Bionano Genomics Q3 2025: Contradictions Emerge on Utilization Targets, Operating Expenses, and Instrument Strategy

Date of Call: November 13, 2025

Financials Results

• Revenue: $7.4M, up 21% YOY (core +12% after adjusting for $0.5M write-down in 2024)
• Gross Margin: 46% non-GAAP, compared to 26% non-GAAP in Q3 2024

Guidance:

• Reiterating full-year 2025 revenue guidance of $26M–$30M.
• Q4 2025 revenue expected to be $7.5M–$7.9M.
• Expect to exceed prior guidance of 20–25 system installations, likely surpassing the high end.
• Completed $10M equity offering; cash runway extended into Q3 2026; operating expenses intended to remain roughly flat with selective investments.

Business Commentary:

* Revenue Growth and Strategic Shift: - Bionano reported total revenue of $7.4 million for Q3 2025, reflecting a 21% increase compared to Q3 2024. Adjusted for a write-down, core revenues increased by 12% year-over-year. - The growth was driven by a strategic shift towards focusing on routine users, leading to increased utilization and higher consumables and software sales.

• Increased Flow Cell Sales and Utilization Increase:
• Bionano sold an all-time record of 8,390 flow cells in Q3 2025, reflecting a 7% increase compared to Q3 2024. Flow cells sold to existing customers grew by 6% on a year-over-year basis.

• The increase was due to higher utilization from routine users who repeatedly purchased and used consumables and software at higher rates.

• Non-GAAP Gross Margin Improvement:

• Bionano reported a non-GAAP gross margin of 46% for Q3 2025, a significant improvement from the 26% non-GAAP gross margin reported in Q3 2024.
• The improvement was attributed to cost reductions, improved product manufacturing costs, and higher volumes, as well as a shift in product mix towards consumables and software.

• Operating Expense Reduction:
• Bionano's non-GAAP operating expense for Q3 2025 was $9.7 million, representing a 40% year-over-year reduction from the $16.1 million in Q3 2024.

• The reduction was achieved through disciplined financial management and a focus on operational efficiency.

• Optical Genome Mapping (OGM) Adoption and Reimbursement:

• There were 97 new publications demonstrating the value of OGM in Q3 2025, marking a 10% growth over the same period the previous year. The OGM community has published nearly 11,500 clinical research genomes to date.
• The increase in publications and research genomes is a positive leading indicator of future adoption, contributing to new customer acquisition, expanded applications, and third-party support for OGM in reimbursement.
  

  Sentiment Analysis:

  Overall Tone: Positive

  • Management highlighted Q3 revenue of $7.4M (+21% YOY), record 8,390 flow cells (+7% YOY), non-GAAP gross margin expansion to 46% from 26% prior year, and non-GAAP operating expense down 40% to $9.7M; reiterated FY guidance $26M–$30M and extended cash runway via a $10M offering.

Q&A:

• Question from Yi Chen (H.C. Wainwright): My first question is with respect to increasing utilization of routine use customers, can you talk about what is the potential peak level of utilization for these routine use customers? And how soon do you expect to have these customers achieve the peak level based on the current trend?
  Response: Target average utilization goal is in the low-20s samples/week per routine user (midpoint between typical ~4 and top ~40); labs are not sample-limited and growth will come from validating and expanding assay menus.

• Question from Yi Chen (H.C. Wainwright): Got it. And with respect to the Japanese market, can you tell us how many -- what is the current installed base in Japan? How do you think the market could ramp up in comparison to the U.S. market?
  Response: There is one system in Japan at a service lab; interest is growing and the market should evolve similarly to the U.S. for genetic and oncology applications over time, though adoption will be gradual—pharma/cell & gene therapy may accelerate uptake.

• Question from Yi Chen (H.C. Wainwright): Got it. And with respect to operating expenses, do you expect it to remain relatively stable going forward?
  Response: Management intends to keep operating expenses roughly flat next year, allowing selective investments only where justified.

