Joydeep Goswami
Chief Financial Officer, Chief Strategy and Corporate Development Officer at Illumina
Thank you, Jacob. I'll start by reviewing our consolidated financial results, followed by segment results for core Illumina and GRAIL and then conclude with my remarks on our current outlook for 2023. I will be discussing non-GAAP results, which includes stock-based compensation. I encourage you to review the GAAP reconciliation of these non-GAAP measures, which can be found in today's release and in the supplementary data available on our website. As Jacob noted, in the third quarter, consolidated revenue of $1.12 billion was flat year-over-year and up 1% on a constant currency basis. Consolidated revenue was down 5% from the second quarter of 2023. Although we correctly anticipated a sequential decrease in high-throughput consumables revenue due to the NovaSeq X transition, we placed fewer NovaSeq X instruments than we expected in the quarter as customers purchase constraints led to lengthened sales cycles. Non-GAAP net income was $52 million or $0.33 per diluted share, which included dilution from GRAIL's non-GAAP operating loss of $155 million for the quarter. Despite our lower revenue, non-GAAP EPS exceeded our expectations primarily due to continued execution of expense-reduction initiatives and a higher gross margin than we forecast. GAAP net loss was $754 million or $4.77 per diluted share, which included goodwill and intangible impairments of $821 million related to the GRAIL segment. These impairments were primarily the result of a decrease in Illumina's consolidated market capitalization and a higher discount rate used for the fair value cancellation of the GRAIL segment.
Our non-GAAP tax rate was 39.7% for the quarter, which decreased from 43.2% in Q3 2022 with both quarters reflecting the impact of R&D capitalization requirements. The year-over-year decrease was primarily due to a decrease in the non-GAAP tax expense, impact of R&D capitalization requirements given increased amortization of capitalized R&D expenses. Our non-GAAP weighted average diluted share count for the quarter was approximately 158 million. Moving to segment results. Core Illumina revenue of $1.11 billion was flat year-over-year on both a reported and constant currency basis and included anticipated reductions of approximately seven percentage points from two primary categories: one, the decrease in COVID surveillance and the effect of sanctions in Russia that together represent approximately 3.5 percentage points; and two, the year-over-year reduction in China revenue, that also is approximately 3.5 percentage points. COVID surveillance contributed approximately $4 million in total revenue in Q3 2023 compared to $28 million in Q3 2022. Core Illumina sequencing consumables revenue of $695 million was down 4% year-over-year. The decrease was primarily driven by a 12% decline in sales to research customers. These customers were impacted by the NovaSeq X transition and are reducing NovaSeq 6000 consumables purchases before they have fully ramped up activity on NovaSeq X. Total sequencing consumables revenue was also impacted by the COVID, Russia and China factor, I noted previously, as well as the impact of macroeconomic conditions and customers' purchasing power and project planning. Strength in sales to clinical customers partially offset the decline in research with clinical sequencing consumables growing 10% year-over-year, led by continued momentum in oncology and genetic disease testing.
Turning to sequencing activity. Total sequencing gigabase output connected high- and mid-throughput instruments grew 5% from Q2 2023 and 29% year-over-year. We are encouraged by the trends we are seeing across both research and clinical high-throughput customers that have a NovaSeq X installed. As expected, these customers show higher overall growth in sequencing output than high-throughput customers that have not yet adopted the NovaSeq X, both on a quarter-over-quarter and a year-over-year basis. As a reminder, we believe this data is a useful reference that shows the general activity trends across our installed base and is directionally correlated with revenue over time. Sequencing instruments revenue for core Illumina of $179 million grew 10% year-over-year driven primarily by NovaSeq X, which more than offset the decline in NovaSeq 6000 shipments. Growth in high-throughput instruments was partially offset by the expected decline in mid-throughput due to increasing capital purchase and cash flow constraints that continue to impact our customers' purchasing behaviors globally as well as by local competition in China. For NovaSeq X, we exited Q3 with more than 310 orders since launch. Our shipments of 97 NovaSeq X instruments in Q3 brought our total installed base to 273 instruments. Core Illumina sequencing service and other revenue of $142 million was up 15% year-over-year driven primarily by higher instrument service contract revenue on a growing installed base as well as an increase in lab services revenue.
