Vendor Questions - Govt Responses final 100617.pdf

Questions Re: FDA RFP 10-223-SOL-00105 Legacy Data Conversion Services

Question

1. Within Appendix 1 of the Task Order Attachment 7 (p. 119) there is a table listing approximately 179 studies and 4,800 data sets potentially included. Can you please confirm that the first 18 month work order is expected to include the completion of this quantity of data?

Govt Response: The Government confirms that conversion of the “approximately 179 studies and 4,800 data sets” must be completed during the Task Order performance period. However, the Government is extending the task order period of performance from 18 months to 36 months.

2. Section C.3.D (p. 7) – Within the Data Security Assurances section there are references to a number of requirements around the systems the vendor might use. Will the FDA plan to conduct an audit of the vendor’s systems they will use in execution of the work?

Govt Response: The Government confirms that, if the contractor plans to process sensitive data on the contractor’s systems, FDA is planning to conduct an audit of the vendor's system, in accordance with the Federal Information Security Management Act, 2002, prior to the contractor processing sensitive data.

3. The work order references the creation of integrated ADaM data sets within the scope of work. Does the scope of work include the creation of analysis data sets at the individual study level, the integration of multiple studies, or both?

Govt Response: The Government confirms the work includes the creation of analysis datasets at the individual study level. The contractor should ensure consistency across analysis datasets in a particular therapeutic area to allow integration across studies.

4. The statement of work (p. 114) references the use of OpenCDISC for validating the data creating over the course of the project. In our work with this tool we have identified a number of issues with the robustness and scalability of this solution. Is the FDA open to using other tools for validating data?

Govt Response: The Government plans to use the OpenCDISC tool functionality in the future Janus implementation as well as for development of a publicly-available validation service.

Validation functions for use of the tool in Janus are in the process of being defined. We are also planning to use the OpenCDISC validation tool to validate SDTM submissions during the interim period while the tool is modified and integrated into the Janus architecture. In light of this, FDA would prefer use of the OpenCDISC validation tool to ensure consistency of results as well as feedback needed to inform the modification of the tool for future use in Janus.

5. Within the data conversion work is it expected that the vendor will deliver the code that is generated as well as the data, validation results, and define.xml? If the code must be delivered it is expected to be SAS code or whatever code is appropriate for the standard or format being used?

Govt Response: The Government is not expecting that the vendor deliver the code that is generated during the data conversion process. Consistent with the requirements in the SOW, the contractor is expected to document transformations for traceability.

6. We have a question regarding the proposal solicitation 10-223-SOL-00105. Per SF133 the proposal is due on 6/28/2010, but on page 85 it states that references will be contacted between 6/7/2010 and 6/21/2010. Are these dates erroneous? If so, will you please let me know the time frame during which our references can anticipate being contacted? If the dates are not erroneous, should we plan to submit our references now?

Govt Response: References will likely be called during the period between 6/28/10 and 7/2/10 during normal business hours.

7. Will you please confirm the number of studies to be migrated? On page 119 of the RFP, it appears that there are 178 studies to be migrated.

Govt Response: The Government has identified 178 studies to be converted . See Govt.

response to question 1.

8. Will you please confirm the number of Diabetes studies to be migrated for CDER? The RFP states that there are 120 with an average of 30 datasets/study.

Govt Response: The Government confirms there are 120 Diabetes studies.

9. How many NDAs were involved with the CDER diabetes studies?

Govt Response: 11 NDAs were involved with CDER diabetes studies

10. The SDTM domain Subject Elements (SE) was not identified as needing to be included in the grid. This is a special purpose domain and is typically expected for inclusion in SDTM submissions. Please confirm whether or not it should be included.

Govt Response: The objective is to transform as much data as is available into the appropriate CDISC domains. Any one study may provide data for more or fewer domains. Assume the SE as an optional domain for conversion when the data is available from the sponsor submitted datasets.

11. Pharmacokinetic Concentrations (PC) and Pharmacokinetic Parameters (PP) domains were not identified as needing to be included in the grid. Please confirm this is accurate.

Govt Response: The Government confirms that PC and PP will not be included.

12. Is an affiliation with CDISC necessary/required for vendors offering data conversion services?

Govt Response: An affiliation with CDISC is not necessary or required of any vendor offering data conversion services. FDA staff familiar with the respective study datasets to be converted as well as CDISC standards will be available to provide feedback and clarifications during data conversion activities.

