P03.J _ A - 10X_Genomics_Chromium Connect System.pdf

VHAPM Part 813.106 Simplified Acquisition Procedures: Soliciting from a Single Source Attachment 1: Single Source Justification for SAP under the SAT

VHAPM Part 813.106 Page 1 of 3 Original Date: 08/30/17 Revision 02 Eff Date: 03/31/2020

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:__561-24-1-1674-0001

1. Contracting Activity: Department of Veterans Affairs, VISN2, New York/New Jersey VA

Health Care Network, VA New Jersey Health Care System (East Orange, NJ), Neurology Service, Dr. Yun-Beom Choi, Neurology Service, yun-beom.choi@va.gov

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

10X Genomics Chromium Connect, Training, Setup, and 1-year service $285,000.00

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

The funds for this requirement is awarded by the Office of Research & Development (ORD) Shared Equipment Evaluation Program (ShEEP). The named vendor, Namocell under ProteinSimple, was also included in the original grant application.

The combined system required is a single-cell analysis system that requires a Namocell Pala Single Cell Dispenser and a 10X Genomics Chromium Connect. The Namocell Pala Single Cell Dispenser will provide dissociated cells that are then input into the 10X Genomics Chromium Connect. The 10X Chromium instrument adds marker bar code (oligonucleotides-short sequences) to the nucleic acids in such a way that the nucleic acids from each cell have a specific bar code unique to that particular cell. The RNA-sequencing will identify thousands of different cells and be able to report gene expression levels for every gene in every cell. This solves a problem examining expression levels in tissue samples that complicate analyses because different cell types are present.

10X Genomics Chromium Connect is the only commercially available compact instrument which automates the Chromium Single Cell Gene Expression workflow. It is the only instrument that can perform all steps of the workflow, from cell partitioning to library construction, without the need for manual intervention. Fully automated workflow: The Chromium Connect automates all steps of the Chromium Single Cell Gene Expression workflow, from cell partitioning to library construction. This reduces hands-on time and the risk of human error. High throughput: The Chromium Connect can process up to 8 samples simultaneously, with a maximum throughput of 192 samples per day. This makes it ideal for large-scale single cell gene expression studies. Reproducible results: The Chromium Connect is designed to generate reproducible results, even across multiple users and instruments.

This is important for ensuring the quality of your data and the reliability of your results.

VHAPM Part 813.106 Page 2 of 3 Original Date: 08/30/17 Revision 02 Eff Date: 03/31/2020

Flexible workflow options: The Chromium Connect offers a variety of workflow options, including the ability to generate cDNA libraries or perform automated library construction.

This gives you the flexibility to choose the workflow that best meets your needs. Ease of use: The Chromium Connect is easy to use, even for users with limited experience in single cell sequencing. The instrument is controlled by a touchscreen interface that guides the user through each step of the workflow.

Cell recovery: Typically 65-85% of input cells successfully encapsulated and barcoded.

Viability: >80% of recovered cells remain viable.

Doublets: Doublet rate usually <5% allowing confident single cell identification.

Reads per cell: Median of 50,000 reads/cell, allowing detection of >1000 genes per cell.

Sequencing saturation: >90% of transcripts detected with maximum sequencing depth.

UMI counts: Median of 25,000-50,000 UMIs/cell enables high confidence gene quantification.

Gene detection: Median of 2000-3000 genes detected per cell.

Data quality: High cell-to-cell reproducibility (r > 0.9) and low technical noise with

UMI barcoding.

QC metrics: Reports useful quality control metrics like number of cells, reads, genes detected and percentage of reads in cells.

Sensitivity: Capable of detecting biological differences as small as 10-20% between conditions.

Throughput: Up to 100,000 cells in a single run with results in 1-2 days.

Labor, travel, sorting cartridge kits, tools to install the dispenser equipment, and training 1 year service contract

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

10X Genomics Chromium Connect research was performed by consulting multiple sources as PubMed, PitchBook, SelectScience, and NIH Reporter.

The Chromium Connect is the only single-source instrument that can fully automate the Chromium Single Cell Gene Expression workflow.

Published literature: PubMed on October 8, 2023 returns no other device with Chromium Connect’s capabilities. PitchBook, a market research site, lists Fludigm’s C1 single cell auto prep system, Pacific Biosciences’s SMRT technology, and Beijing Genomics Institute (BGI) as 10x Genomics’ competition. PitchBook’s listing of Fluidgm’s C1 is unsuitable as a market competitor as the C1 cannot complete upstream tasks of single-cell template preparation

VHAPM Part 813.106 Page 3 of 3 Original Date: 08/30/17 Revision 02 Eff Date: 03/31/2020 that the Chromium Connect can complete. Pacific Bioscience’s SMRT technology is an unsuitable comparison as PacBio's SMRT is a sequencing technology, while 10x Genomics' Chromium Connect is primarily an automated library preparation system for single-cell RNA transcriptomics. 10X Genomics is based in the United States whereas BGI is based in China.

SelectScience website: https://www.selectscience.net/products/chromium-connect?prodID=226588#tab-2 lists no other instrument that performs like Chromium Connect.

While there are no VA ShEEP users that list Chromium Connect, there are two VA ShEEP awards (VA Palo Alto, CA and VA Charlie Norwood, Augusta, GA) for Chromium Controller which is a subcomponent in Chromium Connect Outside of the VA and at extramural NIH, Dr. Michael Snyder of Stanford University, lists and describes the Chromium Connect on NIH Reporter, “We predict that use of the Chromium Connect System will approach maximum capacity due to the high demand and need for cost-effective library preparation. Data generated by sequencing libraries prepared with the proposed instrument will positively impact a broad cross section of human disease research, notably: cardiovascular disease, pulmonary hypertension, type 2 diabetes mellitus, inflammatory bowel diseases, developmental defects, cancer, sleep disorders, obesity, and aging.” We embark on similar mission and agree with Dr. Snyder on Chromium Connect’s unique position in the market.

10X Genomics is the only manufacturer and distributor of the Chromium Connect, which is only single-source instrument that can fully automate the Chromium Single Cell Gene Expression workflow, necessary to run in conjunction with the Namocell Pala Single Cell Dispenser for on-going studies. This is the last unit to be manufactured.

Due to urgent nature of requirement, J & A will be posted with award notice.

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.

Millicent Covert Contracting Officer

MILLICENT

COVERT

Digitally signed by MILLICENT

COVERT

Date: 2023.12.08 14:58:38 -05'00'