Nilanjan Chatterjee

Genetic and Cellular Architecture of Breast Cancer Risk Across Ancestries

This study analyzes breast cancer GWAS across multiple ancestries, finding similar heritability and genetic correlations, and identifies shared regulatory and cellular contexts.

TLS-Tractor: A transfer learning framework for incorporating summary-statistics into local ancestry-aware GWAS in admixed populations

TLS-Tractor integrates external GWAS summary statistics with individual-level data for ancestry-aware association analysis in admixed populations, improving power and calibration.

Local ancestry-informed rare variant burden testing improves gene discovery in admixed populations

Tractor-Burden improves gene discovery in admixed populations by incorporating local ancestry in rare variant burden testing, identifying additional genes and pathways for type 2 diabetes.

Contextualizing the Utility of Polygenic Risk Scores using Absolute Risk Models in Diverse Ancestry Populations

This paper evaluates polygenic risk scores (PRSs) in diverse populations using absolute risk models, finding that PRSs can provide greater utility in risk stratification for certain diseases in non-European populations.

Estimation of Direct and Indirect Polygenic Effects and Gene-Environment Interactions using Polygenic Scores in Case-Parent Trio Studies

This paper introduces PGS-TRI, a framework to estimate direct and indirect polygenic effects and gene-environment interactions in case-parent trio studies, applied to autism and orofacial clefts.

A genome-wide meta-analysis identifies a sex-specific genetic effect for platelet aggregation in response to agonists

This study identifies a sex-specific genetic variant affecting platelet aggregation in response to low-dose epinephrine across multiple cohorts.

Evaluating Individual Level Performance of Polygenic Risk Scores Using Early Onset High Genetic Risk Coronary Artery Disease as a Benchmark

The paper evaluates individual-level performance of polygenic risk scores (PRSs) using a benchmark cohort of early-onset coronary artery disease patients, showing variability in PRS accuracy and highlighting the need for individual-level validation.

Ancestrally diverse genome-wide association analysis highlights ancestry-specific differences in genetic regulation of plasma protein levels

The paper identifies ancestry-specific and shared genetic regulators of plasma proteins in European and African populations, revealing novel causal relationships and shared pQTLs.

Genome-Wide Large-Scale Multi-Trait Analysis Characterizes Global Patterns of Pleiotropy and Unique Trait-Specific Variants

This study identifies pleiotropic variants and trait-specific susceptibility variants using GWAS data from 116 traits, revealing widespread pleiotropy and unique genetic contributions to specific traits.

Joint Modeling of Gene-Environment Correlations and Interactions using Polygenic Risk Scores in Case-Control Studies

This paper develops a method to jointly model gene-environment correlations and interactions using polygenic risk scores in case-control studies, showing improved performance over standard approaches in detecting breast cancer risk interactions.

An Ensemble Penalized Regression Method for Multi-ancestry Polygenic Risk Prediction

This paper introduces PROSPER, an ensemble penalized regression method for multi-ancestry polygenic risk prediction, showing improved performance across diverse populations.

MUSSEL: Enhanced Bayesian Polygenic Risk Prediction Leveraging Information across Multiple Ancestry Groups

MUSSEL improves polygenic risk prediction across populations by integrating GWAS summary statistics and using Bayesian hierarchical modeling with ensemble learning.

Subset-based method for cross-tissue transcriptome-wide association studies improves power and interpretability

The paper introduces CSTWAS, a subset-based meta-analysis method for cross-tissue transcriptome-wide association studies that improves power and identifies active tissues for gene-trait associations.

Admix-kit: An Integrated Toolkit and Pipeline for Genetic Analyses of Admixed Populations

Admix-kit provides tools for genetic analysis of admixed populations, enabling simulation, association testing, and polygenic scoring.

Mendelian Randomization Analysis Using Multiple Biomarkers of an Underlying Common Exposure

This paper introduces MRLE, a method for Mendelian Randomization analysis of latent exposures using multiple biomarkers, showing improved power and evidence for inflammation's causal role in diseases.

A new method for multi-ancestry polygenic prediction improves performance across diverse populations

The paper introduces CT-SLEB, a method for multi-ancestry polygenic prediction that improves performance in non-European populations using GWAS summary statistics and simulation studies.

A Polygenic Score for Reduced Kidney Function and Adverse Outcomes in a Chronic Kidney Disease Cohort

The paper assesses if a polygenic score for reduced kidney function predicts adverse outcomes in chronic kidney disease patients, finding significant associations but no improvement in prediction over existing risk equations.

The miR-124-AMPAR pathway connects polygenic risks with behavioral changes shared between schizophrenia and bipolar disorder

This study identifies the miR-124-AMPAR pathway as a common mediator linking polygenic risks to shared behavioral changes in schizophrenia and bipolar disorder.

Aggregative trans-eQTL analysis detects trait-specific target gene sets in whole blood

This study introduces ARCHIE, a method to identify trait-specific gene sets through trans-eQTL analysis, finding 71 gene networks with significant trans-associations across 29 traits.

Pathogen exposure misclassification can bias association signals in GWAS of infectious diseases when using population-based common controls

This study shows that using population-based common controls in GWAS of infectious diseases can lead to biased effect estimates and spurious associations due to unaccounted pathogen exposure.

Plasma proteome analyses in individuals of European and African ancestry identify cis-pQTLs and models for proteome-wide association studies

The paper identifies cis-pQTLs and develops models for proteome-wide association studies using plasma proteome data from European and African ancestry populations.

Genome-wide association studies of 27 accelerometry-derived physical activity measurements identifies novel loci and genetic mechanisms

This study identifies 5 novel genetic loci associated with physical activity using 27 accelerometry-derived phenotypes from 88,411 UK Biobank participants.

Smoking Interaction with a Polygenic Risk Score for Reduced Lung Function

This study investigates whether smoking modifies the effect of a polygenic risk score on reduced lung function, finding significant gene-by-smoking interactions in FEV1/FVC.

Improving reporting standards for polygenic scores in risk prediction studies

ClinGen and the PGS Catalog expand the GRIPS guideline into a 22-item Polygenic Risk Score Reporting Statement covering study populations, model construction, evaluation, and clinical interpretation.

A Powerful Method for Pleiotropic Analysis under Composite Null Hypothesis Identifies Novel Shared Loci Between Type 2 Diabetes and Prostate Cancer

A Comprehensive Evaluation of Methods for Mendelian Randomization Using Realistic Simulations and an Analysis of 38 Biomarkers for Risk of Type-2 Diabetes

This paper evaluates Mendelian randomization methods using realistic simulations and real GWAS data, finding that performance varies with sample size, instrument validity, and InSIDE assumption.

Polygenic Risk Scores for Kidney Function to the Circulating Proteome, and Incident Kidney Diseases: the Atherosclerosis Risk in Communities Study

This study develops a polygenic risk score for eGFR and shows its association with kidney disease outcomes and plasma proteins in the ARIC study.

Genome-wide association and multi-omic analyses reveal new mechanisms for Heart Failure

This study identifies one known and two novel genetic variants associated with heart failure through GWAS and multi-omic analyses, revealing potential causal mechanisms and shared heritability with musculoskeletal traits.

iCARE: An R Package to Build, Validate and Apply Absolute Risk Models

iCARE is an R package for building, validating, and applying absolute risk models using user-defined inputs and SNP data, demonstrated with breast cancer.

A mixed-model approach for powerful testing of genetic associations with cancer risk incorporating tumor characteristics

The paper introduces a mixed-model approach to test genetic associations with cancer risk, incorporating tumor characteristics, and shows it outperforms existing methods in identifying heterogeneous associations.