CIDR_JOFOC_06-14-2012 final posted.pdf

Attachment C

Justification for Other than Full and Open Competition

“Source Selection Information – see FAR 2.101 and 3.104”

1. Identification of the agency and contracting activity

a. Federal agency and contracting activity.

HHS / NIH

b. Sponsoring organization:

The National Human Genome Research Institute

c. Project Officer information.

NIH, NHGRI

Gloria Dunnigan 333 Cassell Drive, Suite 1200 Baltimore, MD 21224

410-550-2740

Email: gloriad@nhgri.nih.gov

2. Nature and/or description of the action being approved.

a. Acquisition purpose and objectives.

The purpose of the acquisition is to continue to provide high quality, high throughput human and mouse genotyping and sequencing services to the scientific community on a peer-review basis. Determining the exact state of genetic variation in a human or model organism forms the foundation of efforts to map and identify genes and the variants within these genes that increase susceptibility to many common and rare diseases. The identification of genes that predispose or are responsible for a variety of human diseases will greatly benefit the programs of the National Human Genome Research Institute and the Institutes that comprise the National Institutes of Health. The identification of genes associated with diseases and other health related traits has allowed scientists to better understand the disease process. Identifying specific genetic variants that cause, or are associated with, disease traits can lead to new DNA-based diagnostic and prognostic tests. The use of this paradigm to identify disease genes has illuminated the molecular, biochemical and physiological pathways of several disorders and provided insights that led to the development of both preventive and therapeutic interventions. It is expected that most, if not, all human diseases have a genetic component. Thus, the continued search for disease genes will lead to improvements in public health. This acquisition is expressly focused on providing ready access to data production and data analysis services to the NIH community. Johns

Hopkins University (JHU) is the only contractor capable of providing study design, sample preparation, and collection, cleaning, interpretation, and dissemination of the data for CIDR program investigators as an integrated unit.

b. Project background.

The Center for Inherited Disease Research (CIDR) was created in 1996 through a sole source contract with Johns Hopkins University. The CIDR contract has been renewed twice. On each occasion, no other qualified source was identified for the goal of competition and JOFOCs were approved for award to JHU. The current contract number HHSN268200782096C/HHSN268201100011I is for the period June 1, 2007 through May 31, 2012. The total amount obligated to date is $66,855,914. CIDR is a centralized facility that provides a suite of services and deliverables focused on understanding the genetic contribution to human phenotypes. These services are provided to investigators and include SNP genotyping, DNA sequencing, epigenomic analyses, statistical genetics services and the deposition of data into NIH data repositories. CIDR is available to all scientists through competitive peer review by a chartered CIDR Access Committee (CAC). Applications are evaluated by the CAC for scientific merit. These applications and the CAC's recommendations are reviewed by the Board of Governors (BOG).

The BOG determines which projects are granted access to CIDR. All projects require prior approval from an institute liaison before an application is submitted to CIDR. This process ensures that the highest quality science is produced.

Upon its establishment, CIDR was supported by eight of NIH’s Institutes.

The success of the CIDR model has spread beyond the founding Institutes. CIDR is now supported by fourteen NIH Institutes: National Human Genome Research Institute (NHGRI), National Cancer Institute, National Institute of Dental and Craniofacial Research, National Institute of Neurological Disorders and Stroke, National Institute of Child Health and Human Development, National Eye Institute, National Institute of Environmental Health Sciences, National Institute on Aging, National Institute on Alcohol Abuse and Alcoholism, National Institute of Deafness and other Communication Disorders, National Institute of Mental Health, National Institute of Diabetes and Digestive Kidney Diseases, National Institute on Drug Abuse, and the National Institute of Arthritis and Musculoskeletal and Skin Diseases. Institutes have continued to join CIDR because of the high data quality and low cost of studies. While NHGRI provides the scientific and administrative oversight of CIDR, the science is driven by the research goals of the 14 member Institutes.

The basis for the approval of the previous JOFOCs was that JHU remained the only source capable of performing this work based on its unique experience, resources, and internationally recognized organizational staff.

