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Within the application, add this dataset (accession NG00135) in the “Choose a Dataset” section.
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This dataset involves whole exome, genome, and genotyping array data (both pre-imputation and post-imputation data) from the University of Alabama at Birmingham (UAB) Alzheimer’s Disease Research Center. Participants are enrolled as either cognitively unimpaired, MCI, or a target of mild dementia and followed longitudinally. The cohort aims to recruit a substantial fraction of self-reported African American / Black participants. There were total of 81 subjects that were enrolled in the study and the specifications for each data type are provided below.
Whole genome sequencing data includes 15 samples that were prepared by Covaris shearing, end repair, adapter ligation, and PCR using standard protocols. Library concentrations were normalized using KAPA qPCR prior to sequencing.
Whole exome Sequencing data includes 17 samples and the variants were genotyped using Integrated DNA Technologies xGen Exome Hyb Panel v2 at 100x coverage.
Genotyping SNP array data includes 64 samples variants were genotyped using the Illumina Global Diversity Array plus Neuro consortium content. PLINK v1.90 and PLINK v2.00 were used to annotate the data with hg19. One set of the data was pre-imputed, the other was imputed using the TOPMed Imputation Panel and Server v1.3.3. For the imputed set, the Pre-Imputation script located here:
Pre-imputation script (https://github.com/HudsonAlpha/Pre-Imputation-QC-Pipeline)was used on the data before submitting to the imputation server. Post-Imputation script (https://github.com/HudsonAlpha/Post-Imputation-Pipeline) was used after imputation to recover the typed only variants.
Sample Summary per Data Type
|UAB WGS||fsa000059||NG00135.v1||Whole Genome Sequencing data|
|UAB WES||fsa000060||NG00135.v1||Whole Exome Sequencing data|
|UAB Pre-Imputation||fsa000061||NG00135.v1||Genotyping SNP Array|
|UAB Post-Imputation||fsa000062||NG00135.v1||Genotyping SNP Array|
|UAB ADRC Documentation||fsa000063||NG00135.v1||Phenotype File and README|
View the File Manifest for a full list of files released in this dataset.
This dataset contains 15 samples that have Whole Exome sequencing, 17 samples Whole Genome Sequencing in FASTQ format. Also, 64 samples were genotyped using the Illumina Global Diversity Array plus Neuro consortium content. PLINK v1.90 and PLINK v2.00 were used to annotate the data with hg19. One set of the data was pre-imputed, the other was imputed to GHRCh38 using the TOPMed Imputation Panel and Server v1.3.3. The UAB ADRC cohort aims to recruit a substantial fraction of self-reported African American / Black participants. Participants are enrolled as either cognitively unimpaired, MCI, or a target of mild dementia and followed longitudinally.
|Sample Set||Accession Number||Number of subjects|
|Consent Level||Number of Subjects|
Visit the Data Use Limitations page for definitions of the consent levels above.
Acknowledgment statement for any data distributed by NIAGADS:
Data for this study were prepared, archived, and distributed by the National Institute on Aging Alzheimer’s Disease Data Storage Site (NIAGADS) at the University of Pennsylvania (U24-AG041689), funded by the National Institute on Aging.
Use the study-specific acknowledgement statements below (as applicable):
For investigators using any data from this dataset:
Please cite/reference the use of NIAGADS data by including the accession NG00135.
For investigators using University of Alabama at Birmingham Alzheimer’s Disease Research Center (sa000036) data:
Funding for genome sequencing was provided by the HudsonAlpha Memory and Mobility program. Funding for exome sequencing was provided by the Alzheimer’s Association. Funding for array genotyping was provided by NIA grant 5P20AG068024.
Wright AC., et al. Contributions of rare and common variation to early-onset and atypical dementia risk. medRxiv. 2023 Feb 8. doi:10.1101/2023.02.06.23285383.Pubmed Link