Small Business Sources Sought: Whole genome sequencing for HANDLS participants

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; and (4) availability of domestic sources manufactured in the United States in sufficient and reasonably available commercial quantities and of a satisfactory quality. For equipment/supply requirements, responses must include the place of manufacturing (i.e. address if supply/equipment is a domestic end product and include country of manufacture). For equipment/supply requirements, small businesses must also address the size status of the manufacturer under the applicable NAICS code (i.e. address Non-Manufacturer Rule). 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 notice is strictly for research and information purposes only. Background: Health disparities in age-related chronic conditions such as obesity and chronic kidney disease (CKD) are well documented. Importantly, diseases such as obesity and CKD have been linked to accelerated aging, the risk for age-associated conditions at younger ages than usual. Although genetics may contribute to observed health disparities, there are only limited studies in the racial and ethnic minority populations. The objective of this work is expanding our current research to examine health disparities associated with age-related diseases through whole genome sequencing to investigate the contributions of genomics to the disproportionate burden of disease incidence, prevalence, morbidity, and mortality in minority groups within the United States. The long term goal is to create a consistent dataset of whole genome sequencing to complement the longitudinal HANDLS behavior and health data. Purpose and Objectives: Investigators in the Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) study require whole genome sequencing (WGS) data to expand our current research examining whether rare genetic variants present in racial minority populations contribute to observed health disparities in age-related 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. A contract is required because the Government does not have available facilities or resources to perform this work consistent with other WGS performed on HANDLS samples. Project Requirements: The contractor will deliver plates to the Government sufficient to run 95 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 6000 platform using 150 bp paired end runs and NovaSeq 6000 S4 v1.0 Reagent Kit with NovaSeq Xp v1.0 4-Lane kit or standard workflow 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 v4.0.3 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 Supply the whole genome sequencing data in a mutually acceptable electronic format that preserves study participants confidentiality. Data delivered will include: per sample CRAMs per sample gVCFs per sample VCFs joint-called multi-sample VCF per sample structural variant and CNV calls QC report and data dictionary Sample manifest with flagged problems Following data delivery and upon request by the Government, the contractor shall provide attendance at Government laboratory staff meetings and the contractor shall provide technical consultations as needed. Delivery or Deliverables: The contractor will provide the following deliverables: Analytic plates delivered to the Government at the Biomedical Research Center in Baltimore, MD Written summaries and documentation of the methods used to perform the whole genome sequencing pipeline Whole genome sequencing data in a mutually acceptable electronic format that preserves study participants confidentiality. Data delivered will include: per sample CRAMs per sample gVCFs per sample VCFs joint-called multi-sample VCF per sample structural variant and CNV calls QC report and data dictionary Sample manifest with flagged problems Return any leftover DNA on dry ice by overnight shipping to the Government at the Biomedical Research Center. Upon the Government's request, attend staff meetings and provide technical consultations as needed. Government Responsibilities: The Government will provide genomic DNA samples with a minimum concentration of 500 nanograms (ng; per sample) to the contractor for quality control metrics, library preparation, and sequencing. The Government will load the genomic DNA samples on contractor-provided plates. Other important considerations: The National Institute on Aging shall have unlimited rights to and ownership of all deliverables provided under this contract, including reports, data updates and statistical results. This includes the deliverables provided under the basic contract and any optional task deliverables exercised by the contracting officer. In addition, it includes any additional deliverables required by contract change. The definition of - unlimited rights is contained in Federal Acquisition Regulation (FAR) 27.401, - Definitions. FAR clause 52.227-14, - Rights in Data-General, is hereby incorporated by reference and made a part of this contract/order. In case domestic sources are available and capable of fulfilling the Government's need, and a future solicitation is published, the Government will use evaluation preferences in accordance with FAR 25. Capability statement /information sought. Companies that believe they possess the capabilities to provide the required products or 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 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. The response must be submitted to Kaitlyn Landi, Contract Specialist, at e-mail address contact@example.gov. The response must be received on or before August 13, 2024, at 4:00 p.m., Eastern Time. - 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).