John J. Farrell

A multi-ancestry polygenic risk score for Alzheimer disease is associated with cognitive decline, hippocampal atrophy and neuropathological hallmarks in diverse populations

This paper develops an APOE-independent polygenic risk score for Alzheimer's disease that shows associations with cognitive decline and neuropathological markers across diverse populations.

A Specialized Reference Panel with Structural Variants Integration for Improving Genotype Imputation in Alzheimer's Disease and Related Dementias (ADRD)

The paper develops an imputation panel integrating structural variants for Alzheimer's disease and related dementias, improving genotype imputation and identifying new genetic associations.

Alzheimer's Disease Sequencing Project Release 4 Whole Genome Sequencing Dataset

The paper provides a whole-genome sequencing dataset of 36,361 ADSP participants, including variant annotations, phenotypes, and a linkage disequilibrium panel for Alzheimer's Disease research.

Association of Common and Rare Variants with Alzheimer's Disease in over 13,000 Diverse Individuals with Whole-Genome Sequencing from the Alzheimer's Disease Sequencing Project

The paper investigates the association of common and rare variants with Alzheimer's Disease in 13,371 diverse individuals using whole-genome sequencing, identifying significant genetic loci and population-specific associations.

Structural Variation Detection and Association Analysis of Whole-Genome-Sequence Data from 16,905 Alzheimer's Diseases Sequencing Project Subjects

The paper identifies structural variations in whole-genome sequencing data from 16,905 ADSP subjects and finds associations with Alzheimer's disease and related endophenotypes.

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.

A comparative study of structural variant calling strategies using the Alzheimer's Disease Sequencing Project's whole genome family data

The paper evaluates deletion calling accuracy using two pipelines on ADSP whole genome family data, finding Scalpel better for small deletions and Parliament for larger ones, with 78.1% of predicted deletions validated by Sanger sequencing.

An Association Test of the Spatial Distribution of Rare Missense Variants within Protein Structures Improves Statistical Power of Sequencing Studies

POKEMON improves statistical power for detecting associations between rare missense variants and phenotypes by analyzing their spatial distribution on protein structures.

Cell-type Specific Expression Quantitative Trait Loci Associated with Alzheimer Disease in Blood and Brain Tissue

The paper identifies cell-type specific eQTLs associated with Alzheimer's disease in blood and brain tissue, finding shared genes and pathways relevant to AD risk.

Genome-Wide Meta-Analysis of Late-Onset Alzheimer's Disease Using Rare Variant Imputation in 324,809 Subjects Identifies Novel Rare Variant Locus NCK2: The International Genomics of Alzheimer's Project (IGAP)

A robust benchmark for germline structural variant detection

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

Cis- and Trans-Acting Expression Quantitative Trait Loci Differentially Regulate Gamma-Globin Gene Expression

The paper identifies cis- and trans-acting eQTLs influencing HBG2 and HBG1 expression and suggests BCL2L1 as a potential trans-acting HbF activator.