j.isci.2024.109325.

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