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Isis Pharmaceuticals Inc. reported a net loss of 27 cents per share in the third quarter of 2011, well above the year-ago loss of 13 cents and the Zacks Consensus loss Estimate of 21 cents. Revenues came in at $20.7 million, well below the Zacks Consensus Estimate of $25 million and the year-ago revenues of $27.8 million. Higher operating expenses and lower revenues led to the wider third quarter 2011 loss.

Quarter in Detail

Revenues, which include license fees, milestone-related payments and other payments, fell 27.6% from the year-ago period in the third quarter of 2011. Revenues were impacted by lower revenue from Bristol-Myers Squibb (BMY - Free Report) and no revenue from Alnylam Pharmaceuticals (ALNY - Free Report) as the amortization of upfront fees ended in 2010.

Operating expenses increased 14.5% during the quarter to $43 million mainly due to the advancement of Isis Pharma’s pipeline. While research and development expenses increased 15% to $39.9 million, general and administrative expenses increased 8.8% to $3.1 million. We expect operating expenses to continue increasing as the company moves its pipeline candidates into advanced stages of clinical development.

Isis Pharma earned a $5 million milestone payment from GlaxoSmithKline (GSK - Free Report) for identifying ISIS-AATRx as a development candidate – this amount will be recognized in the fourth quarter of 2011.

Kynamro Filed in the EU

Isis Pharma and partner Genzyme -- now a part of Sanofi-Aventis (SNY - Free Report) – filed for European approval of lead pipeline candidate, Kynamro (mipomersen). The companies are seeking approval for patients with homozygous familial hypercholesterolemia (FH) and severe heterozygous FH.

The US application, which will be submitted later this year, will be for the homozygous FH indication. Isis Pharma said that Genzyme is preparing for the EU and US launch of Kynamro, potentially next year.

Isis Pharma, along with Genzyme, intends to conduct a 12-month study (FOCUS FH - saFety and atherOgeniC lipoprotein redUction of mipomerSen in FH). This study will be conducted to support the expansion of the FH patient population to include severe heterozygous FH in the US, support an alternative dosing regimen (three times a week), and broaden the FH indication beyond severe in Europe.

The acceptance of the new drug application (NDA) filing in the US will trigger a $25 million milestone payment from Genzyme.

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