Germline-RFP 36C10X24R0051_Final.docx

36C10X24R0051

1. REQUISITION NO.

2. CONTRACT NO.

3. AWARD/EFFECTIVE DATE

4. ORDER NO.

5. SOLICITATION NUMBER

6. SOLICITATION ISSUE DATE

a. NAME

b. TELEPHONE NO. (No Collect Calls)

8. OFFER DUE DATE/LOCAL

TIME

9. ISSUED BY

CODE

10. THIS ACQUISITION IS

UNRESTRICTED OR

SET ASIDE:

% FOR:

SMALL BUSINESS

HUBZONE SMALL

BUSINESS

SERVICE-DISABLED

VETERAN-OWNED

SMALL BUSINESS

WOMEN-OWNED SMALL BUSINESS

(WOSB) ELIGIBLE UNDER THE WOMEN-OWNED

SMALL BUSINESS PROGRAM

EDWOSB

8(A)

NAICS:

SIZE STANDARD:

11. DELIVERY FOR FOB DESTINA-

TION UNLESS BLOCK IS

MARKED

SEE SCHEDULE

12. DISCOUNT TERMS

13a. THIS CONTRACT IS A

RATED ORDER UNDER

DPAS (15 CFR 700)

13b. RATING

14. METHOD OF SOLICITATION

RFQ

IFB

RFP

15. DELIVER TO

CODE

16. ADMINISTERED BY

CODE

17a. CONTRACTOR/OFFEROR

CODE

FACILITY CODE

18a. PAYMENT WILL BE MADE BY

CODE

TELEPHONE NO.

UEI:

EFT:

PHONE:

FAX:

17b. CHECK IF REMITTANCE IS DIFFERENT AND PUT SUCH ADDRESS IN OFFER 18b. SUBMIT INVOICES TO ADDRESS SHOWN IN BLOCK 18a UNLESS BLOCK BELOW IS CHECKED

SEE ADDENDUM

19.

20.

21.

22.

23.

24.

ITEM NO.

SCHEDULE OF SUPPLIES/SERVICES

QUANTITY

UNIT

UNIT PRICE

AMOUNT

(Use Reverse and/or Attach Additional Sheets as Necessary)

25. ACCOUNTING AND APPROPRIATION DATA

26. TOTAL AWARD AMOUNT (For Govt. Use Only) 27a. SOLICITATION INCORPORATES BY REFERENCE FAR 52.212-1, 52.212-4. FAR 52.212-3 AND 52.212-5 ARE ATTACHED. ADDENDA

ARE

ARE NOT ATTACHED.

27b. CONTRACT/PURCHASE ORDER INCORPORATES BY REFERENCE FAR 52.212-4. FAR 52.212-5 IS ATTACHED. ADDENDA

ARE

ARE NOT ATTACHED

28. CONTRACTOR IS REQUIRED TO SIGN THIS DOCUMENT AND RETURN _______________

29. AWARD OF CONTRACT: REF. ___________________________________ OFFER

COPIES TO ISSUING OFFICE. CONTRACTOR AGREES TO FURNISH AND

DATED ________________________________. YOUR OFFER ON SOLICITATION

DELIVER ALL ITEMS SET FORTH OR OTHERWISE IDENTIFIED ABOVE AND ON ANY

(BLOCK 5), INCLUDING ANY ADDITIONS OR CHANGES WHICH ARE

ADDITIONAL SHEETS SUBJECT TO THE TERMS AND CONDITIONS SPECIFIED

SET FORTH HEREIN IS ACCEPTED AS TO ITEMS:

30a. SIGNATURE OF OFFEROR/CONTRACTOR 31a. UNITED STATES OF AMERICA (SIGNATURE OF CONTRACTING OFFICER) 30b. NAME AND TITLE OF SIGNER (TYPE OR PRINT) 30c. DATE SIGNED 31b. NAME OF CONTRACTING OFFICER (TYPE OR PRINT) 31c. DATE SIGNED

AUTHORIZED FOR LOCAL REPRODUCTION

(REV. NOV 2021)

PREVIOUS EDITION IS NOT USABLE

Prescribed by GSA - FAR (48 CFR) 53.212

7. FOR SOLICITATION

INFORMATION CALL:

STANDARD FORM 1449

SOLICITATION/CONTRACT/ORDER FOR COMMERCIAL PRODUCTS AND COMMERCIAL SERVICES

OFFEROR TO COMPLETE BLOCKS 12, 17, 23, 24, & 30

36C10X24R0051 8-2-2024 LaShawn Knight | lashawn.knight@va.gov

See Block 20

36C10X Strategic Acquisition Center - Frederick Department of Veterans Affairs

5202 Presidents Court, Suite 103 Frederick MD 21703

X

621511 $41.5 Million

N/A

VHA National Pharmacogenomics Program

36C10X Strategic Acquisition Center - Frederick Department of Veterans Affairs

5202 Presidents Court, Suite 103 Frederick MD 21703

TBD

VAFSC

U.S. Department of Veterans Affairs Financial Services Center

PO BOX 149971

(see Section B.3 invoicing/payment) Austin TX 78714-8917 1-(877)-489-6135

See CONTINUATION Page Veterans Health Administration (VHA) National Oncology Program-Germline / Pharmacogenomics Molecular Testing

Multiple Award Indefinite-Delivery Indefinite-Quantity (IDIQ) Contract

See Section E for all instructions associated with this Solicitation.

