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

Notice of Intent to Sole Source

This document is a Notice of Intent to Sole Source from the National Institute on Aging (NIA), National Institutes of Health (NIH), Department of Health and Human Services (HHS). It is not a request for competitive quotations or proposals. The agency intends to negotiate and award a firm-fixed-price purchase order on a sole source basis to the Trustees of the University of Pennsylvania for Data Analysis and Harmonization Services in support of the Alzheimer's Disease Sequencing Project (ADSP).

The services required include, but are not limited to:

• Genome analysis and harmonization on Amazon Cloud using ADSP SNV/INDEL and SV calling pipelines.

• Processing raw sequencing data (CRAM to BAM conversion, read remapping, sorting, duplicate marking).

• Base quality score recalibration and realignment around known indels.

• Calling SNVs, indels, and structural variants.

• Performing quality assurance checks (sex, contamination, relatedness).

• Staging sequencing data on Amazon S3 for two months.

• Providing storage of up to 50 GB per genome (CRAM and VCF outputs) on Amazon S3 and Glacier for three years.

• Ensuring comparability of the 4,799 samples with existing ADSP datasets.

• Contract Type: Firm-fixed-price purchase order.

• Period of Performance: August 1, 2026, through July 31, 2027.

• This notice is for informational purposes only. Interested organizations may submit a capability statement demonstrating their ability to meet the requirements.

• Capability statements must address specific abilities related to processing genomes, maintaining methodological continuity, providing secure cloud-based services, and delivering within the period of performance.

• Response Deadline: June 25, 2026, at 11:00 AM Eastern Time.

• Responses should be submitted via email to Linda Smith (linda.smith2@nih.gov) and Danielle Tines (danielle.tines@nih.gov) with the subject line: "Response to NOI Sole Source – ADSP Data Analysis and Harmonization Services".

• This is a sole source acquisition under FAR 13.106-1(b)(1), as only one source is deemed reasonably available.

• The Trustees of the University of Pennsylvania are identified as the sole source due to their established processing and joint-calling pipeline for ADSP, ensuring methodological continuity and consistency with existing datasets. Their Genome Center for Alzheimer's Disease (GCAD) and NIAGADS repository are critical for meeting the requirement.

• This notice does not constitute a solicitation, request for quote, or proposal, and the Government will not reimburse costs associated with responding.

Statement of Work (SOW) / Performance Work Statement (PWS)

To support the NIH-funded Alzheimer's Disease Sequencing Project (ADSP) by performing data processing and data storage for genomic sequencing data, with the goal of uncovering genetic drivers of Alzheimer's disease.

• Perform genome analysis and harmonization on 4799 unaligned raw sequencing data from Vanderbilt University Medical Center and National Alzheimer's Coordinating Center.
• Utilize Amazon Cloud for ADSP genome analysis and harmonization, employing ADSP SNV/INDEL and SV calling pipelines.
• Process raw sequencing data, including converting CRAM to BAM, remapping reads with BWA, sorting reads, and marking duplicates.
• Calibrate base calling quality scores using GATK BQSR and realign reads using GATK IndelRealigner.
• Call SNVs and Indels using GATK HaplotypeCaller and SVs using programs like Streka, Manta, and Smoove.
• Conduct quality assurance checks (sex check, contamination check, relatedness checks).
• Stage sequencing data on Amazon S3 standard storage for 2 months.
• Provide storage for up to 50GB per genome, including up to 30GB for CRAM sequence alignment and up to 10GB each for genomic VCF produced by GATK and ATLAS genotype callers.
• Store data on Amazon S3 and Glacier for three years.
• Ensure the 4799 samples are directly comparable with existing ADSP datasets for methodological continuity.

August 1, 2026 through July 31, 2027

• Contractor must furnish all necessary services, personnel, material, equipment, and facilities.

• Contractor will provide a dedicated project manager.

• Principal place of performance is the vendor's work site; no travel required for contractor employees.

• The government will provide 4799 FASTQ files of unaligned raw sequence data via electronic cloud transfer.

• Monthly recurring meetings with NIA to discuss results.

• A summary of results provided at the end of the contract period.