Data Analysis and Harmonization Services for the Alzheimer’s Disease Sequencing Project (ADSP)

This is a Notice of Intent to Sole Source and is not a request for competitive quotations or proposals. The National Institute on Aging (NIA), National Institutes of Health (NIH), Department of Health and Human Services (HHS), intends to negotiate and award a firm-fixed-price purchase order on a sole source basis to:

Trustees of the University of Pennsylvania
D102 Richards Building
3700 Hamilton Walk
Philadelphia, PA 19104
UEI: GM1XX56LEP58

for Data Analysis and Harmonization Services in support of the Alzheimer’s Disease Sequencing Project (ADSP).

The anticipated period of performance is August 1, 2026 through July 31, 2027.

Authority

This acquisition is being conducted under the authority of FAR 13.106-1(b)(1), Soliciting from a Single Source, as only one source is reasonably available to satisfy the agency’s requirements.

Requirement Description

The Alzheimer’s Disease Sequencing Project (ADSP) is a large NIH-funded effort to identify the genetic architecture of Alzheimer’s disease through sequencing and analysis of DNA from tens of thousands of individuals. The Government requires contractor support for the processing, harmonization, and storage of 4,799 unaligned raw sequencing datasets from Vanderbilt University Medical Center and the National Alzheimer’s Coordinating Center.

Required services include, but are not limited to:

• Genome analysis and harmonization on Amazon Cloud using the ADSP SNV/INDEL and SV calling pipelines
• Processing raw sequencing data, including CRAM to BAM conversion, read remapping using BWA, sorting reads, and marking duplicates
• Base quality score recalibration using GATK BQSR and realignment around known indels using GATK IndelRealigner
• Calling SNVs and indels using GATK HaplotypeCaller
• Calling structural variants using tools such as Strelka, Manta, and Smoove
• Performing quality assurance checks, including sex check, contamination check, and relatedness checks
• Staging sequencing data on Amazon S3 standard storage for two months
• Providing storage of up to 50 GB per genome, including CRAM and genomic VCF outputs
• Providing Amazon S3 and Glacier storage for three years
• Ensuring the Government’s 4,799 samples are directly comparable with the existing ADSP combined sequencing datasets to maintain full methodological continuity

Sole Source Rationale

The Government has determined that the Trustees of the University of Pennsylvania, through the Genome Center for Alzheimer’s Disease (GCAD) and the NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS), is the only source capable of meeting the requirement without unacceptable risk.

GCAD has established and maintained the standardized processing and joint-calling pipeline used across existing ADSP whole genome sequencing data releases. The required work must be performed in a manner fully consistent with the existing ADSP dataset to avoid technical heterogeneity and batch effects that could compromise downstream analyses. NIAGADS is the NIH-designated controlled-access repository for ADSP data and provides the established infrastructure, governance, access controls, and dissemination framework necessary to securely host, manage, and share these data.

While other vendors may possess general cloud-based genomic data processing capabilities, the Government is not aware of any other source that can provide the required full methodological continuity, direct comparability with the existing ADSP dataset, and integration with the established ADSP repository environment.

Responses

This notice is for informational purposes only. Interested organizations may submit a capability statement demonstrating their ability to meet the Government’s requirement as stated in this notice. Capability statements must clearly address the ability to:

1. Process 4,799 genomes using the established ADSP SNV/INDEL and SV calling pipelines;
2. Maintain full methodological continuity with the existing ADSP harmonized dataset;
3. Provide secure cloud-based staging, storage, and dissemination consistent with ADSP and NIH controlled-access requirements; and
4. Deliver the required services within the stated period of performance.

Responses must be received no later than June 25, 2026, at 11:00 AM Eastern Time. Responses received after the closing date and time may not be considered.

Responses shall be submitted via email to both points of contact below with the subject line:
Response to NOI Sole Source – ADSP Data Analysis and Harmonization Services

Primary Point of Contact

Linda Smith
Contracting Officer
[email protected]

Secondary Point of Contact

Danielle Tines
Procurement Technician
[email protected]

Disclaimer

This notice does not constitute a solicitation, request for quote, or request for proposal. This notice is not to be construed as a commitment by the Government to issue an award or otherwise pay for information submitted in response to this notice. The Government will not reimburse any costs associated with responding to this notice. A determination by the Government not to compete this proposed action based on responses to this notice is solely within the discretion of the Government.