Alzheimer’s Disease Sequencing Project Study Design
Funded under a number of cooperative agreements and research grant awards, the Alzheimer’s Disease Sequencing Project (ADSP) involves more than 150 investigators from institutions across the globe. The ADSP is part of the NIA Alzheimer’s Disease Genetics Portfolio. The overarching goals of the ADSP are to:
- Identify new genes involved in Alzheimer's disease (AD)
- Identify gene alleles contributing to increased risk for or protection against the disease
- Provide insight as to why individuals with known risk factor genes escape from developing AD
- Identify potential avenues for therapeutic approaches and prevention of the disease
This study of human genetic variation and its relationship to health and disease involves a large number of study participants and will capture not only common single nucleotide variations but also rare copy number and structural variants that are increasingly thought to play an important role in complex disease.
The ADSP is divided into three phases:
- Discovery Phase. Whole genome sequencing (WGS) and whole exome sequencing (WES) for the Discovery Phase is complete.
- Discovery Extension Phase. WGS is complete for the Discovery Extension Phase. Data analysis is in progress.
- Follow-Up Study Phase. This phase began in 2017 and is to be completed in 2023. Subsequent Phases will follow.
Each of these components has a case-control and a family-based study design.
The initial phase of the ADSP research plan is called the Discovery Phase. Samples were selected from well-characterized study cohorts of individuals with or without an AD diagnosis and the presence or absence of known risk factor genes. Funding for the sequencing was provided by the National Human Genome Research Institute (NHGRI).
The ADSP generated three sets of genome sequence data for these samples as part of the Discovery Phase:
- WGS for 584 samples from 113 multiplex families
- WES for 5,096 AD cases and 4,965 controls
- WES of an enriched sample set comprised of 853 AD cases from multiply affected families and 171 Hispanic controls
Sequence data are available by application to the NIA Genetics of Alzheimer's Disease (NIAGADS) Data Sharing Service (DSS).
Applicants can obtain from the NIAGADS DSS:
- Cleaned, quality control checked sequence data
- Information on the composition of the study cohorts (e.g., case-control, family-based, and epidemiology cohorts)
- Descriptions of the study cohorts included in the analysis
- Accompanying phenotypic information such as age at disease onset, gender, diagnostic status, and cognitive measures
- Epidemiological information such as educational level and certain demographic data available on the participants genotyped
Analysis of the Discovery Phase sequence data, supported by PAR-12-183 and RFA-HG-15-001, revealed many new variations in the genome that may be implicated as new genetic risk or protective factors in older adults at risk for AD. In February 2016, ADSP consultants recommended that subsequent sequencing and analysis be done on whole genomes in lieu of whole exome or targeted sequencing.
Discovery Extension Phase
To further assess the genomes in multiply affected families, under funding provided by NHGRI, an additional approximately 430 samples were sequenced by the NHGRI-funded large-scale sequencing centers in a Discovery Extension Phase. This included 107 additional samples from families studied under the Discovery Phase, 207 samples from 77 new families, and 114 Hispanic controls.
Also under funding provided by NHGRI, additional participants were whole genome sequenced as part of the ADSP Discovery Case-Control Based Extension Study (1,000 each of non-Hispanic white, Caribbean Hispanic, and African American). This included 1,466 cases and 1,534 controls. A total of 739 autopsy samples were sequenced (500 non-Hispanic white and 68 African American cases and 164 non-Hispanic white and 7 African American controls).
The ADSP Discovery Phase has identified a number of variations in the genomes of individuals affected with AD. These findings are being pursued in the ADSP Follow-Up Study (FUS), funded solely by NIA. The long-term goals of the ADSP FUS are to:
- Move the field closer to enabling prediction of who will develop AD
- Fully reveal the genetic architecture of AD in multiple ethnic groups
- Better understand the underpinnings of AD pathogenesis
- Aid the quest for therapeutic targets
- Examine the AD genome in diverse populations
The ADSP Discovery Phase and the ADSP FUS are described under PAR-16-406. The ADSP FUS is leveraging existing infrastructure and collaborations to ensure continuity of ADSP participation. It provides funds for acquisition, archiving, sequencing, quality control, genome wide association studies (GWAS), and data sharing of the large number of samples from individuals affected by AD for WGS, as appropriate. Racial/ethnic diversity continues to be a high ADSP priority. Well-phenotyped participants were selected with an emphasis on autopsy-confirmed and ethnically diverse cases/controls and availability of longitudinal data. Funds are being provided for both sequencing and data analysis. This effort will pursue rare variants as comprehensively as possible, including consideration of statistical power, and exploration of a range of different populations containing those that are currently underrepresented in sequencing studies.
