36C24821Q1573 0001.docx

5. PROJECT NUMBER (if applicable)

CODE

7.

ADMINISTERED BY

2. AMENDMENT/MODIFICATION NUMBER

CODE

6. ISSUED BY

8. NAME AND ADDRESS OF CONTRACTOR

4. REQUISITION/PURCHASE REQ. NUMBER

3. EFFECTIVE DATE

9A. AMENDMENT OF SOLICITATION NUMBER

9B. DATED

PAGE OF

PAGES

10A. MODIFICATION OF CONTRACT/ORDER NUMBER

10B. DATED

BPA NO.

1. CONTRACT ID CODE

FACILITY CODE

CODE

Offers must acknowledge receipt of this amendment prior to the hour and date specified in the solicitation or as amended, by one of the following methods:

The above numbered solicitation is amended as set forth in Item 14. The hour and date specified for receipt of Offers

E. IMPORTANT:

is extended,

(a) By completing Items 8 and 15, and returning __________ copies of the amendment; (b) By acknowledging receipt of this amendment on each copy of the offer submitted; or (c) By separate letter or electronic communication which includes a reference to the solicitation and amendment numbers. FAILURE

OF YOUR

ACKNOWLEDGMENT TO BE RECEIVED AT THE PLACE DESIGNATED FOR THE RECEIPT OF OFFERS PRIOR TO THE HOUR AND DATE SPECIFIED MAY is not extended.

12. ACCOUNTING AND APPROPRIATION DATA

(REV. 11/2016)

is required to sign this document and return ___________ copies to the issuing office.

is not, A. THIS CHANGE ORDER IS ISSUED PURSUANT TO:

Specify authority) THE CHANGES SET FORTH IN ITEM 14 ARE MADE IN THE CONTRACT ORDER NO. IN ITEM 10A.

15C. DATE SIGNED

B. THE ABOVE NUMBERE

D CONTRACT/ORDER IS MODIFIED TO REFLECT THE ADMINISTRATIVE CHANGES

SET FORTH IN ITEM 14, PURSUANT TO THE AUTHORITY OF FAR 43.103(b).

RESULT IN REJECTION OF YOUR

OFFER. If by virtue of this amendment you desire to change an offer already submitted, such change may be made by letter or electronic communication, provided each letter or electronic communication makes reference to the solicitation and this amendmen t, and is received prior to the opening hour and date specified.

C. THIS SUPPLEMENTAL AGREEMENT IS ENTERED INTO PURSUANT TO AUTHORITY OF:

D. OTHER

Contractor

16C. DATE SIGNED

14. DESCRIPTION OF AMENDMENT/MODIFICATION

16B. UNITED

STATES OF AMERICA

Except as provided herein, all terms and conditions of the document referenced in Item 9A or 10A, as heretofore changed, remains unchanged and in full force and effect.

15A. NAME AND TITLE OF SIGNER

16A. NAME AND TITLE OF

CONTRACTING OFFICER

15B. CONTRACTOR/OFFEROR

STANDARD FORM 30

PREVIOUS EDITION NOT USABLE

Prescribed by GSA - FAR (48 CFR) 53.243 (Type or print) (Type or print) (Organized by UCF section headings, including solicitation/contract subject matter where feasible.)

(Number, street, county, State and ZIP Code) (If other than Item 6) (Specify type of modification and authority) (such as changes in paying office, appropriation date, etc.)

(If required)

(SEE ITEM 11)

(SEE ITEM 13)

(X)

CHECK

ONE

13. THIS ITEM APPLIES ONLY TO MODIFICATIONS OF CONTRACTS/ORDERS,

IT MODIFIES THE CONTRACT/ORDER NO. AS DESCRIBED IN ITEM 14.

11. THIS ITEM ONLY APPLIES TO AMENDMENTS OF

SOLICITATIONS

AMENDMENT OF SOLICITATION/MODIFICATION OF CONTRACT

(Signature of person authorized to sign) (Signature of Contracting Officer) None 36C248 Department of Veterans Affairs Network Contracting Office 8 (NCO 8) Orlando VA Healthcare System 13800 Veterans Way Orlando FL 32827 36C248 Department of Veterans Affairs Network Contracting Office 8 (NCO 8) Orlando VA Healthcare System 13800 Veterans Way Orlando FL 32827 To all Offerors/Bidders

36C24821Q1573 09-02-2021

X X X

See CONTINUATION Page X The purpose of this Amendment 0001 is to:

1) Include edits to SOW Section 3. Requirement section.

2) Include edits to CLINs 0001, 0002, 0003, 0004 descriptions.

3) Include "Estimated" Quantity to B.2 Price/Cost Schedule.

