Judy H. Cho

This study shows GM-CSF reduces intestinal inflammation in Crohn's disease by modulating myeloid cell signaling and ILC-like transcriptional states.

The paper uses GenePy scores and clustering to identify genetic clusters in IBD patients, finding NOD2 and NLRP1 as significant drivers with phenotypic associations.

This study identifies 619 IBD risk signals, resolves 81 high-confidence variants, and prioritizes 664 candidate effector genes using GWAS, eQTL, and exome sequencing.

This study uses exome and genome sequencing to identify 68 genes directly associated with inflammatory bowel disease, providing clearer genetic insights and therapeutic targets.

The paper analyzes over 800,000 human genomes to assess penetrance of clinically relevant variants, finding that 95% of pLoF variants in severe diseases have explanations for lack of disease manifestation.

This study investigates how stem cell transplantation (SCT) restores immune function in refractory Crohn's disease by analyzing immune cell remodeling and HSC heterogeneity using single-cell RNA sequencing and functional assays.

Rare-variant depletion in 1kb windows of 76,156 gnomAD genomes, versus feature-adjusted mutation expectations, marks regulatory elements and outperforms seven alternative scores at flagging functional non-coding variants.

The paper develops a method to infer compound heterozygosity from exome sequencing data, achieving high accuracy in phasing rare variants for recessive disease diagnosis.

This study evaluates polygenic risk score methods across diverse biobanks and ancestries, finding that European reference panels often yield better performance, while PRS-CS outperforms P+T for high-heritability traits.

This paper shows that meta-analysis fine-mapping is often miscalibrated due to cohort heterogeneity and introduces a QC method to identify suspicious loci.

Meta-analysis of harmonized GWAS from up to 18 biobanks (six ancestry groups) across 14 endpoints replicated 320 known loci and identified 188 apparently novel loci.

This paper develops a genome-wide polygenic score for chronic kidney disease that incorporates APOL1 risk genotypes and shows consistent performance across four major continental ancestries.

This paper introduces MOI-Pred, a tool for predicting recessive inheritance of missense variants, showing high accuracy in distinguishing recessive disease-causing variants.

This paper predicts the utility of polygenic embryo screening for disease based on selection strategies and finds that selecting the lowest PRS embryo can significantly reduce disease risk.

The paper uses measured and predicted gene expression to identify ulcerative colitis patients at elevated risk of colectomy, showing both methods independently replicate in multiple datasets.

This study links genomic data with EHRs to identify health outcomes enriched in sub-populations, revealing both known and novel associations.

The paper identifies ultra-rare exonic variants in an Ashkenazi Jewish founder population, implicating cadherins in schizophrenia through recurrent mutations and altered purifying selection.

The paper quantifies disease risk associated with 37,772 clinical variants across 72,434 individuals, revealing heterogeneity in penetrance and limitations of current variant classification systems.

This paper reports on a pilot genomic screening program in a diverse population, finding higher return rates for hATTR results in African/African American and Hispanic/Latinx participants.

This study identifies robust gene-phenotype associations by analyzing rare loss-of-function variants in exome-wide data linked to electronic health records.

The paper identifies 7 novel IBD-causing genes in Ashkenazi Jewish IBD patients using exome sequencing and analyzes their overlap with early-onset IBD and other diseases.

From 125,748 exomes and 15,708 genomes, 443,769 high-confidence predicted loss-of-function variants yield LOEUF, a continuous gene intolerance score tracking mouse lethality, cell essentiality, and disease associations.

The paper develops an expression-based annotation metric to improve rare variant interpretation by filtering false-positive loss-of-function variants and identifying pathogenic variants in highly expressed exons.

Short-read genome sequencing of 14,891 diverse genomes yields 433,371 structural variants (SVs) for gnomAD; loss-constrained genes also resist duplication, and clinical SV carrier rates are benchmarked.

The paper analyzes loss-of-function variants in LRRK2 across large genomic datasets to assess the safety of partial LRRK2 inhibition as a Parkinson's disease therapy.

The paper analyzes multi-nucleotide variants (MNVs) in 125,748 exomes and 15,708 genomes, identifying their distribution, mutational origins, and functional implications.

The paper uses exome sequencing and EHR data to find BRCA1/2 pathogenic variants in a diverse biobank population, revealing high prevalence in certain ancestry groups and gaps in knowledge for non-European populations.

This study shows that natural language processing applied to electronic health records can accurately identify patients with non-alcoholic fatty liver disease and detect those at risk for disease progression.

The paper sequenced a population-specific reference panel at high depth to improve imputation accuracy and variant filtering in the Ashkenazi Jewish population.

The paper identifies a common collagen disease in Puerto Ricans using identity-by-descent mapping and genomic data from a health system.