J_A - FAR 13_04212020_Redacted.pdf

DEPARTMENT OF VETERANS AFFAIRS

Justification for Single Source Awards IAW FAR 13.106 1 For

Over Micro Purchase Threshold but Not Exceeding the SAT ($250K)

Acquisition Plan Action ID: 36C261 19 AP 5132

1. Contracting Activity: Department of Veterans Affairs, Program Contracting Activity is procuring the following items on behalf of the VA Palo Alto Health Care System for the new research facility which is currently under construction. 2237# 640 20 1 522 0013 has been submitted and approved for this action.

2. Brief Description of Supplies/ Services required and the intended use/Estimated Amount:

This requirement is for a CODEX instrument, internal computer, software, and training. Total estimated cost is $ .

Item

Description Qty Estimated Price

0001 Codex instrument, external computer, and software, for enhanced fluorescence imaging.

1 $

3. Unique characteristics that limit availability to only one source, with the reason no other supplies or services can be used:

CODEX is a cytometric imaging platform that enables highly multiplexed immunostaining of tissue sections. CODEX utilizes oligonucleotide conjugated antibodies and in situ hybridization of fluorescently labeled DNA probes through iterations of indexing and labeling of different antibody probes. While immunofluorescence is limited to the visualization of a few targets, iterative indexing and labeling allows for the detection of up to 66 antigens within a sample. Thus, using CODEX multi parameter immunostaining will allow characterization of the landscape of a tissue. Using CODEX will enable the detection of differences in the landscape of a tissue, and at the single cell level. The images it produces are analyzed at the single cell level to provide spatial information, which is critical to understanding interactions between individual cells.

The Akoya Biosciences CODEX system is a fluidics system that is an “add on” system to a fluorescent (FL) microscope. The CODEX system enables researchers to look at the tissue or cell and study not only what protein or biomarker is present in the tissue, but also where it is (i.e. inside the cell, on another layer (membrane), in the space between cells, inside the nucleus, and so forth). And how the specific protein interacts with another. The system includes a fluidics based instrument, reagents, and a software analysis suite. It offers a cost effective means to transform VA Palo Alto’s existing fluorescence microscope into an ultra high parameter tissue imaging system. The CODEX system will enable researchers to simultaneously analyze more than 40 protein markers for spatially resolved tissue characterization with single cell resolution, even in challenging samples such as highly auto fluorescent Formalin Fixed Paraffin Embedded (FFPE) and fresh frozen samples. The system offers the flexibility to design custom panels using a combination of Akoya validated, ready to use antibodies and customers’ antibodies of interest.

What is unique about the CODEX system as compared to other similar systems is that it is an “add on” to an existing FL microscope, eliminating the need to purchase a dedicated proprietary microscope. The CODEX system allows users to use the microscope as a traditional FL microscope when the CODEX system is not being used. Hyperion by Fluidigm is a similar system but it requires a dedicated proprietary microscope, and a dedicated person to operate the system. The Hyperion can’t be used as a traditional FL microscope. Moreover, the CODEX System has a small footprint and it can fit easily onto the benchtop eliminating the need for extra large lab space required by alternate systems. As the research building (710) has a limited space availability, the VA requires an instrument with a smaller footprint, allowing more space for the researcher. It is also important to note that CODEX System is part of an end to end solution that includes reagents, software, and specialized support. While Akoya Biosciences offers validated, commercial CODEX antibodies, users also have the flexibility to design custom panels using the CODEX Conjugation Kit. The CODEX Software Suite includes different modules for integration and synchronization with the companion microscope for imaging, image processing (cell segmentation, drift compensation, FCS file generation and more) and storage, and visualization and analysis of images and cell phenotype

The CODEX System enables highly multiplexed imaging with existing fluorescence microscopes, thus eliminating the need for specialized imaging equipment. No other commercial system offers a combination of high multiplexing capability, integration with fluorescence microscopes, affordability and a small benchtop footprint while providing complete spatial context and preserving sample integrity. Alternate commercial solutions involve trade offs in one of these key attributes.

