The ADSP Discovery Phase
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. The ADSP generated three sets of genome sequence data for these samples as part of the Discovery Phase: (1) WGS for 584 samples from 113 multiplex families (two or more affected per family), (2) Whole Exome Sequence (WES) for 5,096 AD cases and 4,965 controls, and (3) WES of an Enriched sample set comprised of 853 AD cases from multiply affected families and 171 Hispanic controls. The Case-Control and Enriched Case Study spans 24 cohorts provided by the Alzheimer’s Disease Genetics Consortium (ADGC) and the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium.
As part of the Discovery Phase, the NIA ADSP genetics investigators funded under PAR-12-183 and the NHGRI funded Large Scale Sequencing and Analysis Centers (LSACs) conducted analysis of sequence data, including quality assessments and variant calling. Analysis of the Discovery Phase sequence data is anticipated to identify many new variations in the genome that may be implicated as new genetic risk or protective factors in older adults at risk for AD.
Because the initial analysis of WGS data in subjects from families multiply affected with AD revealed the occurrence of variations in the genome that were intergenic and intronic, in February of 2016 the external consultants to the ADSP recommended that further sequencing for the project should be of whole genomes.
The fully quality control checked (QC’d) data for the Discovery Phase study using Genome Reference Consortium Human Build 37 (GRCh37) was released in March of 2016 through the database of Genotypes and Phenotypes (dbGaP). Discovery Phase data called on Genome Reference Consortium Human Build 38 (GRCh38) are being shared through NIAGADS. Applicants for sequence data can obtain: (1) cleaned, quality control checked sequence data, (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 analysis, (4) accompanying phenotypic information such as age at disease onset, gender, diagnostic status, and cognitive measures, and (5) epidemiological information such as educational level and certain demographic data available on the subjects genotyped.
The ADSP Discovery Extension Phase
The ADSP Discovery Family-Based Extension Study:
To further assess the genomes in multiply affected families, under funding provided by NHGRI, an additional 427 samples were whole genome sequenced. This included 107 additional samples from families studied under the Discovery Phase, 175 samples from 47 new families, and 145 Hispanic Controls. This portion of the study is called the Discovery Extension Phase. The Family Based Study spans seven cohorts provided by the Alzheimer’s Disease Genetics Consortium (ADGC) and the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium.
The ADSP Discovery Case-Control Based Extension Study:
Under funding provided by NHGRI, an additional 3,000 subjects were whole genome sequenced. This included 1,466 cases and 1,534 controls. Of these 1,000 each of Non-Hispanic White (NHW), Caribbean Hispanic (CH), and African American (AA) descent were sequenced. Of these a total of 739 autopsy samples were sequenced [568 cases (500 NHW cases and 68 AA cases) and 171 controls (164 NHW and 7 AA)]. The Case-Control and Enriched Case Study spans 24 cohorts provided by the Alzheimer’s Disease Genetics Consortium (ADGC) and the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium.
The ADSP Follow-Up Study (FUS)
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, 37 datasets with existing cognitive data with the ability to adjudicate Alzheimer disease status 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). Brief descriptions of the cohorts selected for sequencing are provided below. Cohort collection, phenotypic characterization, and whole genome sequencing are funded by the National Institutes of Health. This and additional information about the ADSP can be found on the National Institutes on Aging site.
The ADSP Follow-Up Study (FUS) 2.0
The ADSP Follow-Up Study 2.0: The Diverse Population Initiative (PAR-21-212) was launched in 2021 to expand the sample set in ADSP to represent more diverse populations. The long-term goals of the ADSP FUS 2.0 are to:
- move the field closer to enabling prediction of who will develop AD;
- fully characterize AD subtypes by studying endophenotypes in diverse populations;
- better understand the differences in the genetic underpinnings of AD pathogenesis among diverse populations; and
- identify specific therapeutic targets based upon diverse population.
Numbers of Hispanic/Latino and Black/African American participants in the US remain insufficient to provide statistical significance for identification of rare or very rare variants. Variants in the Alzheimer’s genome are largely rare or very rare in the population. It is estimated that for 80% certainty for single variant testing for rare variants, ~16,100 cases and ~16,100 controls are needed for a variant with a minor allele frequency of 0.5% in the population; single variant testing for rare variants indicate that for 90% certainty, ~18,500 cases and ~18,500 controls are needed for each population for a variant with a minor allele frequency of 1% in the population. To ensure that there are sufficient numbers of study participants to achieve statistical power for analysis of rare or vary rare variants in the three largest diversity cohorts’ AD/ADRD genome given the available funding, the primary focus of the ADSP FUS 2.0 is on Hispanic/Latino, Black/African American, and Asian populations. Consortia are leveraging cohorts already recruited or in planning for recruitment to obtain sufficient numbers; sharing diversity data across consortia is essential to the success of this effort. Genetic samples and phenotypic data that are analyzed by the ADSP are provided by several consortia, initiatives, centers, and studies.