Whole genome sequencing

This is a Small Business Sources Sought notice. This is NOT a solicitation for proposals, proposal abstracts, or quotations.
The purpose of this notice is to obtain information regarding: (1) the availability and capability of qualified small business sources; (2) whether they are small businesses; HUBZone small businesses; service-disabled, veteran-owned small businesses; 8(a) small businesses; veteran-owned small businesses; woman-owned small businesses; or small disadvantaged businesses; (3) their size classification relative to the North American Industry Classification System (NAICS) code for the proposed acquisition.
Your responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. An organization that is not considered a small business under the applicable NAICS code should not submit a response to this notice. This notice is issued to help determine the availability of qualified companies technically capable of meeting the Government requirement and to determine the method of acquisition. It is not to be construed as a commitment by the Government to issue a solicitation or ultimately award a contract. Responses will not be considered as proposals or quotes. No award will be made as a result of this notice. The Government will NOT be responsible for any costs incurred by the respondents to this notice. This is a 12-month period of performance.  This notice is strictly for research and information purposes only.

National Institutes of Health, National Institute on Aging investigators in the HANDLS study require whole genome sequencing (WGS) data to expand current research examining whether rare genetic variants present in White and African American individuals contribute to age-related chronic diseases. Samples from HANDLS participants have been obtained over the longitudinal study, starting in 2004, and thus some samples are over 15 years old and many are over 10 years old. 

The contractor will be required to deliver plates to the Government sufficient to run 325 samples, some of which have been stored for ten or more years. The contractor will perform whole genome sequencing, and specifically shall sequence libraries on the NovaSeq X-Plus platform with 25B-300 flow cells using 150 bp paired end runs and NovaSeq workflow-series 10B sequencing run, confirm genomic DNA quantity and quality by performing DNA concentration measurements and volume checks, re-attempt sequencing in the case that DNA quality and quantity is sufficient, but sample fails sequencing-based QC, examine agarose gels on all samples as an industry-standard method for screening DNA marker quality prepare PCR-free sequence libraries for all samples, sequence the libraries at a minimum of 30x coverage with 2×150 base pair runs, perform primary and secondary analysis of the sequencing data including but not limited to read alignment, variant calling, and quality control analyses. Quality control checks will include: confirming sex, identifying unexpected duplicates and relatedness, confirming relatedness, providing sample performance information and sample identity confirmation against the sequencing data, in addition to confirming coverage, contamination, mapped reads, and other general quality metrics.  Alignment and variant calling will be performed with the DRAGEN Germline v4.3.6 pipeline. After quality is confirmed, joint variant calling should be performed producing a multi-sample VCF file. Provide written summaries and documentation of the methods used to perform the whole genome sequencing pipeline. 

Capability statement /information sought.

Companies that believe they possess the capabilities to provide the required services should submit documentation of their ability to meet each of the project requirements to the Contracting Officer. The capability statement must specifically address each of the project requirements separately. Additionally, the capability statement should include 1) the total number of employees, 2) the professional qualifications of personnel as it relates to the requirements outlined, 3) any contractor GSA Schedule contracts and/or other government-wide acquisition contracts (GWACs) by which all of the requirements may be met, if applicable, and 4) any other information considered relevant to this program. Capability statements must also include the Company Name, Unique Entity ID from SAM.gov, Physical Address, and Point of Contact Information. The response must include the respondents’ technical and administrative points of contact, including names, titles, addresses, telephone and fax numbers, and e-mail addresses.
Interested companies are required to identify their type of business, applicable North American Industry Classification System (NAICS) Code, and size standards in accordance with the Small Business Administration. The government requests that no proprietary or confidential business data be submitted in a response to this notice. However, responses that indicate the information therein is proprietary will be properly safeguarded for Government use only. Capability statements must include the name and telephone number of a point of contact having authority and knowledge to discuss responses with Government representatives. Capability statements in response to this market survey that do not provide sufficient information for evaluation will be considered non-responsive. When submitting this information, please reference the solicitation notice number. One (1) copy of the response is required and must be in Microsoft Word or Adobe PDF format using 11-point or 12-point font, 8-1/2” x 11” paper size, with 1” top, bottom, left and right margins, and with single or double spacing.  The information submitted must be in and outline format that addresses each of the elements of the project requirement and in the capability statement /information sought paragraphs stated herein. A cover page and an executive summary may be included but is not required.  The response is limited to ten (10) page limit. The 10-page limit does not include the cover page, executive summary, or references, if requested.  All responses to this notice must be submitted electronically to the Contract Specialist and Contracting Officer. Facsimile responses are NOT accepted.

Disclaimer and Important Notes: This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization’s qualifications to perform the work.
Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a presolicitation synopsis and solicitation may be published in www.sam.gov. However, responses to this notice will not be considered adequate responses to a solicitation.  Confidentiality: No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s).