genetics-Amendment 1.pdf

NIH-NIDDK-07-05 1

OMB NO. 0990-0115

SOLICITATION – AMENDMENT ONE (1)

SECTION A - SOLICITATION/CONTRACT FORM

Page 1 of 15 pages

1. Purchase Authority: Public Law 92-218 as amended

2. Request For Proposal (RFP) No. NIH-NIDDK-07-05

3. Issue Date:

October 12, 2007

4. Just In Time:

[X] NO

[ ] YES

5. Set Aside:

[X] NO

[ ] YES

6. TITLE: The NIDDK Genetics Repository - AMENDMENT ONE (1)

7. ISSUED BY:

NIDDK/FIC R&D Contracts Management Branch Office of Acquisitions, NIDDK, NIH, DHHS 2 Democracy Plaza, Suite 700W

6707 DEMOCRACY BLVD MSC 5455

BETHESDA, MD 20892-5455

8. SUBMIT OFFERS TO:

See Part III, Section J, "Packaging and Delivery of the Proposal," ATTACHMENT 1 of this Solicitation.

9. THIS AMENDMENT REVISES SECTION C - ARTICLE C.1. STATEMENT OF WORK and SECTION M –

EVALUATION FACTORS.

The deadline for submission of proposals remains 3:00pm local time on Thursday, November 15, 2007.

Offers will be valid for 120 days unless a different period is specified by the offeror on the Attachment entitled, "Proposal Summary and Data Record, NIH 2043." ANY QUESTIONS RELATED TO THIS RFP MUST BE SUBMITTED IN WRITING (via Fax or Email) TO THE CONTACT IN BLOCK 12 BELOW NO LATER THAN OCTOBER 17, 2007. AMENDMENT TWO (2) TO THIS SOLICITATION WILL BE ISSUED RESPONDING

TO ALL QUESTIONS RECEIVED ON OR ABOUT OCTOBER 24, 2007.

10. THIS SOLICITATION REQUIRES DELIVERY OF PROPOSALS TO THE OFFICIAL POINT OF RECEIPT

FOR THE PURPOSE OF DETERMINING TIMELY DELIVERY AS STATED IN ATTACHMENT 1,

"PACKAGING AND DELIVERY OF THE PROPOSAL." IF YOUR PROPOSAL IS NOT RECEIVED BY

THE CONTRACTING OFFICER OR HIS DESIGNEE AT THE PLACE AND TIME SPECIFIED, THEN IT

WILL BE CONSIDERED LATE AND HANDLED IN ACCORDANCE WITH SUBPARAGRAPH (c)(3) OF FAR CLAUSE 52.215-1, ENTITLED, "INSTRUCTIONS TO OFFERORS--COMPETITIVE ACQUISITION"

LOCATED IN SECTION L.1. OF THIS SOLICITATION.

11. Offeror must be registered in the Central Contractor Registry (CCR) prior to award of a contract.

(http://www.ccr.gov)

12. FOR INFORMATION CALL: Mr. Dana L. Harris

PHONE: (301) 594-9987

e-MAIL: harrisd@mail.nih.gov

COLLECT CALLS WILL NOT BE ACCEPTED.

13. Table of Contents on following page.

Edward J. Kostolansky, Contracting Officer

Office of Acquisitions National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health

SECTION C - DESCRIPTION/SPECIFICATIONS/WORK STATEMENT is amended to read as follows:

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ARTICLE C.1. STATEMENT OF WORK

Independently and not as an agent of the Government, the Contractor shall furnish all the necessary services, qualified personnel, material, equipment, and facilities not otherwise provided by the Government, as needed to perform the Statement of Work, below.

I. Background Information/Project Description

Discovery of disease related genes requires a population of individuals with the genetic variant, as well as a population of control (unaffected) individuals. Thus, a repository of genetic materials, including DNA samples, cryopreserved lymphocytes, immortalized cell lines, and accompanying clinical and pedigree data is clearly an invaluable resource for the research community studying diseases related to the mission of the NIDDK. This project, which will be referred to herein as “The Genetics Repository”, continues an important collection begun in 2003 and is conceptually related to repositories in existence at other institutes at the NIH.

The repository will allow the continued storage, maintenance, and quality control, and equitable, ethical distribution of DNA and other resources important to the study of diseases under the mandate of the NIDDK. It facilitates sharing of resources, thus encouraging work by a broad group of investigators and, perhaps, increasing the sample size and the resulting power of a study tidentify genetic determinants of a disease. It helps to ensure that research participants will be making a maximal contribution, and decreases duplicative sampling efforts.

The objective of this contract will be to continue the NIDDK Genetics Repository, in order to accomplish the following in a highly efficient, rapid, and cost-effective manner:

• Receive blood samples from NIDDK funded grants

• Process these data and materials to create cell lines, cryopreserved lymphocytes, and/or DNA or RNA samples

• Receive externally produced immortalized lymphocyte cell lines; and

• Widely distribute all materials to qualified investigators in the scientific community in variety of customized formats.

