Statement of Work_Illumina_DRAGEN.pdf

Version 11-30-2016-1 FAR Part 11—Describing Agency Needs

STATEMENT OF WORK (SERVICES)

(SOW)

GENERAL INFORMATION

Title of Project:

Illumina DRAGEN GCP Lvl 4 1-year License

Statement of Need and Purpose:

This acquisition aims to purchase access to the Illumina DRAGEN (Dynamic Read Analysis for GENomics) platform. This platform is a proprietary suite of advanced algorithms designed to accurately detect variants in human genome data. Access to the DRAGEN platform is needed to analyze whole-genome sequencing data from 10,000 people with neurodegenerative diseases and controls. The critical capabilities of the DRAGEN platform are: 1) ultra-high throughput processing capacity, 2) exceptional accuracy in variant calling, 3) comprehensive data handling and management capabilities, and 4) compatibility with existing Illumina sequencing technologies. The purpose of this purchase is to enable our group to align raw next-generation sequencing data already generated on Illumina sequencers to the human reference genome. Generating highly accurate genetic variant calls is essential for discovering disease-related genetic information and the mission of our laboratory.

Background Information and Objective:

The Neurodegenerative Diseases Research Section (NDRS) is a leading neurogenomics laboratory that specializes in applying modern gene discovery applications to understudied neurodegenerative diseases, such as Lewy body dementia and frontotemporal dementia/amyotrophic lateral sclerosis. NDRS's success rests on its ability to generate and analyze high-quality genome data from patients suffering from these fatal diseases. The laboratory has already generated the raw genome data from 10,000 people using the Illumina sequencing platform. These raw genome data must be processed on the Illumina DRAGEN platform to be usable for gene discovery analyses.

The Illumina DRAGEN (Dynamic Read Analysis for GENomics) platform is a sophisticated system that analyzes next-generation sequencing data from Illumina sequencers. This versatile platform integrates optimized algorithms to process genomic data with high accuracy. The system is designed to be scalable, so thousands of genomes can be rapidly processed. The DRAGEN platform will perform graph-based alignment of the raw sequence data files to the human reference genome (hg38) and apply highly optimized algorithms for accurate and scalable joint variant calling. These alignment data will then be used for the accurate genome-wide detection of single-nucleotide variants, structural variants, copy number variants, repeat expansions, and variants in targeted regions (e.g., HLA locus, GBA locus) using advanced algorithms readily incorporated in the DRAGEN platform. For more information, please see the latest DRAGEN release notice: https://support.illumina.com/content/dam/illumina-https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsupport.illumina.com%2Fcontent%2Fdam%2Fillumina-support%2Fdocuments%2Fdownloads%2Fsoftware%2Fdragen%2Frelease-notes%2F200040845_01_DRAGEN-4.2-Customer-Release-Notes.pdf&data=05%7C02%7Csonja.scholz%40nih.gov%7C66a8c39f053c4172b30608dc6d6dc61f%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638505565841484062%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=D52T0%2BFToQAxtyC4CT355GNkX7kOOd2O6N7SUNJ7Q1E%3D&reserved=0 support/documents/downloads/software/dragen/release-notes/200040845_01_DRAGEN-4.2- Customer-Release-Notes.pdf). The whole genome sequence data from these 10,000 samples will be merged with existing Illumina whole-genome sequence data for additional samples that have already been processed with the same DRAGEN platform. These two datasets can only be merged if they are called on the exact same DRAGEN platform. Merging the two datasets increases the power to find the genetic causes of neurodegenerative diseases. Not calling our current 10,000 samples on the same DRAGEN platform will prevent the merging of the datasets, halt the progress of the project, and prevent the project from being completed, representing a considerable loss of resources to the US Government.

This purchase order requests the processing of 1,300,000 Gigabytes of data, the size of the raw data files from 10,000 human genomes, on the DRAGEN GCP platform. The cost per genome is $11.30, and the total cost is $113,004.

Period of Performance:

The period of performance shall be 12 months.

SCOPE OF WORK

General Requirements:

This purchase order requests access to the DRAGEN platform to allow the processing of 1,300,000 Gigabytes of data. This data amount represents the size of the raw data files from 10,000 human genomes. The processing cost per genome is $11.30, and the total cost is $113,004.

