Sequenom, Inc. (Sequenom), an in vitro diagnostics company, has reported total revenues of $8.7 million for the first quarter of 2009, compared with the total revenues of $10.6 million in the year-ago quarter. It has also reported a net loss of $17.5 million, or $0.29 per share, for the first quarter of 2009, compared with the net loss of $8.6 million, or $0.19 per share, in the year-ago quarter.

The increase in net loss during the first quarter of 2009, against first quarter of 2008, reflects increased general and administrative expenses and expenses associated with the planned launch of various noninvasive prenatal tests.

System revenues were $2.4 million, as against $3.7 million in the prior period while consumable sales rose modestly (1.3%) to $4.7 million. Gross margin was 61% for the first quarter of 2009, compared with 56% for the first quarter of 2008. The increased gross margin was attributable to higher relative sales in consumables (which have higher gross margins), as compared to lower relative system and contract research revenues (which traditionally have lower gross margins).

Research and development expenses were $8.8 million for the first quarter of 2009, as against $4.9 million for the same period of 2008. The increase in research and development expenses for the first quarter of 2009 reflected additional expenses associated with the company’s investment in its molecular diagnostic technology and product development, increased clinical study costs and increased headcount-related expenses (including higher stock-based compensation expense), primarily associated with the building of the company’s infrastructure for its molecular diagnostics business. Selling, general and administrative expenses for the first quarter of 2009 were $14.3 million compared with $9.2 million for the first quarter 2008. The increase in selling, general and administrative expenses in 2009 resulted from increased headcount-related expenses related to the building of the company’s diagnostics sales force, as well as legal fees associated with on-going litigation and acquisition activities. Total operating expenses for the first quarter of 2009 were $23 million, compared with $14.1 million for the first quarter of 2008.

As of March 31, 2009, the company had total cash and short- and long-term marketable securities of $87 million and $7.8 million in accounts receivable.

Updated 2009 Financial Outlook

SEQUENOM is updating its 2009 financial guidance as follows:

Genetic Analysis:

The company projects 2009 revenues to range between $32 million and $35 million

Gross margin is projected to be about 57% in 2009

After corporate allocations Genetic Analysis is projected to report a loss of between $10 million to $12 million, which includes about $5 million in non-cash FAS 123R expense, while incurring a cash burn after corporate allocations of breakeven to $2.0 million.

Molecular Diagnostics

The company is not providing revenue outlook for the molecular diagnostic business. However, Molecular Diagnostics is expected to incur a net loss after corporate allocations of between $52 million to $55 million, which includes about $7 million in non-cash FAS 123R expense, while incurring a cash burn after corporate allocations of approximately $45 million to $50 million.

Consolidated

On a consolidated basis the company is projected to report a 2009 loss of between $62 million to $67 million, which includes about $12 million in non-cash FAS 123R expenses.

On a consolidated basis, the company is projected to have a cash burn of between $45 million to $52 million.