Important due dates/times:

1. Questions – August 09, 2024, at 12:00PM ET.

2. Bid Intentions – August 07, 2024, at 12:00PM ET.

3. Formal Response – August 23, 2024, at 12:00PM ET.

TBD

See CONTINUATION Page

Jacky Jean-Jacques Contracting Officer

Table of Contents

SECTION B - CONTINUATION OF SF 1449 BLOCKS

B.1 CONTRACT ADMINISTRATION

A. Contract Administration

All contract administration matters will be handled by the following individuals:

(1) CONTRACTOR POC: TBD

(2) GOVERNMENT: Jacky Jean-Jacques, Contracting Officer, 36C10X Strategic Acquisition Center - Frederick Department of Veterans Affairs 5202 Presidents Court, Suite 103 Frederick MD 21703

a. The Germline Pgx Molecular Testing (GPGxMT) multiple IDIQ CO is responsible for providing overall scope oversight, maintaining communication between contractors and VA, ensuring contract compliance, administering base contract and modifications. Each task order (TO) will have an identified CO who will be responsible for ensuring that task orders are within the scope of the IDIQ base contracts, administering all task order awards, overseeing payment or rejection of invoices, and ensuring that annual contractor performance evaluations are completed at the TO level and submitted through the Contractor Performance Assessment and Reporting System (CPARS).

b. The CO will designate a Contracting Officer’s Representative (COR) at the IDIQ contract level, and each TO level CO will designate a COR at the individual TO level. The CO will issue a designation letter to the COR and the contractor to ensure that all parties understand the limited authority, role, and responsibilities of the COR.

c. Any reporting requirements will be defined at the TO level.

B. Minimum Guaranteed Amount and Maximum Value

(1) The maximum aggregate value of all awards and TOs under GPGxMT is $99,032,828.20. This ceiling is neither divided nor multiplied by the number of awardees.

(2) The minimum guaranteed amount is $10,000.00.

C. Task Order Procedures

Contractors under VHA PGxMT shall provide services as requirements are identified throughout the ordering period. Fair opportunity under FAR 16.505 will be provided.

The Government anticipates award of an annual firm-fixed price TO that specifies details as they relate to deliverables, price, and other technical items.

(1) Each Task Order Proposal Request (TOPR) will include, at a minimum:

a. the due date and instructions for proposal submission,

b. the place and period of performance, and

c. any additional information deemed necessary by the CO.

(2) No formal evaluation plans are required. COs have wide latitude in developing and establishing the most appropriate evaluation factors given the nature of the TO. Factors, except for Price, may be assigned a confidence rating. In general, TOPRs will be evaluated by analysis of the following factors:

a. Technical Capability. The contractor will be asked to discuss their plan for accomplishing the work of the requirement. This factor may include subfactors such as a management plan, staffing plan, or key personnel.

b. Performance Risk. The contractor will be asked to provide examples of relevant experience and to provide past performance questionnaires which confirm a level of quality. The CO may consider relevant performance on task order awards under VHA GPGXMT and any other information available from Government sources.

c. Price. The Government will evaluate price reasonableness using price analysis techniques as prescribed in FAR 15.404-1(b).

d. Any1 other factors as determined appropriate by the CO.

(3) The task order proposals will be evaluated in accordance with the evaluation criteria as set forth in each TOPR. The CO is not required to prepare formal evaluation plans, post notice on the Federal Business Opportunities webpage or hold discussions/ negotiations with each offeror. The CO will, however, maintain an internal record of the award decision and supporting information. COs may evaluate by directly comparing competitive proposals and make an award decision based upon this comparison.

(4) In accordance with FAR 16.5, the CO has broad discretion in determining which contractor should receive a task order. The CO will issue a task order to the contractor whose proposal is most advantageous to the Government considering the evaluation factors specified in the TOPR. The CO reserves the right to withdraw or cancel the TOPR. In such event, the contractor will be notified, via email, of the CO’s decision.

(5) Upon TO award, the TO will be sent via email to the contractor. The contractor is not authorized at any time to commence TO performance prior to issuance of a signed TO or other written approval provided by a CO. The contractor’s failure to begin performance within the time frame required may result in termination of the task order and reconsideration of other proposals received in response to the TOPR.

(6) IAW with 16.505(b)(6). Contracting Officer SHALL notify unsuccessful awardees when the total price of a task or delivery order exceeds the established threshold.

(i) The procedures at 15.503(b)(1) shall be followed when providing post award notification to unsuccessful awardees. (iii) A summary of the debriefing shall be included in the task or delivery order file.

(7) Task orders may only be modified by written modification, executed by a warranted CO. The contractor shall not perform or provide services that are not expressly stated in the contract or TO. A Contracting Officer’s Representative (COR) does not have the authority or means to obligate the Government or change the terms and conditions of the contract or TO.

