Analyst Conference Summary

conference date: November 2, 2016 @ 1:30 PM Pacific Time
for quarter ending: September 30, 2016 (third quarter, Q3)

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 $13.7 million, up sequentially from $8.7 million, and up from $6.3 million year-earlier. All revenue was from collaborations.

Net income was negative $104.7 million, down sequentially from negative $90.1 million, and worse than negative $76.8 million year-earlier.

Diluted EPS was negative $1.21, down sequentially from negative $1.05, and down from negative $0.91 year-earlier.

Guidance:

End of year cash will be greater than $1.0 billion. R&D expense is likely to continue to increase, but may vary by quarter.

Conference Highlights:

"We continue to advance a broad pipeline of investigational RNAi therapeutics - including 8 programs in clinical development - across a wide range of disease indications with high unmet need. Despite a disappointing outcome in our revusiran program, we remain committed to serving the needs of the ATTR amyloidosis community with patisiran and to developing RNAi therapeutics with our ESC-GalNAc conjugate platform as a new class of innovative medicines," said John Maraganore, CEO.

"We're pleased with new positive clinical results we presented in the third quarter for patisiran for hATTR-PN, fitusiran for hemophilia, ALN-AS1 for porphyria, and ALN-GO1 for primary hyperoxaluria. Now and through the end of the year, we are anticipating a very data rich period - including key clinical data presentations for five distinct programs at the AHA and ASH meetings and at our R&D Day in December - and we look forward to sharing our progress."

All revenue was from collaborators: $2.7 million from The Medicines Company, $7.4 million from Genzyme/Sanofi, and $3.6 million from other sources. Some of this revenue resulted from payments for milestones achieved.

Cash and equivalents balance at the end of the quarter was $1.19 billion, down sequentially from $1.28 billion. $150 million in long-term debt. Expects to end 2016 with over $1 billion cash balance.

Patisiran Phase 3 APOLLO study for the treatment of hereditary TTR-mediated amyloidosis with polyneuropathy (hATTR-PN), also known as familial amyloidotic polyneuropathy (FAP), continued, on recommendation of the data monitoring committee. Topline results should be available in mid 2017. Open-label extension (OLE) Phase 2 reported positive data in the quarter, showing it can "potentially halt or improve neuropathy progression."

Revusiran program will be discontinued due to higher than expected mortality in the treated arm of the trial. All the deaths were of patients who already had advanced heart failure. But there did not seem to be any drug-induced neuropathy. This should not affect the rest of the platform or pipeline.

Alnylam continued a Phase 1 trial 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. Initial data will be reported at R&D Day.

Fitusiran for hemophilia and rare bleeding disorders Phase 1 study interim results were positive, achieving a median estimated annualized bleeding rate of zero for hemophilia A and B. OLE study continued. Data to be presented at ASH in December. Phase 3 studies should start in early 2017. 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 Phase 3 trial will be started in 2017. Positive interim Phase 1 results were reported in the quarter. More data will be presented at ASH in December. Granted Orphan Drug designation.

ALN-CC5 for complement-mediated diseases including PNH continued dosing in a Phase 1/2 trial after reporting positive initial efficacy and safety 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). Will also study in related diseases starting in 2017. Data will be presented at ASH, and we will give an update on our plans on R&D Day.

ALN-AAT for AAT deficiency liver disease reported positive Phase 1/2 initial results, except at the highest doses. May modify before continuing the program.

ALN-GO1 for primary hyperoxaluria type 1 (PH1) Phase 1/2 study in Europe had positive results from the dose-escalation phase.

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

ALN-PCSsc reported positive results from The Medicines Company in Phase 2; the study is ongoing.

ALN-HBV Phase 1 study initial data was initiated.

See also Alnylam pipeline.

Operating expenses of $106.7 million consisted of: $97.9 million for research and development and $22.4 million for general and administrative expense. Interest & other income was $2.2 million. Income taxes $0 million. Unrealized loss on marketable securities was $1.2 million.

Alnylam broke ground for a new manufacturing facility in Norton, Massachusetts.

R&D day will be December 16.

Q&A:

Data safety monitoring, was it unblinded to efficacy? Just the safety data was unblinded.

Fitusiran data at ASH? With and without inhibitor groups. Without are from OLE, have been treated up to 16 months. With inhibitor is an approximately 15 patient cohort. Both groups had a 50 mg or 80 mg dosing schedule.

Fitusiran competition, what do you need? We could go to less frequent dosing. For now we are sticking with monthly dosing. The important thing for patients is to not bleed, the monthly dosing is a plus.

Patisiran gating factors? We will need a rigorous database, then share data with regulators, then writing up the NDA. Many parts of the NDA are already complete.

TTR mutations are variable, the patisiran trial covers a spectrum of them. Cardiomyopathy would require a completely different study.

Idea of bringing one new program per year? We have "an amazingly compelling pipeline" and are getting ready to file an NDA. On December 16 R&D Day we will go through our plans in detail.

ABR values in low single digits would be highly competitive.

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