Q301--Genome Sequencing (VA-22-00058417)

SOURCES SOUGHT

The purpose of this sources sought is to conduct market research to determine if responsible sources exist by determining if this effort can be successfully competed and/or set-aside for Small Businesses. The proposed North American Industry Classification System (NAICS) Code is 541380-Testing Laboratories. The size standard is 16,500,000 or 621511 Medical Laboratories, size standard $35 million. The Department of Veterans Affairs will use this information to determine the best acquisition strategy for this procurement. The Government is interested in all large and small businesses to include 8(a), Service-Disabled Veteran-Owned, HubZone and Women-Owned small business concerns.

The Department of VA, Office of Research & Development, Million Veterans Program is seeking potential sources to provide high-throughput whole genome sequencing for human biological samples. The human biological samples will be de-identified/coded and sent to the contractor facility from a designated VA Biorepository. VA will provide the contractor with coded human biological samples. 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 policy VA handbook 65001. The acceptable method of destroying biological samples is by bleaching and certified to completion of the destruction in writing to the VA PM. The contractor MUST meet the following requirements:

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 working using Illumina next generation sequencing by synthesis technology

Ability to conduct high-throughput WHOLE GENOME sequencing (for research purposes ONLY) of up to 3300 VA human biological 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

Ability to conduct high-throughput WHOLE GENOME sequencing (for research purposes ONLY) of up to 900 VA human biological samples at >100x depth or another qualitative metrics mutually agreed upon by the contractor and VA PM and over 90% coverage of the mutually agreed upon reference genome per month utilizing a sequencing by synthesis method within the contract period.

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

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.

The contractor must be able to store samples 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 policy VA handbook 65001. The acceptable method of destroying biological samples is by bleaching and certified to completion of the destruction in writing to the VA PM.

The contractor shall not use VA Data for any purposes other than generation and shipping the data to VA. Once VA has received the data and validated within VA and upon request from the VA PM 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

Contractor shall have the ability to provide monthly written reports to 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 biological 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.

Contractor shall supply completed whole genome sequence data for the VA samples including the data requirements in below in section M and generated in a secure manner in one or all of the requested formats below. The contractor may have to complete VA Contractor Security Control Assessment on an annual basis.

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 of 5 TB and 45TB in size.

In addition to the external drives above, data should also be transferred to VA approved secure cloud storage location as requested in writing by the VA.

Contractor shall test biological specimen sample 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% coverage 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 biological samples at >100x with 90% coverage of mutually agreed upon reference.

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)

This is not a solicitation. This information is for planning purposes only and is not to be construed as a commitment by the Government, implied or otherwise, to issue a solicitation or award a contract. Potential sources responding to this sources sought notice are advised their responses do not ensure participation in future solicitations or contract awards. The Government will not reimburse any company or individual for any expense.

Potential sources who are interested should provide the following:

1. Business name, address, SAM UNIQUE ID#, number; point of contact; business size and business socio-economic category; register in SAM (http://www.sam.gov).

2. Provide a service capability statement that clearly demonstrates your ability to meet the requirements in sections A-M and subsections.

3. Send written responses electronically in Word format to Lynn.Portman@va.gov by 5/10/22. Telephone responses will not be accepted.  Â

*This notice is to assist in determining sources only--a solicitation is not currently available.