Analyst Conference Summary

conference date: May 2, 2016 @ 1:30 PM Pacific Time
for quarter ending: March 31, 2016 (first quarter 2016, Q1)

Forward-looking statements

Overview: Development stage company continues to make progress with its RNAi therapies. It is running deep in the red due to R&D expenses.

Basic data (GAAP):

Revenue was $7.3 million, down sequentially from $7.6 million, and down from $18.5 million year-earlier. All revenue was from collaborations.

Net loss was $103.0 million, down sequentially from loss of $90.7 million, and down from loss of $50.8 million year-earlier.

Diluted EPS was negative $1.21, down sequentially from negative $1.07, and down from negative $0.62 year-earlier.

Guidance:

At year end expects to have more than $1.0 billion in cash remaining. That will include $150 million from a credit agreement made in April.

Revenue from collaborators is expected to increase during the remainder of 2016, including a potential milestone payment.

R&D expense are expected to increase v. 2015.

Conference Highlights:

Has 10 clinical stage programs; 2 are in Phase 3. By year end that should be 12 and 3.

Advancing a very robust RNAi pipeline addressing major unmet medical needs. Expects 10 major clinical readouts in 2016, plus 3 new IND filings to advance candidates into clinical trials. Fitusiran Phase 3 trials should start in 2016.

All revenue was from collaborators: $2.7 million from The Medicines Company, $4.4 million from Genzyme, and $0.2 million other. Some of this revenue resulted from payments for milestones achieved.

Cash and equivalents balance at the end of the quarter was $1.21 billion, down sequentially from $1.28 billion.

Strategic program "Alnylam 2020" provides guidance for the commercialization of RNAi therapies through 2020, assuming the clinical data supports that. Expects to have 3 commercial products by 2020, with a robust follow-up pipeline of 10 clinical programs.

Patisiran Phase 3 APOLLO study for the treatment of hereditary TTR-mediated amyloidosis with polyneuropathy (hATTR-PN), also known as familial amyloidotic polyneuropathy (FAP), completed enrollment. Data is expected in mid-2017. The Phase 2 OLE study data presented interim positive results for preventing neuropathy progression.

ALN-PCSsc is partnered with The Medicines Company, which continued enrollment in a Phase 2 trial. ALN-PCSsc targets PCSK9 to treat hypercholesterolemia (high cholesterol). Results may support quarterly dosing. Initial Phase 2 ORION-1 data could be available in late 2016, with a Phase 3 start possible in 2017.

Revusiran Phase 3 ENDEAVOR study continued to enroll ATTR amyloidosis FAC (familial amyloidotic cardiomyopathy) patients. Enrollment should complete in late 2016 with data in 2018. OLE data should be presented in July.

Alnylam filed a Clinical Trial Application (CTA) for ALN-TTRsc02, an ESC-GalNAc-siRNA conjugate targeting TTR for the treatment of ATTR amyloidosis, which is expected to enable a once-quarterly subcutaneous dosing regimen.

ALN-AT3 (fitusiran) for hemophilia and rare bleeding disorders continued a Phase 1 study and a Phase 1 extension study. Interim results were positive, giving evidence for restoration of hemostasis in severe hemophilia A and B. Phase 3 studies should start in mid-to-late 2016. Genzyme is a partner in the ALN-AT3 program, with goal of commercializing outside of U.S. and Europe.

ALN-AS1 for acute hepatic porphyrias is expected to report initial Phase 1 data in late 2016. If the data is positive a Phase 3 trial will be started in 2017.

ALN-CC5 for complement-mediated diseases including PNH continued dosing in a Phase 1/2 trial after reporting positive initial data. A new phase 2 PNH study should start in 2016. A phase 3 trial for aHUS and mysasthenia gravis could start in 2017. Could be used with or without eculizumab (Alexion's Soliris). Data presentations will be made at 3 meeting midyear.

ALN-AAT for ATT deficiency liver disease continued a Phase 1/2 trial.

ALN-GO1 for primary hyperoxaluria type 1 (PH1) is started a Phase 1/2 study in Europe. It received Orphan Drug Designation from the FDA. There are about 5,000 potential patients worldwide.

ALF-F12 targeting factor XII is now in development for the treatment of hereditary angioedema and for thromboprophylaxis.

ALN-HBV Phase 1 study could begin soon. One-third of the world population is infected.

See also Alnylam pipeline.

Operating expenses of $117.4 million consisted of: $96.3 million for research and development and $21.1 million for general and administrative expense. Interest & other income was $7.1 million. Income taxes $0 million. Unrealized loss on marketable securities was $13.3 million.

Q&A:

Is the strategy for ALN-CC5 around eculizumab one you will use for other complement mediated diseases? In other indications we believe monotherapy may be the best path forward. But there may be other settings where using it in combination with eculizumab or anti-C5 antibodies generally speaking would be warranted as well.

Would your strategy change with different outcome from 1210? We don't have specific data on 1210 yet. It would not have too much influence. For now both monotherapy and combination approaches are viable. We will evaluate those going forward. There are patients who are not adequately controlled in these diseases.

Is there more data that led to your CC5 decision, like knock-down? We have an oral presentation coming that has a data embargo. The data will be presented on June 11.

ENDEAVOR study dropout and compliance? Enrollment is going far better than expected. We are over 50% into enrollment. 60 or so sites online worldwide. The clinical hold that Ionis is suffering has removed competition for test subjects.

AS1 data, what are you looking for give Phase 3 could be soon? For acute hepatic porphyrias are due to heme pathway defects. You get a build up of ALA and other toxic metabolites. That results in pain and other symptoms. We are blocking an upstream enzyme in the pathway. We are looking for good knockdown of ALA & other indicators. In part C we will enroll a small cohort of patients who are actually having attacks. We should have data by the end of the year. In Phase 3 the endpoints would likely relate to the frequency or severity of the attacks.

What percent of PNH patients are considered poor responders to eculizumab alone? Our understanding is 20% to 30%. Some of the part C data gives us confidence, it will be released June 11. Poor responders are measured across several variables, including the need for dose escalation or symptoms between doses, or an LDH level that is not controlled.

The unmet need for ATTR amyloidosis may be larger than previously thought, given our ease of enrolling patients in the trial.

How long to build the new manufacturing plant? We will be operational in 2018. 200,000 square foot facility in Norton, Massachusetts. This should do us for 5 or 6 years. It would allow us to scale well for diseases with larger numbers of patients.

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