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Bionano Genomics, Inc. (BNGO)·Q2 2025 Earnings Summary

Executive Summary

  • Q2 2025 revenue was $6.733M, up sequentially vs Q1 2025 and above Wall Street consensus; non-GAAP and GAAP gross margin expanded to 52%, a notable step-up from 46% in Q1 and 42% in Q4, driven by cost reductions and manufacturing improvements .
  • EPS beat consensus as losses narrowed; management reiterated FY’25 revenue guidance ($26–$30M) and initiated Q3 revenue guidance ($6.7–$7.2M); new OGM installations guidance was raised to 20–25 for FY’25 .
  • Strategic pivot to “routine users” is showing traction: flowcells sold rose 17% YoY to 7,233, consumables and software revenues increased 16% YoY, and non-GAAP operating expense fell 53% YoY to $8.834M .
  • Catalysts: margin above 50%, raised install guidance, second Category I CPT code for constitutional genetic disorders, and VIA/Solve/Stratys Compute upgrades enabling AI-driven workflows and higher utilization .

What Went Well and What Went Wrong

  • What Went Well

    • Gross margin hit 52% (GAAP and non-GAAP), reflecting improved manufacturing costs and cost discipline; management expects margins to remain around current levels near term .
    • Routine-user focus drove utilization: 7,233 flowcells (+17% YoY), consumables/software revenue +16% YoY; installed base at 378 (+4% YoY) despite taking back eight rentals .
    • Strategic progress: second Category I CPT code established for constitutional genetic disorders (effective Jan 1, 2026), supporting reimbursement and broader clinical adoption; VIA 7.2 adds AI-driven workflow for constitutional disorders .
    • Quote: “Bionano has become a digital pathology company… One critical component… is AI driven software, such as our VIA software.”

  • What Went Wrong

    • Total revenue declined 13% YoY due to discontinued clinical services ($0.7M prior-year) and lower instrument revenue ($1.4M vs $2.3M prior-year) under the strategy shift .
    • Installed base declined by one sequentially (to 378) as eight reagent-rental systems were returned after evaluation, highlighting sensitivity of research-oriented placements to funding constraints .
    • Continued net loss of $(6.857)M, although markedly improved YoY; instrument sales decelerated as mix shifts away from new placements toward consumables/software .

Financial Results

MetricQ4 2024Q1 2025Q2 2025
Revenue ($USD Millions)$8.163 $6.457 $6.733
Wall Street Consensus Revenue ($USD Millions)*$6.200$6.250$6.563
GAAP Gross Margin %42% 46% 52%
Non-GAAP Gross Margin %42% 46% 52%
Net Loss ($USD Millions)$(20.125) $(3.102) $(6.857)
Revenue vs ConsensusBeatBeatBeat
EPS vs EstimatesQ4 2024Q1 2025Q2 2025
Primary EPS Consensus Mean ($USD)*$(6.00)$(3.02)$(2.67)
Actual EPS ($USD)*N/AN/A$(1.97)
EPS vs ConsensusN/AN/ABeat

Notes: Asterisk denotes values retrieved from S&P Global.

Segment breakdown:

Revenue Breakdown ($USD Millions)Q4 2024Q1 2025Q2 2025
Product Revenue$7.649 $6.004 $6.310
Service & Other Revenue$0.514 $0.453 $0.423
Total Revenue$8.163 $6.457 $6.733

KPIs and operating metrics:

KPIQ4 2024Q1 2025Q2 2025
Flowcells Sold (units)8,058 6,994 7,233
Installed Base (units)371 379 378
New OGM Systems Installed (units)N/A9 7
Systems Returned (units)N/AN/A8
Non-GAAP Operating Expense ($USD Millions)$10.639 $8.450 $8.834
Cash, Cash Equivalents & AFS Securities ($USD Millions)$20.9 $29.2 $27.4

Guidance Changes

MetricPeriodPrevious GuidanceCurrent GuidanceChange
RevenueFY 2025$29.0–$32.0M (Q4’24) $26.0–$30.0M (Q2’25) Lowered (from Q4), Maintained vs Q1
RevenueQ3 2025N/A$6.7–$7.2M Initiated
New OGM InstallationsFY 202515–20 (Q1’25) 20–25 Raised
Cash RunwayInto Q1 2026Into Q1 2026 (Q1’25) Into Q1 2026 Maintained

