Get ready, bargain shoppers. The Nasdaq Biotechnology Index has plummeted 24% since the beginning of October and it looks like this pair received more lashes than they deserved. 

Agenus Inc. (NASDAQ:AGEN) and Gilead Sciences Inc. (NASDAQ:GILD) look like bargains right now, but market-beating gains are far from guaranteed. Here's what you need to know about potential calamities on their paths to growth.

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Agenus Inc.: Shots on goal

This biotech has taken a lot of shots on goal that have sailed wide, but its recently depressed market cap seems a little too pessimistic right now. A recent $150 million cash injection from Gilead Sciences for rights to three early stage cancer therapy candidates only pushed the stock's market cap up to around $277 million at recent prices.

Agenus has two checkpoint inhibitors in development that just might find a partner desperate enough to license them, but it's the company's partnered early stage assets that make this stock look like a risky bargain right now. Agenus' collaboration with Merck & Co. moved an undisclosed candidate into clinical trials this summer, and success would trigger significant milestone payments.

Gilead's surprising upfront payment will keep Agenus from asking shareholders for more money in 2019, and perhaps much longer. The new collaboration partners have three oncology candidates nearly ready to enter clinical trials. Beginning the studies will trigger milestone payments that begin small and could eventually total $1.7 billion. 

Biotech collaboration partners rarely recognize a fraction of potential milestone payments. That said, Agenus' partners are taking a lot of shots on goal. Positive results from any one of several early stage clinical trials could send this stock soaring from its present levels.

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Gilead Sciences Inc.: Let's try oncology again

In 2017, Gilead's $12 billion foray into the oncology space seemed bold, but investors are increasingly worried the biotech made a huge mistake. Yescarta launched in October 2017, but sales during the three months ended this Sept. 30, 2018, reached just $75 million.

The stock's fallen 18% since the beginning of October, but a new CEO on the way could give it some lift in the new year. Daniel O'Day will step down as head of Roche's pharmaceutical segment to become chairman and CEO of Gilead in March.

Once he arrives, Gilead's pipeline could have plenty of new directions to take. In addition to a handful of oncology candidates from Agenus, Gilead recently paid Scholar Rock $80 million upfront for options to license three fibrosis-inhibiting candidates.

O'Day will also have everything the company needs to move these early stage assets forward at top speed, and acquire more. Gilead Sciences finished September with $30.8 billion in cash and securities after generating $7.9 billion in free cash flow over the past year. 

Gilead's hepatitis C antiviral sales fell to just $902 million during the third quarter, a frightening drop from $2.2 billion a year earlier. Now that Gilead leans on hepatitis C sales for around 17% of total revenue, the company's HIV franchise will find it a lot easier to pull this entire train uphill. 

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Biktarvy launched this February as the first single-pill regimen for HIV-infected adults who are virally suppressed with another treatment or new to HIV treatment altogether. Unlike hepatitis C, HIV still requires lifelong treatment to keep the virus at bay. Biktarvy makes it so easy for patients and their doctors that EvaluatePharma thinks the tablet will add $6.1 billion in sales to Gilead's top line in 2024.

By then, Gilead could launch a treatment with similar sales expectations. Filgotinib is behind similar oral rheumatoid arthritis treatments in late-stage development, but a superior safety profile that we've seen so far in pivotal studies could send it to the top of the class.

Gilead is still incredibly profitable, and Bikrtarvy and filgotinib could return this company's bottom line to growth in the years ahead. The stock has been beaten down so far that you can scoop up the shares at just 10.2 times free cash flow generated over the past 12 months.

Something for everyone

Agenus is a long way from safe, but it's going to have plenty of chances to bounce back before it has to visit the equity tap again. Swinging for the fences with Agenus could more than double your money in a couple years, or clinical trial setbacks could cause investors to lose everything.

Gilead Sciences is poised to generate heaps of cash, and it isn't shy about sharing profits with investors as dividends they can keep. This biotech might not have what it takes to skyrocket, but a lot needs to go wrong before this stock drags your portfolio down.

This article represents the opinion of the writer, who may disagree with the “official” recommendation position of a Motley Fool premium advisory service. We’re motley! Questioning an investing thesis -- even one of our own -- helps us all think critically about investing and make decisions that help us become smarter, happier, and richer.