Illumina, Inc. (NASDAQ:ILMN) today announced, based on management’s preliminary financial review, second quarter revenue of approximately $161 million compared to guidance of $168 to $173 million. It should be noted that this revenue estimate is preliminary and remains subject to review by our independent registered accounting firm.

Lower than expected revenue relative to the first quarter was a direct result of a shortfall in our array business. As we mentioned in our first quarter earnings call, we expected the growth of our microarray business to moderate, but the following factors resulted in a sequential revenue decline in arrays:

• Customers delaying the start of new Genome Wide Association studies in anticipation of new, rare variant content arrays;
• The impact of reduced foundation funding in a few key accounts; and
• Order delays directly related to stimulus funding under the American Recovery & Reinvestment Act (ARRA).

In the quarter, our sequencing business once again saw significant sequential growth, but was insufficient to offset the decline in the array business. As we saw in Q1, the ARRA resulted in order delays in our sequencing business.

We expect the stimulus funding to have a significant positive impact on Illumina’s business in Q4 and in 2010. However, in the short-term the program has caused order delays as customers wait to learn whether and to what extent they will receive incremental funding. We believe this situation reduced our revenue by approximately $10M to $15M in the first half of the year and has created uncertainty in our Q3 forecast.

Despite the challenges we saw in Q2, we believe the fundamentals in our markets remain intact and that our competitive position, execution and new product flow are as strong as ever. Given the Q4 upside opportunities related to the stimulus, offset by the near-term weakness in the array business, we are resetting our fiscal 2009 outlook to the original range we provided entering the year of $690 to $720 million. We will provide more details regarding our financial guidance on our second quarter earnings call later this month.

Jay Flatley, President & Chief Executive Officer and Christian Henry, Senior Vice President & Chief Financial Officer will hold a brief conference call for investors to discuss our preliminary revenue estimate at 2:00pm Pacific Time (5:00pm Eastern Time) today, Wednesday, July 1, 2009.