3. Description of the supplies or services required to meet the agency’s needs (including the estimated value).

a. Project title.

High Throughput Genotyping and DNA Sequencing for Studying the Genetic Contributions to Human Disease Renewal 2012-2017

b. Project description.

The CIDR program is dedicated to providing high quality, high throughput genotyping in support of efforts to locate and identify gene variants responsible for human disease. The identification of the locations of genes that predispose or are responsible for a variety of human diseases will greatly benefit the programs of the National Human Genome Research Institute and the Institutes that comprise the National Institutes of Health. The identification of genes associated with diseases and other health related traits will allow scientists to better understand the disease process. Identifying specific genetic variants that cause, or are associated with, disease traits can lead to new DNA-based diagnostic and prognostic tests. The use of this paradigm to identify disease genes has illuminated the molecular, biochemical and physiological pathways of several disorders and provided insights that led to the development of both preventive and therapeutic interventions. It is expected that most, if not all, human diseases have a genetic component. Thus, the continued search for disease genes will lead to improvements in public health.

The purpose of this acquisition is to provide high quality, high throughput human and mouse genotyping and, genomic DNA sequencing services, and statistical genetics expertise dedicated towards finding the genetic basis for disease. The acquisition also contains a significant research and development component. As existing technologies improve, these improvements will be evaluated and adopted. The acquisition also includes tasks related to the ongoing evaluation of new technologies that may significantly increase the efficiency and yield of genetic studies. All efforts described in the SOW are designed to enhance the extramural and intramural research programs supported by the fourteen participating Institutes.

Requirement type. Check the appropriate box:

Research & development (R&D) R & D support services Support services (non-R&D) Supplies/equipment Information technology (IT) Construction Architect-engineer (A & E) services Design-build Other (specify): ____________________

Type of action.

New requirement Follow-on Other (specify): ______________________

Proposed contract/order type.

Firm-fixed-price Other fixed-price (specify, e.g., fixed-price award-fee, fixed-price incentive-fee): __________ Cost-plus-fixed-fee Other cost reimbursement (specify, e.g., cost-plus-award-fee, cost-plus-incentive-fee): ___________ Time and materials Indefinite delivery: Indefinite quantity Other (specify): ___________ Completion Form Term form

Acquisition identification number. RFP No: HHSN-NIH-NHLBI-

HG-12-20.

c. Total estimated dollar value and performance/delivery period.

The total estimated dollar value of this acquisition is $101,892,223 and the total period of performance is for five years from June 1, 2012 through May 31, 2017. This amount is for the maximum order or ceiling of an IDIQ task order contract. A cost reimbursement severable task order will be issued for Program Management (Task Area One), while multiple non-severable fixed price task order(s) (Task Area Two) will be used to fund a variety of genotyping projects over the five year period of performance for the participating member Institutes of the CIDR program.

4. Identification of the statutory authority permitting other than full and open competition.

This acquisition is conducted under the authority of 41 United

States Code (U.S.C.) 3304(a)(1) as set forth in Federal Acquisition Regulation (FAR) 6.302- 1 and HHSAR 306-302-1.

This acquisition is conducted under the authority of section 4202 of the Clinger-Cohen Act of 1996.

This acquisition is conducted under the authority of the Services

Acquisition Reform Act of 2003 (41 U.S.C. 428a).

5. Demonstration that the proposed contractor(s) unique qualifications or the nature of the acquisition requires use of the authority cited.

a. Name and address of the proposed contractor(s).

Johns Hopkins University School of Medicine 733 N. Broadway, Suite 117 Baltimore, MD 21205

b. Nature of the acquisition and proposed unique qualifications of the contractor(s).

