Andrea Ganna

Sex-related signatures in the plasma proteome not attributable to XX and XY chromosomes and their impact on health and disease

The paper introduces the Proteomic Sex Index (PSI), a continuous measure of plasma proteome alignment with chromosomal sex, showing its association with health and disease traits.

A Genome-Wide Association Study in the Chilean admixed population reveals four new loci for COVID-19 severity and susceptibility

The paper conducts a genome-wide association study in a Chilean admixed population to identify genetic loci associated with COVID-19 severity and susceptibility, finding four new loci.

Quantifying the contribution of genetic variation to healthcare expenditure across diverse healthcare systems

This study identifies genetic variants associated with healthcare costs across multiple systems, finding polygenic influences and large effects from specific loss-of-function variants.

Machine learning augmented genome-wide meta-analysis of prescription opioid use in 860,000 individuals

The paper uses genome-wide meta-analysis and machine learning to study prescription opioid use in 860,000 individuals, identifying genetic loci and distinguishing between pain-related and dose-intensity traits.

Reducing misclassification bias in electronic health record-based GWAS of psychiatric traits using the SuperControl framework

The paper reduces misclassification bias in EHR-based GWAS of psychiatric traits using SuperControl and PRISMA, increasing locus discovery and biological specificity.

Joint profiling of cell morphology and gene expression during in vitro neurodevelopment

The paper jointly profiles neuronal morphology and gene expression during iPSC differentiation to better understand neuronal development and disease modeling.

Removing genetic effects on plasma proteins enhances their utility as disease biomarkers

The paper removes genetic effects from plasma proteins to enhance their utility as disease biomarkers, showing improved associations with diseases and environmental factors.

Effect of a Dietary Intervention on Weight Loss in Adults with High vs Low Genetic Predisposition to Higher BMI: A Randomized Diet Intervention Trial

This study evaluates if weight loss from a dietary intervention varies by genetic predisposition to higher BMI, finding no significant interaction between polygenic scores and intervention effectiveness.

Limited overlap between genetic effects on disease susceptibility and disease survival

The paper compares genetic effects on disease susceptibility and progression, finding limited overlap and suggesting larger samples or different progression measures are needed.

The impact of polygenic score and socioeconomic status in predicting risk for 19 complex diseases

This study examines how polygenic scores and socioeconomic status jointly influence risk for 19 diseases, finding distinct and partly interacting effects across populations.

Polygenic risk score prediction accuracy convergence

This study assesses the progress and limitations of polygenic risk score prediction accuracy for common diseases, showing diminishing returns from recent GWAS and highlighting the need for broader variant coverage.

Prevalence and disease risks for male and female sex chromosome trisomies: a registry-based phenome-wide association study in 1.5 million participants of MVP, FinnGen, and UK Biobank

This study identifies prevalence and disease risks for male and female sex chromosome trisomies using registry data from 1.5 million participants, finding shared phenotypic associations across trisomy subtypes.

Transferability and accuracy of electronic health record-based predictors compared to polygenic scores

This study compares EHR-based phenotype risk scores (PheRS) and polygenic scores (PGS) for predicting 13 diseases, finding they capture independent information and improve prediction when combined.

Family-GWAS reveals effects of environment and mating on genetic associations

Family-based GWAS meta-analysis of 34 phenotypes shows standard GWAS effects carry sizeable confounding uncorrelated with direct genetic effects, while assortative mating likely inflates SNP heritability and genetic correlations.

Association between plausible genetic factors and weight loss from GLP1-RA and bariatric surgery: a multi-ancestry study in 10 960 individuals from 9 biobanks

This study investigates genetic factors influencing weight loss from GLP1-RA and bariatric surgery in 10,960 individuals across 9 biobanks, finding no strong genetic associations with GLP1-RA effectiveness but a modest link between BMI polygenic scores and reduced bariatric surgery weight loss.

High incidence and geographic distribution of cleft palate cases in Finland are associated with a regulatory variant in IRF6

The paper identifies a regulatory variant in IRF6 associated with increased cleft palate risk in Finland and shows it disrupts IRF6 enhancer function.

Non-linear genetic regulation of the blood plasma proteome

The paper identifies non-linear genetic regulation of plasma proteins using a deep learning method, finding dominance and epistasis effects in large cohorts.

50,000 years of Evolutionary History of India: Insights from ~2,700 Whole Genome Sequences

This study analyzes 2,762 whole genome sequences from diverse Indian populations to reconstruct 50,000 years of evolutionary history, revealing major admixture events and archaic hominin gene flow.

Evaluation of polygenic scoring methods in five biobanks reveals greater variability between biobanks than between methods and highlights benefits of ensemble learning

This study evaluates polygenic scoring methods across five biobanks and finds that biobank differences outweigh method differences, with ensemble learning improving performance.

ADuLT: An efficient and robust time-to-event GWAS

ADuLT is a time-to-event GWAS method that outperforms Cox regression in strongly ascertained studies, finding more genome-wide significant associations in psychiatric disorder analyses.

HAPNEST: efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes

HAPNEST generates and evaluates large-scale synthetic genotype and phenotype datasets for polygenic risk score analysis.

A FinnGen pilot clinical recall study for Alzheimer's disease

The paper demonstrates the feasibility of conducting clinical recall studies from the FinnGen biobank to collect customized clinical data from participants with Alzheimer's disease or mild cognitive disorder.

Development and validation of DNA Methylation scores in two European cohorts augment 10-year risk prediction of type 2 diabetes

The lingering effects of Neanderthal introgression on human complex traits

This study assesses the contribution of Neanderthal introgression to human complex traits using UK Biobank data, finding significant but depleted effects compared to modern human variants.

Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus.

This study identifies 43 genomic loci associated with reproductive success in 785,604 individuals, showing ongoing natural selection at the FADS locus.

Population analyses of mosaic X chromosome loss identify genetic drivers and widespread signatures of cellular selection

This study identifies genetic drivers and cellular selection signatures of mosaic X chromosome loss in women using large-scale population data and polygenic scores.

Genome-wide association study of school grades identifies a genetic overlap between language ability, psychopathology and creativity

This study identifies genetic overlaps between psychiatric disorders, language ability, and creativity through a GWAS of school grades.

Global biobank analyses provide lessons for developing polygenic risk scores across diverse cohorts

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.

A second update on mapping the human genetic architecture of COVID-19

This study updates a genome-wide association study on COVID-19 severity and susceptibility, identifying 51 genome-wide significant loci and mapping three major biological pathways.

Meta-analysis fine-mapping is often miscalibrated at single-variant resolution

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