ID

45492

Description

Principal Investigator: Richard A. Gibbs, PhD, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA MeSH: Alzheimer Disease https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000572 *NOTICE OF CHANGE IN LOCATION FOR ALZHEIMER'S DISEASE SEQUENCING PROJECT (ADSP) GENETIC AND PHENOTYPIC DATA:* ADSP whole exome and whole genome sequence data that are shared through dbGaP were mapped to the Genome Reference Consortium human genome GRCh37 (build 37). These data are from the Discovery Phase of the project (described below) and will continue to be available at this site. Please see the ADSP Design page for the complete study description. All data that are mapped to GRCh38 (hg38) are being shared through the NIA Genetics of Alzheimer's Disease Data Storage Site (NIAGADS) Data Sharing Service (DSS). For instructions on how access the ADSP Build 38 data that are shared through NIAGADS DSS, visit the Application Instructions page. *STUDY DESCRIPTION FOR dbGaP BUILD 37 ADSP DATA: *The overarching goals of the Alzheimer's Disease Sequencing Project (ADSP) are to: (1) identify new genomic variants contributing to increased risk of developing Alzheimer's Disease (AD), (2) identify new genomic variants contributing to protection against developing AD, and (3) provide insight as to why individuals with known risk factor variants escape from developing AD. These factors will be studied in multi-ethnic populations in order to identify new pathways for disease prevention. Such a study of human genomic variation and its relationship to health and disease requires examination of a large number of study participants and needs to capture information about common and rare variants (both single nucleotide and copy number) in well phenotyped individuals. Using existing samples from NIH funded and other studies, three NHGRI funded Large Scale Sequencing and Analysis Centers (LSAC) - Broad, Baylor, and Washington University - produced the DNA sequence data. Variant call data are being made available to the scientific community through NIH-approved data repositories. Statistical analysis of the sequence data is anticipated to identify new genetic risk and protective factors. The ADSP will conduct and facilitate analysis of sequence data to extend previous discoveries that may ultimately result in new directions for AD therapeutics. Analysis of ADSP data will be done in two phases. The Discovery Phase analysis (2014-2018) is funded under PAR-12-183. The entire Discovery dataset contains whole-genome sequencing data on 584 subjects from 113 families, and pedigree data for 4000 subjects; whole exome sequencing data on 5096 cases 4965 controls; and whole exome sequence data on an additional 853 (682 Cases [510 Non-Hispanic, 172 Hispanic]), and 171 Hispanic Control subjects from families that are multiply affected with AD. The Replication Phase (2016-2021) analysis will be funded under RFA-AG-16-001 and RFA-AG-16-002 and is expected to include a combination of genotyping and sequencing approaches on at least 30,000 subjects. Targeted sequencing will be done by the LSACs. *GRCh37 Data Releases* - The *first* ADSP data release occurred on November 25, 2013. It included the whole-genome sequencing data in BAM file format on 410 individuals. - The *second* ADSP data release occurred on March 31, 2014, and included the whole-genome sequencing data in BAM file format for an additional 168 individuals. - The *third* ADSP data release occurred on November 03, 2014 and included whole-exome sequencing data in BAM file format for 10,939 individuals. - The *fourth* ADSP data release occurred on February 13, 2015 and included revised ethnic data for subjects with whole-exome sequencing data. - The *fifth* ADSP data release occurred on July 13, 2015 and included whole-genome genotypes and updated phenotypes as well as changes to pedigree structures and sample IDs. - The *sixth* ADSP data release occurred on December 8, 2015, and included whole-exome genotypes and updated phenotypes as well as changes to subject IDs. This *seventh ADSP data release on April 12, 2016* includes: (1) WES and WGS SNV VCF files (2) WES and WGS Indel PLINK files *ADSP Data Available through dbGaP:* table border="1" tr th/th th*ADSP - Whole Genome Sequencing*/th th*ADSP - Whole Exome Sequencing*/th th*Comments*/th /tr tr tdDNA-Seq (BAM)/td tdn=578/td tdn=10913/td tdSequence data available (plus n=38 replications w/out genotype data)/td /tr tr tdConcordant SNV Genotypes (PLINK format)/td tdN/A/td tdn=10913/td tdQC'ed genotypes that are concordant between the Atlas (Baylor's) and GATK (Broad's) calling pipelines (a subset of the consensus genotype set)/td /tr tr tdConsensus Genotypes (PLINK and VCF format)/td tdn=578/td tdn=10913/td tdQC'ed genotypes that are concordant between Atlas and GATK pipelines as well as those that that were called uniquely by Atlas or GATK/td /tr tr tdConcordant Indel Genotypes (PLINK format)/td tdn=578/td tdn=10913/td tdQC'ed genotypes that are concordant between the Atlas and GATK calling pipelines/td /tr tr tdPhenotype Data/td tdn=4735/td tdn=10913/td tdData of n=53 phenotype variables available (plus administrative data), including APOE genotype. WGS phenotypes include data of connecting family members./td /tr /table Please use the release notes provided by dbGaP to obtain detailed information about study release updates. The ADSP data portal provides a customized interface for users to quickly identify and retrieve files by covariates, phenotypes, and data properties such as sequencing facility or coverage. For more information about the ADSP study and the data portal, please visit https://www.niagads.org/adsp/.