JHU is the only contractor capable of providing a uniquely integrated service in the areas of study design, sample preparation, data collection, data cleaning, data interpretation, and data dissemination for CIDR program investigators. JHU’s uniquely integrated service was developed as a result of the long term collaboration with the NIH community when this program was developed. No other contractor is currently capable of providing all of these services as an integrated unit. The separation of these services into individual service components to be performed at separate institutions is not possible as this could compromise the integrity of the data if multiple transfers were required. For example, the statement of work under the contract requires, as mandated by NIH policy (see http://gwas.nih.gov/), the deposition of genome wide association (GWAS) data into a public data base, dbGAP, the National Library of Medicine’s data base of genotype and phenotype information. 100% of the studies performed under CIDR have been deposited into dbGAP due to JHU’s efficient work relationship with the dbGAP staff at the National Library of Medicine and the secure data submission process developed by JHU which includes a phenotypic (i.e., the traits or diseases under study) data certification step that is carried out prior to generating the genotype data (the testing of the DNA). JHU’s secure data connection to the National Library of Medicine would have to be duplicated and vetted if another contractor were to be selected. Switching contractors would endanger the CIDR’s ability to have GWAS data made available to other investigators in a timely fashion and make it difficult to fulfill the NIH data sharing mission “to foster science for the benefit of the public through the creation of a centralized NIH GWAS data repository.”

Commitments to the general scientific community to make CIDR services available are planned 9-24 months in advance of the actual service(s) being rendered. During the planning stage, many researchers around the United States submit grant applications to NIH, start research projects, begin gathering samples, and communicate with contractor staff in anticipation of having their samples genotyped at CIDR. This process produces an expectation that CIDR services would continuously be available when needed. Switching contractors would cause the Government to incur duplicate costs related to planning because previously initiated projects would need to repeat the initiation process under the new contractor. For example, each project initiation requires approximately 2.5 days time from a senior FTE. This person consults with the investigator and the CIDR Liaison from the member Institute funding the study. The current system that JHU uses to successfully manage these projects has been developed in collaboration with NHGRI staff and cannot be easily transitioned to another contractor. If a similar system were developed for a new contractor, it would consume many hours of time from NIH senior staff which would adversely impact their primary duties, i.e., managing reviews and project flow, and cause unacceptable technical delays to the CIDR program.

Projects that pass through the CIDR program are supported by extramural grants and intramural funds. These NIH funding mechanisms have pre-approved the collection of samples to be tested at CIDR. The process of granting access to CIDR during the peer review process is contingent upon the fact that the uninterrupted service will remain available to the general scientific research community. To assure that this commitment is realized and to avoid unacceptable delays to the program, it is essential that the contractor has both the technical expertise and well established collaborations with the participating CIDR member Institutes. It is the member Institutes that fund grants and programs and mandate CIDR as the genotyping service. JHU is the only contractor that has the technical expertise, established collaborations with the CIDR member Institutes, and the quality assurance, quality assessment and quality control measures to produce the data for genetic association studies required by the CIDR. Also, JHU has developed this technical pipeline via a decade of experience carrying out genetic disease research and the development of high throughput genotyping protocols. The JHU staff has the unique ability to produce genetic data for thousands of samples using CLIA (Clinical Laboratory Improvement Amendments (http://wwwn.cdc.gov/clia/regs/toc.aspx ) certified procedures. CLIA certification requires oversight from individuals that are Board Certified in human molecular genetics by the American Board of Medical Genetics.

Board Certification requires a minimum of 24 months of training and a passing grade on the Board Exams (~1/4 applicants fail the exam).

Having staff that are Board Certified may be common in low volume clinical laboratories but rare in the research labs, and simply not found in high throughput labs other than the CIDR lab under JHU. This certification allows NIH funded investigators to propose long term projects in which the clinical utility of genetic and genomics can be studied.

Should JHU be replaced, the grants awarded contingent upon the genotyping at CIDR would need to be re-evaluated by the Program Staff at the CIDR member Institutes and would result in the duplication of costs and unacceptable delays in fulfilling NIH’s requirements.

CIDR projects are completed under a two phase project design as approved by peer reviewers. Since several projects that pass through CIDR using the “SNP” process must be completed in phases, the continuity of quality control is critical to the scientific research community.

