Updated throughout with new information, including comments from Amarin.

MYSTIC, Conn. ( TheStreet) -- Amarin ( AMRN) plans to appeal a "surprise" rejection of a U.S. patent application for the company's experimental drug AMR101 that lowers levels of fat or cholesterol in the blood, a spokesman said Thursday.

Shares of Amarin are down 81 cents, or 6.5%, to $11.58 Thursday amidst a broad and sharp market sell off. The stock also fell 5% Wednesday -- and was down as much as 10% intraday -- after news broke yesterday that the U.S. Patent and Trademark Office (USPTO) issued a "final rejection" notice on an Amarin patent application for AMR101.

While the final rejection notice was posted to the USPTO's web site, Amarin has not yet received a copy of patent office's decision and can't comment on specifics, according to Amarin spokesman David Schull.

"The posting was a surprise, but a final rejection doesn't mean an ultimate rejection of the patent," said Schull. "The company is waiting to receive the letter and then will address the USPTO's concerns. This is part of the back-and-forth patent process and Amarin has a significant intellectual property portfolio around AMR101 ," he added.

Amarin has filed for multiple method-of-use patents that would grant additional years of exclusivity to AMR101 as a treatment for patients with very high levels of triglycerides, or soluble fats in the blood. Amarin is expected to file an approval application with FDA for AMR101 in this patient population before the end of September and launch the drug next year, if approved.

Under FDA law, Amarin would get five years of exclusivity -- likely extended by another 18 months -- to sell AMR101 without further patent protection once the drug is approved. But getting additional patent protection to keep generic competitors on the sideline is important for peak sales of AMR101 and Amarin's valuation.

"Amarin is not getting bought for $100 a share with eight years of exclusivity," said Monness Crespi Hardt analyst Avik Roy. Concerns about AMR101's patent situation -- and the hurdle that may put n front of a lucrative marketing partnership or acquisition -- is a big reason for why Roy has a neutral rating on the stock. He models generic competition in 2021, assuming a 2013 drug launch.

Amarin shares have been a big winner this year in part because investors believe the company is a likely takeover target due to the billion-dollar sales potential of AMR101.

"This is not a big deal but is just typical Wall Street focusing on a marginal issue," said one institutional investor who owns Amarin but asked to remain anonymous because his fund doesn't allow employees to speak to the media.

Specifically, this investor believes AMR101 will receive further patent protection on data showing that the drug not only lowers triglyceride levels but does so without raising levels of LDL, or bad" cholesterol. This claim is not included in the patent just rejected by the USPTO and it's a clinical benefit of AMR101 that similar drugs, including GlaxoSmithKline's ( GSK) Lovaza, have not been able to demonstrate.

Amarin also has other patent applications pending, including on use of the drug in patients with lower baseline levels of triglycerides.

Thursday, several sell-side analysts, including those from Jefferies, Lazard and Canaccord Genuity, defended Amarin and said AMR101 patent concerns were overbown or were being mis-interpreted.

AMR101 is an ultra-purified form of the omega-3 fatty acid called EPA, derived from fish oil. Across two phase III clinical trials, AMR101 has demonstrated the ability to significantly lower triglyceride levels without raising LDL, or "bad" cholesterol levels.

It's not precisely clear why U.S. patent examiners issued a final rejection notice on the AMR101 patent, but a previous "non-final" rejection issued in June said the claims in the AMR101 patent overlapped similar claims made in an existing patent issued for Epadel, another fish-oil derived EPA drug sold by the Japanese drug firm Mochida.

--Written by Adam Feuerstein in Boston.

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