The cell immortalization and other tasks outlined in this statement of work are highly technical, and require extensive experience and expertise. The success rate for cell immortalization is extremely variable. It depends, in large measure, on how well the established methods are implemented. As the entire value of many genetics studies rests on the ability to analyze the DNA of sib-pairs and other relatives, inability to recover DNA from any particular sample may negate the value of multiple samples. Therefore, it is essential that the success rate for establishing cell lines be as close to 100% as possible. Furthermore, the ability to track thousands of genetic samples, preventing sample mix-ups and cross-contamination while maintaining a high-throughput processing system, is crucial to the integrity of the studies being supported. The Contractor’s project director must have extensive experience in successfully providing these genetics and sample processing services, including blood cell immortalization and DNA extraction and distribution, to a large group of investigators. The Contractor’s staff must be highly trained to carry out exacting technical tasks accurately and reproducibly. As all the work is with samples from human subjects, all staff must be familiar with human subjects protections and be sensitive to the bioethical and safety issues involved in handling human biosamples. Finally, the Contractor must have a demonstrable long-term interest in providing these services, to ensure that there is continuity throughout the period of the contract.

II. Number of Samples

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Since investigators cannot determine the exact number of subjects or the anticipated analytic strategies for samples over a 12-month period of time, estimates are used for predicting the number of subjects per year and the number of various types of sample distributions.

For the purpose of constructing fixed price schedules, Contractors shall anticipate:

A. Receiving blood samples from 2500-3500 subjects per year. For proposal preparation purposes, the projected number of blood samples to be received 3100 per year. Of those, it is anticipated that:

1. 900 will be used to create immortalized cell lines from which DNA is extracted

2. 300 will be used to produce cryopreserved lymphocytes

3. 1900 will be used to extract DNA directly, preserving the plasma.

B. Receiving 3500 externally produced cell lines for long-term storage each year for the first two years of this contract, from which DNA will be extracted.

C. Distributing 10,000 samples per year in a variety of formats, including:

1. 1000 small sets of individual samples aliquots

2. 2-5 large sets of samples arrayed for automated analysis

D. Preparing 500 RNA samples from immortalized cell lines annually, and carrying out 250 pedigree analyses.

E. Preparing 250 Whole Genome Amplified DNA samples per year.

III. Description of Tasks to be Performed

Task 1. Establish biospecimen preparation, shipping, receipt, and tracking systems for numerous individual multi-center clinical studies.

a. The Contractor shall work with representatives of studies designated in writing by the Project Officer, with the

NIDDK Biosample and Data Repositories to develop appropriate aliquoting, packaging and labeling systems for blood, DNA, and frozen cell line samples. A copy of each study-specific protocol shall be provided to the NIDDK Project Officer within 2 weeks of being finalized by the Contractor and the study.

b. The Contractor shall develop systems to ensure the receipt of approximately 30 mls of whole blood from adult study subjects or smaller volumes from pediatric study subjects, by preparing appropriate blood collection kits as needed for shipment to investigators and sites in participating studies designated in writing by the Project Officer.

c. The Contractor shall develop systems to ensure receipt of DNA samples or externally produced frozen cell lines from central processing laboratories or other study sites,

d. The Contractor shall develop biosample packaging, marking and shipping systems that are in accordance with

Standard Industry Practice, FDA Requirements, approved Standard Operating Procedures, city, state, and/or Federal regulations, and any special instructions given.

e. The Contractor shall develop notification systems to anticipate shipments and be responsible for recording and monitoring the location of all specimens that are being shipped to minimize delay or loss. The Contractor shall establish procedures for monitoring and maintaining information on the status of specimens upon receipt, including accidental thaws and other adverse conditions, and actions to be taken when such problems occur.

f. The Contractor shall designate specific individuals, and alternates, to be responsible for after-hours specimen receipt and manipulation.

g. Detailed descriptions of all the systems described in part (b) shall be provided to the Project Officer within 8 weeks of contract award. Revisions specified by the Project Officer will be completed within 2 weeks, and the final version will then be submitted for approval by the Project Officer.

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h. The Contractor shall work with the Project Officer and with investigators from studies designated in writing by the

Project Officer to modify and adapt these systems to suit the specific needs of individual projects.