13. On page 86 it states: ii. Data Conversion iii. Therapeutic Area Study Data Conversion (for each Therapeutic Area specified in the Task Order) We are attempting to determine the difference between Data Conversation and Therapeutic Area Study Data Conversion. In Appendix 1 the Therapeutic Areas are listed (which relates to iii. Therapeutic Area Study Data Conversion) but how does this differ from (ii. Data Conversion)?

Govt Response: Please refer to the requirements in Attachment 7 of the solicitation.

“Data Conversion Plan” and “Study Data Conversion Plan” requirements are described in “Specific Tasks” Item 2 (Page 111) with associated deliverables (Page 113).”

14. For ADaM dataset development, please clarify the number of unique groupings/pooling for integrated analysis datasets needed (e.g., if 6 flu studies are grouped and 4 medical device studies are grouped that would be 2 unique grouping for analysis).

Govt Response: The Government is requesting the creation of analysis datasets at the individual study level. The contractor should ensure consistency across analysis datasets in a particular therapeutic area to allow integration across studies.

15. Do you have an estimate of the amount of legacy data that is to be converted?

Govt Response: Please refer to Appendix 1 (page 119)

16. On page 85, L.5.4.1 states “References will likely be called during the weeks of 6/7/10 through 6/21/10”. Are those dates correct?

Govt Response: See Govt. response to Question 6.

17. Page 87 states “There is significant historical information from past projects of a similar nature to estimate the types and quantities of labor that will be required over the life of the contract.” Where can this data be located?

Govt Response: This information is found within various government financial systems and is not available to the public.

18. L.4.2.5. The proposal shall not exceed 100 pages in length. The page limitation excludes the cover letter, table of contents, list of figures, tables and drawings, printout of Certifications and Representations, and all documentation as specified under Key Personnel and Staffing (see below).

Govt Response: Vendor has not submitted a question. No response necessary.

19. Is this a new effort or re-compete?

Govt Response: This RFP is for a new effort.

20. System certification requirement is mentioned on Page 43 of the Solicitation Recovery ARRAOS pdf document. Would certification from a 3rd party, for e.g., ISO, be considered desirable, even though it may not be required?

Govt Response: The government will evaluate the offeror’s systems and processes against the security requirements in the solicitation. There is no specific preference for industry or government standards other than those stated in the solicitation.

21. On pages 111 and 112 of the document (Attachment 7), the first point under Scope mentions that the contractor will furnish materials including computers, while the last point mentions that the FDA will provide laptops with VPN access. Could you please clarify if the contractor is expected to use its own systems and tools, and if so, how will the data be shared and what sort of connectivity to FDA systems will be expected?

Govt Response: FDA will provide laptop computers with VPN access to allow access to a shared area(s) providing access to the legacy datasets (e.g. SAS.XPT files) and background materials (e.g. clinical protocols, statistical analysis plans, etc) as requested by the contractor. FDA confirms that the contractor is expected to use its own systems and tools for the data conversion process. Also, the contractor is expected to use FDA-furnished computers with VPN access to provide contract deliverables.

22. The table in Appendix 1 lists a total of 178 studies to be converted. Please confirm that these studies should be converted over a period of 5 years not during the first 18 months of the project. If these studies are to be converted over the 5 year period, how many studies are expected to be converted for the first Task Order?

Govt Response: The period of performance for the first task order-ARRAOS task (Attachment 7) has been revised to 36 months. All 178 studies that are currently identified in the Appendix 1 ARRAOS SOW will be converted during the 36 month performance period. If the Government has need for the conversion of additional data that is not currently identified, those services will be procured through subsequent task orders within the 5 year ordering period of the basic contract.

23. There are 120 diabetes studies from CDER to be converted. How many sponsor companies (NDA submissions) submitted data for this group of studies? To date, are there results from metadata analysis available? If no metadata analysis has been performed, will the data for all 120 studies be available to the contractor to perform metadata analysis and identify the degree of similarity between studies? This will be critical to define optimal conversion strategies and facilitate work planning

Govt Response: The Government has identified 11 NDAs covering the diabetes studies.

To date, metadata analyses have not been conducted on these studies.

24. Is there an option to request information from the sponsor companies when issues with the source data can’t be resolved?