The majority of the samples from the ADSP Discovery and Discovery Extension phases were non-Hispanic white in origin, making the addition of ethnically diverse samples to the study critical to identification of both shared and novel genetic risk factors for AD between populations. Collection and sequencing of ethnically diverse cohorts is emphasized in the ADSP FUS, the goal being that additional existing cohorts with unrelated AD cases that encompass the richest possible ethnic diversity be given the highest priority for inclusion. For the United States this includes augmenting African American, Hispanic, and Asian cohorts.
AD is not a single genetic entity; it is a genetic spectrum with a number of sub-phenotypes (endophenotypes). Endophenotypes will likely vary by ethnicity. Important instances of ethnically unique AD/ADRD genetic variation have been identified in Hispanic and African American cohorts. Variants for AD are rare and can only be identified with a larger number of participants. Variants occur at different frequencies in different populations and certain risk variants may be much easier to detect in some populations. ADSP studies in ethnic groups including African American and Hispanic, remain statistically underpowered, so the genetics of these populations remain largely unstudied. Therefore, a major effort is being undertaken to augment the numbers of cases and controls in ethnically diverse populations in the United States. In order to understand the underlying substructure of the diversity populations, global studies are a key component of this effort.
The global effort brings important population sectors that are not presently well represented in the ADSP including Central and South America, the Iberian Peninsula, Iceland, Africa, and Asia. Examples of the expected types of sequencing and analytical assessments include continuing activities as outlined in the parent FOAs (PAR-19-234 and PAR-17-214). Proposed approaches will not only increase the numbers of participants and the volume of data, but also will require novel methods to perform in-depth and subgroup analyses of diverse ethnic backgrounds, as well as integrated analyses to completely unravel the architecture of the AD genome.
To fulfill the goals of this ADSP FUS, eight existing cohorts of African American and pan-Hispanic ancestry, with a total of 13,745 samples (2,456 African American AD cases and 4,126 African American controls and 2,588 Hispanic AD cases and 4,475 Hispanic controls), are being whole genome sequenced at the American Genome Center at the Uniformed Services University of the Health Sciences (USUHS) in coordination with existing NIH-funded AD infrastructure including the National Cell Repository for Alzheimer’s Disease (NCRAD), NIAGADS, and the Genome Center for Alzheimer’s Disease (GCAD). In addition, 1,500 non-Hispanic white autopsy cases and 1,500 controls are also being sequenced. Brief descriptions of the cohorts selected for sequencing are provided below. Cohort collection, phenotypic characterization, and whole genome sequencing were funded by the National Institutes of Health.
ADSP FUS Cohort Descriptions
- The Alzheimer’s Disease Genetics Consortium (ADGC) African-American Cohort is a cohort of 1,240 cases and 1,643 controls collected from several cohorts including from the GenerAAtions Study, Indianapolis-Ibadan Study, Rush University, University of Miami, Case Western Reserve University, North Carolina A&T University, and the Mirage Study.
- The Mexican Health and Aging Study (MHAS) is prospective study of health and aging in Mexico that began in 2001. The ADSP FUS will sequence 200 cases and 2,600 controls from this study starting in 2018.
- The REasons for Geographic and Racial Differences in Stroke (REGARDS) Study is a national study of risk factors for stroke in adults 45 years old or older that includes measurements of traditional stroke risk factors such as blood pressure and cholesterol levels, and an echocardiogram of the heart. The ADSP FUS will sequence 1,000 African American cases and 1,500 African American controls from this study starting in 2018.