Task 2. Maintain the confidentiality of subjects by removing all traditional personal identifiers from samples

a. Traditional personal identifiers that may be utilized to establish the identity of individual subjects (e.g., surname, address, social security number, etc.) shall not be provided nor accepted by the Contractor. Instead, the Contractor shall work with the NIDDK Data Repository and with researchers submitting samples to develop an identifier code for each subject that will link the sample to the clinical and descriptive data associated with the sample. Thus, all data and biological materials received by the Contractor shall be untraceable to their original sources.

b. Neither the investigators receiving samples from the Contractor, nor the Contractor him/herself will use information collected under this contract to establish the identity of a given subject or query the databases and retrieve information for an individual subject whose identity is known from some other source.

c. The Contractor shall apply to the Office for Human Research Protections (OHRP) at the Department of Health and

Human Services for a project assurance number, if such a number has not been assigned to the Contractor. Obtaining a project assurance number represents a binding commitment to minimum standards for the protection of human subjects, which safeguards the rights and welfare of all human research subjects. The Contractor shall submit the relevant documentation showing that a project assurance number has been issued and that submitting investigators have IRB approval to the Project Officer for review and approval before samples are accepted.

d. The Contractor shall assure that all investigators have adequate approval from an Institutional Review Board (IRB), for the collection and use of samples submitted to the analysis facility. The Contractor shall obtain blank copies of all the informed consent forms used in the collection of the samples received by the Contractor. The Contractor shall maintain an electronic record-keeping system to track the consents and the status of their approval by the NIDDK Project Officer.

Task 3. Establish one or more subcontracts for timely and cost-effective shipping of biosamples between multiple sites and the repository.

The Contractor shall establish subcontracts with commercial carriers for overnight shipping of biosamples between multiple sites, domestic and international, and the repository in accordance with Standard Industry Practice, FDA Requirements, approved Standard Operating Procedures, city, state, and/or Federal regulations, and any special instructions given. All shipments of blood collecting materials to these projects and samples from these projects shall be paid for by the Contractor and charged to the contract.

Task 4. Create and store viable cell lines via Epstein-Barr virus transformation of lymphocytes from blood samples, with a success rate of 97% or greater and expanding the lymphoblastoid cell lines.

a. The Contractor shall process blood drawn from each subject and shall establish high-quality lymphoblastoid cell lines via Epstein-Barr virus transformation of lymphocytes from blood samples, with a success rate of 97% or greater for samples from domestic collection sites. The transformation success rate for samples shipped from international sites shall be 90% or greater.

b. All cell lines shall be free of contamination by bacteria, fungi, mycoplasma, other cells, etc.

c. An aliquot of blood shall be frozen for future verification of sample identity. In addition, live cells from each sample shall be cryopreserved for backup in the event of a transformation failure.

d. In the event of cell transformation failure, where a cell line cannot be established for a subject from a blood sample received (including the use of cryopreserved blood), the Contractor shall

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i. Notify the Project Officer within 2 calendar weeks of the determination of failure and the suspected reason for failure.

ii. Notify the submitter within 2 calendar weeks of the determination of failure and the suspected reason for failure.

iii. Request that the submitter obtain additional blood from the subject, with the goal of correcting the reason for failure on re-submission, for up to total of three attempts for a given sample. After three attempts, the sample will be considered unsuitable for transformation and nor further attempts will be made.

e. The lymphoblastoid cell lines shall be expanded for DNA extraction and aliquoted for long-term storage. An aliquot of each stored cell line shall be checked to ensure viability.

f. The Contractor shall submit, within 8 calendar weeks of award, a detailed protocol of sample processing, lymphocyte transformation, cell line storage, quality control, re-growth, safety, and facilities for this work. The work plan shall document the precise transformation methods that will be employed including the rationale for method selection, reliability, feasibility, and documented evidence that the method has been successful. In addition, the work plan shall describe the actions to be taken to maximize the transformation success rate and to ensure that it is maintained at a minimum of 98% for domestic samples during the performance of the contract. Finally, the work plan shall describe the procedures that will be used to ensure freedom from contamination by bacteria, fungi, mycoplasma, other cells, etc. Revisions specified by the Project Officer will be completed within 2 weeks, and the final version will then be submitted for approval by the Project Officer.

Task 5. Receive and store lymphoblastoid cell lines prepared at other facilities and carry out quality control assessments.

a. As directed by the Project Officer, the Contractor shall receive lymphoblastoid cell lines prepared by other laboratories for long-term storage.

b. An aliquot of each stored cell line shall be checked to ensure viability, and the regrown cells aliquoted and put into long-term storage.

c. In the event that a cell line fails to grow, the Contractor shall:

i. Notify the Project Officer within 2 calendar weeks of the determination of failure and the suspected reason for failure.

ii. Notify the submitter within 2 calendar weeks of the determination of failure and the suspected reason for failure.

iii. Request that the submitter provide an additional aliquot of the cell line.

d. The Contractor shall ensure that all cell lines received and stored are free of contamination by bacteria, fungi, mycoplasma, other cells, etc. In the event that any contamination is detected in any of the received cell lines, the Contractor shall:

i. Notify the Project Officer within 2 calendar weeks of the determination of contamination and the suspected contaminant

ii. Notify the submitter within 2 calendar weeks of the determination of contamination and the suspected contaminant

e. The Contractor shall submit, within 8 calendar weeks of award, a detailed protocol of cell line storage, quality control, re-growth, safety, and facilities for this work. The work plan shall document the precise methods that will be employed including the rationale for method selection, reliability, feasibility, and documented evidence that the method has been successful. Revisions specified by the Project Officer will be completed within 2 weeks, and the final version will then be submitted for approval by the Project Officer.

