NG00065 - ADSP Discovery Case/Control Association Results


The Alzheimer's Disease Sequencing Project (ADSP) undertook whole exome sequencing in 5,740 late-onset Alzheimer disease (AD) cases and 5,096 cognitively normal controls primarily of European ancestry (EA), among whom 218 cases and 177 controls were Caribbean Hispanic (CH). An age-, sex- and APOE based risk score and family history were used to select cases most likely to harbor novel AD risk variants and controls least likely to develop AD by age 85 years. ~1.5 million single nucleotide variants (SNVs) and 50,000 insertion-deletion polymorphisms (indels) were tested for association to AD, using multiple models considering individual variants as well as gene-based tests aggregating rare, predicted functional, and loss of function variants.

This dataset contain results for single variant and gene-based rare variant aggregation tests, performed separately by ancestry (European ancestry, Caribbean Hispanic) and meta-analyzed. Three sets of covariate adjustment models were employed in the genotype-phenotype association analyses:
Model 0 included only principal components and sequencing center;
Model 1 further adjusted for sex and age at AD or last-known dementia-free age for controls;
Model 2 further adjusted for APOE E2 and E4 genotypes.

Rare variants were aggregated by Ensembl genes, with variants selected using various filtering strategies based on predicted function. All analyzes were performed using seqMeta.

April 23, 2019 UPDATE: There was an error discovered in the dataset which is currently being corrected. Please wait to download the summary statistics until the error is fixed. If you have downloaded data already, you will need to download the new version.

July 24, 2019 UPDATE: The previously released gene-based test files for SKAT-O CADD analyses were all the same (the CADD-15 model 0 results). The files have been corrected for each result and are available again for download. 

Molecular Data Type


Submission date: 
ADSP Discovery Case/Control Association Results | NIAGADS


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