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Basic Science and Pathogenesis.

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Heterogeneity in Alzheimer's Disease (AD) cohorts, including age and APOE profiles, was identified. Optimizing these diverse cohorts improved AD gene discovery and recovery, offering new research opportunities.

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Area of Science:

  • Genetics
  • Neuroscience
  • Bioinformatics

Background:

  • Alzheimer's Disease (AD) affects millions, necessitating advancements in gene discovery and therapeutics.
  • The Alzheimer's Disease Sequencing Project (ADSP) has amassed extensive sequencing data via the National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (NIAGADS).
  • Observed phenotypic heterogeneity (sex, APOE, age) within NIAGADS sub-cohorts prompted this investigation.

Purpose of the Study:

  • To address cohort heterogeneity hindering robust AD risk discoveries.
  • To generate a unified dataset from diverse NIAGADS WES (R2) and WGS (R4) data.
  • To identify and validate novel AD candidate genes.

Main Methods:

  • Utilized 56,000 AD and healthy subject samples from NIAGADS R2 and R4 datasets.
  • Performed quality control, including genetic ancestry prediction.
  • Analyzed sub-cohorts by sex, age, age of onset, and APOE genotypes, identifying and removing outlier sub-cohorts.
  • Applied pipelines to identify and computationally/experimentally validate AD candidate genes.

Main Results:

  • Confirmed significant differences in APOE and age distributions between AD and healthy subjects.
  • Identified and removed outlier sub-cohorts with diverse age and APOE profiles.
  • Removing outliers enhanced AD gene discovery, improving replication of known AD genes (p < 1.2e-3 for R2, p < 8.6e-5 for R4) and STRING network connectivity (z > 5.6).
  • Analysis of extreme age-of-onset cases within remaining cohorts further facilitated gene discovery.

Conclusions:

  • NIAGADS R2-R4 cohorts exhibit significant heterogeneity in APOE and age distributions.
  • Optimizing cohorts based on these distributions demonstrably improves AD gene recovery.
  • Cohort heterogeneity presents opportunities for studying specific subgroups (e.g., age of onset, APOE profiles).
  • These findings can inform standard criteria for AD case/control selection, advancing future research.