Link

dbGap study = phs000572

Keywords

Versions (2)
  1. 10/27/22 10/27/22 - Simon Heim
  2. 12/13/22 12/13/22 - Kristina Keller
Copyright Holder

Richard A. Gibbs, PhD, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA

Uploaded on

December 13, 2022

DOI

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License

Creative Commons BY 4.0
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dbGaP phs000572 Alzheimer's Disease Sequencing Project (ADSP)

English

Eligibility Criteria

9 forms  
  1. StudyEvent: SEV1
    1. Eligibility Criteria
    2. The subject consent data table includes subject IDs, consent information, and subject aliases.
    3. This pedigree data table contains family relationships in the format of family IDs, subject IDs, father IDs, mother IDs, subjects's sex, and family group ethnicity.
    4. This subject sample mapping data table includes a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs.
    5. Family Subject Phenotypes (WGS) year 1: AD affection status, Braak stage, presence of APOE allele combinations, availability of autopsy material, and general sociodemographic (race and ethnicity) data of participants for whom whole genome sequencing (WGS) data are available.
    6. This sample attributes table includes body site where sample was collected, analyte type, tumor status, and sequencing center.
    7. Connecting Family Subject Phenotypes year 1: participants' family members' AD affection status, Braak stage, APOE allele presence, availability of autopsy material, and general sociodemographic data (race and ethnicity).
    8. Case Control Enriched Phenotypes (WES) year 0: prevalent and incident AD status, AD diagnosis, selection criteria, age (n=2 variables; baseline, onset or last exam), APOE genotype, availability of autopsy data, Braak stage, and general sociodemographic (race and ethnicity) of participants for whom whole exome sequencing (WXS) data are available.
    9. Case Control Enriched Phenotypes (WES) year 1: prevalent and incident AD status, AD diagnosis, selection criteria, age (n=2 variables; baseline, onset or last exam), APOE genotype, availability of autopsy data, Braak stage, and general sociodemographic (race and ethnicity) of participants for whom whole exome sequencing (WXS) data are available.
Inclusion and exclusion criteria
Description

Inclusion and exclusion criteria

The samples for the ADSP have been selected from well-characterized cohorts of individuals characterized for AD diagnosis as well as having known AD genetic risk factors. Investigators in the ADSP will obtain from the NIH approved data repositories: (1) quality control checked and 'cleaned' sequence data. 'Quality control checked and cleaned' means a set of routine checks have been performed for sample information, phenotype, and GWAS data to ensure the sequence data are of high quality and are ready for downstream genetic analysis and that likely sources of false-positives have been ruled out, and that samples that are outliers which may skew project-level analyses have been identified; (2) information on the composition of the study cohorts (e.g. case-control, family based, and epidemiology cohorts); (3) descriptions of the study cohorts included in the study; and (4) accompanying phenotypic information such as age at disease onset, self-reported race/ethnicity, gender, diagnostic status, and cognitive measures. The ADSP will determine what additional information, if any, is needed by its members to facilitate the project.
Description

The samples for the ADSP have been selected from well-characterized cohorts of individuals characterized for AD diagnosis as well as having known AD genetic risk factors. Investigators in the ADSP will obtain from the NIH approved data repositories: (1) quality control checked and 'cleaned' sequence data. 'Quality control checked and cleaned' means a set of routine checks have been performed for sample information, phenotype, and GWAS data to ensure the sequence data are of high quality and are ready for downstream genetic analysis and that likely sources of false-positives have been ruled out, and that samples that are outliers which may skew project-level analyses have been identified; (2) information on the composition of the study cohorts (e.g. case-control, family based, and epidemiology cohorts); (3) descriptions of the study cohorts included in the study; and (4) accompanying phenotypic information such as age at disease onset, self-reported race/ethnicity, gender, diagnostic status, and cognitive measures. The ADSP will determine what additional information, if any, is needed by its members to facilitate the project.