D. On-Ramp/ Off-Ramp

(1) On-Ramping The Government reserves the right to “on-ramp” additional contractors throughout the ordering period to ensure adequate competition. Should the Government exercise this right, a new solicitation with tailored requirements, terms, and conditions will be issued to the Government Point of Entry (GPE) at SAM.gov. New awardees will be added to the pool of GPGXMT IDIQ contractor holders for future TO competitions.

Contracts awarded via the “on-ramp” process will share in, but not increase, the previously established ceiling. The “on-ramping” process will not extend the ordering period.

“On-ramping” and “off-ramping” processes may occur independently and are not guaranteed as a result of the other. The decision to “on-ramp” and “off-ramp” is at the sole discretion of the Government. The Government anticipates three (3) “On-Ramp” periods during the life of the vehicle.

(2) Off-Ramping The Government may off-ramp contractors at any time during the contract period for performance issues, responsiveness, or eligibility at its discretion.

Contractor performance will be assessed/evaluated at the TO level and submitted through the CPARS. In the event of severe and/or multiple performance failures not remedied to the Government’s satisfaction, the Government reserves the right to off-ramp the contractor at no cost to the Government.

E. Invoicing

a. All payments by the Government to the contractor will be made in accordance with 52.232- 33, Payment by Electronic Funds Transfer – System for Award Management.

b. Specific invoicing instructions will be specified at the TO level.

F. Place of Performance

a. Contractor facility

G. Period of Performance

a. The IDIQ contract POP is through September 30, 2024, through September 29, 2029. Each TO shall specify the period of performance that will govern a particular task order awarded under the IDIQ contract.

36C10X24R0051 ********************END of B.1 IDIQ CONTRACT ADMINSTRATION DATA*************** Page 1 of

B.2 PERFORMANCE WORK STATEMENT

GERMLINE GENETIC TESTING SERVICES FOR

VETERANS HEALTH ADMINSTRATION NATIONAL ONOCOLOGY PROGRAM (NOP)

1.0 INTRODUCTION AND SCOPE

1.1 OVERVIEW

On behalf of the Department of Veterans Affairs (VA), the VHA National Oncology Program (NOP) intends to secure specialized, comprehensive reference laboratory germline genetic testing for Oncology and Medical Genetics and pharmacogenomic (PGx) testing. The contract will be administered through the VHA National Oncology Program.

The objective of this request is to ensure national access to germline genetic testing for Oncology and Medical Genetics and PGx testing for patients eligible to receive care throughout the VA enterprise in accordance with testing guidance established by the National Oncology Program (NOP), the National Genomic Medicine Program (GMP), and The National Pharmacogenomics Program (NPP).

The contractor shall provide all personnel, equipment, supplies, facilities, tools, materials, supervision, trainings and other items and services necessary, as defined in the Performance Work Statement (PWS), except for those items specified as government furnished property and services. The contractor shall perform to the standards in this contract and maintain compliance with policies and procedures with the Health Insurance Portability and Accountability Act (HIPAA), the Clinical Laboratory Improvement Act (CLIA), and accreditation with the American College of Medical Genetics and Genomics (ACMG) or the College of American Pathologists (CAP) or Joint Commission (JC) and maintain the relevant laboratory and personnel state licensure to offer testing across the United States and its territories.

1.2 SCOPE

The contractor’s laboratory shall have the ability to perform collection kit delivery, sample intake, processing, analysis, interpretation, reflex testing and reporting for one or more germline genetic test and PGx tests, as described herein. The Contractor must demonstrate capacity to service all VA Oncology, Medical Genetics and PGx practice sites (>170) including growth as additional Medical Centers and other practice sites needing testing services (in all 50 states and US territories).

These services require a CAP- or ACMG-accredited, CLIA-certified laboratory with the ability to perform complex genetic testing (as evidenced by staff board certification and current license). In addition, the contractor shall have a New York State licensure compliant laboratory or demonstrate the willingness to perform tests for Veterans Health Administration as a federal entity, regardless of any state requirements. Services require the ability to provide single gene testing as well as PGx gene panels including whole exomes and whole genomes curated by the laboratory that are updated regularly in accordance with national guidelines and with the ability to customize orders for the gene panels (e.g., add and remove genes from already curated panels). For germline testing, evaluation of variants of uncertain significance (VUS) through a variety of methods (e.g., RNA sequencing, family resolution studies) will be made available by the contractor’s laboratory with no additional billing if additional specimen is not needed (Ex: If RNA sequencing is needed, it would incur additional costs if initial testing was DNA). Appropriateness of VUS evaluation will be determined by the ordering provider in collaboration with the contractor laboratory. Reclassification of variants (e.g., VUS, likely pathogenic, likely benign) will be performed by the laboratory including upgrading and downgrading of the clinical significance of variants with notification to the ordering provider, associated VA laboratory and NOP to ensure all clinical and raw data collected both prospectively and retrospectively is up to date and consistent across delivery platforms. The VA would also like knowledge of and access to any future technology or recommended additions to the PGx panel as evidence arises. Time from initial report to reclassification as well as methods used for reclassification should be described in detail the proposal. Post award, the reclassification process may be subject to alterations that would be mutually agreed upon between the contractor and National Oncology Program (NOP) to meet NOP needs.

