David W. Fardo

Rare extreme polygenic risk scores strongly indicate Alzheimer's disease risk

The paper identifies individuals with extreme polygenic risk scores (PRS) for Alzheimer's disease (AD) and shows they have significantly elevated AD risk across multiple ancestries and APOE diplotypes.

Alzheimer's Polygenic Risk Scores Are Not Interchangeable: Evidence from 1,752 Models

The paper evaluates 1,752 polygenic risk score models for Alzheimer's disease and finds significant variability in results across methods and ancestries.

Systematic contextual biases in SegmentNT potentially relevant to other nucleotide transformer models

The paper identifies contextual biases in the SegmentNT model, showing how input sequence length and nucleotide position affect predictions and suggests ways to mitigate these biases.

scVIP: personalized modeling of single-cell transcriptomes for developmental and disease phenotypes

scVIP models single-cell transcriptomes to predict phenotypes and infer trajectories in development and disease.

Whole genome sequence association analysis of brain structural volume measures in the NHLBI TOPMed Program highlights novel loci in diverse participants

This study uses whole-genome sequence data from diverse participants to identify novel genetic loci associated with brain structural volumes, highlighting the importance of diverse cohorts in uncovering genetic architecture.

Clustering individuals using INMTD: a novel versatile multi-view embedding framework integrating omics and imaging data

INMTD integrates omics and 3D imaging data to produce unconfounded individual subgroups with biologically meaningful embeddings.

Genomic and phenotypic correlates of mosaic loss of chromosome Y in blood

The paper identifies genetic and phenotypic correlates of mosaic loss of chromosome Y in blood using whole genome sequencing data from the TOPMed program.

Systematic review and meta-analysis of bulk RNAseq studies in human Alzheimer's disease brain tissue

This study systematically reviews and meta-analyzes bulk RNAseq studies in human Alzheimer's disease brain tissue to identify differentially expressed genes and pathways.

Novel multi-omics deconfounding variational autoencoders can obtain meaningful disease subtyping

The paper introduces four VAE-based deconfounding frameworks for multi-omics clustering, showing they reduce confounding effects and improve biological clustering.

Multi-ancestry genome-wide meta-analysis of 56,241 individuals identifies LRRC4C, LHX5-AS1 and nominates ancestry-specific loci PTPRK, GRB14, and KIAA0825 as novel risk loci for Alzheimer disease: the Alzheimer Disease Genetics Consortium

This study identifies novel Alzheimer's disease risk loci by analyzing multi-ancestry GWAS data from diverse populations, highlighting the importance of including underrepresented groups in genetic research.

Manifestations of genetic risk for Alzheimer's Disease in the blood: a cross-sectional multi-omic analysis in healthy adults aged 18-90+

This study identifies blood-based biomarkers associated with Alzheimer's disease genetic risk variants in a large cohort of healthy adults, showing effects from early adulthood and sex-specific patterns.

Region-based analysis of rare genomic variants in whole-genome sequencing datasets reveal two novel Alzheimer's disease-associated genes: DTNB and DLG2

This study identifies two novel Alzheimer's disease-associated genes, DTNB and DLG2, by analyzing rare variants in whole-genome sequencing data from AD family datasets.

A New Functional F-Statistic for Gene-Based Inference Involving Multiple Phenotypes

The paper introduces an exact alternative to the Shen and Faraway F-statistic for gene-based multi-phenotype analysis, showing it performs well in small sample sizes and identifies novel associations in neurodegenerative disease data.

Genetic Variants and Functional Pathways Associated with Resilience to Alzheimer's Disease

This study identifies genetic variants and pathways associated with cognitive resilience to Alzheimer's disease, finding a novel locus linked to bile acid metabolism and methylation changes.

A/T/N polygenic risk score for cognitive decline in old age

The paper develops a polygenic risk score integrating AD biomarkers and shows it better predicts cognitive decline than a clinical AD-based PRS.

Noninvasive sleep monitoring in large-scale screening of knock-out mice reveals novel sleep-related genes

The paper identifies 122 novel sleep-related genes from a large-scale knockout mouse study using non-invasive sleep monitoring.

Genetic data and cognitively-defined late-onset Alzheimer’s disease subgroups

The paper identifies genetic loci associated with cognitively-defined subgroups of late-onset Alzheimer’s disease using SNP data from multiple studies.