JHU’s specific quality control methods, unique ability to provide a variety of technical platforms, and their final data analysis procedures cannot be duplicated by another contractor. Should another contractor be used, the protocol for quality control will have to be recreated and approved by the peer reviewers before implementation. This would cause a major disruption in the program because procedures would need to be vetted by running the same samples through JHU’s process and the process offered by the new contractor. This duplication of effort would be prohibitively expensive and would result in unacceptable technical delays to the program.

JHU owns the Laboratory Information Management System (LIMS) which is used to control and document all processes carried out in the CIDR lab.

The LIMS includes a large number of custom software modules which are essential to the CIDR program. This system covers all aspects of the project and sample handling. The instrumentation that produces the data also generates measures related to signal intensity, values for internal standards and reproducibility. The LIMS system gathers these metrics from each of the instruments and attaches them to the sample data. This allows laboratory staff and the ultimate end users of the data to assess all of the manipulations that occur as the samples move through the process. In addition, the LIMS system records all information for each batch of sample. This provides the CIDR staff and the investigator with information for the overall project quality. Another important function of LIMS is the custom integrated data collection performed on each of its data producing and sample handling instruments which allows for the flagging of machine specific anomalies. These anomalies trigger the event reporting functions of the LIMS which prevents the production of substandard data. The LIMS has also been designed to record and provide data in cases where the instrument noise baselines drift over time. As multiple instruments are used in parallel, it is critical that they are capable of producing the same quality data. JHU is the only contractor that has access to the types of custom integrated data collected under LIMS over the last ten years which makes it uniquely capable of providing any custom data queries required by CIDR users.

The re-creation of a new LIMS system by another contractor will result in the duplication of costs, unacceptable delays to the program, and the loss of CIDR legacy knowledge.

The current CIDR program is extremely successful because JHU has been able to successfully integrate NIH equipment into its existing research infrastructure. For example, the current research space, some IT, and nearly all telecommunications infrastructure at JHU are compatible with the existing NIH equipment used for CIDR. If a similar infrastructure had to be recreated at a new contractor’s site, it is most likely that there would be equipment compatibility and infrastructure renovation issues that would result in the transition costs that are not expected to be recovered through competition and unacceptable technical delays in meeting CIDR’s research objectives. See item 9 for our conservative estimate of these transition costs.

6. Description of the efforts made to ensure that offers are solicited from as many potential sources as practicable. Indicate whether a FedBizOpps notice was or will be publicized as required by FAR Subpart 5.2 and, if not, which exception under FAR 5.202 applies.

Federal Business Opportunities (FedBizOps) small business sources sought and research and development sources sought synopses were posted on September 8, 2011 to determine if any small businesses or other than small businesses were capable to perform this work. No capability statements were received in response to the small business sources sought notice. However, three capability statements were received in response to the research and development sources sought synopsis: One from Expression Analysis, Inc. which is a small business under the designated NAICS 541712 code and two identical generic brochures from CD Genomics. The capability statements were assessed by a team of experts in accordance with the NIH Interim Guidance on the Justification for Other than Full and Open Competition (JOFOC) Process (July 2009). It was determined by the team of experts that each potential Offeror was not capable of fulfilling the requirement. A HHS Form 653 was submitted to the OSDBU and the OSDBU Small Business Specialist and SBA Procurement Center Representative concurred with the decision that the incumbent contractor is the only organization capable of performing the requirement. A pre-solicitation notice notifying the public of our intent to negotiate on a non-competitive, sole source basis was issued in FBO on October 6, 2011. Only one response was received from CD Genomics by October 20, 2011, the expiration date of the notice, which was identical to the two capability statements already previously received under the research and development sources sought synopsis. Since it was identical to their previous submissions, it was not necessary to review it again.

