Q--Genomic Sequencing

The VHA provides healthcare services for the nations Veteran population. One of the charges of the VHA is to promote research and development dedicated to improving the health and lives of Veterans. The Office of Research and Development (ORD) created the Genomic Medicine Program (GMP) in 2006 to support and lead VA as it moves into the venue of genomic or precision medicine. ORD has an upcoming requirement for Whole Genome sequencing for human DNA samples for the Department of Veterans Affairs (VA) Veterans Health Administration (VHA), Office of Research and Development s Million Veteran Program. The purpose of this synopsis is to gain knowledge of potential qualified sources who can meet the salient characteristics below and their size classification (large business, small business, 8(a), SDVOSB, etc.), relative to NAICS code 334516. Responses to this synopsis will be used by the Government to make appropriate acquisition decisions. General Scope The VHA Million Veteran Program requires the services of High-throughput human whole genome sequencing. The field of genomics and particularly genomic medicine is a new and rapidly evolving one. The VA stands at this cutting edge and needs resources to ensure that the Veterans receive the benefit of the latest technology and research. This upcoming requirement is to secure a combination of WHOLE GENOME sequencing services to support the objectives of the VA s Million Veteran Program (MVP). The following overview contains, but is not limited to, the tasks associated with this upcoming requirement. The human DNA samples shall be sent to the contractor facility from the MAVERIC Biorepository in Boston or another VA biorepository. Contractor Qualifications The contractor shall have the following qualifications, capabilities, and be able to document the following: Headquarters and laboratory facilities where work to be conducted in is located within the Continental United States. No work shall be performed outside of the United States or in any locality outside of the jurisdiction of the laws of the United States. Ability to conduct high-throughput WHOLE GENOME sequencing (for research purposes ONLY) of up to 2500 VA human DNA samples at >30x depth over 90% of the mutually agreed upon reference genome per month utilizing a sequencing by synthesis method within the contract period .THIS IS A CRITICAL REQUIREMENT. OR, Ability to conduct high-throughput WHOLE GENOME sequencing (for research purposes ONLY) of up to 900 VA human DNA samples at >100x depth over 90% of the mutually agreed upon reference genome per month utilizing a sequencing by synthesis method within the contract period for somatic samples. THIS IS A CRITIAL REQUIREMENT. Ability for Sample tracking and management utilizing bar coding to ensure security & traceability of VA samples. Ability to produce documentation of sample handling and processing attributes/audit trail, etc. that would address sample mixing and sample error tracking. The contractor shall demonstrate that they are certified in Good Laboratory Practice (GLP) and CLIA certification Contractors shall be required to submit for a NACI low level background investigation and security clearance in accordance with the VA IT Security Clause and complete the required training and procedures to comply with these requirements. TASKS/REQUIREMENTS. Tasks: The contractor shall provide a detailed Project Management Plan in their proposal to address the following tasks necessary to complete the whole genome sequencing, and shall address the capabilities to provide specific requirements: Additionally, the contractor shall not propose primary and alternative methods within a single proposal. If alternate methodologies are going to be proposed, it is suggested that the contractor submit multiple proposals. Task 1: Provide a detailed DNA Sample Security and Data Security Plan: All materials and samples utilized during the course of the contract are the property of the Department of Veterans Affairs and must be handled in a confidential and secure manner. The contractor shall outline in their response: their planned lab Standard operating procedures (SOPs) methods for handling and securing of samples including paper and electronic documents, the methods, assurances and processes for destruction of samples and data, details of proposed shipping requirements like method/conditions for shipping, receipt & acknowledgement of shipments, encryption of hard drives (if that is the VA requested delivery method); documentation of security of electronic data delivery (if that is VA requested delivery method) as well as the contractors ability to perform in accordance with and subject to: VA Handbook 6500.1 - Electronic Media Sanitization, VA Directive 6300 Records and Information Management and its Handbook 6300.1 Records management Procedures, National Archives and Records Administration(NARA), FISMA, HIPAA, NIST, and related VA security and privacy control requirements applicable with provisions and clauses within this requirement. This plan shall address how the contractor plans to meet these requirements and shall be required at the time of submitting the proposal. Simply stating or acknowledging the references is unacceptable. Task 2: Attend an initial contract kick-off meeting, and attend as needed meetings through the life of the contract. A kick off meeting will be held in Washington, DC at the Department of Veterans Affairs within 14 days after contract award and shall be attended by all staff on contract. This meeting may take place via teleconference if preferred. The contractor shall