HHS-NIH-NIDA-SSSA-CSS-17-075_Question_and_Answer.pdf

Solicitation Number: NIH-NIDA-SSSA-CSS-17-075 Questions & Answers (Q&A)

January 19, 2017

1. What are the proposed gene targets (1-10) to be tested for in this genotyping project?

NIA has approximately 175 genes of interest. The (1-10) gene targets refers to the number of potential genes for a single tissue submission.

A list of 172 currently anticipated genes of interest and associated primers is attached to this solicitation titled “List of Anticipated Genes of Interest.” Additional genes may be added to this list periodically to the approximate number of 175.

2. Can you provide an example of the annotation results expected with genotyping results?

Yes. Please find attached two examples of annotation results when using traditional gel PCR methods. This method of annotation is expected for use with traditional gel PCR methods.

If performing qPCR assays, the above-described annotation is not necessary; instead a report of the presence or absence of the gene of interest along with the zygosity of the alleles for that gene is required.

Contractors may propose traditional PCR, qPCR, or a combination of methods, for this requirement.

3. The Government’s Project Requirements state that the online bioinformatics database “must be provided and hosted by the contractor.” Is it acceptable for the offeror to subcontract-out web hosting of the bioinformatics database?

Yes, the offeror may subcontract database hosting.

4. Will the Government make “the existing genotyping protocols and other documentation developed for the rodent samples, such as construct sequences and manuscripts” available for contractor review reasonably in advance of the response date of January 23, 2017?

No. The Government will not provide the existing genotyping protocols and other documentation developed for the rodent samples, such as construct sequences and manuscripts in advance of the solicitation response date. This information is not available in full. As much information as possible will be provided to the successful offeror following award.

However, many of the strains in use are commercially available and testing protocols are available through the Mouse Genome Informatics database.

http://www.informatics.jax.org/ http://www.informatics.jax.org/

5. To assist with pricing, should the offeror assume that the 72 hours allowed for sample processing/ reporting include hours on weekends and federal holidays? Or is the 72 hours conserved to Mon-Fri, non-holiday?

Yes. The 72 hours allowed for sample processing and reporting includes weekends and holidays.

6. What assumption should the offeror make as to the frequency and volume of samples submitted? For example, should the offeror assume that the 25,200 – 34,200 samples per year will be submitted in approximately equal batches 3 times per week? Or is there a possibility of 10,000 samples being submitted at one time?

There will not be a mass submission of samples at one time. Typically, approximately 2,700 samples are submitted monthly. Weekly sample submissions may not be equal.

Please find attached an Excel file titled “Historical Submission and Reaction Data” showing the historical number of samples submitted and reactions performed for the most recent twenty months. Of note, fewer samples were submitted in 2015 than in 2016. Please focus on the average anticipated number of 2,700 samples being submitted monthly when preparing pricing.

7. The Technical Evaluation Factor 1 includes the ability “to assist with genotyping assay development”, which is not discussed in the Project Requirements section. Will the government further explain the role/level of effort the offeror is expected to have in assay development?

The Government expects the successful offeror to assist the National Institute on Aging investigators with assay development for problematic genes as needed. This requirement is added to the Solicitation Project Requirements.

A list of historically problematic genes is attached to this solicitation with the title “Historically Problematic Strains” for reference; however other genes may be problematic in the course of this requirement.

8. What assumption should the offeror make as to the number of new assays that will need to be developed or manufactured by the offeror per year?

Please assume that approximately 30 to 40 new assays may require development annually. This includes assays that may need to be developed due to importation of unique mouse strains from other institutes, new strain development, and addition of new commercially available strains.

9. What assumption should the offeror make as to the average number of genes and sample reactions to be tested per sample? The solicitation states between “one and ten genes”, which is a broad range. Are the assays typically able to be multiplexed, or should it be assumed that “ten genes” may be ten separate assays?

Historical data indicates an average of 1.7 reactions performed per sample submitted.

Please use this average when preparing pricing and see the attached Historical Submission and Reaction Data spreadsheet for reference.

Historical data indicates that at least 90% of historical submissions were duplexed rather than performed as individual separate assays. Multiplexing beyond two genes at a time has not been performed to date but may be possible for some samples. Please use this information when preparing pricing.

10. Should the offeror’s firm-fixed unit price for “One Sample” include contingencies for performing any number of assays from one to ten?

