Frequently Asked Questions

Solicitation Frequently Asked Questions

Question 1: Are investigators from (military or other government laboratories) , who are conditional federal employees, eligible for funding  under your recent solicitation for POC assays for chlamydia? 

Answer 1:  Yes.  Investigators from all sources which are eligible for government funding are eligible for funding under this mechanism.   Under the eligibility section 1.I., it states: "Awards under this solicitation may be made only to NIH-eligible applicants ".  If you are unsure if you are eligible, please review the information at the web site given (http://grants.nih.gov/grants/policy/nihgps_2003/NIHGPS_Part4.htm#_Ethical_and_Safe)

Question 2: Is direct experience with Chlamydia preferred for the application?

Answer 2:  No, specific expertise in working with Chlamydia species is not required though expertise in handling biological organisms must be demonstrated for the project to be successful. 

Question 3: In the proposal, can we focus on the detection side or do you expect successful applications to cover the whole process from sample preparation to target detection?

Answer 3:  As stated in the proposal, the technology must be able to achieve a time from sample collection to detection of less than 4 hours.  If the detection technology is rapid but requires an extensive sample preparation time which exceeds the stated time requirement, the technology would not be considered responsive to the proposal.  The technology does not have to address sample preparation if extensive sample preparation is not required and the technology can achieve a detection time of less than 4 hours using existing rapid methods.  The technology will be evaluated from the time the sample is collected to the time that the result is disclosed.

Question 4: The Quad chart asks for a ROM for cost? What is this?

Answer 4: ROM is Relative Order of Magnitude cost.  This number should be the best estimate of direct and indirect costs to complete the project as proposed.  ROM costs are not binding and therefore do not require formal budget and pricing information to support the figure supplied.  However, ROM costs should be a realistic reflection of the true cost of the proposals.  ROMs which are too low, too high or are grossly inaccurate estimates of the full proposal costs may result in the rejection of a pre-proposal or of a full proposal.

Question 5: Has a budget been set for this solicitation or has there been an indication of the potential number of awards?
 
Answer 5: As noted in the solicitation, APL will award at least one contract.  There is no limit on the number of contracts which may be made although not more than four awards are anticipated.  The number of awards made and funding levels for each will be evaluated based on the needs for each technology presented for award.  Technologies which are at a basic science level (6-1) or technologies which are promising but require significant development and funding beyond the scope of this solicitation will be referred on to other funding opportunities.

Proposal Frequently Asked Questions

Proposal Question 1:     Can you recommend specific literature references to confirm pertinent group specific antigens for Herpes, Chlamydia and Gonorrhea STD? 

Answer 1: We suggest a good literature search to make sure you have access to all the available information regarding clinical tests for STDs. Below are listed a subset of articles which discuss both genetic and immuno assays for Chlamydia and some other STDs.

a) Comparison of polymerase chain reaction, monoclonal antibody based enzyme immunoassay, and cell culture for detection of Chlamydia trachomatis in genital specimens. Wu CH, Lee MF, Yin SC, Yang DM, Cheng SF.  Sex Transm Dis. 1992 Jul-Aug;19(4):193-7
b) Molecular genetic methods for diagnosis and characterisation of Chlamydia trachomatis and Neisseria gonorrhoeae: impact on epidemiological surveillance and interventions. Fredlund H, Falk L, Jurstrand M, Unemo M.APMIS. 2004 Nov-Dec;112(11-12):771-84. Review
c) Urine nucleic acid amplification tests for the diagnosis of sexually transmitted infections in clinical practice.Gaydos CA, Quinn TC.Curr Opin Infect Dis. 2005 Feb;18(1):55-66. Review
d)The accuracy and efficacy of screening tests for Chlamydia trachomatis: a systematic review.Watson EJ, Templeton A, Russell I, Paavonen J, Mardh PA, Stary A, Pederson BS.J Med Microbiol. 2002 Dec;51(12):1021-31. Review
e)Confirmation of BD ProbeTec Neisseria gonorrhoea reactive samples by Gen-Probe APTIMA assays and culture.Hardwick R, Gopal Rao G, Mallinson H.Sex Transm Infect. 2008 Oct 1.