Task 6. Cryopreserve blood cells for eventual transformation and/or DNA extraction

a. Some studies may choose not to establish cell lines immediately for each subject. Instead, for those studies, identified in writing by the Project Officer, the Contractor shall prepare and cryopreserve blood cells from the submitted blood samples. The cryopreservation should be carried out in such a manner as to maximize the potential to immortalize the frozen cells in the future.

b. At the beginning of the designated study, and annually thereafter, the Contractor shall assay 25 cryopreserved samples to determine the transformation success rates. The success rate for transformation of cryopreserved samples shall be greater than 85%. The Project Officer may approve a lower cell line establishment rate if data provided by the

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Contractor and by an independent laboratory document that underlying medical conditions of subjects or sample shipment conditions preclude the possibility of achieving 85% success in immortalization.

Task 7. Extract and store DNA from cell lines or from isolated blood cells and, with designated samples, separating the white blood cells (buffy coat) from the plasma.

a. The Contractor shall extract DNA from lymphoblastoid lines in sufficient quantities for genetic analysis (i.e., at least 1 mg).

b. The Contractor shall extract DNA directly from blood samples or frozen blood cells, in varying amounts depending on the volume of the starting material. The method used must produce a yield of at least 3 micrograms per ml of whole blood, and the Contractor must have a success rate of at 95%in achieving that yield. The Project Officer may approve a lower yield rate if data provided by the Contractor and by an independent laboratory document that underlying medical conditions of subjects or sample shipment conditions preclude the possibility of achieving extraction efficiencies of at least 3 micrograms of DNA per ml of whole blood.

In the event of low DNA yields AND where the total DNA recovered is less than 30 micrograms, the Contractor shall:

i. Notify the Project Officer within 4 calendar weeks of the determination of failure and the suspected reason for failure.

ii. Notify the submitter within 4 calendar weeks of the determination of failure and the suspected reason for failure.

iii. Request that the submitter obtain additional blood from the subject, with the goal of correcting the reason for failure on re-submission.

c. Extracted DNA shall be aliquoted and shall be of high quality, with a 260/280 OD ratio of 1.6-2.0, and high molecular weight, and suitable for molecular genetic analysis. The Contractor shall store the extracted DNA samples during the time of the contract.

d. As directed by the Project Officer, the Contractor shall save the plasma from the initial blood separation and aliquot it as directed by the protocol developed by the submitting study and approved by the Project Officer. Aliquoted samples will be delivered to the NIDDK Biosample Repository. For each study requiring this task, the Contractor shall submit a written detailed protocol of aliquoting volumes, labeling methods, and shipping schedule to the NIDDK Project Officer. Revisions specified by the Project Officer will be completed within 2 weeks, and the final version will then be submitted for approval by the Project Officer.

Task 8. Receive externally produced DNA As directed by the Project Officer, the Contractor shall receive DNA produced externally, and carry out quality control assessments as directed by the Project Officer.

Task 9. Carry out whole genome amplification, pedigree analyses and RNA extraction.

a. The Contractor shall develop methods and carry out whole genome amplification of DNA samples, as directed by the

Project Officer. These methods shall use validated technologies that achieve the highest possible fidelity and extent of amplification, and produce DNAs that are suitable for standard genotyping assays.

b. The Contractor shall develop methods and carry out RNA extraction from lymhpoblastoid cells, as directed by the

Project Officer. These methods shall use validated technologies for the highest possible yield and quality of RNA.

c. The Contractor shall develop methods and carry out limited genotyping , primarily to verify sample identity or for pedigree testing, on samples designated by the Project Officer. These methods shall use validated technologies that produce high quality data and are cost-effective.

d. The Contractor shall submit, within 8 calendar weeks of award, a detailed protocol for this work. The work plan shall document the precise methods that will be employed including the rationale for method selection, reliability, feasibility, cost-effectiveness and documented evidence that the method has been successful. In addition, the work

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plan shall describe the actions to assess the quality and integrity of the resulting DNA or RNA or genotyping product.

Revisions specified by the Project Officer will be completed within 2 weeks, and the final version will then be submitted for approval by the Project Officer.