Testing must be supported by the contractor’s field team across the VA enterprise to ensure rapid sample processing turnaround times. Clinical results return must occur on a web portal but can also be delivered through use of various methods such as fax or other appropriate means, as a backup option. Contractor must have the ability and willingness to work towards test ordering and results return integration with VA Electronic Health Record (EHR) systems (currently VISTA CPRS (and in a future state with Cerner) through HL7 messaging, Application Programming Interface (API), Fast Healthcare Interoperability Resources (FHIR) or other technical interface capabilities. Finally, the Contractor shall return all raw and finished data generated as a result of testing (both clinical and Research Use Only (RUO)) to the National Oncology Program (NOP). Results return is typically via Amazon Web services. For Oncology tests, contractor must return un-used or residual blocks and/or slides to send out laboratories, and residual extracted materials back to the National Oncology program office lab.

1.3 GENERAL REQUIREMENTS

The National Oncology Program seeks to contract with germline genetic and PGx testing laboratories that can receive, process, and report results for the test types in diagnostic areas as described in the attached Genetic Test Requests document. Tests listed as mandatory shall be available through the contractor and access to most preferred tests is also expected. Since the genetic testing field is dynamic, when a new type of test or test methodology is released by the contractor laboratory that is relevant to the required clinical areas, the VA shall have access to that offering through a contract modification.

1.3.1 Germline Genetic Test offering for Oncology and Medical Genetics Germline genetic test offerings and expertise are mandatory for, but not limited to the following clinical areas: cancer, cardiovascular diseases, gastrointestinal disorders, neurological disorders, endocrinology and metabolic conditions, ophthalmologic disorders, renal disorders, allergy and immunologic disorders, autoimmune and rheumatologic disorders, connective tissue and skeletal disorders, birth defects, and preconception carrier screening. Preferred areas of test offerings and expertise include chromosomal disorders, non-invasive prenatal testing, mitochondrial disorders, and polygenic risk scores. The list of mandatory and preferred oncology and medical genetics tests are listed separately (see Genetic Tests Requests document).

1.3.2 Mandatory and preferred methodologies:

· Mandatory methodologies: DNA-based testing such as multi-gene panels, whole exome sequencing, whole genome sequencing, single gene assays, and single allele assays using next generation (massively parallel) sequencing, Sanger sequencing, or other methodologies with a description of the platform on which each test is performed.

· Preferred methodologies (include but are not limited to): NGS sequencing of DNA (whole exome, whole genome, single/multi-gene panels) and RNA, DNA/RNA microarrays, karyotyping, fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and other PCR-based methods.

1.3.3 Pharmacogenomic Test Offerings:

· A focused PGx panel is required that includes the following genes at a minimum to be included in the panel and clinical report:

· A preferred, comprehensive PGx that includes all mandatory genes listed above and in addition the following additional genes:

· PharmGKB Tier 1 and Tier 2 genes

· For each gene within a PGx panel, the list of reported alleles (including structural variants such as copy number variation) must comply with required standards according to Association for Molecular Pathologists (AMP) Tier 1 and Tier 2 alleles for those genes where AMP standards exists. For other genes where AMP guidelines are not available, the assay should be designed to capture all known functional alleles/haplotypes (defined by the Clinical Pharmacogenomics Implementation Consortium [CPIC] or equivalent alternative resource if CPIC function is unavailable) that have > 0.01% frequency in any one of the following ancestries: European, African American, Hispanic, or East Asian ancestries.

2.0 SUMMARY OF KEY DELIVERABLES

2.1 Testing

2.1.1 The Contractor shall offer the following testing methodologies (at minimum):

2.1.1.1 Molecular analyses including DNA-based tests such as next generation sequencing (NGS) for the required and preferred tests described in the Genetic Test Requests attachment.

2.1.1.2 NOTE: Contractor shall provide new type(s) of test content, interpretation, or methodology relevant to the required clinical areas, as the molecular testing field matures by mutual agreement between the contractor and VA.

2.1.2 Provide all mandatory tests and at least 75% of preferred tests within at least one of the three categories (Oncology, Medical Genetics, or Pharmacogenomics) as described in the Genetic Test Requests attachment. Gene lists for panels must comply with required genes according to ACMG, European Society of Molecular Oncology (ESMO) and other published standards for germline genetic testing. The proposal must include reference to how well contractor gene lists overlap with published standards.

2.1.3 Offer ordering provider created custom gene panels (ability to add/subtract genes from already curated panels) at no additional cost.

2.1.4 Have the ability to reflex to a larger panel of genes associated with phenotype at no additional cost when no additional specimen is needed.

2.1.5 Offer STAT testing with expedited turnaround times when needed.

2.1.6 Provide site specific mutation testing utilizing a previous family member’s test.

2.1.7 Provide evidence of current CAP/CLIA accreditation with certificates.

2.1.8 Offer testing and interpretation on site or at wholly own subsidiaries.

2.2 Portal

2.2.1 Conduct an evaluation of online portal with NOP leadership to identify needed enhancements within 30 days of contract award.