Data type

boolean

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C0599755
UMLS CUI [1,3]
C0002395
UMLS CUI [2,1]
C1512693
UMLS CUI [2,2]
C0010995
UMLS CUI [2,3]
C0449416
UMLS CUI [2,4]
C3847505
UMLS CUI [2,5]
C0034378
UMLS CUI [2,6]
C0486616
UMLS CUI [3,1]
C1512693
UMLS CUI [3,2]
C0678257
UMLS CUI [3,3]
C0599755
UMLS CUI [4,1]
C1512693
UMLS CUI [4,2]
C0031437
UMLS CUI [4,3]
C0206132
UMLS CUI [4,4]
C0015031
UMLS CUI [4,5]
C0079399
UMLS CUI [4,6]
C1546922
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Similar models

Eligibility Criteria

9 forms
  1. StudyEvent: SEV1
    1. Eligibility Criteria
    2. The subject consent data table includes subject IDs, consent information, and subject aliases.
    3. This pedigree data table contains family relationships in the format of family IDs, subject IDs, father IDs, mother IDs, subjects's sex, and family group ethnicity.
    4. This subject sample mapping data table includes a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs.
    5. Family Subject Phenotypes (WGS) year 1: AD affection status, Braak stage, presence of APOE allele combinations, availability of autopsy material, and general sociodemographic (race and ethnicity) data of participants for whom whole genome sequencing (WGS) data are available.
    6. This sample attributes table includes body site where sample was collected, analyte type, tumor status, and sequencing center.
    7. Connecting Family Subject Phenotypes year 1: participants' family members' AD affection status, Braak stage, APOE allele presence, availability of autopsy material, and general sociodemographic data (race and ethnicity).
    8. Case Control Enriched Phenotypes (WES) year 0: prevalent and incident AD status, AD diagnosis, selection criteria, age (n=2 variables; baseline, onset or last exam), APOE genotype, availability of autopsy data, Braak stage, and general sociodemographic (race and ethnicity) of participants for whom whole exome sequencing (WXS) data are available.
    9. Case Control Enriched Phenotypes (WES) year 1: prevalent and incident AD status, AD diagnosis, selection criteria, age (n=2 variables; baseline, onset or last exam), APOE genotype, availability of autopsy data, Braak stage, and general sociodemographic (race and ethnicity) of participants for whom whole exome sequencing (WXS) data are available.
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Inclusion and exclusion criteria
The samples for the ADSP have been selected from well-characterized cohorts of individuals characterized for AD diagnosis as well as having known AD genetic risk factors. Investigators in the ADSP will obtain from the NIH approved data repositories: (1) quality control checked and 'cleaned' sequence data. 'Quality control checked and cleaned' means a set of routine checks have been performed for sample information, phenotype, and GWAS data to ensure the sequence data are of high quality and are ready for downstream genetic analysis and that likely sources of false-positives have been ruled out, and that samples that are outliers which may skew project-level analyses have been identified; (2) information on the composition of the study cohorts (e.g. case-control, family based, and epidemiology cohorts); (3) descriptions of the study cohorts included in the study; and (4) accompanying phenotypic information such as age at disease onset, self-reported race/ethnicity, gender, diagnostic status, and cognitive measures. The ADSP will determine what additional information, if any, is needed by its members to facilitate the project.
Item
The samples for the ADSP have been selected from well-characterized cohorts of individuals characterized for AD diagnosis as well as having known AD genetic risk factors. Investigators in the ADSP will obtain from the NIH approved data repositories: (1) quality control checked and 'cleaned' sequence data. 'Quality control checked and cleaned' means a set of routine checks have been performed for sample information, phenotype, and GWAS data to ensure the sequence data are of high quality and are ready for downstream genetic analysis and that likely sources of false-positives have been ruled out, and that samples that are outliers which may skew project-level analyses have been identified; (2) information on the composition of the study cohorts (e.g. case-control, family based, and epidemiology cohorts); (3) descriptions of the study cohorts included in the study; and (4) accompanying phenotypic information such as age at disease onset, self-reported race/ethnicity, gender, diagnostic status, and cognitive measures. The ADSP will determine what additional information, if any, is needed by its members to facilitate the project.
boolean
C1512693 (UMLS CUI [1,1])
C0599755 (UMLS CUI [1,2])
C0002395 (UMLS CUI [1,3])
C1512693 (UMLS CUI [2,1])
C0010995 (UMLS CUI [2,2])
C0449416 (UMLS CUI [2,3])
C3847505 (UMLS CUI [2,4])
C0034378 (UMLS CUI [2,5])
C0486616 (UMLS CUI [2,6])
C1512693 (UMLS CUI [3,1])
C0678257 (UMLS CUI [3,2])
C0599755 (UMLS CUI [3,3])
C1512693 (UMLS CUI [4,1])
C0031437 (UMLS CUI [4,2])
C0206132 (UMLS CUI [4,3])
C0015031 (UMLS CUI [4,4])
C0079399 (UMLS CUI [4,5])
C1546922 (UMLS CUI [4,6])
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