Task 10. Distribute cell lines and biosamples to investigators granted access by the PO, including arraying in a variety of formats, packaging, handling, and coordinating sample shipments to domestic and international sites.

a. As directed in writing by the Project Officer, the Contractor shall return a viable cell line and a designated quantity of

DNA prepared from the submitted sample, without charge, to sample submitters at regular intervals (e.g. semi-annually) when a sufficient number accumulates or when requested. For each study requiring this task, the Contractor shall submit a written detailed protocol of aliquoting volumes, labeling methods, and shipping schedule to the NIDDK Project Officer. Revisions specified by the Project Officer will be completed within 2 weeks, and the final version will then be submitted for approval by the Project Officer.

b. The Contractor shall distribute DNA in a variety of formats, including formats that allow high-throughput, automated analyses, along with appropriate electronic shipping manifests. The tubes shall be appropriately labeled, in accordance with a system worked out by the receiving site. The formats for arrayed samples must be approved in writing by the NIDDK Project Officer

c. The Contractor shall charge an access fee and shipping charges per sample. The Contractor shall establish an appropriate system for the accounting and reporting of fees in accordance with the fee schedule established jointly with NIDDK. The Project Officer retains the right to waive the access charge for a recipient. In these cases, the Contractor shall pay any and all shipping charges. The Contractor shall establish a process, with approval of the Contracting Officer, to ensure that all such fees are promptly collected and accounted for accurately, and offset against contract costs in a proper and timely manner. The Contractor shall not distribute materials before payment in full is received, unless the Project Officer has waived the fees. Payment shall be in the most expeditious format (e.g., check, purchase order) possible. Income received from fees charged for access to cell lines and DNA shall be utilized to offset contract costs. Such income shall be reflected on the Contractor’s invoice for the month it is received.

d. The Contractor shall not use the biosamples for any purpose other than that specified in this contract, without written approval of the PO.

e. Packaging, marking and shipping shall be accomplished in accordance with Standard Industry Practice, FDA

Requirements, approved Standard Operating Procedures, city, state, and/or Federal regulations, and any special instructions given. The Contractor shall guarantee that all required materials be delivered in immediate usable and acceptable condition. The Contractor shall be responsible for recording and monitoring the location of all specimens that are being shipped through use of an electronic tracking system of all requests and specimens.

f. The Contractor is responsible for monitoring and shipping of specimens to minimize delay or loss. The Contractor shall have a procedure for the notification of recipients of anticipated delivery time, and the Contractor shall follow-up with the recipient to ensure that specimens are received at the anticipated delivery time. If a specimen shipment is not received within four hours of expected delivery time, the Contractor shall inform the intended recipient by telephone or electronic mail. The Contractor shall then initiate immediate tracking to locate the delinquent specimen shipment.

Upon finding the delinquent specimen shipment, the Contractor shall notify the intended recipient with the location and new expected delivery time.

g. When samples are requested by investigators granted access by the Project Officer, the Contractor shall ship samples within 2 weeks of requests for less than 100 DNA samples, 4 weeks for requests of more than 100 DNA samples and 3 weeks for cell lines, unless shipment within this window would jeopardize the viability of the sample due to holidays, natural disasters, or other factors.

Task 11. Withdraw and destroy samples from the repository as directed in writing by the Project Officer

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During the course of a study, or after a study is concluded, a subject may choose to withdraw from the research project.

When notified by an investigator who submitted the sample that the subject (identified by the identifier code) has withdrawn from the study, the Contractor shall request confirmation from the Project Officer. Upon receiving written confirmation, the Contractor shall withdraw and destroy all biosamples, cell lines, DNA, and other materials associated with that subject’s identifier code, and record the materials as “withdrawn” in the database.

Task 12. Establish and maintain Quality Assurance (QA) and Quality Control (QC) programs.

a. The Contractor shall develop and implement QA/QC programs covering activities critical for the successful operation of the repositories.The QA/QC programs shall include, but not be limited to:

i. Each protocol used for the processing and storage of biosamples

ii. Mechanical functioning of freezers and other storage equipment, including alarm and back-up systems

iii. Cell immortalization, viability of frozen cells, quality of extracted DNA, preservation of biosamples.

iv. Storage of an aliquot of each sample of whole blood to verify sample identity

v. Monitoring the flow of biosamples into and out of the repository.

vi. Packaging and shipping of materials to domestic and international sites.

vii. Accuracy of data entry and database maintenance in the inventory database, including regular comparisons of shipping and receipt records with the study’s data coordinating center, and regular comparison of informed consent approvals with NIDDK records.

b. The Contractor shall conduct a physical inventory of not less than one-tenth of one (0.1) percent of the repository samples annually. The Project Officer will assist the Contractor in selection of a representative sample to be inventoried.

The inventory shall include both samples handled in the previous 12 months and freezer positions that may or may not include samples. As part of the inventory, the Contractor shall assess the viability of randomly selected frozen cell lines and the quality of randomly selected DNA samples.

The Contractor shall submit, within 8 calendar weeks of award, a detailed protocol for QA/QC. Revisions specified by the Project Officer will be completed within 2 weeks, and the final version will then be submitted for approval by the Project Officer.