Proposal Question 2: Are there commercial tests (manufacturer and part number) which establish a benchmark for Lower Limit of Detection of the proposed POC Test?  Are these commercial tests used or modified by JHU to increase sensitivity or specificity? 

Answer 2:  The commercial tests are not POCT. However, the POCT test must be comparable in specificity and sensitivity to currently used tests for detection of chlamydia and gonorrhea. The clinical laboratory tests currently in use are:

a) Aptima Combo2  (transcription Mediated Amplificatin [TMA])2 by GenProbe, San Diego, CA
b) ProbeTec  (Strand Displacement [SDA]) by Becton Dickinson, sparks, MD
c) Amplicor (polymerase chain reaction [PCR]) by Roche Molecular diagnostics, Indianapolis, IN.

Proposal Question 3: Is PCR the accepted “Gold Standard” for clinical testing of STD samples?  Can you identify the PCR probe specifications?

Answer 3: PCR is an accepted gold standard for STD detection.  For acceptable probes, we suggest you look at the probes used in the forementioned commercial assays, as well as other published research assays.

Proposal Question 4: Concerning the mentioned “pre-clinical materials” available (in small quantity) from JHU/APL,

a. What is the sample matrix; blood, serum, exudates? 

Answer 4a: Pre-clinical testing does not require the use of sample matrices mentioned.  Clinical testing is performed in revelant matrices.  Clinical evaluation is not part of Core 2 efforts, but is the primary function of Core 1 efforts.   JHU/APL  will provide materials as cultured samples.

b. Will the “pre-clinical” samples be characterized? 

Answer 4b:Yes, the pre-clinical samples will be characterized and the concentration, strain information and culture fluid information will be provided with the samples.  For facilities without the appropriate biosafety level facilities, only killed specimens will be provided.

c. What would be the typical sample volume provided for each STD? 

Answer 4c: Clinical sample volumes range from 100 microliters to 200 milliliters based on whether the test is performed on vaginal swabs (resuspended in 1 ml buffer) or urine samples (10 ml).

Proposal Question 5: Regarding Enclosure 1

a. IV – Foreign Persons. Atlas Genetics is a foreign (British) company. The Foreign Persons definition shown (Non-US Citizens in the US on Temporary INS Visas) does not apply to any of us. Do we need to specifically identify in the proposal that we are all foreign persons? In general, are there any areas of likely problems that we will encounter as a foreign company applying for NIH funds under this program?

Answer 5a: Please include the statement regarding your company and its employees in your proposal.  There are no known problems with the eligibility of foreign entities for award at this time; however, all parties will be screened against the US Government restricted party lists.

b. V – Contractor Business Systems Approval
     i. Accounting System. Our accounting system has not been approved by a US Government Agency. We use the Sage Instant Accounts software package which incorporates Sage Payroll. This is a recognized accounting software package. Is this acceptable?
     ii. Purchasing – Our purchasing system has not been approved by a US Government Agency. Our purchasing system is compliant with ISO 9001:2000, although the company is not yet certified under this standard. Is this acceptable?
     iii. DCAA/DCMA Approved Rates. We have no US Government Audit Agency. Our indirect costs are auditable and we can provide open book accounting if required. Is this acceptable?

Answer 5b: It is understood that the business systems of foreign entities have not been audited and approved by the U.S. Government.  All Offerors should state the status of their  business systems approvals in the cost section of your proposal, including any approvals by your country’s government.  JHU/APL and the selected Contractor(s) will enter into discussions regarding the best way forward should the selected Contractor(s) not have approved business systems. 

Proposal Question 6: Regarding Enclosure 4, the sample contract 

a. Article 5 – contract information. Are we required at this stage to provide any of:
     i. Defense Priority and Allocation System (DPAS) rating?
     ii. DoD security classification?

Answer 6a: Offerors are not required to provide information for any of the blank spaces in Enclosure 4.  The DPAS rating and DOD security classification are based on the prime contract and will be specified by JHU/APL at the time of award.  It is anticipated that both the DPAS rating and DOD security classification will be “not applicable” for this procurement. 


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