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Region-based analysis with functional annotation identifies genes associated with cognitive function in South Asians
Hasan Abu-Amara1, Wei Zhao1, Zheng Li1
1University of Michigan.
Research Square
|August 16, 2024
Summary
Genetic risk factors for dementia in South Asians are understudied. This study found that some Alzheimer's disease (AD) risk genes in European Ancestry populations are also associated with cognitive function in South Asians from India.
Area of Science:
- Genetics
- Neuroscience
- Population Health
Background:
- Dementia prevalence is high in South Asians (7.4% in those ≥60 years), but genetic risk factors remain largely unknown.
- Most identified Alzheimer's disease (AD) risk loci originate from European Ancestry (EA) studies, limiting applicability to diverse populations.
Purpose of the Study:
- To investigate genetic risk factors for cognitive function in South Asians using whole-genome sequence data.
- To identify gene-based associations with cognitive measures, including the Hindi Mental State Examination (HMSE) and general cognitive function.
Main Methods:
- Analyzed whole-genome sequence data from 2680 participants in the Longitudinal Aging Study of India (LASI-DAD).
- Performed gene-based association tests on 84 AD-associated genes from EA populations, examining missense/loss-of-function (LoF) and promoter/enhancer variants.
- Utilized the variant-Set Test for Association using Annotation infoRmation (STAAR) with and without annotation weights.
Main Results:
- Three genes showed significant associations with cognitive function measures (FDR q<0.1) in the missense/LoF analysis: *APOE* (4 measures), *PICALM* (HMSE score), and *TSPOAP1* (executive function).
- Identified specific variants, including the rare missense mutation rs779406084 in *PICALM*, which is more prevalent in the South Asian cohort than in EA.
- No significant associations were found for brain-specific promoter/enhancer variants.
Conclusions:
- Missense/LoF variants in genes previously linked to AD in EA populations are associated with cognitive function in South Asians from India.
- Whole-genome sequencing facilitates the discovery of potential novel causal variants that may be enriched in South Asian populations.
- Findings highlight the importance of studying diverse populations to understand the genetic architecture of dementia and cognitive decline.
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