Task 13. Provide security and back-up systems and a plan for disaster recovery.

a. The Repository shall have an adequate number of empty, functional storage units, constantly running, to serve as back-up units in the event of freezer failures. The back-up units shall be appropriate to the sample inventories at respective temperatures, including mechanical and liquid nitrogen freezers.

b. The Repository shall store aliquots of each cell line and DNA sample in a back-up facility located at a second site, so that there is independent back-up storage of each and every sample in case of catastrophic loss.

c. The Contractor shall ensure that the repository is equipped with fire, smoke, and mechanical failure alarms, and appropriate fire control equipment. The Contractor shall ensure that key repository personnel can be contacted at any time in case of fire, mechanical failure of one or more freezers, or other emergency.

d. The Contractor shall ensure that the repositories have emergency back-up generators with the capabilities of handling the complete power supply, notably all freezers and facility HVAC, in the case of electrical power failure, except as noted below. The Contractor shall ensure that at a minimum, 72 hours of fuel is available for the generator(s). The Contractor shall conduct biweekly tests of the generators to ensure proper operation.

e. The Contractor shall establish systems to ensure data security and to prevent loss of inventory data in case of physical damage or equipment failure.

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f. The Contractor shall submit, within 8 calendar weeks of award, a detailed protocol for recovery of stored materials and data following a natural or man-made disaster. Revisions specified by the Project Officer will be completed within 2 weeks, and the final version will then be submitted for approval by the Project Officer.

Task 14. Maintain high quality, secure information systems to allow detailed tracking and reporting of sample receipt, processing, storage and distribution, rapid retrieval of samples, storage of QA/QC information associated with the sample, seamless interaction with the Database Repository, and listing of investigators using the repository.

a. The Contractor shall maintain accurate databases that are regularly updated and verified. The databases shall allow real-time tracking of samples as they are received, processed, stored and distributed. In addition, the databases should also permit flexible, Web-based reporting to NIDDK of samples received, produced, discarded and distributed, as well as yield of DNA, and other QA/QC data.

b. The Contractor shall maintain a regularly updated database of information about qualified investigators using the repository who submit and/or receive data and biological materials, as well as the informed consents provided by those investigators. The database shall minimally include for each investigator the following information:

a. Name of the principal investigator

b. Title of the research project, and whether it is ancillary to an existing study

c. Name and approval date of ancillary study, if relevant

d. NIH grant, contract, or cooperative agreement # of project

e. Administrative official mailing address, telephone number, fax number, e-mail address, and recipient institution.

f. Samples submitted

i. Date of submission

ii. Sample Id

g. Samples withdrawn

i. Dates of withdrawal

ii. Charges and date fees paid

iii. Ids of samples withdrawn

h. Informed consent

i. Version and date

ii. Date approved by NIDDK

c. The databases shall be organized to permit rapid and efficient downloading and uploading of information, and shall be designed to facilitate transfer of information with researchers or other entities submitting or receiving samples, and with the NIDDK Data and Biosample Repositories. The Contractor shall assure that the NIDDK Project Officer can view customized reports via a Web-based interface. The Contractor shall maintain a daily backup of all electronic databases to protect against the accidental data loss. In addition, the Contractor shall ensure that the information systems include standard security measures, and that new security measures are implemented as they become available.

d. The Contractor shall submit, within 8 calendar weeks of award, a detailed description of the proposed information systems, including a description of security and back-up provisions. Revisions specified by the Project Officer will be completed within 2 weeks, and the final version will then be submitted for approval by the Project Officer.

Task 15. Work in a cooperative fashion with the Project Officer, the External Advisory Committee, and the Steering Committee.

a. The Contractor shall cooperate with the Project Officer, the External Advisory Committee, and with Contractors and their representatives from the NIDDK Data and Biosample Repositories, through participation in the Steering Committee

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and through other activities. This includes, but is not limited to, cooperation in developing a sample labeling system, methods for cross-referencing, and database integration. In addition, the Contractor shall facilitate site visits by the Project Officer, the Steering Committee, and other groups, as directed in writing by the Project Officer.

b. The Contractor shall also assist the NIDDK Data Repository in developing a public website that includes data regarding the Genetics Repository’s inventory, policy, forms, procedure, and other information.

Considerations:

I. Ownership and Property

The government shall own cell lines and all equipment used to store the cell lines, as well as all other products (e.g., DNA, databases, documentation) produced under this contract.

The guidelines regarding ownership and intellectual property as published ashttp://ott.od.nih.gov/NewPages/RTguide_final.html apply to this repository.

Patents on materials generated from the repository resources shall follow the guidelines as published at http://www.nih.gov/news/researchtools/appendd1.htm.

The Project Officer shall maintain rights to be included as an author on publications resulting from the repository or regarding the repository, provided that s/he has made substantial contributions to:(a) conception and design, or analysis and interpretation of data; and (b) the drafting of the article or critical revision for important intellectual content.