2.2.2 Complete any required modifications to the Vendor Portal to ensure all required fields as outlined in this RFP are captured within 105 days of contract award. This includes testing, validation and demo of updated portal modifications and new features.

2.2.3 Provide user friendly ordering fields and an online portal customizable to VA’s needs as described in the PWS (including tracking of sample status from placement of an order to a clinical report being issued and returned to the provider and ability to limit ordering of test types to those within the scope of contract).

2.2.4 The portal must include tiered access controls and ability to control user access by VA station, individual or national settings and offer “view only” options for support staff. Contractor must also have the ability to capture and provide audit logs of portal use when requested related to access patterns for individual users or sites. Portal must also have the ability to limit access to only VA users with a va.gov address only and de-activate access when notified by NOP that users no longer have an active VA affiliation.

2.3 Lab

2.3.1 Provide documentation addressing how the testing facility, processes and methodologies meet the requirements described in the PWS.

2.3.2 Perform sample collection kit delivery with associated supplies and return shipping materials, sample intake, processing, analysis, interpretation, and clinical reporting for all tests, as described in this PWS.

2.3.3 Provide evidence of:

2.3.3.1 CAP or TJC accredited, CLIA-certified Laboratory

2.3.3.2 NYS state licensure compliant laboratory, or acknowledge willingness to provide services to VA facilities in the State of NY

2.3.3.3 Laboratory with the ability to perform complex molecular testing (as evidenced by staff board certification and current laboratory licenses).

2.3.4 Provide documentation addressing how the testing facility is capable of handling volumes of 10,000 – 20,000 specimens processed annually for the VA.

2.3.5 Offer testing and interpretation on site or at wholly own subsidiaries meeting licensure requirements as described in the PWS.

2.3.6 Provide evidence of appropriate Medical Director qualifications outlined in a resume/CV.

2.3.7 Ensure any residual tissue can be sent to VA practice sites and all residual nucleic acids (DNA or RNA) are returned to the National Oncology Program Office Laboratory.

2.3.8 Deliver residual materials return manifest template within 105 days of contract award.

2.4 Specimen Transport and Laboratory Test Request Form Requirements

2.4.1 Patient data: The contractor is required to facilitate the transport of specimens by providing customized laboratory test request forms. These forms must include the information required by the VA. Please refer to the list below for the specific details that must be included. It is mandatory that these ordering forms are made available in both paper-based (pdf) and online formats. Ordering provider information (Name, address, NPI)

Patient information: Full name | date of birth | social security number/MRN or second identifier and EDIPI(when applicable) | sex (biological) | gender | test(s) to be performed | specimen collection date/time | specimen type | VA Station Name (patent and provider) | VAStation ID (patient and provider) |diagnosis | ICD-10 code (if, applicable)

2.4.2 Collection and Handling Instructions:

Special instructions for collection and handling of specimen including media for fibroblast culture. Description of specimen types that can be accepted for each test. Specimen collection supplies for specialized testing. Mailing account number to cover the costs of shipping within the US. Contractor shall cover sample shipping costs and will not restrict shipping/receiving days or dates. The Government is not responsible for these costs, nor can they be billed to the Government.

2.4.3 Maintenance and Notification of Point of Contact (POC) and Shipping Information Changes:

Maintain up to date POCs and shipping information and timely notification to all NOP staff and VA portal users of any changes in specimen delivery processes/information.

2.5 Laboratory Operations and Service Requirement

2.5.1 Sample tracking and management (e.g., utilizing bar coding) to ensure security and traceability of VA samples in accordance with good laboratory practices.

2.5.2 Analyze samples and report within a specified, expected turn-around time (TAT). Any test that has a longer TAT than 3 weeks should be explained in the proposal.

2.5.3 Ability to order STAT testing in special cases, with sample analysis completed no later than 1 week. Please indicate per panel or assay the TAT when STAT is ordered.

2.5.4 Overall order status tracking to allow for tracking orders from the time they are placed to completed. This will also include tracking for failed orders and in those instances provide reason for failure (ex: tissue insufficient). NOP must also have the ability to cancel orders programmatically at any stage in the ordering process up until the time the sample has been received by the contractor.

2.5.5 The Contractor must demonstrate capacity to service all VA Medical Centers (approximately 170) in all 50 states (including Hawaii and Alaska) as well as US territories (including but not limited to Puerto Rico and Guam) and have a mechanism to identify tests requested specifically under this contract across VA facilities.

2.5.6 Contractor shall assume all packing and shipping costs. This includes the cost of shipment of kits to VA Medical Centers, samples from the VA Medical Centers to the Contractor as well as shipment of residual nucleic acids to NOP designated central laboratory or designee. This includes all 50 states (including Hawaii and Alaska) as well as US territories (including Puerto Rico and Guam).

2.5.7 Provide an excel sheet shared via secure email containing patient and rest level reconciliations for tests run and resulted that month. This will be broken out into up to 3 categories: 1.) Medical Genetics, 2.) Oncology 3.) Pharmacogenomics. This Pre-invoice excel shall delineate all testing reported within the specified month and shall include the following information:

· Indication

· Quantity

· Amount

· Submit approved invoice once pre-invoice reconciliation process completed in VA within a month of service completion.

