With no drugs on the market, Alnylam Pharmaceuticals' (NASDAQ:ALNY) third-quarter earnings were all about the pipeline progress it's made and plans going forward. During the conference call, there were 16 slides based on its pipeline and one devoted to financial results.

That's the kind of ratio investors should want to see.

For the record, the company lost $44.0 million, or $0.58 per share, on a GAAP basis. The more important number -- how much cash the company has -- was rock solid, coming in at $915 million. With a plan to burn $55 million in the fourth quarter, Alnylam has years of cash in the bank even while the cash burn rate should increase as its drugs push further into development.

In October, Alnylam released positive phase 2 data for its lead program, patisiran. In patients with familial amyloidotic polyneuropathy taking patisiran for six months, the drug caused a slight decrease of 0.95 points in the modified Neuropathy Impairment Score. There wasn't a placebo control group, but Alnylam estimates that untreated patients would have increased 7 to 10 points over six months.

Alnylam has already started a phase 3 trial in patients with familial amyloidotic polyneuropathy. The trial is placebo controlled, so it'll give a more definitive answer about whether patisiran is helping patients. The trial tracks patients for 18 months, so getting it fully enrolled is critical to being able to complete the trial. CEO John Maraganore said he's "pleased with the pace of enrollment."

Management clearly has confidence in the company's second program, revusiran, which treats familial amyloidotic cardiomyopathy. Enrolment in the phase 2 trial just completed, and the early enrollees who have already completed dosing are being rolled over to an extension trial, but management is already ramping up for a phase 3 trial to start by the end of the year. Investors will get to see the initial data at the American Heart Association meeting later this month.

We'll get to see data from another one of Alnylam's clinical-stage compounds, ALN-AT3 -- you can tell by the code name it's further behind -- next month at the American Society of Hematology meeting. Unlike the rare diseases that its lead programs treat, ALN-AT3 treats hemophilia patients, a market worth more than $9 billion. The phase 1 trial is mostly to test safety and tolerability but will measure thrombin generation, a biomarker for efficacy in hemophelia patients.

Finally, there's ALN-PCS, designed to lower cholesterol by targeting PCSK9. The target has already been validated by Amgen (NASDAQ:AMGN) and by the team of Regeneron Pharmaceuticals (NASDAQ:REGN) and Sanofi (NYSE:SNY), which already have phase 3 data showing that their PCSK9 inhibitors can lower cholesterol. ALN-PCS can knock down up to 96% of PCSK9 expression, which could allow it to be dosed as infrequently as four times a year. We should see initial clinical data for the subcutaneous version of the drug in the middle of next year.

All the rest of Alnylam's pipeline is still in preclinical development, but there are nine drugs there, so the clinical pipeline should be full fairly quickly.

Alnylam Pharmaceuticals is still a few years away from having a drug on the market. Pushing in that direction is all investors can ask for, and so far Alnylam is delivering.

Brian Orelli has no position in any stocks mentioned. The Motley Fool recommends Alnylam Pharmaceuticals. Try any of our Foolish newsletter services free for 30 days. We Fools don't all hold the same opinions, but we all believe that considering a diverse range of insights makes us better investors. The Motley Fool has a disclosure policy.