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Data Notices

May 11, 2020- Location Change for ADSP Data 

Please go to NIAGADS DSS to apply for build 38 ADSP genetic and phenotypic data.  See Background below for more details.  For instructions on how access the additional ADSP data that are shared through NIAGADS DSS, visit the Application Instructions page.

Background: Additional sequencing data are continuously being generated by the ADSP. These data are mapped to the latest Genome Reference Consortium human genome build GRCh38 (hg38) and are being shared through the NIA Genetics of Alzheimer's Disease Data Storage Site (NIAGADS) Data Sharing Service (DSS). As of May 1, 2020, there are 4,789 whole genomes and 19,922 whole exomes available to the research community. Later in 2020 there will be a total of  ~17,000 whole genomes and 19,922 whole exomes available through NIAGADS DSS (ng00067). The total number of genomes from multi-ethnic cohorts is anticipated to exceed 50,000.  Please see the ADSP Design page for the complete study description. 

ADSP whole exome and whole genome sequence data that were shared through dbGaP were mapped to the GRCh37 (build 37). These data are from the Discovery Phase of the project and will continue to be available at dbGaP.


 

September 7, 2018 - NIAGADS Data Sharing Service Now Accepting Applications

The NIAGADS Data Sharing Service (DSS) is now ready to accept applications. The DSS hosts sequencing data mapped to GRCh38, while ADSP Discovery data mapped to GRCh37 can still be accessed here at dbGaP. The NIAGADS DSS currently hosts ADSP Discovery+ Extension whole genome data from 854 subjects in 159 families and an additional 1433 cases and 1654 controls as well as 809 whole genomes from ADNI-WGS-1. The first release includes the GATK called CRAMs and gVCFs generated by Genome Center for Alzheimer’s Disease (GCAD) and corresponding phenotypes and pedigree structures. The second release will include the ADSP quality controlled GATK project level VCF. Look for additional sequencing studies later this year.


August 3, 2017- IRB Data Use Limitations

The data use limitations for the ADSP were recently broadened [provide link to attached]. In addition, effective May 1, 2017, NIH will began permitting access to data with an “Alzheimer’s disease only” data use limitation if the data access request includes research on Alzheimer’s disease or the ADRDs delineated above. Updating the definition of Alzheimer's disease used to establish data-sharing criteria will allow advancement of research on dementia-causing disease processes that are commonly embedded in and/or are difficult to distinguish from AD during life. This clarification will allow approved users of Alzheimer's disease genomic data to pursue research that is fully congruent with the <a href="https://aspe.hhs.gov/national-alzheimers-project-act>NAPA</a> definition and the current state of the science in the field. Please see the following for additional information: <a data-cke-saved-href=" https:="" grants.nih.gov="" grants="" guide="" notice-files="" not-ag-17-007.html"="">NIH NOT-AG-17-007.html.

Detailed information can be found here.

 


November 4, 2016- Review and Proposed Actions for False-Positive Association Results in ADSP Case-Control Data

Some SNVs in the publicly released whole exome sequence (WES) QCed “consensus-called” data (which systematically integrated genotype calls from two pipelines: Atlas at Baylor College of Medicine and GATK at the Broad Institute) may have biased genotype calls resulting from sequence data generated/processed at the Broad Institute. This issue was identified by follow-up on likely “false-positive” genetic associations with genome-wide statistical significance in case-control analysis. It is not yet clear if this issue also affects WGS data.

Detailed information can be found here.

 


 

October 28, 2016- dbGaP News phs000572.v7.p4 ADSP Data Use

This notice describes a new issue with the whole-exome (WES) and whole-genome sequence (WGS) concordant and consensus genotype files released to Authorized Access Users.
It was recently discovered that heterogeneity in pre-variant-calling BAM processing has resulted in systematic biases in the GATK WES variant calls, and thus in the released WES concordant and consensus genotype files. 
ADSP WES data were independently and uniformly reprocessed as part of the Atlas variant pipeline, so the Atlas WES variant calls do not manifest this bias. We are currently examining the impact of this heterogeneity on the WGS data, but expect that these biases will need to be addressed in all WGS variant sets. 
Any analyses performed on ADSP BAM files downloaded from dbGaP may manifest these biases unless the data were reprocessed from a pre-mapped state (i.e., FASTQs). 
The ADSP will release an updated data set for both WGS and WES in the December 2016 dbGAP release which may consist of HGSC Atlas-only called variants or the current data sets with additional filters applied.
Researchers using the current data set are reminded that there are many possible sources of heterogeneity in any dataset/analysis that may generate false positive results and that findings should be verified by looking closely at primary data and via replication.

November 4, 2016- Review and Proposed Actions for False-Positive Association Results in ADSP Case-Control Data

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