The Contractor will be not included as a co-author on publications resulting from repository resources unless s/he has made substantial contributions to: (a) conception and design, or analysis and interpretation of data; and (b) the drafting of the article or critical revision for important intellectual content. However, the repository shall be cited, and the repository website, sample identification data, and other data shall be included in publications resulting from utilization of repository resources. The Contractor shall monitor resulting publications to assure that the NIDDK and the Contractor are cited within scientific and other publications.

II. Transition Planning

1. Three months prior to the completion of the contract, an updated full inventory of samples shall be provided to the Project Officer. A detailed plan, with milestones, for the transfer of all biological materials to a storage facility or successor Contractor shall be provided at least twelve months before the expiration date of this contract. If there is a successor Contractor or if this function is be to taken over by the Government, the Contractor shall inform and assist the Project Officer or successor Contractor in the transition and day-to-day operation to enable the successor to gain detailed working knowledge of procedures utilized in order to assure proper and successful transition.

2. Three months prior to the completion of the contract, an updated full inventory of all electronic databases shall be provided to the Project Officer and any successor Contractor. A detailed plan, with milestones, for the transfer of all electronic databases and files to a successor Contractor shall be provided at least twelve months before the expiration date of this contract. If there is a successor Contractor or if this function is be to taken over by the federal government, the Contractor shall inform and assist the Project Officer or successor Contractor in the transition and day-to-day operation to enable the successor to gain detailed working knowledge of procedures utilized in order to assure proper and successful transition.

3.The Contractor shall fully cooperate with any successor Contractor and NIDDK to ensure the smooth and efficient transfer of all such data and biological materials.

REPORTING REQUIREMENTS

a. Technical Progress Reports

In addition to those reports required by the other terms of this contract, the Contractor shall prepare and submit the http://ott.od.nih.gov/NewPages/RTguide_final.html http://www.nih.gov/news/researchtools/appendd1.htm

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following reports during the period of performance of this contract:

The contractor is required to provide 4 (1 Original and 3 Copies) copies of these reports as follows:

1. Monthly: The first reporting period consists of the first full month of performance plus any fractional part of the initial month. Thereafter, the reporting period shall consist of each calendar month. Each monthly report submitted to the Project Officer shall include the following:

a. The number of samples received from each research project during that month, broken down by sample type

b. Processing activities carried out each month, including number of samples processed

c. The success rate for cell line transformation during the month.

d. Clear documentation of all unsuccessful attempts at cell line transformation during the month to date, including corrective action taken. Requests to research projects during that month for blood re-draws shall be clearly documented.

e. The success rate for DNA extraction during the month

f. Clear documentation of all unsuccessful attempts at DNA extraction during the month, including corrective action taken. Requests to research projects during that month for blood re-draws shall be clearly documented.

g. Samples shipped during the month, by study and recipient

h. Samples discarded during the month and reason for discard

i. Income generated during that month, used as offset against that month’s charges.

2. Quarterly: This report shall include a summation of the monthly progress reports. A monthly report will not be submitted for the final month of the quarter. The first reporting period consists of the first full three months of performance including any fractional part of the initial month. Thereafter, the reporting period shall consist of three full calendar months. Each quarterly report shall contain:

a. The cumulative number of samples, and sample types, received from each research project over the past quarter and for the entire project history, broken down by year;

b. The cumulative success rate for cell transformation during the quarter and for the entire project period, by study and in aggregate;

c. The cumulative success rate for DNA extraction during the quarter and for the entire project period, by study and in aggregate;

d. Processing activities carried out for the quarter and for the entire project period, broken down by study and by activity, as well as cumulative data;

e. Samples shipped, by study and recipient, for the quarter and for the entire project period;

f. Budget report for the quarter and for the entire project period, broken down by study and billable activities.

3. Annually: This report shall include a summation of the results of the entire contract work for the period covered.

An annual report will not be required for the period when the Final Report is due. A monthly report shall not be submitted when an Annual Report is due. A brief annual report shall be compiled to summarize the inventory, NIH-NIDDK-07-05 12 processing success rate and budget information contained in that year’s monthly and quarterly reports, and shall also include a full inventory of samples, and a full inventory of all electronic databases, including a description of each database, the DBMS used, and a list of relevant files. In addition, the annual report should contain a summary description of major changes over the past year, including new facilities, major laboratory equipment, information systems and security systems added during the year, as well as any planned major expansions or system changes.

4. Final report: This report shall consist of the work performed and results obtained for the entire contract period of performance as stated in Section F of this contract. This report shall be in sufficient detail to describe comprehensively the results achieved. The Final Report shall be submitted on or before the last day of the contract performance period. An annual report shall not be required for the period when the Final Report is due. A final report, including an executive summary, shall summarize all of the activities conducted under the contract, at the time of the contract end or contract transfer to another Contractor.

b. Summary of Salient Results

The Contractor will be required to prepare and submit, with the final report, a summary (not to exceed 200 words) of salient results achieved during the performance of the contract. This report will be required on or before the expiration date of the contract.