CONTINUATION PAGE

A.1 PRICE/COST SCHEDULE

ITEM INFORMATION

ESTIMATED

QUANTITY

POLYMERASE CHAIN REACTION (PCR) , NEXT GENETIC SEQUENCING (NGS) EQUIPMENT ARRAY EQUIPMENT, SERVICE AND REAGENTS Solid Tumor Testing: Equipment, software, licenses, reagents, consumables, service , validations, and training Cost per Test for a reportable result.

PRINCIPAL NAICS CODE: 325413 - In-Vitro Diagnostic Substance Manufacturing PRODUCT/SERVICE CODE: 6515 - Medical and Surgical Instruments, Equipment, and Supplies LOCAL STOCK NUMBER: None

Hematology Cancer Testing: Equipment, software, licenses, reagents, consumables, service , validations, and training Cost per Test for a reportable result .

PRINCIPAL NAICS CODE: 325413 - In-Vitro Diagnostic Substance Manufacturing

Pharmacogenomic Testing: Equipment, software, licenses, reagents, consumables, service , validations, and training Cost per Test for a reportable result.

Ancillary Equipment: Equipment, software, licenses, reagents, consumables, service , validations, and training Cost per Test for a reportable result.

STATEMENT OF WORK

PCR, NEXT GEN SEQUENCING AND ARRAY EQUIPMENT AND REAGENTS

COST PER TEST

Orlando VA Healthcare System, Orlando, FL

PATHOLOGY AND LABORATORY

1. PURPOSE

Department of Veterans Affairs, Orlando Veterans Affairs Healthcare System (OVAHCS) has a requirement to establish a Cost Per Test (CPT) contract to implement Polymerase Chain Reaction (PCR) and Next Generation Sequencing (NGS) testing and Pharmacogenomic testing. The OVAHCS Pathology and Laboratory Medicine Service (PLMS) has been tasked with implement Cancer Precision (Personalized) Medicine testing for genetic tumor profiling. This state-of-the art technology shall allow the detection of mutant genes involved in cancer by PCR and NGS testing that will assist providers in selecting targeted therapy that is more likely to help the veterans based on the genetic understanding of their disease.

2. SCOPE

The OVAHCS requires a Fixed Cost Requirements contract for the testing of Polymerase Chain Reaction (PCR) and Next Generation Sequencing (NGS) testing and Pharmacogenomic testing.

To perform these studies, the OVAHCS will need to acquire specialized testing equipment, reagents and consumables needed to analyze specimens such as biopsies or excision of soli organs, blood and bone marrow. DNA or RNA genetic material is extracted from these samples, amplified by specialized PCR methodology, electrophoresed, purified, and fragmented in preparation for NGS testing in analyzer instruments. Similarly extracted DNA or RNA material and prepared for analysis on array-based scanner for Pharmacogenomics studies (PGx) that will enhance the efficacy and reduce to abolish drug adverse events in veterans with commonly prescribed medications.

All work shall be performed in accordance with the guidelines established by Federal, State, and local ordinances, with the Federal Drug Administration (FDA) and manufacturer’s guidelines and with all terms, conditions, provisions, schedules, and specifications provided herein.

3. REQUIREMENT

The contractor shall provide the following material:

Two Next Generation Sequencing analyzers are required:

1) The first sequencer will be utilized mostly for solid organ (lung, breast, colon, etc.) cancer testing requiring large gene panel kits. This system must be open, flexible and highly scalable, capable of handling different throughput levels. The scalability of this platform must be upgradable to handle exome or whole genome sequencing as the future needs and testing volume of the lab increases. Sequencer must be highly accurate utilizing industry proven technology and chemistry that minimizes phasing errors. To further clarify, the chemistry to be utilized must be able to perform both single and paired end reads to avoid homopolymer errors. Accuracy score Q30 must exceed 75%. Amplification must be fully automated and allow cluster generation. This sequencer must be able to run cytogenetic and methylation arrays for future use. The reagent gene panel assay kit to be utilized on this instrument must be compatible with this sequencer and its content must be comprehensive and large enough to include solid tumor biomarkers encompassing at least 1 Mb of coding genome (over 500 genes), including HLA and TMB biomarkers in addition to MSI, small variants, splice variants and fusion genes. To further clarify, this sequencer must be able to run in vitro diagnostics (IVD) and research only use (RUO) content from both the manufacturer and other partners IVD menu. This allows flexibility and versatility in the utilization of reagent gene panels for future use or upgrades. This is better achieved on an IVD-cleared sequencer. The reagent panel must capture fusions and translocations from RNA, including both known and novel fusions. To further clarify, the technology employed for fusion detection should be able to characterize the identity of the unknown (novel) fusion partners, should yield good results with both optimal and degraded samples, must not limit the ability to call novel fusions and must not require additional confirmatory testing such as FISH. Specimen compatibility included fresh and formalin-fixed paraffin-embedded (FFPE) samples. Turn-around-times to complete this assay on this instrument must be no more than 5 days. The manufacturer of this sequencer must offer sign out service for ease of reporting of results in a true clinical (and not an RUO) report with constant update on curation database. This service should also be able to offer input on validation and review of cases.

