Attach_3-DNA_Sequencing-SOW_Jul_16_2019.pdf

Attachment 3

DNA SEQUENCING SERVICES

Statement of Work for the National Institutes of

Environmental Health Sciences (NIEHS)

July 16, 2019

A. Introduction

The National Institute of Environmental Health Sciences (NIEHS) (http://www.niehs.nih.gov/index.cfm), located in Research Triangle Park (RTP), North Carolina, is one of 27 research institutes and centers that comprise the National Institutes of Health (NIH) (http://www.nih.gov/). The mission of the NIEHS is to reduce the burden of human illness and disability by understanding how the environment influences the development and progression of human disease.

In support of this mission, NIEHS seeks to establish a reliable, rapid and cost-effective Sanger Method capillary-based DNA sequencing services contract which supports investigators within the intramural research program at NIEHS. This sequencing information will provide vital information to ongoing investigations regarding environmental disease mechanisms and the genetic component involved in causes, outcomes, and progression of environmental diseases.

This contract will provide high quality DNA sequencing of individual samples and accompanying bioinformatics support. The majority of the biological samples will be yeast colonies, plasmid DNA and Polymerase Chain Reaction (PCR) generated samples from a variety of species that include, but are not limited to, human, rodent and recombinant DNA isolated from various tissue sources and cell lines. The contractor shall provide sample storage and preservation which are critical for subsequent nucleic acid analysis. Information needed to assist the contractor in their ability to perform the service correctly will be provided prior to sequencing;

data analysis will be performed by NIEHS.

All references to the term “user” within this statement of work shall be inclusive of government users such as investigators, the COR, or other approved government personnel.

B. Requirements/Specifications

Independently and not as an agent of the Federal Government, the contractor shall supply services, qualified personnel, materials, equipment and facilities not otherwise provided to the contractor by the Government under terms of this contract, as required to perform work set forth below:

1. Contractor shall perform high-throughput Sanger DNA resequencing using robotic automation and sample barcode tracking, sufficient to support an estimated average monthly volume of 7,500 samples.

2. Contractor shall provide sequence data from user-provided agar plates containing yeast colonies, 96 well plates or PCR strip tubes containing PCR amplifiable material, which may be genomic DNA or plasmid DNA. The requirement for PCR amplification prior to cycle sequencing will be specified, at the time of sample submission, by the sample submitter/user for each sample within a given plate or tube. The contractor shall verify (by gel electrophoresis) success of PCRs required to produce the DNA template for successful sequencing.

Note: Samples requiring PCR for the production of the DNA template for sequencing will be provided additional time for this process. The contractor will not be required to isolate genomic DNA from cells or tissues. Successful PCR amplifications require production of a single DNA band of the appropriate size.

3. Contractor shall normalize DNA template(s) for PCR amplification and sequencing when requested by the submitter/user.

4. Samples which fail to produce data due to capillary failure or other contractor technical problems shall be repeated immediately.

Note -Successful sequencing runs shall cover the desired region in length for PCR products, at least 600 bases for plasmid DNA while achieving a quality score for each base of > 20.

5. Contractor shall employ staff trained in bioinformatics to perform successful primer design for new sequencing projects.

6. Contractor will be required to develop assays necessary to determine the

DNA sequence as requested by the user. This includes, but is not limited to, primer design, PCR optimization, and sequence reaction optimization. DNA reference sequence(s) or accession number(s) will be provided. The government retains all rights to use developed assays and must be provided all technical information, including but not limited to:

• formulations of reagents used in assay;

• instrumentation type used;

• all settings and calibrations of instrument regarding each assay.

Technical information shall be delivered within 24 hours of receipt of a written request from the user.

7. Contractor shall provide a reliable method of sample transport both to and from the NIEHS campus and contractor’s laboratory/facility. This may be achieved by: in-house courier, local contracted courier, or through FedEx or UPS. Samples shall be picked up daily at the NIEHS main campus at the following address:

111 TW Alexander Dr.

Durham, NC 27709.

8. Contractor shall provide all necessary sample collection material and information for the shipment of samples, including but not limited to:

a) sample collection plate or vial;

b) identification of refrigerated storage method of samples prior to sequencing analysis;

c) appropriate pre-paid shipping containers;

d) a record of the tracking system/method used for samples.

9. Contractor shall provide a web-based ordering platform/system which allows for efficient ordering of DNA services and communication between the Contractor and government end users.

