John R. Shaffer

The paper performs trio-based GWAS on cleft lip subtypes to identify novel genetic loci associated with specific phenotypes.

This study uses a pleiotropy-informed GWAS method to identify new orofacial cleft risk loci by leveraging genetic associations with facial shape.

This study identifies novel genetic drivers of orofacial clefts by analyzing de novo variants in 2,497 trios and integrating findings across subtypes and syndromic status.

The paper uses 3D craniofacial data and genome-wide association analysis to link craniofacial variation to genetic diversity, evolutionary processes, and clinical conditions in modern humans.

The paper investigates gene-environment interactions involving maternal exposures and orofacial cleft risk in Filipinos, identifying suggestive interactions with smoking and vitamin use.

This study identifies three new genetic loci associated with orofacial cleft risk and confirms known risk genes, providing insights into the molecular mechanisms of facial development.

This study compares univariate phenotyping strategies for 3D facial shape in GWAS, finding that inter-landmark distances and AE-derived dimensions show higher heritability than facial resemblance to gestalts.

This study identifies DNA methylation sites associated with cognitive function in early-stage hormone receptor-positive breast cancer patients using epigenome-wide association analyses.

The paper identifies a SNP that regulates facial shape and disease risk by affecting PKDCC expression during chondrogenesis, showing its impact on both normal variation and clefting.

This paper introduces a method to extract genetically relevant facial phenotypes by optimizing trait heritability, showing higher heritability and better GWAS performance compared to principal components.

This study performs a joint multi-ancestry and admixed GWAS on cranial vault shape, identifying 30 genome-wide significant loci and highlighting genetic pathways involved in craniofacial development.

The paper identifies gene-environment interactions associated with orofacial cleft risk, highlighting VGLL2 and PRL as key genes interacting with alcohol and smoking, respectively.

The paper investigates genetic differences between bilateral and unilateral cleft lip and palate subtypes using genome-wide association studies and finds distinct genetic architectures.

The paper investigates the impact of low-frequency coding variants on facial shape in Europeans, identifying seven genes associated with facial morphology and showing a specific variant's effect on chin shape.

This study identifies 203 genomic regions associated with facial variation using GWAS on multivariate shape phenotypes, revealing novel regions and epistatic interactions.

This study identifies shared genetic loci influencing brain and facial shape, distinct from cognitive traits, suggesting a developmental link between brain and face formation.

The paper develops a DNA methylation QC protocol and compares blood and CSF methylation profiles in aSAH patients, finding low global correlation and suggesting blood is not a suitable surrogate for CSF.

This study identifies 24 genetic loci associated with facial shape variation in humans through GWAS and confirms 13 of them in a multi-ethnic cohort.

The paper develops a framework to analyze subtype-specific and shared genetic effects in orofacial clefting and applies it to identify loci associated with different subtypes.

The paper introduces a fully-adjusted two-stage method for rank normalization in genetic association studies to reduce Type I errors and improve power by adjusting for covariates in both stages.

The paper investigates genetic overlap between non-syndromic cleft lip/palate and facial morphology using polygenic risk scores and Mendelian randomization, finding a causal relationship with philtrum width.

This paper conducts a consortium-wide GWAS to identify genetic variants associated with childhood dental caries, finding two significant loci but low heritability estimates.