It's been a year of ups and downs for these two drugmakers. Shares of Ionis Pharmaceuticals (NASDAQ:IONS) and Bellicum Pharmaceuticals (NASDAQ:BLCM) tanked to begin the year, but the latter had notched a significant gain until a recent dive.

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At the time of writing, Ionis and Bellicum were down 26% and 19% this year, respectively, despite giving investors reasons to cheer. It looks like an opportunity to pick up a couple great stocks at bargain prices, but which is the better pick overall? Let's look closer at both to find out.

The case for Ionis Pharmaceuticals

With an FDA approval for Kynamro under its belt, Ionis has a leg up on clinical-stage Bellicum. Unfortunately, lackluster sales of the cholesterol-lowering therapy narrow this advantage to a doll-sized limb.

Luckily, Ionis also has immense value in a bulging pipeline, which could begin gushing sales in the near future. One of many partners, Biogen, recently submitted applications for Spinraza, and a speedy approval is widely expected. The well-tolerated therapy is the first to show a significant benefit for patients with the leading genetic cause of infant mortality in the U.S., spinal muscular atrophy.

Stellar data in the most severe form of the disease led to peak annual sales projections of around $1.5 billion for Spinraza. Following the presentation of equally impressive results in patients with less severe forms of the disease, though, its addressable patient population could be much larger than hoped. With this in mind, achieving more than $2 billion in annual sales isn't too far-fetched.

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If Biogen's sales force succeeds, Ionis could receive about $150 million in milestone payments and royalties in the mid-teens. Spinraza cash flows would help support development of Ionis' wholly owned lipid-lowering candidate, volanesorsen. It's in a late-stage study that could support an application if results fall in line with previous observations.

Most companies the size of Ionis Pharmaceuticals would be thrilled with two candidates like volanesorsen and Spinraza, but there's plenty more coming through the pipe. A total of about 30 clinical-stage candidates in development is enough to make some of the world's largest biopharmas jealous.

The case for Bellicum Pharmaceuticals

This clinical-stage biotech doesn't have nearly as many irons in the fire as Ionis does, but it does have a very interesting lead candidate. Stem cell transplants have long been an effective way to treat a variety of diseases, but often fatal graft-versus-host disease (GvHD) complications severely limit the treatment option. Bellicum's BPX-501 aims to change this paradigm by employing a "safety switch" to control GvHD attacks before they become serious.

Generally, patients receiving stem cells from parents -- which are nearly always available -- encounter GvHD far more frequently than those grafted with cells from siblings -- which are often unavailable. Depleting patient t-cells ahead of the transplant helps, but this also increases exposure to deadly opportunistic infections. BPX-501 operates on two fronts by allowing physicians to safely add back infection-fighting t-cells post-transplant. If the modified t-cells begin running amok and symptoms of GvHD surface, simple administration of rimiducid triggers their swift demise.

The process might sound like science fiction, but it appears to work. Bellicum recently presented data from 85 children treated with BPX-501 monitored for at least 100 days post-transplant. There was just one patient death, unrelated to the cells themselves, which is an incredible improvement over historical mortality rates for patients receiving similar transplants. Adding back t-cells appeared to dramatically reduce infections, and healthcare providers were able to stop five cases of acute GvHD with rimiducid before they became fatal.

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According to Bellicum, European regulators appear keen to usher BPX-501 through the regulatory process, and they will allow an application based on the ongoing study if the company adds more patients. In order to succeed, BPX-501 must significantly reduce risk of GvHD, infection, and death. Based on the data so far, it looks like a slam-dunk.

Running the numbers

Bellicum Pharmaceuticals stock has fallen about 22% since Juno Therapeutics announced two more patient deaths in a trial with its lead candidate. Juno's candidate employs modified t-cells to attack cancer, but it's otherwise unrelated to Bellicum's BPX-501. If approved, annual sales of the stem cell transplant solution could very well top $1 billion. That makes the company's recent market cap of $441 million seem awfully cheap.

An influx of milestone payments pulled Ionis Pharmaceuticals' bottom line into positive territory during the third quarter, but we'll need to measure its relative value based on potential sales and a market cap around $5.46 billion. It looks like Spinraza, volanesorsen, and perhaps another candidate will need to succeed to justify Ionis' valuation. With plenty of shots on goal, I'd say it's a chance worth taking.

I'll keep my eye on BPX-501, but without another promising candidate in mid- to late-stage development, it might be best to keep Bellicum on a watchlist for now. That makes Ionis Pharmaceuticals the better buy.