NIH-NIDDK-07-05 13

SECTION M - EVALUATION FACTORS FOR AWARD is hereby amended to read as follows:

1. GENERAL

The Government intends to evaluate the offeror’s proposal and award a contract without discussions (except clarifications as described in FAR 15.306(a) ). Therefore, the offeror(s) initial proposal should contain the offeror’s best terms from a cost or price and technical standpoint. The Government reserves the right to conduct discussions if the Contracting Officer later determines them to be necessary. If the Contracting Officer determines the number of proposals that would otherwise be in the competitive range exceeds the number at which an efficient competition can be conducted, the Contracting Officer may limit the number the number of proposals in the competitive range to the greatest number that will permit an efficient competition among the most highly rated proposals.

The technical portion of the proposal will be the most important single consideration in the award of the contract, and should be as complete and specific as possible. The evaluation of the proposals will be based on the administrative capabilities of the offeror to the needs of the project and realism of the level of effort in relation to the work done. Specific evaluation factors are shown below. The Government reserves the right to make an award(s) to that offeror(s) whose proposal provides the overall best value to the Government.

2. Technical Evaluation Criteria

A) The technical proposal will receive paramount consideration in the decision to award a contract for this acquisition, but not to the exclusion of cost/price. All evaluation factors other than cost or price, when combined are significantly more important than cost or price. The technical evaluation of the proposal, in accordance with the technical evaluation criteria specified below, will be based on the technical capabilities of the offeror in relation to the requirements of the project, as stated in the Statement of Work, and the realism of the proposed level of effort and direct costs.

B) The technical evaluation criteria for the review of each proposal are specified below, together with their relative weights of importance:

1. Personnel ................................................................................................................................................40%

Experience, training and appropriateness of the proposed personnel will be evaluated in the following areas:

i) Project Director .......................................................................................................................................... 10% The Project Director must demonstrate extensive successful experience in running a comparable facility that provides cell immortalization and DNA extraction services to a large group of investigators, and which carries out more than 500 cell immortalizations and more 2000 automated DNA extractions annually. This experience shall include training and supervising a staff of technically skilled managers and technicians. The Project Director must have experience and understanding of the technical and scientific issues that are involved in culturing mammalian cells, cell immortalization, DNA extraction, and molecular genetics and be able to evaluate and implement new protocols, reagents and techniques as they become available. The Project Director must be familiar with, and have implemented, information systems for tracking samples as they are being processed and when they are stored. The Project Director must have experience in interacting successfully with a diverse group of investigators. In addition, the Project Director shall have at least 5 years’ experience working with human biosamples and extensive knowledge in the area of human subjects protection and protection of subject confidentiality. Finally, the Project Director shall have extensive experience and knowledge in the area of job safety and risk reduction.

NIH-NIDDK-07-05 14

ii) Project Manager ........................................................................................................................................ 10% The Project Manager must demonstrate extensive successful experience in day-to-day supervision and management of a comparable facility that provides cell immortalization and DNA extraction services to a large group of investigators, including training and supervising a staff of skilled technicians. The Project Manager must have experience and understanding of the technical and scientific issues that are involved in culturing mammalian cells, cell immortalization, and molecular genetics, and the challenges in receiving and processing more than 100 samples per week. This individual must also be highly trained in the use of information systems for tracking samples as they are being processed and after they are stored. In addition, the Project Manager shall have at least 3 years’ experience working with human biosamples, and be highly trained in the area of human subjects protection and protection of subject confidentiality, and in safety aspects and risk reduction on the job. Finally, the Project Manager must have experience in interacting successfully with a diverse group of investigators.

iii) Information Systems Manager .................................................................................................................. 5% The Information Systems Manager must demonstrate extensive successful experience designing, implementing, and maintaining information systems for a biomedical facility. S/he must be familiar with multiple databases and platforms, data security and transmission, and be able to supervise computer/informatics staff, as well as interact successfully with many different researchers and non-specialists. The Information Systems Manager shall have at least 3 years’ experience working with sample or inventory tracking systems, especially with systems that allow detailed Web-based reporting. In addition, the Information Systems Manager must be familiar with protection of human subjects.

iv) Administrator.............................................................................................................................................. 5% The Administrator must demonstrate extensive successful experience as an administrator of a facility providing laboratory services to a large group of investigators. S/he must be able to interact with many different researchers successfully, as well as be skilled in using an information system that tracks samples. In addition, s/he must have experience in arranging the logistics of conference calls and small meetings.

v) Technical Staff.............................................................................................................................................. 5% Technical staff – the technicians must be highly trained to carry out exacting tasks accurately and reproducibly in order to receive, process, aliquot, analyze and store biosamples and input data from sample analyses. As all the work is with samples from human subjects, all staff must be highly trained in the ethical standards of protecting subject confidentiality and rights, as required by federal government. The Contractor shall also ensure that staff is well trained in the safety aspects and risk reduction on the job.

vi) Business Manager .......................................................................................................................................