2.5.8 Provide access to a local account representative (e.g., a genetic counselor, pharmacist or other genetic or laboratory professional) for provider consultation regarding test results for VA genetics teams and interpretation by telephone and email, as needed, during regular business hours. Contractor is not expected to interact with or support direct genetic counseling or consultation for VA patients. Field team is also expected to handle issues related to sample acquisition to ensure rapid turnaround times.

2.5.9 A variant evaluation/interpretation program, for:

2.5.9.1 Oncology and Medical Genetics requirements:

At a minimum, the program conforms to ACMG Standards and guidelines for the interpretation of sequence variants. Such a program should include a periodic refresh of variant interpretations in light of new evidence that may increase or decrease the clinical significance of variants. The refresh shall result in an updated clinical report and updated structured data and a workflow to notify NOP Staff (prior to implementation) and ordering providers in real time of the change via the online results portal and email notification. Use of the variant interpretation program will apply to all retrospective and prospective data collected under this contract. A variant resolution program for germline testing that includes family studies (i.e., provides for testing of family members whose results may help inform variant reclassification) or functional studies (e.g., RNAseq).

2.5.9.2 Pharmacogenomic Testing:

The pharmacogenomics testing process is designed to conform to the recommendations set forth by the Pharmacogene Variation Consortium (PharmVar) and Clinical Pharmacogenomics Implementation Consortium (CPIC) recommendations for annotating variants and assigning gene phenotypes, respectively. In addition, the interpretation program should provide therapeutic recommendations in terms of medication dosing/alternatives should be based on CPIC, Dutch Pharmacogenomics Working Group (DPWG), and/or Food and Drug Administration (FDA) package insert. The reference source (e.g, CPIC) should be transparent on the clinical report so that providers are aware of which knowledgebases were used to translate genotypes to phenotypes to therapeutic recommendations. Such a program shall include a timely refresh of variant interpretations considering new evidence that may increase or decrease the clinical significance of variants, their impact on gene function, and medication recommendations. In addition, within 90-days of updated CPIC, DPWG, or FDA changes made publicly available, the vendor shall update its interpretation program to reflect these changes in both newly issued reports as well as updating historical results. The refresh of historical data shall result in an updated clinical report and updated raw data and a workflow to notify NOP Staff and ordering providers or relevant VA staff of the change via the online results portal and email notification.

2.5.10 A proficiency testing program. The VA reserves the right to request the results of any proficiency testing to which the contractor subscribes.

2.6 Processes and Procedures:

2.6.1 The Contractor Laboratory shall have the following processes and procedures in place:

2.6.1.1 Ensure testing is completed at the prime Contractor’s facilities, to include wholly owned subsidiaries. Special exception can be made for fibroblast cultures if that work is done by a second party contactor. If so, please state as such and include details of that contractor in the proposal. Ensure that samples are not further transported to any other facility for testing, nor interpreted by any other personnel than the prime contractor employed, medical directors, laboratory or medical geneticists, or molecular pathologist. These professionals must be employees of the Contractor’s facility or wholly owned subsidiary and be available at the site to remedy quality concerns and testing challenges.

2.6.1.2 Accept and store the National Provider Identifier (NPI) for ordering providers. All are licensed healthcare providers in the VA, including genetic counselors, nurse practitioners, pharmacists, and physicians.

2.6.1.3 Accept orders without requiring additional signed consent from patients beyond a provider’s attestation on the test requisition form.

2.6.1.4 Provide a list of tests currently available with a price list.

2.6.1.5 Provide a secure online, user-friendly ordering portal, and the need for a VA-specific portal to support this contract, demonstrated to NPP within 30 days of contact award (ideally during contract kickoff meeting). If during the demo it is determined that the existing contractor portal does not meet NPP specific needs (as outlined in this PWS), contractor will make, test, validate and demo all needed modifications to the portal within 105 days of contract award. During this period, VA will allow use of existing, online portals provided by the vendor so long as 1) they are allowable for use by VA providers using their VA credentials to order tests for VA patients and 2) provided that all reporting and invoicing requirements herein are adhered to.

2.6.1.6. Customized VA NOP portal must include:

· Tests searchable by test or panel name and/or gene (s) included in the panel.

· Full list of genes for each panel must be listed online.

· Portal should allow for creation of customizable gene panels.

· Portal should automatically alert ordering providers and relevant VA staff when test results are available via email or other electronic means.

· Portal test ordering fields must be customizable for VA’s needs and organizational structure, allowing for providers to place orders and review results at multiple sites, VISN level or nationally as needed. The portal must have the ability to track sample status from placement of an order to a clinical report being issued and returned to the provider. The portal should also allow customization for which fields/tests are viewable by specific ordering provider types.

· The portal must allow for a results search feature to query patients by patient identifiers, panel, disease, gene, and variant and by provider or facility.

· The portal must allow for user-friendly download of report PDFs individually or in batches and search queries described above.

