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Seer, Inc. (SEER)·Q3 2025 Earnings Summary

Executive Summary

  • Q3 revenue was $4.12M (+2% y/y; +1.7% q/q) with gross margin 51%; EPS was $(0.32) vs S&P Global consensus $(0.30), and revenue modestly beat the $4.00M consensus, resulting in a mixed quarter (slight EPS miss, slight revenue beat)* .
  • Management maintained FY25 revenue guidance of $17–$18M and indicated results likely land in the lower half given NIH/government uncertainty and a U.S. government shutdown overhang; long-term gross margin target remains 70–75% .
  • Execution positives: third straight strong instrument shipment quarter; first joint sale closed with Thermo Fisher; record third-party publications (66 to date; 13 in Q3) signal accelerating adoption .
  • Liquidity remains a key differentiator: $251.2M cash, cash equivalents, and investments at 9/30; cumulative repurchases of ~$21.9M reduced net shares outstanding by ~14%; management reiterated belief cash is sufficient to reach cash flow breakeven .
  • Potential stock catalysts: incremental large biobank wins (including NIH-funded multi-omics program selection), Thermo Fisher co-selling momentum, and visibility on macro/government funding resolution .

What Went Well and What Went Wrong

  • What Went Well

    • Strong instrument demand and utilization for Proteograph ONE drove another solid shipments quarter; ~3x instruments shipped in 9M25 vs all of 2024; CEO: “robust demand and utilization…another strong quarter for instrument shipments” .
    • Scientific validation accelerating: 66 customer publications to date, with a record 13 in Q3, including notable cohort studies demonstrating capabilities vs affinity platforms .
    • First joint sale with Thermo Fisher; growing co-selling pipeline and pursuit of large biobank opportunities; CFO expects benefits moving into 2026 .

  • What Went Wrong

    • Macro headwinds: tariff policy shifts, NIH/government funding uncertainty, and a government shutdown slowed academic spending and elongated sales cycles .
    • EPS missed consensus modestly on continued operating losses despite lower opex; Q3 EPS $(0.32) vs $(0.30) consensus; net loss $(18.2)M *.
    • Guidance bias to low end reflects near-term visibility challenges; management noted potential Q4 shipment delays if shutdown persists .

Financial Results

MetricQ3 2024Q2 2025Q3 2025Q3 2025 Consensus
Revenue ($USD Millions)$4.03 $4.05 $4.12 $4.00*
Gross Margin %48% 52% 51% —
Operating Expenses ($USD Millions)$26.26 $22.64 $21.46 —
Net Loss ($USD Millions)$(21.33) $(19.42) $(18.23) —
Diluted EPS ($)$(0.35) $(0.33) $(0.32) $(0.30)*
  • Estimates marked with an asterisk are sourced from S&P Global consensus (Values retrieved from S&P Global).

Segment revenue breakdown

Metric ($USD Millions)Q3 2024Q2 2025Q3 2025
Product Revenue$2.92 $2.73 $2.76
Service Revenue (ex-Related Party)$0.66 $0.80 $0.91
Related Party Revenue$0.37 $0.41 $0.30
Other Revenue$0.09 $0.12 $0.15
Total Revenue$4.03 $4.05 $4.12

KPIs and balance sheet

KPIQ1 2025Q2 2025Q3 2025
Gross Profit ($USD Millions)$2.06 $2.11 $2.11
Publications/Preprints (cumulative)42 52 66 (13 in Q3)
Cash, Cash Equivalents & Investments ($USD Millions, period-end)$285.0 $263.3 $251.2
Share Repurchase (Cumulative since May’24)—~$20.0M; ~13% net share reduction ~$21.9M; ~14% net share reduction

Guidance Changes

MetricPeriodPrevious GuidanceCurrent GuidanceChange
RevenueFY 2025$17–$18M (Q1/Q2 reiterated) $17–$18M; likely lower half given macro Maintained; skew to lower half
Gross Margin (Long-term)LT70–75% target 70–75% target Maintained
Free Cash Flow LossFY 2025$(40)–$(45)M (as of Q1/Q2) Not reiterated in Q3N/A
Capital Return (Repurchase)Program$25M authorized (May 2024); ~$20M used by Q2 ~$21.9M used by 9/30; ~14% net share reduction Increased utilization

