Loren Data's SAM Daily™

SAMDAILY.US - ISSUE OF JULY 23, 2021 SAM #7174
SOURCES SOUGHT

99 -- Whole Exome Sequencing of 160 tumors and associated normal blood DNAs

Notice Date

7/21/2021 2:32:02 PM
 

Notice Type

Sources Sought
 

NAICS

541380 — Testing Laboratories
 

Contracting Office

NIH National Cancer Institute Rockville MD 20850 USA
 

ZIP Code

20850
 

Solicitation Number

SBSS_75N91021Q00175
 

Response Due

7/27/2021 1:00:00 PM
 

Archive Date

08/11/2021
 

Point of Contact

Jolomi Omatete, Phone: 2402766561, Elizabeth Tucker
 

E-Mail Address

jolomi.omatete@nih.gov, elizabeth.tucker@nih.gov
(jolomi.omatete@nih.gov, elizabeth.tucker@nih.gov)
 

Description

This Small Business Sources Sought Notice (SBSS) is for information and planning purposes only and shall not be construed as a solicitation or as an obligation on the part of the National Cancer Institute (NCI). The purpose of this Sources Sought Notice is to identify qualified Small Business concerns including 8(a), HUBZone or Service-Disabled Veteran-owned businesses that are interested in and capable of performing the work described herein. The NCI does not intend to award a contract on the basis of responses received nor otherwise pay for the preparation of any information submitted. 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 requirement is assigned North American Industry Classification System (NAICS) code 541380 with a size standard in dollars is $16.5M. As a result of this Sources Sought Notice, the NCI may issue a Request for Quotation (RFQ). THERE IS NO SOLICITATION AVAILABLE AT THIS TIME.� However, should such a requirement materialize, no basis for claims against NCI shall arise as a result of a response to this Sources Sought Notice or the NCI�s use of such information as either part of our evaluation process or in developing specifications for any subsequent requirement. BACKGROUND The Urologic Oncology Branch of the NCI has spent many years recruiting patients with a hereditary predisposition to kidney cancer.� Over time we have been very successful in identifying the underlying genetic causes for many of these patients, but a large number of patients still require investigation.� In addition, once the germline mutation has been identified it is important to catalogue and understand what other additional somatic (acquired) changes are occurring within the tumor.� Whole exome sequencing (WES) has provided an excellent platform for investigating both the underlying germline changes and the additional somatic changes.� Commercial WES has become more and more economic and effective at providing high quality data and providing established pipelines for the initial analysis of the raw data.� This is very important as this initial analysis step can take up a huge amount of time for the researchers at the NIH so they benefit from using a well-established pipeline.� Data derived from these studies can be invaluable for patient management and care.� Once germline mutations are identified patients can be more effectively managed.� They can have appropriate kidney screening and possibly addition screening for additional symptoms associated with the identified mutation.� The decision to perform surgery or utilize active surveillance and the choice of systematic therapy is influenced by the germline alterations that are found.� The somatic mutations are also essential for our understanding and therapeutic targeting of specific tumors.� Some somatic mutations are directly associated with more aggressive disease, influencing patient management, or with responses to specific drugs, influencing treatment.� Understanding what pathways and mechanisms are mutated in the tumors can also give us a wider view of what has gone wrong within the tumor and what pathways could be therapeutically targeted due to our increased understanding. As with all next generation sequencing performed at the NCI, these data will be added to a publicly available database, such as dbGAP, upon submission for publication and will provide a resource for further research. OBJECTIVE The primary objective of this project is to perform human whole exome sequencing and analysis on 160 tumors and associated normal blood DNAs using the NovaSeq 6000 PE150 system to provide 12 G of raw data per sample that will translate to an average of 100x coverage per tumor.� The bioinformatic analysis is to be performed by the vendor and will include: Data quality control: filtering reads containing adapter or with low quality, Alignment with reference, statistics of sequencing depth and coverage, SNP and InDel calling, annotation and statistics, Somatic variant detection - SNP calling, annotation and statistics, InDel calling, annotation and statistics, CNV calling, annotation and statistics SCOPE The contractor will perform human whole exome sequencing of 160 tumors and associated normal blood DNAs and provide bioinformatic analysis of the raw data acquired.� This will be a one-off analysis and once the samples have been received by the contractor and shown to be of sufficient quality, the project should be completed in 36 days.� The contractor will provide the raw data and bioinformatic analysis report at the end of this projected 36-day timeframe. CONTRACT REQUIREMENTS/ AND PERSONNEL QUALIFICATIONS The Contractor shall perform the following tasks: Whole Exome Sequencing The contractor will perform a quality control check on the received DNA and report the findings before proceeding.� The contractor will then perform human whole exome sequencing using NovaSeq 6000 PE150 system to provide 12 G of raw data per sample that will translate to an average of 100x coverage per tumor. The Raw data will be provided to NCI. Bioinformatic Analysis The raw data will be processed by the contractor using their established pipelines and provide a report detailing the Data quality control (filtering reads containing adapter or with low quality), Alignment with reference, statistics of sequencing depth and coverage, SNP and InDel calling, annotation and statistics, Somatic variant detection - SNP calling, annotation and statistics, InDel calling, annotation and statistics, CNV calling, annotation and statistics This report will be provided in full to NCI. How to Submit a Response: Page Limitations: Interested qualified small business organizations should submit a tailored capability statement for this requirement not to exceed 10 single sided pages including all attachments, resumes, charts, etc. (single spaced, 12 �point font minimum)� that clearly details the ability to perform the requirements of the notice described above.� All proprietary information should be marked as such.�� Responses should include a minimum of two pages demonstrating experience over the past two years meeting the requirements of this notice.� Statements should also include an indication of current certified small business status; this indication should be clearly marked on the first page of your capability statement (preferable placed under the eligible small business concern�s name and address).� Responses will be reviewed only by NIH personnel and will be held in a confidential manner. Due Date:� Capability statements are due no later than 4:00 PM. EST on July 27, 2021. Delivery Point: All information furnished must be in writing and must contain sufficient detail to allow the NCI to determine if it can meet the unique specifications described herein. Written responses can be emailed to Jolomi Omatete, Contracting Officer at Jolomi.Omatete@nih.gov or mailed to the address located under Point of Contact.� All questions must be in writing and submitted via email.� A determination by the Government not to compete this requirement based upon responses to this notice is solely within the discretion of the Government.� Information received will be considered solely for the purpose of determining whether to conduct a competitive procurement.� In order to receive an award, contractors must have valid registration and Representations and Certifications Application at www.sam.gov.� No collect calls will be accepted.� Please reference number SBSS_75N91021Q00175 all correspondence. 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, an RFQ may be published.� However, responses to this notice will not be considered adequate responses to a solicitation(s). � Point of Contact: Inquiries concerning this Notice may be direct to: Jolomi Omatete Jolomi Omatete@nih.gov 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.
 

Web Link

SAM.gov Permalink
(https://beta.sam.gov/opp/d6e81469bf2f4daaa63a102d4c807c13/view)
 

Place of Performance

Address: Rockville, MD 20850, USA

Zip Code: 20850

Country: USA
 

Record

SN06069525-F 20210723/210721230134 (samdaily.us)
 

Source

SAM.gov Link to This Notice
(may not be valid after Archive Date)

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