· The portal must include access controls that allow NOP system wide access to all VA orders under the contract. Ability to control user access by VA station or at the level of the individual provider is also required. Vendor must also have the ability to capture and provide audit logs when requested related to access patterns for individual users or sites.

· The portal must have the ability to filter orders by provider and VA site.

· The portal must have the ability to flag clinical reports with positive results.

· The portal must have the ability to indicate if a previous clinical report has been updated from when it was first issued to ease review for providers assessing impact of report updates to patient care.

· The portal must have the ability to store care team information so results can be shared with appropriate individuals.

2.6.1.7 Work with NOP for portal account set up only with approved providers as identified by NOP.

2.6.1.8 Perform testing on VA patient specimens for the tests requested using clinically validated tests. The Contractor shall bill only for the tests specified in the request sent by VA medical centers and ordered by authorized providers.

2.6.1.9 Provide a reference test manual and report of test results, upon award, describing the full scope of its laboratory operations.

2.6.1.10 Provide individual VA facilities and their respective outpatient clinics with any specimen collection tubes, supplies, or kits required for testing that are not routinely available in standard clinical laboratories (e.g., blood collection tubes with specialized preservatives other than EDTA, citrate, or heparin; saliva or buccal swab collection devices; or media/containers for fibroblast culture, etc.). In addition, postage paid transport shipping kits will be required. These supplies are to be used by VA laboratories only in connection with specimens being sent for testing to the contractor. Access to a mobile phlebotomy service is preferred. Saliva collection requirements are discussed below.

2.6.1.11 Carry out its functions hereunder in full compliance with all local, state, and federal laws or regulations. Provide test report electronically or by fax in an encrypted fashion compliant with HIPAA requirements. Preferred ability to offer cascade testing for family members up to 180 days after initial test resulted when there is a positive pathogenic variant.

2.6.1.12 Ability to send raw molecular data files (e.g., FASTQ, BAM, BAI and VCF files) as well as final reported data files in a structured data format (e.g., report json, xml, csv, txt) is required within 3 months of contract award. This includes filtered and unfiltered BAM files when applicable depending on assay technology, Contractor must have the ability to securely perform cloud-based transfer of these files electronically to VA on a weekly basis at a minimum (daily preferred). Contractor to provide technical files describing the format and size of each file, including genomic annotation (e.g., BED) files. Data storage location and transfer mechanisms must comply with VA’s IT security and privacy requirements that are based on NIST standards.

2.6.1.13 Ability to interface with the VA laboratory information system to facilitate test ordering and reporting is required within 9 months of contract award. This could include Vista CPRS and Cerner Millennium). This requirement is in addition to, not in lieu of, the “Reporting of Test Results” and “Reporting of Clinical Structured Data and Raw Data” requirements listed below.

2.6.1.14 Provide a point of contact including names and telephone number(s) to make inquiries on weekdays. Laboratory Directors, technicians, and other laboratory personnel must be made available for consultation.

2.6.1.15 Immediate (within 24 hours) notification must be given to VA upon adverse action by a regulatory agency.

2.6.1.16 Ensure compliance with the Cures Act, and that germline genetic test results are not released to anyone other than the ordering healthcare provider, staff/clinical team associated with the order, or NOP staff, or designees of NOP for contract management, quality improvement, IRB-approved research, or other indications. The only exception to release of results is for select VA staff in charge of oversight as identified by NOP. Prior to release to a VA oversight unit, (VA OIG, VA OIT, etc.), permission must be granted from NOP. All records shall be treated as confidential, to comply with all state and federal laws regarding the confidentiality of patient’s records. This provision shall survive termination of the resulting contract award.

2.6.1.17 Certify and ensure that all laboratory employees, officers, or agents comply with standards set forth in the Health Insurance Portability and Accountability Act (HIPAA). The contractor must provide evidence of staff HIPAA training compliance.

2.6.1.18 Provide at least weekly summary reports that provide information to the VA regarding test orders, order status, sample status and results at the test level. Summary reports must provide an in-process test summary, broken down by test type and at the test level indicating the stage each sample is at in the testing process (e.g., analysis started, sample not received etc.) in addition to an aggregate count of how many samples are in each stage of that process. The report shall also include an indication of whether orders are via the online portal or a paper-based mechanism. Tests on hold due to the sample not being received should be highlighted with an indication of how many days have elapsed since the order was received. For reported samples, the summary should also indicate the turnaround time for each sample and whether that aligns with contracted expectations.

2.6.1.19 30 days after the close of each period of performance the contractor shall prepare monthly reports that provide information to the VA regarding genetic test orders and results at the patient and test level. Monthly reports should include a single month’s data for all completed testing (both raw and summary level) Reporting requirements for both weekly and monthly data include but are not limited to:

· Patient first and last name

· Patient MRN or SS#

· Patient Date of Birth

· Vendor assigned Requisition Number

· Vendor Billing / Account code75

· Patient VA facility name and station number

· Medical record number

· Ordering provider name and NPI

· Specimen type

· Date of specimen collection

· Date of test result report

· Order status and associated dates with current order status indicated.

