Participating for Illumina today will be Jay Flatley, President and Chief Executive Officer; Marc Stapley, Senior Vice President and Chief Financial Officer; and Christian Henry, Senior Vice President and GM of our Genomic Solutions business. This call is being recorded, and the audio portion will be archived in the investor section of our website.It is our intent that all forward-looking statements regarding our expected financial results and commercial activity made during today's call will be protected under the Private Securities Litigation Reform Act of 1995. Forward-looking statements are subject to risks and uncertainties. Actual events or results may differ materially from those projected or discussed. All forward-looking statements are based upon current information available, and Illumina assumes no obligation to update these statements. To better understand the risks and uncertainties that could cause actual results to differ, we refer you to the documents that Illumina files with the Securities and Exchange Commission, including Illumina's most recent Forms 10-Q and 10-K. Before I turn the call over to Marc, I want to let you know that we will participate in the Morgan Stanley Global Health Care Conference in New York the week of September 10 and the UBS Global Life Sciences Conference also in New York the week of September 17. For those of you unable to attend these conferences, we encourage you to listen to the webcast presentations, which will be available through the Investor Relations section of our website. With that, I will now turn the call over to Marc. Marc Stapley Thanks, Kevin. Good afternoon, everyone, and thank you for joining us today. During this section of today's call, I will review our second quarter financial results and our guidance for the remainder of the year. I will then turn the call over to Jay to provide an update on our commercial progress and the state of our business and market.
We have continued our positive revenue and earnings momentum with our third consecutive quarter of sequential growth in both revenue and earnings per share. In Q2, we had record operating margins and record orders of the both the MiSeq instrument and MiSeq sequencing consumables. Second quarter 2012 revenue increased 3% sequentially to $281 million due to another successful quarter of MiSeq shipments, higher service revenue and continued growth in sequencing consumables.Revenue for the quarter decreased 2% compared to Q2 2011 as last year's quarter included a greater number of HiSeq sales. Instrument revenue for the second quarter was $72 million compared to Q2 2011. Instrument revenue was down 32%, again primarily due to decrease in sequencing and microarray instrumentation. Consumable revenue for the quarter was $184 million, up 6% sequentially and up 16% compared to the second quarter of 2011. Consumable revenue now represents 65% of our total revenue compared to 55% this time last year. We are very pleased with this trend, which results from a larger install base of both HiSeq and MiSeq and a sequentially improved average annualized quarter on HiSeqs. In particular, record shipments of our [indiscernible]product including TruSeq and Nextera contributed to the sequential growth consumable revenue. Services and other revenue, which includes genotyping and sequencing services, as well as instrument maintenance contract, was $22 million for the quarter compared to $18 million from Q2 of last year. This growth is also encouraging. In our discussion of gross margin and operating expenses, I will highlight our adjusted non-GAAP results, which exclude non-cash stock competition expense, restructuring charges and in-process R&D charge and other non-cash items. I encourage you to review the GAAP reconciliation of non-GAAP measures included in today's earnings release. Our adjusted gross margin for the second quarter was 70.9%. This compares to 69% in both last quarter and the second quarter of 2011. The sequential improvement was attributable primarily to a favorable mix of consumable versus instrument revenue and improved absorption. The year-over-year gross margin increase was also driven by a favorable product mix. We continue to expect gross margins of approximately 70% for the full year as improvements in consumable mix are somewhat offset by expected MiSeq care [indiscernible] reduction as our trade-in program continues to gain traction and by increasing FastTrack Services revenue.
Adjusted research and development expenses for the quarter was $41 million or 14.7% of revenue compared to 14.9% of revenue in the first quarter and 14.1% of revenue in the second quarter of 2011. Adjusted SG&A expenses were $55 million or 19.4% of revenue compared to 18.9% of revenue in the first quarter and 19.1% of revenue in the second quarter of 2011.Adjusted operating margins were a record 36.7% of revenue in the quarter compared to 35.8% of revenue in the second quarter of 2011 as we gain leverage from the improved gross margin performance. Our non-GAAP tax rate for the quarter was 33.8% compared to 34.7% in the second quarter of last year. This quarter's tax rate was higher than the expected annualized rate as a result of the delay in the passage of the U.S. R&D tax credit. We anticipate the non-GAAP tax rate will continue to be approximately 34% until the R&D tax credit is passed and retroactively applied at some point this year. Non-GAAP net income was $53 million for the quarter, and non-GAAP earnings per share was $0.40. This compares to non-GAAP net income and EPS of $52 million and $0.38, respectively, in the second quarter of 2011. We reported GAAP net income of $23 million or $0.18 per diluted share in the second quarter compared to $31 million or $0.22 per diluted share in the prior-year period. This includes an impairment charge this quarter of $21.4 million related to a technology asset acquired in 2010 and $6.7 million of ongoing unsolicited tender offer expenses. Read the rest of this transcript for free on seekingalpha.com