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Alnylam Pharmaceuticals (ALNY -1.20%) and Juno Therapeutics (JUNO) have garnered significant interest among biotech investors because their clinical pipelines are both oriented toward exceptionally high-growth markets.

Alnylam, for instance, is in the process of building a pipeline of RNAi therapeutics for the treatment of rare diseases -- a niche market that comes with several advantages such as extended periods of exclusivity and shorter development timelines. 

For its part, Juno is quickly becoming a leader in the emerging field of adoptive T cell therapies such as chimeric antigen receptor (CAR-T) and high-affinity T-cell receptor technology (TCRs). Although the potential for these types of therapies to make an impact in the realm of solid tumors remains an open question, they do appear to be game-changers when it comes to treating blood-based disorders. 

As these two clinical-stage biotechs are both on track to transition into revenue-generating entities within the 2017 to 2018 time frame, I think now is a good time to consider which stock offers investors the best opportunity right now. So, let's get started.

Alnylam is a rare-disease specialist with tremendous upside potential
Although Alnylam sports eight clinical-stage programs in total -- with more on the way -- all eyes are on the company's two late-stage product candidates patisiran and revusiran indicated for transthyretin (TTR)-mediated amyloidosis.

As patisiran's ongoing late-stage trial is forecast to wrap up in 2017, Alnylam could have its first product on the market by 2018. Revusiran, with its later start, is expected to produce top-line data in 2018, implying that its commercial launch is likely to kick off in 2019. Taken together, these two drugs have the potential to generate close to $2 billion in peak sales for the company within the next decade.

Besides its emerging late-stage clinical program, Alnylam is also in decent financial shape, exiting 2015 with $1.08 billion in cash and short term investments. So at current burn levels, the company shouldn't need to raise additional funds until patisiran's commercial launch is close at hand.

The downside, though, is that Alnylam isn't the only antisense drugmaker targeting TTR-mediated amyloidosis. For example, Ionis Pharmaceuticals' (IONS -0.82%) late-stage drug, IONIS-TTR, could hit the market at nearly the same time as patisiran. Moreover, IONIS-TTR covers the same indications as both patisiran and revusiran, potentially dampening their commercial potential. 

Juno is a top dog in the emerging adoptive T-cell therapy space
Juno's value proposition mainly centers around its CD-19 directed T-cell therapies indicated for blood-based disorders such as acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia, and non-Hodgkin lymphoma in the second-line setting. After all, these three initial indications alone are believed to be worth upwards of $5 billion in potential sales, according to Juno's management.

Right now, the biotech has an ongoing pivotal stage trial for its lead CAR T-cell product candidate, JCAR015, as a treatment for adult relapsed/refractory ALL that could lead to the company's first FDA approval by 2017. The possible hang-up is that CAR T therapies in general have run into serious problems when it comes to safety. JCAR015, for instance, induced several cases of severe cytokine release syndrome and/or neurotoxicity in an early-stage study.

Looking ahead, Juno is developing two follow-up products to JCAR015 -- JCAR017 and JCAR014 -- that are so far exhibiting superior efficacy profiles. Unfortunately, their safety profiles don't appear to be any less concerning than JCAR015's:

Source: Juno Therapeutics.

Complicating matters further, Juno is in a tight race with Kite Pharma (NASDAQ: KITE) to be the first to commercially launch an adoptive T-cell therapy. Kite, for example, believes that its lead product candidate, KTE-C19, could be on the market by 2017 -- roughly the same time as JCAR015.

On the bright side, Juno does have a strong balance sheet, with $1.17 billion in cash and short term investments at the end of third quarter of 2015. Moreover, its blue-chip biotech partner Celgene (CELG) could choose to opt in to further the development of Juno's CAR T product candidates in the near future, which would bring in additional milestone payments in the process.

Is Alnylam or Juno the better stock?
While both stocks are inherently risky, I think Alnylam wins this match-up because antisense drugs have reached the market in the past -- with Ionis Pharmaceuticals' cholesterol-lowering drug Kynamro gaining a regulatory approval in 2013. CAR T-cell products appear likely to do the same based on their impressive response levels across a host of B-cell malignancies, but they remain a more speculative bet than antisense-based drugs right now. 

Another important factor to consider is Juno's $1 billion research partnership deal with Celgene. From an outsider's perspective, this huge deal looks an awful lot like a prelude to a buyout -- that is, if this technology leads an approved product. Put simply, Juno's upside potential over the long term might be limited because of a tender offer from Celgene, especially compared with what Alnylam offers investors if its lead product candidates succeed in their ongoing late-stage studies.