In accordance with FAR Part 10.002(b)(2)(i), another technique for conducting market research is “contacting knowledgeable individuals in Government and industry regarding market capabilities to meet requirements”. The PO contacted a number of scientific staff within NHGRI who are knowledgeable about the genomic industry to determine if there were other organizations besides JHU that could perform the required services. Market research was also conducted by reviewing information from other organizations on the Internet. This included numerous academic and commercial laboratories purported to offer genotyping services. Representatives from other OPDIVs, whose grantees have experience using some of these other sources, were also consulted. No other organization was found that could perform the entire range of services required under this contract. While there are other organizations who may be able to perform some of the required services, these services covered under this contract are uniquely integrated, which makes it unfeasible to have them performed by more than one organization. The integrity of the data would be compromised if the services were performed by more than one organization. In addition, market research determined that no other organization’s facilities were suitable for NIH’s needs because they either lacked flexibility or had chosen genotyping platforms that were less than adequate. For example, commercial genotyping technology facilities are “wedded” to their own proprietary platforms and would not be able to offer genotyping on platforms invented by their competitors (even if they were better, faster, and cheaper.) JHU has a proven track record of being able to objectively evaluate and adopt new technologies. No organization could be identified that could duplicate JHU’s specific methods, technical platforms and final data analysis procedures. Other large genotyping facilities run more on samples in-data out basis but lack the staffing and experience at the post-production genotyping phase and the ability to interact directly with individual investigators. These conclusions were also confirmed upon reviewing the 2 capabilities statements that were received in response to the sources sought announcement.

7. Determination by the Contracting Officer that the anticipated cost/price to the Government will be fair and reasonable. An independent government cost estimate (IGCE) has been developed using certified cost information obtained, in accordance with FAR 15.403, from the contractor during our recent negotiations to bring the current contract into fiscal compliance effective June 1, 2011. The IGCE and certified current cost and pricing data which will be obtained from the contractor during contract renewal negotiations shall be used to perform the cost analysis. In addition, a cost realism analysis will be performed to determine if the proposed costs are realistic and consistent with the scope of work. The cost analysis and the cost realism analysis will be used to document the pertinent issues to be negotiated and will establish our pre-negotiation objectives. Based on the above, the Contracting Officer will be able to negotiate fair and reasonable costs and an audit should not be necessary.

8. Description of the market research conducted (see FAR Part 10) and the results, or a statement of the reasons market research was not conducted.

A Federal Business Opportunities (FedBizOps) small business sources sought and research and development sources sought synopse were posted on September 8, 2011 to determine if any small businesses or other than small businesses were potentially available to perform this work. No capability statements were received in response to the small business sources sought notice. However, three capability statements were received in response to the research and development sources sought synopsis: One from Expression Analysis, Inc., a small business under the designated NAICS 541712 code, and two identical generic brochures from CD Genomics. Two capability statements, one from each organization, were assessed by a team of experts in accordance with the NIH Interim Guidance on the Justification for Other than Full and Open Competition (JOFOC) Process (July 2009). It was determined by the team of experts that the two potential Offerors were not capable of fulfilling the requirement.

9. Any other facts supporting the use of other than full and open competition.

a. Transfer of the work would result in substantial cost duplication that is not expected to be recovered through competition. (See attached duplication of cost estimate.) Further, transfer would result in unacceptable delays in accomplishing the Government’s goals for the program. It would also threaten the program’s ability to achieve its research objectives. It is therefore recommended that this acquisition be non-competitively negotiated with the existing contractor. The reasons for this recommendation are:

i. Transfer of the CIDR responsibilities to a new contractor would entail months to years of delay to recruit and train new staff. It would be impossible to duplicate the more than ten years of experience by the John Hopkins University in terms of understanding the contents of the data, knowing its possibilities and limitations, and applying statistical analyses to the data set.

This irreplaceable experience is at both the individual and organizational level. Study data would need to be thoroughly documented before transfer to a new contractor. A learning period of at least a year would be necessary before the new contractor could gain familiarity with software, hardware, and the data set to assume management of new data, and provide quality assurance and quality control measures. On-going data analyses and publication efforts would be interrupted. The continuity of projects that are being completed in phases would be disrupted.

The net result would be cost duplications and unacceptable delays, postponing the continued data collection activities, and slowing the pace of discovery.

ii. Data management and protocol adherence require close collaboration between the contractor and the Government.