In accordance with the authority prescribed in Federal Acquisition Regulation (FAR) 6.302 1, only one source is available, and no substitutions are possible.

4. Description of market research conducted and results or statement why it was not conducted:

Researchers at the VA Palo Alto Research Department spoke with scientist colleagues to get their input, conducted Internet searches, and spoke to sales reps, as well as communication with core facilities managers within Stanford, and other universities.

The tissue needs prepared before examining it under a microscope. Methods to do that are:

a. FFPE: A very reliable method that preserves the sample forever. However, it can break some of the proteins or change the protein structure thus making it “invisible” when we test it.

b. Frozen section (with or without fixation): Freeze the tissue immediately in a specific polymer, and tissue is the kept in ultra low temperature ( 80 degrees Celsius). Throughout the process of the researcher has to keep the tissue in ultra low temperature. As you can imagine, it’s harder to work with, and more costly to preserve BUT some proteins can only be viewed under frozen section as it doesn’t change the protein structure.

The following competitors were reviewed that offer multiplexing analysis, based on AACR abstracts:

1. Lunar 2 This is a platform to screen multipole biomarkers from a blood test. This is not a tool to enhance microscopy and study tissues and solid cells.

2. GeoMx/NanoString: With this system, the image is limited to only one method of sample preparation, FFPE, while the CODEX can work on both frozen section and FFPE. Unfortunately, many proteins are destroyed when using FFPE, thus limiting to only one method of sample prep also limits the ability to study some curial proteins. Additionally, to visualize only 4 colors when, and the multiplexing is done the GeoMAx is limted to channels, and the multiplexing is then achieved by genetic analysis of the barcodes. This mean we need another instrument to be able to analyze the sequence, which we don’t have.

3. Fluidigm/Hypron: This instrument requires a fully dedicated person to operate, unlike the codex that is easier to use and doesn’t require a dedicated person. This instrument is significantly more expensive. Both of those stamen are the result of the detection methodology time of flight (TOF) mass spectrometer coupled to cytometer.

4. Akoya: Offers two options including, the Perkin Elmer Vectra and the Codex. The Perkin Elmer unit is also limited to FFPE treat tissue, it offers some automation but can analyze less biomarker per assay. CODEX is the one that can work on multiple (40 and over analytes) and on cells, FFPE and frozen tissue.

5. Ulitvue: Limited to FFPE and only 16 analytes at a time.

6. Cell Idx: Limited to 16 analytes at a time from FFPE tissue

7. MultiOmyx: Only works only on FFPE tissue.

8. IONPath: Like the Hypron, the IONPath instrument requires a dedicated person for operation.

Additionally, it can only use FFPE tissue.

9. RNAScope by ACD: This is a way to study gene expression, basically multiplexing gene expression assay. It is a way to “count” how many copies of a particular gene are present in the cell. It uses FFPE and frozen but is limited to 12 analytes at a time.

10. Readcore is another Fluorescent in situ Sequencing (FISSEQ) similar to RNA scope.

Akoya has one competitor for the Codex, the Hyperion by Fluidigm. However this system costs approximately $1.2 million as it requires a dedicated microscope, whereas the Codex will allow the use of an existing, in house, FL microscope. Additionally, Codex is the only brand that offers true multiplexing with more than 30 analytes on both frozen and FFPE.

Market Research was conducted to locate authorized distributors, specifically SDVOSBs and VOSBs who could fulfill this requirement. Akoya Biosciences is a small business manufacturer and does not have authorized distributors in the United States. As a result, SDVOSBs and VOSBs and would not be in compliance with Gray Market and Non Manufacturing Rule regulations.

5. Contracting Officer's Certification: Purchase is approved in accordance with FAR13.106 1(b). I certify that the foregoing justification is accurate and complete to the best of my knowledge and belief. Price reasonableness will be determined IAW FAR 13.106 3.

Grace E Kelly Date Contracting Officer

Grace E. Kelly-Burnsworth 1384242

Digitally signed by Grace E. Kelly-Burnsworth 1384242 Date: 2020.04.21 16:29:51 -04'00'