10. Contractor shall provide appropriate training to government users on the proper methods required to successfully submit DNA samples for sequencing and retrieval of generated data using the contractor’s website.

11. At the time of sample submission, the user shall provide plate key or tube label information containing sample names with sample identifiers.

Multiple sequencing runs may be requested per template as specified by the user.

12. The contractor shall return data to the investigator via the Internet or by email as attachments and shall return all data to the COR using a data transfer solution provided by the Government that meets the Government’s requirements for throughput, security, integrity, and reliability. Data file types to be sent include the .ab1, .seq, and the qscrl file Data shall be returned to the user and the COR via the Internet or by email as attachments as follows:

• within two (2) working days of receipt of plasmid DNA or PCR amplicon samples;

• within five (5) working days of receipt of genomic DNA. This will require generation of the DNA template by PCR, then DNA sequencing of that product.

Data shall be generated using appropriate software compatible in both PC and Mac formats for data analysis as specified by the COR.

NOTE: Turnaround time for data is calculated according to receipt of samples at Contractor’s facility. The Contractor shall notify the user and the COR of receipt of materials on the same day as receipt.

13. Except as explicitly authorized by the COR, the Contractor shall maintain the confidentiality of all sequencing data generated by this contract. The Contractor shall not publish or use the data and results for any purpose other than those expressly authorized by the COR.

14. Contractor shall promptly identify to the COR any concerns or barriers to performance within 24 hours of identification of any issue. The Contractor shall develop and implement solutions within 24 hours of COR contact.

15. The COR shall promptly identify to the Contractor any concerns or barriers to performance within 24 hours of identification of any issue. The Contractor shall develop and implement solutions within 24 hours of COR contact.

16. Contractor shall provide any requested information and respond to the

COR’s comments and suggestions within 24 hours of contact.

17. The COR may require some data to be transferred using a secure file transfer method. In such cases, the Contractor shall be required to use a government provided file transfer system.

18. Contractor shall provide a Weekly Status Report delivered via email to the

COR in Excel format. The weekly report shall be due on each Monday at 9:00 A.M. EST and shall list the following information:

a) number of samples received, including date received;

b) number of samples successfully sequenced, including date data was sent to the user and/or COR;

c) number of samples unsuccessfully sequenced, including the cause of failure and the date that notification was sent to the user;

d) number of samples requiring PCR amplification;

e) number of samples requiring PCR purification;

f) number of samples requiring modified sequencing protocols and the type of modification;

g) number of samples requiring DNA normalization;

h) status of Quality Control data, including the week’s success and error rate.

19. Contractor shall provide a monthly written report delivered via email to the COR in Excel format. The monthly report shall be due within five (5) business days of the end of each billing cycle and shall summarize the following information:

a) sequencing activities to include the number of samples sequenced;

b) the number of samples requiring PCR amplification;

c) the number of samples requiring PCR purification;

d) the number of samples requiring modified sequencing protocols and the type of modification;

e) the number of samples requiring DNA normalization; and

f) the number of assays developed.

20. Contractor shall submit invoices to the COR and Contracting Officer within ten (10) business days of the end of each billing cycle in accordance with invoicing instructions provided in the contract. Revisions to invoices requested by the COR shall be submitted to the COR and Contracting Officer within two (2) business days after notification of needed revisions by the

COR.

21. Contractor shall comply with Section 508 of the Rehabilitation Act of 1973

(29 U.S.C. 794d) which requires Federal agencies to purchase Electronic and Information Technologies (EIT) that meet specific accessibility standards. All electronic deliverables including reports, data entry, audio and video shall be Section 508-compliant; drafts do not need to be compliant. Detailed data that is meant to be processed by a program and not meant to be read by people does not need to be Section 508 compliant.

22. Contractor shall maintain confidentiality of all data and secure back-up of all essential data, including but not limited to, all DNA sequencing data generated, sample tracking and storage information, and Quality Control information.

23. Contractor shall have no access, and shall not attempt access, to any type of personal identifiers or other form of identifying information with the human samples provided.

24. Contractor shall return or destroy, as instructed by the COR, all DNA from users no sooner than 180 days after completing sequencing, or as agreed upon and approved by the COR. Remaining unused primers shall be returned to the COR for long term storage.

NOTE: This includes primers produced and synthesized by the contractor for use in the performance of this contract.