· Test name

· Indication of reflex testing (when applicable),

· Procedure/test type

· Genes names included in panel and associated CPT codes

· IDC-10 codes

· Diagnosis

· Stage (for patients with cancer)

· Report release date

· Summary of results (weekly)

2.6.1.20 Monthly reports will expand on above to include a structured breakdown of results from the validated clinical report (to be discussed more upon award to span all eligible test types covered in this contract).

2.6.1.21 Weekly reports shall be available no later than 3 business days after the end of the week. Monthly reports shall be available within 15 calendar days after the end of each month. These reports should be submitted in Microsoft Excel or similar format.

2.6.1.22 Updates to a patient's prior test results should be appropriately flagged in this report to allow distinction between the original and updated interpretations or corrections to patient identifiers, for example, and include date update made.2.3.1.23. For Pharmacogenomics testing daily reports are needed and should only include additions or modifications (I.e., new data) that had not previously been reported.

2.6.1.23 Prepare an annual report (due 30 calendar days after the close of each year of performance) that summarizes germline genetic test utilization and costs overall and by ordering provider and VA facility.

2.6.1.24 NOP will generate and provide the contractor with regular lists of approved providers who can then place orders upon contract award. Contractor will only grant account access to individuals identified by the program office. NOP will oversee development and communication on guidelines outlining when testing is appropriate for ordering oncology tests per evidence-based guidelines (when applicable for the test). Weekly reports from the contracted laboratory as outlined above are required to facilitate an auditing of both providers and test types to ensure:

1) only NOP approved providers place orders and

2) that tests ordered follow the NOP programmatic guidelines for patient eligibility. This will be performed by NOP staff or NOP designated VA employees again to ensure specified providers are ordering testing according to evidence-based guidelines or best practices, as outlined by the National Oncology Program (NOP), Genomic Medicine Program, or National Pharmacogenomics Programs.

2.7 Test Sample Preparation

VA laboratories shall be responsible to provide laboratory specimens prepared in accordance with the contractor’s Laboratory User’s Manual. All specimens will be properly identified and labeled for testing to include at least two identifiers (e.g., patient full name, medical record number, date of birth). The contractor shall provide an adequate supply of requisition forms, special instructions, and a current list of tests with specimen requirements. These requirements shall be defined in the laboratory user’s manual.

2.8 Transport of Specimens

The contractor laboratory client services will provide a mailing account number to send specimens directly to the contractor’s laboratory. The contractor will also send blood collection kits to the local VA labs if/when needed. The contractor laboratory must have the ability to send saliva kits and/or buccal swab kits directly to a patient’s home and provide packaging/mailing supplies as well as postage for the patient to send a specimen directly back to the contractor laboratory, or to the local VA facility who will collect the specimen.

The contractor laboratory must also have the ability to send fibroblast culture media along with appropriate shipping materials needed for assay. As this is not a common procedure, the Government will allow this to be subcontracted out, but would need details of this workflow and subcontractor to be indicated as such in the proposal. Additionally, subcontractors are also required to meet compliance and security requirements as laid out in the RFP. The contractor laboratory will not use patient address for any other purpose beyond mailing specimen collection supplies, if requested by VA. Access to a mobile phlebotomy service is preferred.

The regulations governing the packaging and shipment of biological, infectious, and hazardous substances are primarily found in 49 CFR parts 100-185 and 397. The parts of 49 CFR specifically dealing with biological and infectious specimens are 107, 171, 172, and 173. While the majority of shipments packaged and processed by the clinical laboratories are classified as diagnostic specimens, all specimens, as well as any select agents and toxins that are identified, must be packed and shipped in accordance with the applicable guidance provided in 49 CFR. Contractor or Subcontractors that package, transport, or ship biological, infectious, and hazardous substances shall comply with all laws, regulations, and policies of Federal, State, and Local governments, the Centers for Disease Control (CDC), Department of Transportation (DOT), International Air Transport Association (IATA), and the Department of Veterans Affairs.

2.9 Reporting of Test Results

A clinical report is defined as a printed final copy of a genetic test result interpreted by individuals with training in genetics and signed out by a AMGG board-certified geneticist or molecular genetic pathologist. Consult reports shall be sent by contractor electronically or by fax to the ordering provider, VA laboratory and made available to NOP staff in batch for all orders placed under this contract. Each clinical report shall, at a minimum, indicate the following information:

· Patient’s full name

· Patient’s date of birth

· Patient’s unique medical record number

· Patient’s VA Station and Station ID

· Ordering provider’s name

· Ordering provider’s NPI

· Purchase order/ billing/ account number

· Test(s) ordered, including list of genes analyzed

· Date/time of specimen collection (when available)

· Date/time specimen received in Reference Lab

· Date test signed and reported

· Type of specimen/source

· Test result(s)

· Flag abnormal results

· Comments on interpretation for variants of uncertain significance, likely pathogenic, and pathogenic results, which may include but are not limited to: Clinical summary, comments on familial testing, variant effect on protein, ClinVar entries, in silico models, experimental studies, reference to population databases.

· Flag and date for any associated amendments

· Methodology used and limitations of listed methodology

· Name of testing laboratory (contractor and/or wholly owned subsidiary), address, CLIA number

· Testing laboratory…