Yes, please provide firm-fixed unit pricing for “one sample” which includes contingencies for performing any number of assays from one to ten. Please develop this price with the assumption that an average of 1.7 reactions will be performed per sample submitted but that up to 10 reactions may be required.

11. Will the Government relieve the contractor of stewardship responsibility and liability, per FAR Clause 52.245-1(f)(1)(vii)(C), for Government furnished rodent biological tissue samples?

FAR Clause 52.245-1(f)(1)(vii)(c) is removed from the solicitation and will not be included in any resultant contract, per the response to question 20 below.

However, please note that in the project requirements section of the solicitation the Government requires that all provided samples and biological tissues remaining after assays are performed must be preserved by the Contractor for six months after receipt from the Government. Stored samples and remaining tissues shall be maintained in such condition that subsequent nucleic acid analyses may be performed. Stored samples shall be returned to the Government upon request. Upon holding for 6 months, the contractor shall obtain approval from the Government to either return or destroy samples.

12. To assist with pricing, please specify if the PCR analysis required is qrtPCR, end point PCR, or a combination. If a combination, what percentage of sample tests should we assume are qrtPCR?

The Government expects contractors to propose PCR analysis plans which will provide the information identified as required in this solicitation.

For reference, approximately 94% of historical strains could be analyzed using only endpoint/traditional PCR techniques and approximately 6% using only qrtPCR/qPCR techniques.

13. What is the format in which the samples will be submitted? (i.e. 96 well plate, single vials, strip tubes)

The Government requires offerors to indicate in its proposal which sample format it proposes processing samples from. The offeror may indicate the 96 well plate format, single vial format, or strip format. The Government will consider the proposed format’s efficiency when performing the technical evaluation. The solicitation has been updated to reflect this response.

For reference when determining the sample format to be proposed, please note that most tissue samples submitted shall be from ear snips as tail snipping is discouraged at the NIA.

14. Can you provide more details on the “drop box” requirements? Does the box need to be kept under cold chain or ambient temperatures?

Offerors are expected to propose a means of efficient and sample-safe shipping between the National Institute on Aging and the contractor site. This may include a “drop box” located at the NIA or another method. The transportation method may be kept cold or under ambient temperature depending on the offeror’s proposed analysis processes so long as the method is efficient and sample-safe. The Government shall evaluate the transportation mechanism proposed for ease of use, efficiency, and sample safety.

The solicitation has been updated to reflect this response.

15. Does the expected quality assurance analysis entail independent retesting of the samples with identical assays?

Quality assurance analysis entails re-testing of the sample(s) in question, however use of an identical assay is not required, nor is use of an independent testing service.

In the event that re-test continues to fail or return questionable results after two re-tests, however, the Government may require re-test be performed by an independent testing service at the Contractor’s expense.

The solicitation has been updated to reflect this response.

16. The RFQ Project Requirements state “Provide results of DNA Extraction and PCR assays and analyses with annotation.” Please define what you mean by “annotation”?

Please find attached two examples of annotation results when using traditional gel PCR methods. This method of annotation is expected for use with traditional gel PCR methods.

If performing qPCR assays, the above-described annotation is not necessary; instead a report of the presence or absence of the gene of interest along with the zygosity of the alleles for that gene is required.

Contractors may propose traditional PCR, qPCR, or a combination of methods for this requirement.

17. Please confirm whether this will be a 5 year IDIQ contract or a one year contract with 4 Option years? The RFQ states that it will be a 5 year contract; however, the Genotyping Support Services Quotation table includes a base period with 4 options, and the FAR clause regarding option years is included. If there will be option periods, please confirm that each option period will be for one year.

The Government confirms that this will be a Five (5) - Year indefinite-delivery indefinite-quantity contract. The solicitation has been revised to remove the option period language and clauses.

18. Our commercial pricing for these services is on a calendar year basis (i.e., prices increase each January 1st). Is it acceptable to present pricing this way, or does pricing need to be based on the contract year/option year periods of performance.

Please provide pricing based on contract year.

19. The RFQ Project Requirements note that the contractor database must be able to interface with the NIA Progeny Database.

a. Please provide examples of what are “XML comparable languages” (e.g., are Excel or JSON acceptable)?

XML-comparable languages that are acceptable are JSON, XML, YAML, and CSV. Excel is not acceptable.