Govt Response: Government will provide advice when there are issues with the source data; the COTR will work with the reviewers from the respective therapeutic area to address and resolve these issues in a timely manner as they arise on a case by case basis.

25. Are there studies where the raw data has already been converted to an SDTM-like structure and the actual raw data are not available?

Govt Response: There may be instances where sponsors have chosen, prior to application submission, to convert their non-standard tabulation (or raw) data sets into SDTM and then to submit those to the FDA as part of their registration application. In these cases, typically, no tabulation/raw data sets other than the SDTM data sets are usually available.

26. There will be two levels of standardization. The structural standardization will be following the CDISC /HL7 standards. What will be the expectations around content standardization? Examples; Will the content of the RACE variable be standardized across all 178 converted studies or within the group of studies from a given submission? Will the standardized unit for each lab test be the same across all 178 converted studies?

Govt Response: It is expected that sponsors will use accepted terminologies for the data conversion process. This will typically involve use of CDISC-specified standard terminology as indicated in the NCI EVS. However, there may be instances where no standard terminology exists, and in these cases, it is expected that the contractor will work with the FDA Subject Matter Experts (SMEs) to identify/define acceptable terminology for use.

27. Standards development organizations (e.g. CDISC, HL7) make consensus-based decisions. There are currently no specified turn-around times from the standards development organizations (SDO) regarding updates and additions to the standards.

The contractor will be obligated to deliver according to the timelines outlined in the project plan. If the contractor establishes a governance review board with representatives from the FDA (subject matter experts) and the SDO’s in support of the legacy conversion project, will this board be empowered to make decisions (e.g., custom domain names, variable names, controlled terminology)? These decisions can be made available to the public through an open forum.

Govt Response: The government is requesting that the contractor submit to the COTR the necessary supporting documentation to recommend or request a change to the SDO in accordance with the ARRAOS Task Order Paragraph 3 on Page 113 of the Solicitation.

The Government will then work with the SDO to follow up on such recommendations or requests. For this effort, ultimate decisions about data standards conversion issues (such as terminology, modeling methods, custom domain creation, use of suppqual, etc) will remain with the FDA.

28. Does this effort require recoding of the adverse events across all 178 studies to one MedDRA version and concomitant medications to one version of the WHO Drug dictionary? If the recoding is not required across all 178 studies should the coding within a specific submission be to one version of the medical dictionaries?

Govt Response: Any analysis of adverse events across studies will require that the adverse events be coded to a single version of MedDRA. Coding methods should involve coding of the verbatim terms (instead of preferred terms) to a single version of MedDRA, particularly when the original preferred terms were coded using dictionaries such as COSTART or WHOART.

29. Under this solicitation, is the Contractor required to provide operational support for loading the converted studies into Janus?

Govt Response: No

30. Appendix 1 indicates that the ADaM analysis data should be created from the source legacy data. Please verify this statement to confirm that that the legacy source data, not the standardized SDTM data, should be used as the source for the creation of the ADaM datasets.

Govt Response: Analysis datasets will be created using the standardized SDTM data where possible. In some instances it may be necessary to use the original legacy analysis datasets.

31. When analysis based on the ADaM datasets are performed, will the expectation be that the newly created analysis results match the legacy analysis results or is it acceptable that the differences between the newly created results and the legacy results are explained?

Govt Response: It is acceptable that the differences between the newly created results and the legacy results are explained.

32. Who will be responsible for creation of an Integrated Statistical Analysis Plan (ISAP)?

Govt Response: The ISAP is not part of this solicitation.

33. Usually an ISAP can be finalized only after detailed review and analysis of all raw data to be integrated. That process may require additional time, in particular if numbers of studies is large and they are quite different. However to plan raw data conversion into SDTM format the ISAP will be very helpful to avoid any potential SDTM data deficiencies in the future. What is FDA approach to handle this issue?

Govt Response: The ISAP is not part of this solicitation.

34. Because of the shortened schedule due to the holiday and the requirement that the proposal be delivered on a Monday, will the government grant a 5 day extension to the proposal delivery schedule to July 2, 2010?

Govt Response: No, the deadline for proposal submission will remain unchanged.

Proposals are due on or before 28 June 2010, 4:OO CST. Through the issuing of amendment 000001 of the solicitation the Government has offered some clarifications to vendor inquiries, however none of them were so significant that it would greatly increase the amount of time needed for proposal development.

