NG00135 – UAB ADRC Genetic Data

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.