be required to communicate with Program staff on an as needed basis throughout the life of the contract via teleconference or videoconference. Task 3: Receipt and storage of VA DNA samples for sequencing The contractor shall include in proposal in their response to this PWS the outer boundaries of needed DNA sample quality, quantity and shipping requirement which will then be discussed and finalized at the Kick-off meeting. VA will provide the contractor with coded human DNA. The samples shall be stored by the contractor at -20 degrees Celsius in locked upright or chest freezers (with emergency back-up power) until the samples are processed for sequencing. Any unused samples are to be destroyed by the contractor as specified by VA policies. (See task 6 for detailed instructions on unused DNA and sequence data) Sample tracking and management process shall be in place to ensure security of VA samples. Task 4: Whole Genome Sequencing Contractor shall test DNA for quality sufficient to proceed with vendor sequencing procedures, and to confirm quality from VA reporting sent with samples, and to identity match samples before and after sequencing. Contractor shall provide the following services when a task order is issued for RESEARCH specimens: A. Research Whole Genome Sequencing (>30x depth of >90% of current, bilaterally agreed upon reference genome) DNA alignments and quality scores (Phred) of variants relative to a human genome reference sequence provided by the contractor in FASTQ or similar output file format, OR complete raw sequence files in FASTQ format, depending upon the specific requests of the task order Variant calls (if requested in task order) BAM files of each sequenced genome (if requested in task order) B. Research Whole genome sequencing of samples at >100x DNA alignments and quality scores (Phred) of variants relative to a human genome reference sequence provided by the contractor in FASTQ or similar output file format, OR complete raw sequence files in FASTQ format, depending upon the specific requests of the task order Variant calls (if requested in task order) BAM files of each sequenced genome (if requested in task order) Task 5: Provide reports and required Data 1. Monthly Written Report: - This report shall be delivered electronically via email no later than the 1st day of the following month. The report shall track parameters, including: Number of samples completed to desired parameters as requested per the task order Average depth of sequencing for each sample Quality control measurements of sequence data (including number of samples that did not meet QC measurement standards) These reports will include any non-compliance issues, to include if and the number of DNA samples that do not meet contractor s QC standards. And, in accordance with the most current industry standards, any other data that may be deemed beneficial to VA by contractor. 2. Required Sequenced Data Contractor shall supply completed whole genome sequence data for the VA samples including the data requirements in Task 4, and generated in a secure manner in one or all of the requested formats below: VA approved encrypted hard drives. Encryption shall be in accordance with VA security standards, VA Handbook 6500.6, by shipment of encrypted physical hard drives to VA location (provided by COR) by courier or overnight shipping, and including signature delivery confirmation. Currently the approved hard drives are 45TB in size. or by secure electronic transfer to VA approved secure cloud storage location; or by secure electronic transfer to VA approved federal partner location. Electronic Data and/or physical hard drives shall be sent to the VA or to approved cloud location or federal partner location within one week upon completion of each task order unless a specific schedule is mentioned in the individual task order. The vendor should have the capacity to begin shipments of task orders with the encrypted hard drives, but be able to switch to electronic data delivery within the contract period. Task 6: Destruction of Unused DNA and sequence data The contractor shall destroy or return unused DNA samples, in compliance with relevant sections of VA Handbook 6500.1 and per direction with written approval of the Contracting Officer s Representative or Contracting Officer. The acceptable method of destroying DNA samples is by bleaching and certified to that effect. The contractor shall destroy all data associated with VA sample as per direction and with approval of the VA COR/Contracting Officer and in full compliance of the VA Handbook 6500.1 specifically paragraphs 5 and 6. Once the data is received, the VA COR will notify the vendor in writing of the same. The data on the vendor s end shall be destroyed by the vendor within 30 days after documented completion of initial QC checks by the VA. Type of Contract: Firm Fixed Price This notice is not a request for competitive proposals, however; any responsible source who believes it is capable of meeting the requirement may submit a capability statement to the contracting office no later than Friday, March 10, 2017 at 4 PM, EST. Interest/capability statements may be sent to Lynn Portman at contact@example.gov and should include company name, address, point of contact, business size, SDVOSB/VOSB status, and product information. No telephone responses will be accepted. This notice is to assist the Government in determining sources only. A solicitation is not currently available. If a solicitation is issued, all interested parties must respond to that solicitation announcement separately from the responses to this announcement.