Black Friday is just a few days away, which means that millions of consumers are gearing up to score huge discounts off their holiday shopping list. That's great, but we Fools get far more excited when high-quality stocks go on sale instead.

With that in mind, I scoured the biotech sector to identify stocks that are currently trading at highly discounted prices. Read on to see why I think the blue-light special is flashing on shares of Gilead Sciences (NASDAQ:GILD)Illumina (NASDAQ:ILMN), and Regeneron Pharmaceuticals (NASDAQ:REGN).

Image source: Getty Images.

A victim of its own success

Gilead Sciences' sales and profits have been under pressure all year long, which has caused its stock to plunge. Shares have fallen nearly 40% from their 2015 highs, which has pulled its valuation down to absurdly cheap levels.

So why has this biotech giant's financials been heading in the wrong direction? The blame can be placed squarely on the shoulders of its hepatitis C franchise. A few years back, Gilead launched its hepatitis C cures Sovaldi and Harvoni to market, both of which saw instant success. Gilead's sales and profits immediately skyrocketed, allowing Gilead's stock to follow suit. However, recent competitive launches from AbbVie and Merck have forced management to give in on pricing in order to maintain market share. That has the market worried that this company's best days are behind it.

Image source: Gilead Sciences.

While management has admitted that hepatitis C sales have likely already peaked, there are still reasons to remain optimistic. For one, the company continues to crank out billions in annual profits, which it is using to reward shareholders with buybacks and dividends. In addition, sales in its HIV franchise continue to grow rapidly, which will help to offset its hep C sales declines. Finally, the company continues to invest heavily in research and development in an effort to enter new disease areas, which could pay off huge down the road.

Gilead's near-term results are likely to remain under pressure, but shares could start to rebound once year-over-year comparisons start to become easier.

When double-digit growth isn't good enough

Shareholders of the genomic-sequencing leader Illumina have had a rocky 2016. Everything was going just fine until management warned investors that third-quarter sales were going to come in a bit light. The news caught the markets off-guard, sending traders heading for the exits

So what went so horribly wrong? Management said that it didn't close as many sales of its high-throughput systems as it had previously anticipated. As a result, management projected that sales were only going to grow by 10% in the third quarter and that they would be "flat to slightly up sequentially" in the fourth.

While most companies would be happy with double-digit revenue growth, Illumina's investors demand more. That's fair, as Illumina's stock was trading at more than 60 times trailing earnings before the news came out, so it was priced for high growth.

With shares now down 30% year to date, Illumina's price-to-earnings ratio has finally dropped to a more reasonable level. While 45 times earnings might not seem like a bargain, it's actually one of the cheapest opportunities for investors over the last five years.

ILMN PE Ratio (TTM) Chart

ILMN P/E ratio (TTM) data by YCharts.

While Illumina's recent hiccup shouldn't be ignored, the total demand for gene-sequencing machines is likely to continue to grow rapidly over time. In fact, predictions currently for the market to reach $20 billion by 2020 and that figure could expand rapidly if the the company's investments in GRAIL and Helix work out. 

As long as Illumina remains the top dog in the industry, then its future is looking bright.

Missing the forest for the trees

Regeneron Pharmaceuticals is another biotech giant that the markets have cast aside. Shares have dropped more than 26% since the start of the year in response to the company posting a string of negative headlines.

So what's gone wrong? First, data from a phase 2 study showed that its experimental compound rinucumab failed to improve upon the current standard of care treatments for neovascular age-related macular degeneration. Next, the Food and Drug Administration placed a clinical hold on its phase 2b study of fasinumab, a compound that is being researched with partner Teva Pharmaceuticals as a potential treatment for osteoarthritis pain and chronic low back pain. Finally, Regeneron and Sanofi announced that the FDA had rejected their submission for sarilumab for the treatment of rheumatoid arthritis due to manufacturing issues. 

Image source: Getty Images.

That's a lot of setbacks to throw at investors, so it is no wonder shares have headed in reverse year to date. However, I believe that this bad news is just a temporary setback, and that the company's long-term future is still looking bright. Here's why:

First, the problems with sarilumab and fasinumab appears to be fixable, so while these drugs are down, they are not out. Second, sales of the company's blockbuster drug Eylea continue to be strong, and its next-generation cholesterol-busting drug Praluent also looks like it is starting to pick up steam. Finally, an FDA decision on Dupixent, a potential blockbuster treatment for atopic dermatitis, is expected by the end of March. If it gets the green light, then investors enthusiasm for the company's shares could return.

In other words, Regeneron's future continues to look as bright as ever. That's why I think it's a great time to consider joining me as a shareholder.

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.