Earnings Call Themes & Trends

TopicPrevious Mentions (Q4 2024 & Q1 2025)Current Period (Q2 2025)Trend
AI/technology initiatives (VIA/Solve/Stratys Compute)Stratys system full release; VIA updates highlighted VIA 7.2 adds AI-driven workflow for constitutional disorders; Solve DB expansion; Stratys Compute GPU updates doubling capacity Strengthening capability; enabling easier workflows and higher throughput
Strategy pivot to routine usersStrategy outlined: lower OpEx, focus on recurring revenue Routine-user utilization driving +17% flowcells YoY and +16% consumables/software revenue Execution traction, mix shifting to recurring
Reimbursement & guidelinesCategory I CPT code established for hematologic malignancies; ISCN and ACMG recognition Second Category I CPT code for constitutional disorders established (effective Jan 1, 2026) ; management monitoring pricing Expanding reimbursement pathway; potential pricing upside
Instrument placementsInstalled base grew to 379 (Q1), strategy deemphasizes new placements 7 installs, 8 returns (rentals); installed base 378; conservative H2 install outlook Selective placements; rentals subject to attrition
Macro/funding sensitivityCustomers faced capital constraints in 2024 Returns concentrated in research-oriented rentals amid funding constraints Persistent headwind for research placements
Publications/community momentum2024 publications: 336; largest single-institution study at MD Anderson Record 119 publications in quarter; ESHG conference content across regions -Growing validation and awareness

Management Commentary

  • Strategic focus: “We have become a digital pathology company… Optical genome mapping consolidates these workflows… One critical component… is AI driven software, such as our VIA software.”
  • Cost and margin progression: “We have taken out over a $100,000,000 of annual non GAAP operating expense… margin expansion… to 52% this quarter” .
  • Utilization narrative: “Flow cells… grew 17%… a strong indicator for our efforts towards driving utilization within this routine customer group” .
  • Reimbursement: AMA established a second Category I CPT code for constitutional genetic disorders, expected to be effective Jan 1, 2026 ; management noted hematologic malignancy code priced at $1,263 and that customers have petitioned CMS for increases .
  • Confidence/guidance: “We are reiterating our full year revenue guidance of 26 to 30,000,000… raising expectations for new OGM installations… 20 to 25” .

Q&A Highlights

  • VIA adoption and AI: Adoption is ~one-third across entire installed base but higher among routine users; significant opportunity remains to expand and deepen use. AI accelerates database analysis and variant interpretation workflows .
  • Instrument returns/rentals: Returns largely from research-oriented rentals after evaluation periods; routine-user strategy aims to reduce attrition; purchase vs rental mix ~50/50; premature to quantify new-segment return rates but “very close to zero” .
  • CPT code/pricing: Second Category I CPT code covers constitutional disorders; draft pricing expected around September; hematologic malignancy code priced at $1,263; potential for pricing differentiation .
  • Install guidance conservatism: H2 install guidance seen as conservative due to installation timing potentially spilling into 2026 despite potential Q4 budget flush .
  • Strategic alternatives: Company is “on the radar” of strategics; emphasizes executing digital pathology transformation while acknowledging industry M&A dynamics .

Estimates Context

  • Revenue: Actuals beat S&P Global consensus in Q4 2024 ($8.163M vs $6.200M*), Q1 2025 ($6.457M vs $6.250M*), and Q2 2025 ($6.733M vs $6.563M*), consistent with routine-user utilization and consumables/software mix shift .
  • EPS: Q2 2025 actual EPS of $(1.97)* beat the $(2.67)* consensus; loss narrowing complements margin expansion. EPS actuals for Q4 2024 and Q1 2025 were not disclosed in the press releases reviewed.
    Notes: Asterisk denotes values retrieved from S&P Global.

Key Takeaways for Investors

  • Mix shift toward consumables/software is working: sequential revenue growth and repeated consensus beats reflect the pivot to routine users and higher utilization .
  • Margins inflect: GAAP/non-GAAP gross margin reached 52% from 46% in Q1 and 42% in Q4; management expects near-term margins around current levels as manufacturing and cost efficiencies hold .
  • Reimbursement expanding: Second Category I CPT code for constitutional disorders alongside hematologic malignancies strengthens the clinical adoption case and may support future pricing .
  • Install discipline: Raised FY install guidance to 20–25, but with conservative H2 timing; expect continued emphasis on placements that translate into sustainable consumables demand .
  • Operating leverage: Non-GAAP OpEx is down >50% YoY and holding near $8.5–$8.8M quarterly, supporting runway into Q1 2026 and path to reduced burn .
  • Watch catalysts: VIA 7.2 AI capabilities, Stratys Compute GPU upgrades, publication momentum (119 quarterly publications), and Q3 revenue delivery within $6.7–$7.2M guide .
  • Trading implications: Positive estimate beats and >50% margin can be re-rating drivers; monitor CPT pricing decisions and Q3 utilization progression for sustainability signals .