Contradiction Point 1

Utilization Expansion Targets

It directly impacts expectations regarding operational planning and investor expectations related to the company's utilization growth strategy.

What is the potential peak utilization level for routine use customers and how soon can it be achieved based on current trends? - Yi Chen (H.C. Wainwright)

20251114-2025 Q3: Our target is to achieve average utilization in the low-20s range across routine users. - Robert Holmlin(CEO)

What is the potential peak utilization level for routine-use customers, and how soon can they reach it based on current trends? - Yi Chen (H.C. Wainwright & Co, LLC, Research Division)

2025Q3: The goal is to reach the midpoint, which is around 20 samples per week on average across all routine users. - Robert Holmlin(CEO)

Contradiction Point 2

Operating Expense Strategy

It involves changes in financial strategy, specifically regarding operating expense management, which are critical for organizational planning and investor expectations.

Will operating expenses stay relatively stable moving forward? - Yi Chen (H.C. Wainwright)

20251114-2025 Q3: We plan to keep operating expenses flat, except where opportunities justify additional investment. - Robert Holmlin(CEO)

Do you expect operating expenses to remain stable going forward? - Yi Chen (H.C. Wainwright & Co, LLC, Research Division)

2025Q3: We intend to keep operating expenses stable, with some potential investment areas. The focus is on maintaining a flat expense structure, except where opportunities justify additional spending. - Robert Holmlin(CEO)

Contradiction Point 3

Instrument Installation and Utilization Strategy

This contradiction involves differing statements about the company's strategy regarding the installation of new instruments and the utilization of those instruments, which can impact revenue projections and market penetration.

What is the potential peak utilization level for routine users, and how soon can it be achieved given current trends? - Yi Chen (H.C. Wainwright)

20251114-2025 Q3: The average utilization is about 4 samples per week, with some users running up to 40 samples per week. Our target is to achieve average utilization in the low-20s range across routine users. - Robert Holmlin(CEO)

Are you marketing VIA to non-OGM users? - Michael Okunewitch (Maxim Group LLC)

2025Q2: It takes 6 to 9 months for labs to reach routine-use status with OGM. - Robert Erik Holmlin(President, CEO, CFO & Director)

Contradiction Point 4

Gross Margin Stability

It involves expectations for gross margin stability, which is a critical financial indicator for investors.

Will operating expenses remain stable going forward? - Yi Chen (H.C. Wainwright)

20251114-2025 Q3: We expect gross margin to remain stable in the 40% range for the remainder of the year. Continual improvements are likely, but they may be gradual due to ongoing cost structure adjustments. The current stability is seen as a positive outcome. - Erik Holmlin(CEO and Principal Financial Officer)

Is the mid-40% gross margin range sustainable for the rest of the year? Is there potential for further upside? - Sung Ji Nam (Scotiabank)

2025Q1: We expect gross margin to remain stable in the 40% range for the remainder of the year. Continual improvements are likely, but they may be gradual due to ongoing cost structure adjustments. The current stability is seen as a positive outcome. - Erik Holmlin(CEO and Principal Financial Officer)

Contradiction Point 5

Operating Expenses Stability

It involves expectations for operating expenses, which directly impact the company's financial health and cost management.

Will operating expenses remain stable going forward? - Yi Chen (H.C. Wainwright)

20251114-2025 Q3: Yes, we plan to keep operating expenses flat, except where opportunities justify additional investment. We are in the process of finalizing our detailed operating plan for next year. - Robert Holmlin(CEO)

How will the 50% revenue growth mentioned last quarter and projected instrument production by year-end impact manufacturing capacity or potential export tariffs? - Sung Ji Nam (Scotiabank)

2025Q1: The increase in operating expenses in Q3 mainly included research and development expenses related to the development of the Saphyr system and related products, and the stock-based compensation expense increase. - Erik Holmlin(CEO and Principal Financial Officer)