- The Northern Manhattan Study (NOMAS) is a study focused on stroke or related neurological syndromes. The ADSP FUS will sequence 88 Hispanic cases and 175 Hispanic controls, and 22 African American cases and 43 African American controls from this study starting in 2019.
- The Puerto Rican 10/66 Study is an Alzheimer’s Disease International study of dementia in Puerto Rico that began in 2007. The ADSP FUS will sequence 1,000 Puerto Rican cases and 1,000 Puerto Rican controls from this study starting in 2021.
- The Puerto Rican Alzheimer’s Disease Initiative (PRADI) is a study of late-onset AD focused on the Caribbean-Hispanic Puerto Rican population. The ADSP FUS will sequence 500 cases and 500 controls from this study starting in 2020.
- The Research in African American Alzheimer’s Disease Initiative is a study focused on identifying genetic factors for AD within the African American population in order to detect new targets for drug development and improve accessibility to AD education within the community. The ADSP FUS will sequence 300 cases and 300 controls from this study starting in 2020.
- The Estudio Familiar de Influencia Genetica en Alzheimer (EFIGA) Study is a study of late-onset AD patients with Caribbean-Hispanic ancestry. The ADSP FUS will sequence 800 cases and 300 controls from this study starting in 2019.
- The Alzheimer’s Disease Center Autopsy (ADC) Cohort includes 1,500 cases with autopsy and 1,500 controls from the National Institute on Aging’s ADRCs. These individuals are well-phenotyped and will help to increase the currently underpowered non-Hispanic white sample with WGS data from the ADSP Discovery and Discovery Extension Phases (1,212 cases and 524 controls).
- Additional cohorts will be added as the study progresses.
Some Additional ADSP Collaborations
- Alzheimer’s Disease Neuroimaging Initiative (ADNI)
- Anti-Amyloid Treatment in Asymptomatic Alzheimer’s Disease (A4 Study)
- ASPirin in Reducing Events in the Elderly (ASPREE-US and Australia)
- Diagnostic Assessment of Dementia (DAD) for the Longitudinal Aging Study of India (LASI) (LASI-DAD)
- Gwangju Alzheimer's & Related Dementias (GARD) Study (South Korea)
- Indianapolis-Ibadan Study
- International Genomics of Alzheimer's Project (IGAP)
- Long Life Family Study (LLFS)
- The Reykjavik Study (Iceland)
- The VA Million Veteran Program
- Individually funded investigators and other organizations/websites designed to store and distribute data related to AD
ADSP FUS Sequencing, Quality Control, and Data Sharing
The workflow for the acquisition, processing, and sharing of ADSP data is:
- ADSP investigators identify, assemble, and send DNA samples from well-phenotyped participants affected with AD for WGS to NCRAD.
- NCRAD receives and prepares DNA, performs quality control checks, retains aliquots of DNA, plates and ships samples to sequencing centers, and tracks samples through the sequencing process.
- NCRAD acquires and archives appropriate documentation for compliance of sample and data handling with NIH policy and ensures that standard operating procedures for sample handling are followed.
- Sequencing centers perform GWAS and WGS and process sequence data.
- GCAD receives and processes data and performs quality control checks, variant calling, and harmonization with other ADSP data, and provides this processed data to NIAGADS.
- NIAGADS receives and manages the WGS and GWAS datasets and coordinates ADSP phenotype and GWAS data collection, sequence data production, and delivery to the research community.
Sequence data will be available through NIAGADS Data Sharing Service.
In order to meet time constraints, financial considerations, and the milestones provided under the National Alzheimer's Project Act (NAPA), sequence data from unaffected participants were drawn from existing WGS data from sequencing projects performed in large, well-characterized age-matched cohorts with documented appropriate cognitive function testing such as a subset of the cognitively tested age-matched cohorts in the Trans-Omics for Precision Medicine (TOPMed) program. Samples from AD participants were selected from existing cohorts and sample sets where possible. Samples come from all types of epidemiology study designs, existing case/control, family-based, and other sample sets where AD is the underlying form of dementia. Collection of samples, genetic sequencing, quality control, variant calling, and data harmonization are supported under RFA-AG-16-001, PAR-16-406, PAR-19-288, and PAR-20-110.