Whole Genome Sequencing (WGS) Data

In July 2012 the Brin-Wojcicki Foundation and the Alzheimer’s Association donated funds to support whole genome sequencing (WGS) of 818 ADNI participants (at the time, 128 with AD, 415 with MCI, 267 controls and 8 of uncertain diagnosis). Samples were sent to Illumina where non-CLIA WGS, as well as Illumina Omni 2.5M genome-wide association study (GWAS) single nucleotide polymorphism (SNP) arrays, were performed on each sample and completed in the spring of 2013. Basic quality control checks were then performed and others continue to be performed.

Summary of Whole Genome Sequencing Data

Available Data Description File size File Format Method of Obtaining
WGS (GATK Call) – SNV + Indel These variants were called using Broad’s Best Practices (BWA & GATK HaplotypeCaller). 117GB VCF Download from ADNI Data Archive.
WGS (CASAVA Call) – SNV These variants were called using Illumina’s CASAVA software. 52GB VCF Download from ADNI Data Archive.
Sequenced alignment data These are aligned sequencing data. Users can obtain these data to re-call variants or realign the reads if necessary. Over 150TB BAM Send hardware to LONI.

 

*There are 809 individuals in the CASAVA VCF files and 808 individuals in the GATK VCF files.

Summary of WGS Project Activity

Task Count
Requests Received 27
Requests Filled 14
Requests Copying or Pending 2
Requests Withdrawn/ Non-responsive 11
Average Time for Data Transfer and Return 3-4 weeks

Revised 2015-05-26

Obtaining WGS Data

WGS SNPs data is available to authorized ADNI investigators from within the ADNI Data Archive. To obtain SNPs data, go to the Access Data webpage to apply for an account or login. Once logged in, the data is located on the Download Genetic Data page.

WGS Assembly data amounts to approximately 100 TB, and cannot be reasonably distributed through the ADNI Data Archive. Investigators seeking to obtain the WGS Assembly data must:

Instructions for Requesting WGS Assembly Data

Please follow these steps to acquire WGS Assembly data:

  1. Download, review and sign the ADNI Whole Genome Sequencing Data Use Agreement
  2. Email the completed agreement to adni@loni.usc.edu. Enter “ADNI WGS Data Request” in the subject line. Requests for data will be filled in the order received.
  3. The Laboratory of Neuro Imaging (LONI) will send an email confirmation along with directions for shipping your hardware. Shipping costs to and from the Laboratory of Neuro Imaging are the responsibility of the investigator requesting data. DO NOT ship hardware until you have been contacted to do so.

Investigators will be notified by email when equipment is received at LONI and when return shipment is scheduled. LONI will take all reasonable precautions, but cannot be responsible for damage to equipment during transit.

For information on collection, informed consent, sharing, storage, and quality control of WGS data, please refer to Introduction and Procedures for Accessing Data from Whole Genome Sequencing of ADNI.