David J. Cutler

This study identifies de novo structural variants in individuals with orofacial clefts and finds they contribute to genetic risk, with some variants disrupting known risk genes and suggesting new candidate genes.

This study identifies centromeric structural variants linked to molecular traits and complex diseases in humans using long-read sequencing and haplotype-resolved analysis.

The paper identifies 253 autism-associated genes using rare variation from 62,429 individuals and finds pleiotropy across physiological systems and developmental disorders.

The paper develops a model to analyze X-linked rare variation in ASD, identifying 9 genes associated with ASD and explaining how X-linked variation could contribute to sex-differential prevalence.

This paper introduces KDCA, a framework for differential co-expression analysis of general risk factors, showing improved power and reduced bias compared to existing methods.

The paper identifies rare variants in PRKCI as a novel cause of Van der Woude syndrome and other peridermopathy features through clinical and functional analyses.

CADET improves transcriptome-wide association studies in admixed populations by integrating local ancestry and eQTL data to enhance gene expression prediction and association testing.

The paper identifies protein-altering de novo variants in CP probands, finding higher enrichment in syndromic cases and distinct biological enrichments in single-cell RNA sequencing datasets.

The paper identifies sex-specific genetic risks for cleft palate through genome-wide gene-by-sex interaction analysis in a trio-based cohort.

SCAMPI detects SNP interactions across multiple traits by analyzing trait correlation patterns, improving power over univariate methods in lipid-related traits from UK Biobank data.

This study performs genome-wide association analyses of congenital heart defects in Down syndrome, identifying suggestive loci associated with specific heart defect subtypes.

This paper introduces LIT, a method to detect latent genetic interactions using multiple traits, showing improved power compared to univariate methods in obesity-related traits.

This study performs trio-based GWAS to identify genetic risk factors for cleft palate subtypes, finding a genome-wide significant locus and subtype-specific associations.

The paper estimates the diagnostic yield of sequencing 418 genes in OFC cases and controls, finding a higher prevalence of likely pathogenic variants in cases.

POIROT detects parent-of-origin effects in GWAS by comparing phenotypic covariance matrices across genotypes, showing improved power and robustness to non-normality.

This study identifies rare variants in SEC24D associated with orofacial cleft subtypes and shows they affect transcription factor binding sites.

The paper identifies ten new genes with coding variants linked to Crohn's disease risk using sequencing data from over 30,000 patients and 80,000 controls.

The paper identifies OTUD7A loss-of-function mutations in schizophrenia-associated 15q13.3 deletions and shows they impair synapse development and function in human neurons.

The paper identifies methylation quantitative trait loci (mQTLs) in blood and ileum samples from Crohn's disease patients and finds they are largely consistent across disease states and tissues.

This study investigates the molecular effects of the 3q29 deletion on the human neural transcriptome, identifying convergent and distributed impacts across gene clusters and pathways related to psychiatric disorders.

The paper shows that sex-specific differences in meiotic recombination rates are associated with parental origin biases in recurrent genomic disorders.

The paper identifies pQTLs for brain proteins and finds they differ from eQTLs, suggesting distinct genetic control of mRNA and protein abundance.

This study evaluates 32 individuals with 3q29 deletion syndrome to identify common medical and neurodevelopmental features and provides clinical care recommendations.

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 identifies coding de novo mutations in whole-genome sequencing data from OFC cases and finds enrichment in genes expressed in craniofacial tissues and linked to OFC syndromes.

This paper introduces a new rare-variant association test that incorporates family history information, showing improved performance over standard methods in simulated data and a study of cleft lip and palate.

Bystro provides rapid online variant annotation and natural-language filtering for large whole-genome sequencing experiments, significantly speeding up processing time.

This study investigates the association between copy number variants on chromosome 21 and congenital heart defects in Down syndrome, finding no direct link but suggesting ethnic differences in CNV patterns.

The paper identifies 91 genes associated with neurodevelopmental disorders but highlights critical statistical flaws in the analysis that reduce the validity of the findings.

The paper shows that many de novo protein truncating variants in neurodevelopmental disorders are common in population cohorts and do not contribute to risk, using data from 9246 families and 60,706 adults.