Please find sample code for each acceptable language type below. The fabricated sample data involved in all four examples represents the same set of three theoretical samples with 2 probes and varying presence/absence.

CSV Example:

animalid,reaction1,presence1,reaction2,presence2

123526,CRE L0208-H,Y,TET L0208-H,N

123527,CRE L0208-H,Y,TET L0208-H,N

123528,CRE L0208-H,N,TET L0208-H,Y

XML Example:

<?xml version="1.0" ?> <resultset id="5263FE"> <samples> <sample id="123526" test_time="2017-03-10T09:33:02"> <reactions> <probe name="CRE L0208-H" presence="+" /> <probe name="TET L0208-H" presence="-" /> </reactions> </sample> <sample id="123527" test_time="2017-03-10T09:33:02"> <reactions> <probe name="CRE L0208-H" presence="+" /> <probe name="TET L0208-H" presence="-" /> </reactions> </sample>

<sample id="123528" test_time="2017-03-10T09:33:02"> <reactions> <probe name="CRE L0208-H" presence="-" /> <probe name="TET L0208-H" presence="+" /> </reactions> </sample> </samples> </resultset>

YAML Example:

Order: NIA2017-525 Complete: 2017-05-17 09:32:33 EST Animals:

- ID: 123526

Probes:

- Name: CRE L0208-H Present: Yes

- Name: TET L0208-H Present: No

- ID: 123527

Probes:

- Name: CRE L0208-H Present: Yes

- Name: TET L0208-H Present: No

- ID: 123528

Probes:

- Name: CRE L0208-H Present: No

- Name: TET L0208-H Present: Yes

JSON Example:

{samples:

{"animalid": 123526, "reactions": [["CRE L0208-H", true], ["TET L0208-H", false]]}, {"animalid": 123527, "reactions": [["CRE L0208-H", true], ["TET L0208-H", false]]}, {"animalid": 123528, "reactions": [["CRE L0208-H", false], ["TET L0208-H", true]]}

b. What are the acceptable means of transferring data from the contractor database to the NIA Progeny Database? Are files sent through a secure file transfer protocol (SFTP) or email, to be uploaded into the NIA Progeny Database by NIA staff, acceptable?

Files and two-way data communication sent through a secure file transfer protocol or email are acceptable.

c. Is it a requirement that the contractor database and the NIA Progeny Database must have 2-way communication? If so, please explain what information would be sent to the contractor database. If so, Question 3b also applies to the means of transferring this data.

Yes, the NIA Progeny Database and the database of the offeror must have 2-way communication.

Specifically, the offeror’s database must be able to transmit test results directly into the NIA Progeny database using an XML comparable language as detailed in the response to question 19a above within the first thirty (30) days of the contract.

Following the thirtieth day, the NIA Progeny Database and the successful offeror’s database must have full 2-Way communication.

d. Is there a specific structure or labeling that is required for the data transfer from the contractor database to the NIA Progeny Database? Also, what specific information is required? Please provide examples.

Yes, please see the response the question 19a for examples.

A unique identifier (6-character animal ID number) is generated by the NIA Progeny database and must be used to link the tissue submitted back to the animal. Therefore, the specific information required is the unique animal ID as generated by NIA, the name of the gene tested for, and the results for each gene.

20. The RFQ states that FAR Clause 52.245-1 Government Property shall be applicable to this requirement. Typically this clause only applies when the Government is furnishing supplies or equipment to be used in the contract or in a cost reimbursement contract when the contractor is purchasing equipment on behalf of the Government, not when the contractor is merely receiving samples (with corresponding data) to be tested. Can you confirm whether this clause will be included in the resultant contract?

This clause is removed from the solicitation and shall not be included in any resultant contract.

21. Regarding the Information Systems Security Section and Addendum 1:

a. The specifications listed in these sections are generally required only when the contractor has direct access to NIH IT systems or has access to “sensitive” information. We do not believe that the requirements in these sections are necessary for this contract, as it will not involve sensitive information or access to NIH IT systems. Additionally, there will be no computers dedicated to use on this contract. To implement all of these requirements would incur substantial costs and increase the prices that must be charged to the government. These services are routinely performed for many commercial and government clients without implementing all of these additional security requirements. Can these requirements be removed, in order to provide the most cost effective solution for the government? It is recommended that the standard security clause, 52.204-21

– Basic Safeguarding of Covered Contractor Information Systems be included in the contract to replace these requirements.