Specific Requirements:

The vendor, Illumina Inc, shall provide access to the Illumina DRAGEN GCP Level 4 platform for a one-year period to process approximately 1,300,000 GB of whole-genome sequencing data derived from 10,000 human genomes. The platform must support graph-based alignment to the human reference genome (hg38) and enable accurate variant calling. Required outputs include detection of single-nucleotide variants, insertions/deletions, structural variants, copy number variants, and repeat expansions. The platform must be fully compatible with Illumina-generated sequencing data and existing DRAGEN-processed datasets to ensure seamless integration and down stream analyses.

LEVEL OF EFFORT:

The vendor, Illumina, will provide access to the Illumina DRAGEN platform to allow the processing of 10,000 human genomes, which amounts to 1,300,000 Gigabytes of data.

GOVERNMENT RESPONSIBILITIES

Once access to the Illumina DRAGEN platform has been granted, the investigator will process 10,000 human genomes, which amounts to 1,300,000 Gigabytes of data that have already been generated. Data processing will be completed within one year.

https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsupport.illumina.com%2Fcontent%2Fdam%2Fillumina-support%2Fdocuments%2Fdownloads%2Fsoftware%2Fdragen%2Frelease-notes%2F200040845_01_DRAGEN-4.2-Customer-Release-Notes.pdf&data=05%7C02%7Csonja.scholz%40nih.gov%7C66a8c39f053c4172b30608dc6d6dc61f%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638505565841484062%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=D52T0%2BFToQAxtyC4CT355GNkX7kOOd2O6N7SUNJ7Q1E%3D&reserved=0 https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsupport.illumina.com%2Fcontent%2Fdam%2Fillumina-support%2Fdocuments%2Fdownloads%2Fsoftware%2Fdragen%2Frelease-notes%2F200040845_01_DRAGEN-4.2-Customer-Release-Notes.pdf&data=05%7C02%7Csonja.scholz%40nih.gov%7C66a8c39f053c4172b30608dc6d6dc61f%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638505565841484062%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=D52T0%2BFToQAxtyC4CT355GNkX7kOOd2O6N7SUNJ7Q1E%3D&reserved=0

DELIVERY OR DELIVERABLES

The contractor shall provide: (1) access and operational availability of the DRAGEN GCP platform ; (2) processing capability sufficient to analyze 10,000 genomes within the performance period; and (3) generation of aligned sequence files and variant call outputs (e.g., CRAM and VCF-files) meeting DRAGEN quality standards. All outputs must be suitable for downstream genomic analyses and compatible with previously processed DRAGEN datasets.

REPORTING REQUIREMENTS

The vendor, Illumina, will report when access to the DRAGEN platform has been granted and when the available licenses have been completed. The vendor will be available for ad hoc troubleshooting.

OTHER CONSIDERATIONS

Travel:

There is no travel involved.

Key Personnel:

This purchase order does not include personnel costs.

Information System Security Plan:

This acquisition involved the processing of genomic research data on a cloud-based platform (lllumina DRAGEN on Google Cloud Platform). The contractor shall comply with all NIH, HHS, and NIST information security standards, including appropriate safeguards to ensure the confidentiality, integrity, and availability of data. Data handling will follow NIH/NINDS information security policies, and access to the system will be restricted to authorized users only.

The contractor will not create or maintain a federal system of records, but must ensure secure processing and storage of government-furnished genomic data.

Data Rights:

The genome sequence data have been produced by the Neurodegenerative Diseases Research Section and are a property of the National Institutes of Health. Processed data files are the property of the U.S.

government. The vendor for the Illumina DRAGEN platform does not have the right to use or disclose the data.

Section 508—Electronic and Information Technology Standards:

Section 508 does not apply to this procurement. The acquisition is for a back-end computational genomic platform used for research data processing and does not involve the development, maintenance, or delivery of user-facing electronic and information technology products, public-facing websites, or multimedia content. Therefore, no Section 508 compliance requirements are applicable.

Publications and Publicity:

The vendor will not write or publish articles using data processed on the Illumina DRAGEN platform.

Confidentiality of Information:

The contrast will involve govermment-furnished, deidentified genomic research data. Although the contractor will not create or maintain a system of records, the data must be treated as confidential and protected from unauthorized access, use, or disclosure. Appropriate safeguards shall be implemented to ensure data confidentiality, integrity, and availability throughout processing on the DRAGEN platform.

The contractor shall comply with all applicable federal and NIH data protection and security policies. Any proprietary or sensitive research data provided under this contract shall be used solely for the purposes of performing the requirements of this Statement of Work.