Considerable delays resulting from the selection of a new contractor would contribute significantly to hidden costs in the areas of new staff training, data collection and maintenance, and reporting activities. Coordination and communication inefficiencies would further contribute to unacceptable project delays, negatively impact the execution of the biomedical research projects through disrupted data management, and significantly hamper the project investigator’s ability to publish their findings.

b. A second significant adverse outcome from moving to a new contractor would be the loss of the Government’s joint investment in equipment and computational infrastructure. The genotyping and sequencing pipelines are highly integrated so that all aspects of sample flow and testing can be monitored. There are two critical components of these systems that would be costly to replace:

i. The contract required the establishment of a Laboratory Information Management System (LIMS) to control and document all processes carried out in the lab. This LIMS includes a large number of custom software modules. This entire system would have to be recreated if a new contractor was selected. Retaining the current contractor will allow the government to leverage future advances using this established system.

ii. The equipment used to produce (laboratory equipment with an aggregate value of more than $8 million USD) and record (computers, servers and storage media) the data at CIDR are a mixture of components owned by the government and Johns Hopkins. Replacing the JHU equipment would be costly and this cost would not be recouped by moving to a new contractor.

In accordance with HHSAR 306.302-1(a)(2)(iv), the duplication of cost to the Government is estimated to be at least $1.9 M for the CIDR program. The estimated dollar value for the duplication of costs to the government was developed with the Project Officer. This conservative estimate equals ~56% of the total estimated cost in year one for Program Management (Task Area One) is not expected to be recovered through full and open competition, and is included as an attachment (Program Management Duplication for JOFOC). The Government’s estimate assumes a smooth transfer over a one year period to re-establish CIDR operations at a new site to a minimally acceptable level under a best case scenario. While this estimate is extremely conservative, it represents a substantial duplication of cost that is not expected to be recovered through competition.

10. Listing of sources, if any, that expressed, in writing, an interest in the acquisition.

Three capability statements were received in response to the research and development sources sought synopsis: One from Expression Analysis, Inc. which is a small business under the designated NAICS 541712 code and two identical generic brochures from CD Genomics. The capability statements were assessed by a team of experts in accordance with the NIH Interim Guidance on the Justification for Other than Full and Open Competition (JOFOC) Process (July 2009). It was determined by a team of experts that each potential Offeror was not capable of fulfilling the requirement.

11. Statement of the actions, if any, the agency may take to remove or overcome any barriers to competition before any subsequent acquisition for the required supplies or services.

A continued need for this service beyond the JOFOC period of performance is possible and will be re-evaluated near the end of the contract period. If deemed necessary, market research will be performed to determine if other sources are capable of performing the requirement.

12. Program Office Certification.

This is to certify that the portions of this justification that have been developed by the undersigned program office personnel, including supporting information and/or data verifying the Government’s minimum needs, schedule requirements and other rationale for other than full and open competition, are accurate and complete.

Official Name & Title Signature Date

Project Officer

Gloria Dunnigan, Inherited Disease Branch, NHGRI

Project Officer’s

Immediate Supervisor

Joan D. Bailey-Wilson, Ph.D., Inherited Disease Branch, NHGRI

Head of the Sponsoring

Program Office

Eric Green, M.D., Ph.D., Director of NHGRI

13. Contracting Officer Certification.

This is to certify that the justification for the proposed acquisition has been reviewed and that to the best of my knowledge and belief the information and/or data provided to support the rationale and recommendation for approval is accurate and complete.

Official Name & Title Signature Date

Contracting Officer

Lynn Furtaw, Contracting Officer, COAC Services Branch

OA, DERA, NHLBI

14. Chief of the Contracting Office and Head of the Contracting Activity signature(s).

Official Name & Title Signature Date

Chief of the Contracting

Office

John C. Taylor, Director, OA, DERA, NHLBI

Head of the Contracting

Activity

Diane Frasier, Director, OALM, OA, NIH

15. Competition Advocate signature.

Official Name & Title Signature Date

Competition Advocate

Walter Schaffer, Ph.D., NIH Competition Advocate for R&D

16. HHS Senior Procurement Executive signature.

Official Name & Title Signature Date

HHS Senior Procurement

Executive