responses_to_Questions_for_Solicitation_10_2_2015.docx

Questions for Solicitation Number: 2015-N-17644 Page 2, Section B-Supplies or Services and Prices/Costs:

1. QUESTION: Item 0003: How many samples in total need DNA concentration measurement?

ANSWER: There are 7,129 DNA samples that would require a DNA concentration in the NHANES III collection. Please review additional notes in work breakdown section, number 3, page 9.

2. QUESTION: Item 0004: How many samples in total need DNA concentration measurement?

ANSWER: In the NHANES 2011-12 collection there are 4,171 tube 1 DNA samples and 4,158 tube 2 DNA samples (see table).

3. QUESTION: Item 0005: It looks like Contractor has to provide 7 ultra-low freezers, please confirm?

ANSWER: Yes approximately 7 upright freezers depending on the individual freezer capacity.

4. QUESTION: Item 0006: How many samples need to be normalized and how many plates need to be generated? Is it 500 samples or 500 plates?

ANSWER: This depends on the number of research requests in a year and which NHANES DNA collection is being requested. Some collections (1999-2002 and 2007-08) currently have prepared normalized sets. When these sets are depleted or for the other collections a normalized set would be prepared by the vendor as requested. From a normalized set an aliquot of the normalized DNA would be plated to send to the researcher. Each plate contains 92 samples except for the last plate of a set which may be partially filled.

5. QUESTION: Item 0007: How many samples will be part of Quality Control Sample Plate and how many plates need to be generated?

ANSWER: QC plates will be required for each of the 5 collections. The number of QC samples for each collection will be 5% of the total number of samples. Eg: If a DNA collection consists of 5,000 samples, 5% or 250 samples will be needed for the QC plates. This would require preparation of 3 96-well QC plates.

6. QUESTION: Item 0008: Is contractor supposed to make 510 plates of a normalized set; each plate with 92 samples per plate?

ANSWER: There are 5 unique collections. If a researcher requests all 5 collections, then an aliquot of the normalized DNA (note NHANES III may not be normalized) would be generated from all plates. If a researcher requests all of the other 4 collections, then 237 plates would need to be normalized. If a researcher requests only one collection, an aliquot of the normalized DNA from the requested collection would be plated. There are 92 samples in each plate except for the last plate of a set which may be partially filled.

7. QUESTION: Item 0009: Is contractor supposed to make 100 plates of a normalized custom set with 92 samples /plate?

ANSWER: Aliquots of the normalized DNA sets will be made as requested so the number of plates will vary based on the number of custom sets requested.

8. QUESTION: Item 0010: DNA shipment will be of the prepared plate sets or DNA receptacles/boxes? As shipment is mentioned in terms of boxes, please add some clarification. If boxes stand true then how many boxes (minimum and maximum) will be shipped at any time?

ANSWER: DNA shipment will be of the prepared plate sets. Each collection requested by a researcher will be shipped on dry ice. The shipment will include the prepared aliquot plates of normalized DNA from that collection. The number of boxes required to ship the plates will be determined by the vendor. It is acceptable to ship all plates from a single collection in one shipping box if it does not exceed the capacity of the box. A shipment can be split into separate boxes as needed.

9. QUESTION: For the DNA Samples being received, will the accompanying electronic manifest match the sample vial order in the plates?

ANSWER: Yes.

10. QUESTION: Does the electronic manifest sort by plate ID and vial ID?

ANSWER: Yes, the electronic manifest can be sorted by any column category including plate ID and vial ID.

11. QUESTION: Will CDC reimburse the BioBank for researchers requesting individual shipment of plates containing normalized and QC DNA? Or, will researchers have to pay for this service directly?

ANSWER: Researchers requesting shipment of plates will pay CDC directly. CDC will reimburse the vendor selected for these shipment costs as part of the invoicing process.

12. QUESTION: For the initial sample transfer, will all 50,000+ samples be shipped to the BioBank in one delivery?

ANSWER: No, each collection will be shipped separately and within a collection, a master, secondary and normalized set if available will be shipped separately as a safeguard in the event there is a shipping problem.

13. QUESTION: Is there a CDC database that you envision will be updated by our results and do you wish to link this or otherwise facilitate a handshake between our internal BioBank Database and yours to accomplish seamless transfer of information?

ANSWER: Not at this point. If circumstances change, we may request a modification to the contract.

14. QUESTION: Are DNA samples in individual 1D or 2D coded cryovials? What sort of vial closure is there (threaded cap or sepraseal or other)?

ANSWER: All master and secondary 2.0 ml vials (cryovials) contain both a human readable and 1D barcode. The DNA master stock vials in the NHANES III collection have caps with internal threads. The wells in the normalized deep well plates have caps with internal threads. All other master and secondary stock vials have caps with external threads (NH99-02, 2007-08, 2009-10 & 20011-12). The normalized plates (deep well) from 1999-2002 and 2007-08 have a human readable label and 1D barcode identifier on each plate. Each well (individual sample) within the plate has a 2D barcode (non-human readable) on the bottom. See table.

15. QUESTION: OR, are DNA samples in microwell plates?

ANSWER: Master and secondary stock DNA samples are in 2.0 ml cryovials and normalized DNA samples are in deep well plates.

16. QUESTION: To clarify, CDC will send the BioBank an initial electronic inventory file and an operations manual – is this correct?

ANSWER: CDC will send electronic inventory files for all collections not an operations manual. Note that on the performance-based matrix, page 12, column 1, a desired end result from the vendor is an initial inventory file and operations manual (or vendor process protocol).

17. QUESTION: Will any DNA samples require concentrating or clean up as a follow on to the A260/280 measurement or will DNA that does not meet specification be discarded?

ANSWER: For the NHANES 2011-12 collection, if tube 1 A260/280 test is off then test A260/280 for tube 2, if both tubes are off then would require clean up.

18. QUESTION: The RFP has a due date of 2:00 PM, October 17, 2015. As this is a Saturday, would CDC consider changing the due date to the following first business day, as generally prescribed by FAR, to a new due date of Monday, October 19, 2015?

ANSWER: Yes.

19. Page 10, Section V- Work Breakdown Structure QUESTION: Task 11: Is contractor responsible for coordinating with researchers (making sure shipment is done under cold chain management and regulations) to receive back the unused DNA samples or supposed to arrange for shipment (FedEx) as well?

ANSWER: CDC is responsible for ensuring researchers ship back unused DNA samples. The contractor will be notified of these shipments. CDC is responsible for ensuring the contractor is notified.

20. Page 14, Section F-Deliveries or Performance Work Breakdown Structure QUESTION: Deliverables: Inventory report is due 30 days after DNA samples are received. How many days it will take to receive all the samples to be inventoried?

ANSWER: Each set of DNA samples will be shipped separately. There are 5 total collections with a secondary set for 4 of the 5 collections. The 30 day inventory deadline will start once all samples are received by vendor

(A table has been added that provides a detailed description of the NHANES DNA collection and may help vendors to clarify terminology. See next page.)

Table. NHANES DNA collection description

Normalized set (includes QC plates) Y (2D only)

Normalized set (includes QC plates) Y (2D only)

*Complete set of concentrated stock DNA vials that meet NCHS criteria for distribution and have been arrayed in preparation for normalization. Note: Researchers requesting a NHANES collection receive an aliquot created from the master set of DNA.

** Secondary set of concentrated stock DNA vials that can be considered for use if the master is no longer available

***NHANES 2011-12 concentrated stock DNA has not been assembled into a master set for normalization