The Information Systems Security Addendum 1 has been removed from the solicitation and will not be included in any resultant contract. FAR Clause 52.204- 21 has been added to the solicitation and will be included in any resultant contract.

If some of these requirements remain, we have the following additional questions:

b. This section states that Contractors are required to adhere to the NIH IT rules of behavior. The referenced link isn’t accessible due to log in information needed.

Please provide PDF or log in information to review.

The Information Systems Security Addendum 1 has been removed from the solicitation.

c. This section states that Contractors are required to sign the NIH NDA. We have our own nondisclosure agreement that each of our employees signs, which requires that all client information be kept confidential. We can also certify as a company that we would keep NIA’s information confidential. Would this be sufficient in lieu of the NIH NDA?

d. In Addendum one, it states that Contractor/subcontractor employees assigned to Level 1 positions shall undergo a Suitability Determination and National Check and Inquiry Investigation (NACI), though the text describing that process were not included in the Addendum. It also states that Contractors must report new and departing employees. It does not appear that these requirements should be necessary, since employees would not be dedicated to the contract and would not be accessing sensitive data or have access to NIH IT systems or facilities;

they would only be processing non-human samples for genotyping as part of the contractor’s regular commercial business. Can the requirement that some staff have the NACI investigation, and that Contractors report new and departing employees be removed? If not, what would be the criteria determining whether an employee must have the investigation?

e. Paragraph one in section 6 of the Addendum describes the Standard for encryption language for “sensitive” information. In section 2 of the Addendum this work is listed as Non-sensitive. We recommend this section be removed from the requirements for this contract. Please confirm.

f. The RFQ states that FAR Clause 52.239-1, Privacy or Security Safeguards, is applicable to this RFQ. For reasons stated above, can this be removed from the contract?

22. The RFQ states that HHSAR Clause 352.224-71 Confidential Information is applicable to this RFQ. Confidential Information, as used in this clause, means information or data of a personal nature about an individual, or proprietary information or data submitted by or pertaining to an institution or organization. This contract is for providing genotyping results of various rodent strains. Please explain why this information should be considered proprietary. Alternatively, could this clause be removed from the RFQ/Contract?

This clause has been removed from the solicitation and will not be included in any resultant contract.

23. The RFQ lists FAR Clause 52.222-17, Nondisplacement of Qualified Workers. This clause should not be applicable to this contract, as per FAR 22.1207, this is only required for service contracts "that succeed contracts for performance of the same or similar work at the same location". Please confirm that this is not applicable.

The Government confirms that this is not applicable. FAR Clause 52.222-17 is removed from the solicitation and will not be included in any resultant contract.

24. The RFQ states that FAR Clause 52.237-2—Protection of Government Buildings, Equipment, and Vegetation (April 1984) applies to this acquisition; however, per FAR

37.110 this is only required for services to be performed on Government installations.

Please confirm that this is not applicable.

The Government confirms that this is not applicable. FAR Clause 52.237-2 is removed from the solicitation and will not be included in any resultant contract.

25. The CLOSING INFORMATION section of the RFQ states that the price proposal must include labor categories, an estimate of the number of hours required for each labor category, fully loaded fixed hourly rate or each labor category, breakdown and rationale for other direct sots or materials and the total amount. We assume that this information is not required, since pricing in the tables is based on a fixed unit price rather than labor hours, and will be based on commercial pricing. Lauren: I concur with this statement, it should be based on commercial pricing per sample, we are not interested in how the vendor compensates their staff.

The CLOSING INFORMATION section of the RFQ has been revised to remove the labor category and rate information request. Please use the pricing table included in the solicitation and provide fixed commercial pricing per sample.

26. The RFQ identifies 3 key personnel which are considered to be essential to work performance. The genotyping services required in this RFQ are commercial services that are routinely performed for many clients by a team of personnel supporting our Genotyping Services operation. We don’t feel there would be a need for staff dedicated to the contract and considered “key personnel” as defined in the HHSAR, and ask if we could simply describe our vast (and replaceable) resources.

The Government is interested in point of contact information for use in the event technical concerns must be addressed. Continuity of individual(s) familiar with the NIA account is desirable for ease of communication; however, individuals need not be named key personnel.

The HHSAR Key Personnel clause is removed from the solicitation and will not be included in any resultant contract. Offerors shall describe point of contact resources in their proposals.