Earnings Call Themes & Trends

TopicPrevious Mentions (Q1 & Q2)Current Period (Q3)Trend
Large-scale studiesAnnounced 10k-sample DLS study; launched Proteograph ONE; later 20k Korea Univ. study; AI-driven analytics highlighted Continues; prediction first 100k-sample mass spec study likely in 2026; NIH multi-omics consortium selected Proteograph Improving
Thermo Fisher partnershipTraining US/EU sales; early-stage pipeline; revenue contribution modest in H1 First joint sale(s) in Q3; pipeline of joint opportunities including large biobanks Improving
Demand/adoptionSTACC-to-instrument conversions >50% in Q1/Q2 >2/3 of Q3 instrument shipments from prior STACC users; strong utilization of Proteograph ONE Improving
Macro/NIH fundingTariffs/NIH uncertain; caution near-term Shutdown drove pause in academic spending; guidance bias to low-end Worsening near-term
Publications/validation42 (Q1) → 52 (Q2) cumulative 66 cumulative; record 13 in Q3; superior detection vs affinity tech in cohort work Improving

Management Commentary

  • CEO: “In Q3, we saw robust demand and utilization for our recently launched Proteograph ONE…we have shipped nearly three times as many instruments in the first nine months of this year as we did in all of 2024.”
  • CEO on scientific momentum: “Notably, in the third quarter alone, we achieved a new record of 13 publications and preprints…”
  • CFO: “We ended the quarter with approximately $251M in cash, cash equivalents, and investments. Importantly…we have sufficient capital to reach cash flow breakeven.”
  • CEO on macro: “Shifting government policies around tariffs and research funding…The government shutdown adds yet another headwind.”

Q&A Highlights

  • Thermo Fisher partnership: First joint opportunities closed in Q3; pipeline building; expected to contribute more meaningfully into 2026 while remaining modest near term .
  • Scale of studies: Management expects first 100k-sample mass spec study as early as 2026; multiple biobank discussions underway .
  • Academic end-market: Shutdown drove a near-term pause; ~40% of 9M25 revenue from academic/government; customers cautious amid funding uncertainty .
  • NIH selection: Proteograph chosen after rigorous evaluation for a large, multi-tens-of-millions NIH-funded multi-omics consortium, reinforcing validation .

Estimates Context

  • Q3 2025: Revenue $4.12M vs $4.00M consensus (beat); EPS $(0.32) vs $(0.30) consensus (miss). Actual EBITDA approximately $(17.89)M in Q3 per S&P Global dataset. Estimate breadth is thin (1 estimate for EPS/Revenue), which can increase volatility around reported results*.
  • Forward consensus: Q4 2025 revenue ~$4.60M; EPS $(0.32); Q1 2026 revenue ~$4.50M; EPS $(0.35)*.
  • Implication: Modest beats/misses likely drive limited estimate changes; guidance bias to lower half suggests potential trimming of Q4 expectations if shutdown effects linger .
  • Asterisked values are from S&P Global (Values retrieved from S&P Global).

Key Takeaways for Investors

  • Adoption momentum is real: shipments and utilization strong, with significant STACC-to-instrument conversion and growing third-party validation (66 publications; record 13 in Q3) .
  • Mixed print: slight revenue beat, slight EPS miss; gross margin stable y/y+ and near Q2 levels supports progress toward scale .
  • Guidance intact but cautious: FY25 revenue range maintained with bias to the lower half; watch for shutdown impacts on Q4 shipments and consumables .
  • Strategic leverage: Thermo Fisher co-selling is beginning to translate; larger population-scale studies (incl. NIH) are credible medium-term revenue catalysts .
  • Balance sheet strength and buybacks provide downside support; management asserts cash is sufficient to reach breakeven; ~14% net share reduction to date .
  • Trading lens: Near-term stock moves likely tied to funding headlines and biobank/NIH updates; evidence of additional joint wins or large study starts would be positive catalysts .
  • Medium-term thesis: Proteograph ONE positions Seer as the scalable mass-spec proteomics standard; as large cohorts transition from pilot to production, recurring consumables/services mix should lift margins over time .

Supporting detail excerpts and data

  • Q3 revenue $4.1M; product $2.8M; service $1.2M (incl. $0.3M related party); other $0.15M; GM 51%; opex $21.5M; net loss $(18.2)M; cash $251.2M .
  • FY25 revenue guidance $17–$18M reiterated; management expects lower half; 70–75% LT GM target .
  • Q2 revenue $4.05M; GM 52%; net loss $(19.4)M; cash $263.3M .
  • Q1 revenue $4.21M; GM 49%; net loss $(19.9)M; cash $285.0M .

Notes

  • All company-reported figures are GAAP unless stated; company did not provide non-GAAP EPS adjustments for Q3 in the 8-K.
  • Estimates marked with an asterisk are sourced from S&P Global (Values retrieved from S&P Global).