Jonathan L. Haines

Genetic Architecture of Plasma Amyloid and Tau Biomarkers in the Amish

The paper identifies genetic variants associated with AD-related plasma biomarkers in the Amish cohort using GWAS and linkage analysis.

Evidence for reduced somatic T-cell receptor sequence diversity profiles among Midwestern Amish in an aging cohort study

The paper examines T-cell receptor sequence diversity and HLA alleles in Midwestern Amish participants to explore associations with Alzheimer's disease and cognitive status.

Heritability and rare variant contributions to Alzheimer disease in the Midwestern Amish

The paper estimates heritability and identifies genetic variants, including rare ones, associated with Alzheimer disease in the Amish population.

Heritability of Age-Related Macular Degeneration in the Amish

This study estimates the heritability of age-related macular degeneration in the Amish population using SNP and pedigree-based methods, finding substantial genetic contributions.

Evaluating sequence-to-function deep learning models for ancestry-stratified regulatory variant effect prediction using multi-ancestry blood eQTLs

This study evaluates two sequence-to-function models for predicting regulatory variant effects across ancestries using blood eQTL data, finding better performance for high-confidence variants in African American populations.

Shared Genetic Architecture Between Kidney Function and Alzheimer Disease Across Ancestries

This paper identifies shared genetic loci between kidney function and Alzheimer disease across ancestries, revealing both horizontal and vertical pleiotropy with APOE as the only shared locus.

Local genetic correlation analysis of Alzheimer's disease and stroke implicates PHLPP1 as a shared locus in individuals of African ancestry

Disrupted Lipid Homeostasis as a Pathogenic Mechanism in ABCA7-Associated Alzheimers Disease Risk

This paper investigates the impact of an ancestry-specific ABCA7 deletion on lipid homeostasis in Alzheimer's disease, showing disrupted lipid regulation in neurons.

Multi-ancestry Transcriptome-Wide Association Study Reveals Shared and Population-Specific Genetic Effects in Alzheimer's Disease

This study performs a multi-ancestry transcriptome-wide association study (TWAS) to identify shared and population-specific genetic effects in Alzheimer's disease using RNA-seq and genotype data from multiple cohorts.

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.

Alzheimer disease is (sometimes) highly heritable: Drivers of variation in heritability estimates for binary traits, a systematic review

This study reviews heritability estimates for late-onset Alzheimer's disease, showing significant variation across studies and highlighting the importance of population and methodological context.

Genome-wide pleiotropy analysis of longitudinal blood pressure and harmonized cognitive performance measures

This paper identifies genome-wide pleiotropic loci linking blood pressure and cognitive performance measures using longitudinal data from multiple cohorts.

Sex-Specific Genetic Drivers of Memory, Executive Functioning, and Language Performance in Older Adults

The paper identifies sex-specific genetic loci associated with memory, executive functioning, and language performance in older adults through genome-wide meta-analyses.

Heritability of Alzheimer-related plasma biomarkers in the Amish population

The paper estimates heritability of Alzheimer-related plasma biomarkers in the Amish population, finding moderate genetic contributions to biomarker variances.

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.

Evaluating the association of APOE genotype and cognitive resilience in SuperAgers

This study examines the association between APOE genotype and cognitive resilience in SuperAgers, finding lower APOE-ε4 and higher APOE-ε2 frequencies in non-Hispanic White SuperAgers compared to controls and Alzheimer's cases.

African origin haplotype protective for Alzheimer's disease in APOEϵ4 carriers: exploring potential mechanisms

The paper identifies an African-origin haplotype that reduces AD risk in APOEε4 carriers by 75% and explores its molecular mechanisms through sequencing and methylation analysis.

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.

Methylation Clocks Do Not Predict Age or Alzheimer's Disease Risk Across Genetically Admixed Individuals

The paper evaluates methylation clocks in genetically diverse populations and finds they are less accurate in admixed cohorts and fail to consistently predict age acceleration in Alzheimer's disease cases.

Identifying X-Chromosome Variants Associated with Age-Related Macular Degeneration

This study identifies X-chromosome variants associated with age-related macular degeneration using genome-wide association analysis and pathway enrichment.

Missense and Loss of Function Variants at GWAS Loci in Familial Alzheimer's Disease

The paper examines rare missense and loss of function variants in GWAS loci for Alzheimer's disease across families, finding that many families lack identifiable variants beyond APOE-e4.

Extended genome-wide association study employing the African Genome Resources Panel identifies novel susceptibility loci for Alzheimers Disease in individuals of African ancestry

Spatial Distribution of Missense Variants within Complement Proteins Associates with Age Related Macular Degeneration

The paper analyzes missense variants in complement genes to identify spatial associations with AMD risk using structural and functional metrics.

Domain mapping of disease mutations supports genetic testing of specific SORL1 variants in Alzheimer's Disease

The paper identifies high-priority missense variants in SORL1 associated with increased Alzheimer's Disease risk and earlier onset, suggesting clinical counseling considerations for carriers.

African ancestry APOE e4 non-carriers with higher educational attainment are resilient to Alzheimer disease pathology-specific blood biomarker pTau181.

This study finds that higher educational attainment in African ancestry individuals with AD pathology and APOE e4 non-carriers is associated with greater functional resilience.

A Haptoglobin (HP) Structural Variant Alters the Effect of APOE Alleles on Alzheimer's Disease

The paper investigates how a haptoglobin structural variant modifies the effect of APOE alleles on Alzheimer's disease risk and age of onset in European-descent and African American populations.

Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as novel risk factors for Alzheimers Disease

The paper identifies rare damaging variants in ATP8B4 and ABCA1 as novel risk factors for Alzheimer's Disease using exome sequencing data from 32,558 individuals.

Somatic Loss of the Y Chromosome and Alzheimer's Disease Risk

This study validates the association between mosaic loss of the Y chromosome and Alzheimer's Disease using prospective analyses and Mendelian Randomization across multiple cohorts.

Genetic variants in the SHISA6 gene are associated with delayed cognitive impairment in two family datasets

The paper identifies three SNVs associated with delayed age at onset of cognitive impairment in Amish populations, with one replicated in an independent dataset and linked to the SHISA6 gene.

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.