Moving to regional results for core Illumina. All regions continued to be impacted by two key issues: one, tighter funding and budget pressures that are impacting customer purchasing power and project planning; and two, the impact of high-throughput customers transitioning to NovaSeq X as customers continue to reduce NovaSeq 6000 consumables purchases before they have fully ramped up activity on NovaSeq X. Americas revenue of $650 million grew 10% year-over-year, attributed to NovaSeq X placements as well as clinical testing volume driving greater consumables revenue. Clinical sequencing consumable shipments grew more than 20% year-over-year. Europe revenue of $260 million was flat year-over-year or up 1% on a constant currency basis. Growth in sequencing consumables was driven by mid-teens growth in clinical and strength in mid-throughput consumables, offset by the decline in COVID surveillance and the negative impact of exchange rates. For sequencing instruments, growth in high throughput due to NovaSeq X placements was more than offset by a decline in mid-throughput instruments. EMEA revenue of $98 million declined 22% year-over-year or 19% on a constant currency basis, which included an 11 percentage point impact from sanctions in Russia. The year-over-year decrease was also driven by softness in Japan due to the macroeconomic factors I mentioned earlier as well as the expected slowdown in COVID surveillance. Greater China revenue of $98 million represented a 26% decrease year-over-year or 25% on a constant currency basis, reflecting continued macroeconomic and geopolitical challenges as well as local competition in mid-throughput.
Moving to the rest of core Illumina P&L. Core Illumina non-GAAP gross margin of 66% decreased 290 basis points year-over-year primarily driven by product mix and less fixed cost leverage on lower manufacturing volumes as well as lower instrument margins and higher field service and installation costs due to the NovaSeq X launch, which is typical in a launch year. Core Illumina non-GAAP operating expenses of $481 million were down $33 million year-over-year and were lower than expected primarily due to continued expense-reduction initiatives. As a result of these factors, core Illumina non-GAAP operating margin was 22.5% in Q3 2023 compared to 22.6% in Q3 2022. Despite our lower gross margin, operating margin was approximately flat year-over-year due to our proactive cost management initiatives. Transitioning to financial results for GRAIL. GRAIL revenue of $21 million for the quarter grew 110% year-over-year driven primarily by adoption of Galleri. GRAIL non-GAAP operating expenses totaled $161 million and increased $12 million year-over-year driven primarily by efforts to scale GRAIL's commercial and R&D organizations. Moving to consolidated cash flow and balance sheet items. Cash flow provided by operations was $139 million. Third quarter 2023 capital expenditures were $45 million, and free cash flow was $94 million. We did not repurchase any common stock in the quarter. We ended the quarter with approximately $933 million in cash, cash equivalents and short-term investments.
During the third quarter of 2023, the company used $750 million in cash to repay the outstanding principal of convertible notes that matured in August 2023. Moving now to 2023 guidance. We now expect full year 2023 consolidated revenue to decline 2% to 3% from 2022, including core Illumina revenue that is down 3% to 4% year-over-year. As a reminder, these ranges include anticipated reductions from COVID surveillance of approximately 200 basis points, the impact on our business from sanctions in Russia of approximately 100 basis points, reductions in our business in China as well as a year-over-year negative impact from foreign exchange rates. GRAIL revenue is now expected to be at the low end of the range of $90 million to $110 million for 2023. For fiscal 2023, we now expect core Illumina sequencing instrument revenue to decline 5% to 6% year-over-year driven by capital and cash flow constraints that have continued to impact our customers' purchasing behaviors globally as well as the decline in our business in China. The decrease from our prior guidance is primarily driven by our lower NovaSeq X shipment expectations for 2023. We now expect to ship between 330 to 340 NovaSeq X instruments for the year as customers' purchasing constraints lead to lengthened sales cycles.
We also now expect core Illumina sequencing consumables revenue to decline 5% to 6% year-over-year driven primarily by the decrease in NovaSeq 6000 consumables as customers transition to NovaSeq X, the impact of macroeconomic conditions on customer project planning and budgets, the effect of sanctions in Russia, the slowdown in COVID surveillance, and the decline in our business in China. The decrease from our prior guidance primarily reflects a slower ramp in NovaSeq X consumables, in part due to our lower placement expectations as well as the increasing impacts of macroeconomic constraints. We now expect core Illumina total sequencing revenue to decline 3% to 4% year-over-year. This continues to include intercompany sales to GRAIL of approximately $30 million, which are eliminated in consolidation. We now expect consolidated non-GAAP operating margin of 4% to 4.5% and core Illumina non-GAAP operating margin of 19% to 19.5%. Our revised operating margins reflect our lower revenue expectations for the year, partially offset by continued expense-reduction initiatives. We now expect our non-GAAP tax rate to be approximately 39% for 2023 due to discrete tax benefit recognized in Q3 2023 related to prior year return adjustments. Lastly, we now expect non-GAAP earnings per diluted share in the range of $0.60 to $0.70 for 2023, reflecting non-GAAP diluted shares outstanding of approximately 159 million shares. Dilution from GRAIL's non-GAAP operating loss is now expected to be approximately $660 million as GRAIL continues to manage its expense base in line of its latest revenue outlook. I will now turn it back over to Jacob for his closing remarks. Thank you.