35. When will the government publish its answers to all questions?

Govt Response: 6/17/10, leaving vendors 11 days to review the Government responses and tailor their proposals accordingly.

36. RFP pg. 85, L.5.4.1. Are the Attachment 8 “Past Performance POC Information Sheet(s)” due to FDA at proposal submission on June 28?

Govt Response: This is correct. Offerors are to include their POC Information Sheets with their technical proposals.

37. RFP pg. 85, L.5.4.1. If Attachment 8 “Past Performance POC Information Sheet” is due June 28, please clarify what is meant by “references will likely be called between the weeks of 6/7/10 through 6/21/10, as cited on page 85, Section L.5.4.1.

Govt Response: See Govt. response to question 6.

38. Pg 84 Sec. L.5.4; pg. 76, L.4; pg. 80, L.5.1.1a). Are the “brief, corresponding narratives” to Attachment 8 as described on page 84 (Section L.5.4), the same as the narratives required in proposal section “V.1-T.1.A Technical Experience,” as described on page 80 (Section L.5.1.1a)?

Govt Response: The two narratives do describe the same project that your firm has cited as an example of relevant experience. The “brief, corresponding narratives” to Attachment 8 should be a very brief synopsis of the same project that was provided in the detailed narrative in proposal section “V.1-T.1.A Technical Experience,” as described on page 80 (Section L.5.1.1a).

The idea is that the Government will already have reviewed the lengthy, detailed narrative prior to us calling the POC references for the past performance check. We ask for the very “brief corresponding narrative along with Attachment 8 because we are merely looking for a very brief reminder of the project’s scope before picking up the phone to call the reference about that project.

39. RFP pg. 38. Is the “physical security plan” excluded from the page count?

Govt Response: Physical security plan is no longer required to be submitted with Offeror’s proposal.

40. RFP pg. 38 and 76. Since, “the content of the two volumes MUST be organized ” as indicated in the table on pages 76-77, where within the proposal should the “physical security plan” be placed?

Govt Response: Offerors are no longer expected to submit the physical security plan with its proposal, therefore question is moot.

41. RFP pg. 84, L.5.3 Factor 3: Task Order Approach. Are the project management plan, data conversion plan, and study data conversion plan outline excluded from the page count?

Govt Response: No.

42. RFP pg. 85, L.5.4.3. Are performance recognition documents excluded from the page count?

Is there a page limit for these?

Govt Response: Performance Recognition documents are not excluded from the page count.

There is no page limit on how many recognition documents an Offeror may submit.

43. RFP pg. 119, Attachment 7 Task Order SOW, Appendix 1. There is a table listing approximately 179 studies and 4,800 data sets potentially included. Can you please confirm that Task Order 1 includes the completion of this quantity of data or is this a sample of what could be included?

Govt Response: The Government confirms that Task Order 1 includes the completion of these actual studies.

44. RFP pg. 114, Attachment 7 Task Order #1 SOW. The work order references the creation of integrated ADaM data sets within the scope of work. Does the scope of work include the creation of analysis data sets at the individual study level, the integration of multiple studies, or both?

Govt Response: The Government confirms the work includes the creation of analysis datasets that integrate multiple studies and does not include analysis datasets at the individual study level.

45. RFP pg. 114, Attachment 7 Task Order #1 SOW. Within the data conversion work, is it expected that the vendor will deliver the code that is generated, as well as the data, validation results, and define.xml? If the code must be delivered, is it expected to be SAS code or whatever code is appropriate for the standard or format being used?

The Government is not expecting that the vendor deliver the code that is generated during the data conversion process. Consistent with the requirements in the SOW, the contractor is expected to document transformations for traceability.

46. RFP pg. 114, Attachment 7 Task Order #1 SOW. The Task Order does not provide detailed information regarding the type of domains included within the studies. Can the FDA provide a percentage of the target data sets which will cover the standard SDTM domains vs. customized therapeutic domains that must be developed?

Govt Response: To the extent possible, the Government aims to stay within the construct of the current domains. If there are circumstances where there is difficulty in mapping data to one of the existing domains, FDA's Subject Matter Experts will be consulted and will make the final decision about whether or not a custom domain may be needed for a particular therapeutic disease area.