2) The second sequencer must be FDA approved or pending approval for invitro diagnostic workflows with a smaller footprint, to be utilized mainly for hematological (lymph nodes, blood, bone marrow, etc.) cancer testing including both small or large gene panel kits. The sequencer must be an open and flexible system that is highly scalable, utilizing Amplicon and targeted DNA sequencing methodologies. Sequencer must be highly accurate with industry proven chemistry that minimizes phasing errors and a Q-score of at least 75%. Sequencer must integrate clonal amplification, sequencing, and data analysis all into one instrument, and be small enough to fit as a desktop. The reagent gene panel assay kit must be compatible with that instrument and its content comprehensive enough to detect at least 75 key genes and somatic variants involved in myeloid malignancies. Sequencer must be suitable to fresh and FFPE samples. To further clarify, this panel should be able to detect and characterize fusion. The manufacturer of this sequencer must offer sign out service for ease of reporting of results in a true clinical (and not an RUO) report with constant update on curation database. This service should also be able to offer input on validation and review of cases.

3) The instrument for Pharmacogenomic studies must be a highly sensitive array-based scanner with submicron resolution, broad dynamic range and high throughput of over 5000 sample a week. The array-based scanner must be able to offer methylation and suitable for both fresh and formalin-fixed paraffin-embedded specimens. To further clarify, the technology employed must be a true microarray with beads technology that is able to easily and effectively characterize pseudogenes. Testing kits must be compatible with above instrument and its content should include many biomarkers that allow testing diversity with multiple ethnic groups, in compliance with the “All of Us” Federal Government sponsored project.

4) All required ancillary equipment to accomplish these molecular studies including, reagents, consumables needed to prep, extract , amplify, fragment and optimize a specimen to prepare for testing for sequencing and scanning.

4. PERIOD OF PERFORMANCE AND DELIVERY

This requirement shall be effective from the date of award: Est 09/08/2021.

Delivery to Orlando Veterans Affairs Healthcare System, 13800 Veterans Way, Orlando, FL, 32827

5. RESPONSIBILITIES

Identification: Delivery Orders (DO) issued shall be identified by the applicable contract and purchase order number.

Ordering Method: The (OVAHCS) may order products via Electronic Data Interchange (EDI), telephone, facsimile or other written communication, identifying the products by number, quantity, purchase price, address for delivery, and any special instructions.

***Contractor must be able to provide orders placed during regular work hours (Monday through Friday 6:30 am to 4:30 pm) the next business day after receipt of phoned or faxed orders from the Orlando VAHCS facilities***

Delivery/Scope: Quantities expressed in the schedule are estimates. However, quantities may vary based on patient demand.

· Ordering: Contractor will be furnished the name(s) of individuals authorized to purchase against the Contract. Orlando VAHCS will provide its own Contracting Officer’s Representative (COR).

· Delivery Schedule: Delivery specified by the Government on FOB Destination within consignee’s premises contracts are the dates material is due in, not the shipping dates.

· Emergency call back fees shall not be charged for regular work hours (M-F 6:00 am-4:30 pm) on days not observed as a holiday by the VA, i.e. Christmas Eve, Good Friday, etc.

· Federal Holidays -New Year’s Day -Martin Luther King’s Birthday -President's Day -Memorial Day -Independence Day -Labor Day -Columbus Day -Veterans’ Day -Thanksgiving -Christmas Day -Any other day declared a Federal Holiday by the US President.

· Contractor shall provide any additional technical support deemed necessary for the technical staff, physicians, patient education, etc.

6. PERSONNEL AUTHORIZED TO PLACE ORDERS

The following personnel are authorized to telephone and/or fax orders:

· Supervisory Path & Lab

· Program Support Assistant

· Other VA Medical Center Staff as designated

7. INVOICING

· Contracting Officer’s Representative (COR) shall be provided with a copy of invoice at the end of each week for approval before submission to the Department of Veteran Affairs Financial Services Center for processing. Said invoices will be sent the COR via e-mail and then reviewed for accuracy. The contractor will correct any discrepancies identified within 48 hours. A new invoice will be generated and then sent to the COR before invoice is finalized.

· Contractor shall be paid monthly, in arrears, upon submission of a properly prepared invoice for services/supplies during the period. Contractor shall submit a monthly invoice within 15 days after the end of the month being billed. The invoice will be accurate and include the contract number, date of services, and an itemized listing of charges for each line item.

· Contractor shall submit certified invoices monthly. Invoices at a minimum shall show period covered, billing date, name of preparation, quantity and amount.