What did the market think about Illumina's (ILMN 0.63%) fourth-quarter results and outlook for 2016? A quick look at the genomic sequencing company's stock performance since Illumina announced earnings on Feb. 2 tells the tale. Shares are down more than 14% after the company narrowly missed analysts' earnings expectations.

There's more to the story for Illumina, though -- both positive and negative. The company's management shared details about the fourth-quarter performance and what might be in store in the future during the earnings call last week. Here are five key takeaways from that call (with quotes courtesy of S&P Global Market Intelligence). 

1. Good news and bad news for NIPT
Revenue for Illumina's non-invasive prenatal testing (NIPT) jumped a whopping 50% year over year in the fourth quarter. This growth was helped by an important decision made by Anthem (ELV 1.19%) in 2015.

For a long time, health insurers only approved payment for NIPT for high-risk pregnancies. Anthem changed course in August when it announced that NIPT would be considered medically necessary for average-risk and low-risk pregancies also.

Illumina CEO Jay Flatley said that the company estimates that "25% of the U.S. population has coverage with Anthem and regional Blue Cross Blue Shield carriers who've made a favorable coverage decision for average risk." This presents a solid opportunity for Illumina to generate even more growth from its NIPT business.

Not everything is sunshine and roses for NIPT, though. One of Illumina's largest customers is shifting its testing in-house. This had an impact in the fourth quarter and will continue to hurt service revenue in 2016.

2. Benchtop sales are back on track
Sluggish sales of benchtop sequencing systems contributed to Illumina's disappointing third-quarter results -- but the fourth quarter looked much better.

President Francis deSouza said that "MiSeq orders approached record levels and NextSeq orders were the highest in any quarter since launch." Hints of that strong performance were evident in the third quarter.

MiSeq's success came largely from customers new to sequencing. Over half of MiSeq orders came from these new customers, according to deSouza. Over 40% of NextSeq sales stemmed from clinical and translational centers.  

3. MiniSeq isn't cannibalizing MiSeq too much
One concern about Illumina's benchtop market related to whether the company's new MiniSeq system would take away market share from MiSeq. So far, fears of cannibalization haven't been too big of a factor, according to company management.

Francis deSouza indicated that his team now thinks that there will be only "slight overlap" between MiniSeq and MiSeq. He also stated that expectations are that many customers will purchase multiple MiniSeq units.

Still, though, Illumina admits that there will be some cannibalization. The company thinks that perhaps 20% to 25% of MiniSeq systems sold will be at the expense of MiSeq sales.

4. High expectations for new start-ups
In January, Illumina announced that it was starting a new company called GRAIL to focus on the cancer screening market. A large-scale clinical trial is planned for 2017. Jay Flatley mentioned that recruiting is under way for a CEO for GRAIL and that a potential lab and office space have been found.

If you have any doubt about how important GRAIL is for Illumina, look at a pretty significant management change that just occurred. Longtime board member Dr. William Rastetter stepped down from Illumina's board of directors last week to serve as a board member and to invest in GRAIL. Dr. Rastetter served as chairman of Illumina's board for 11 years.

Illumina's other start-up company, Helix, is also a high priority. Helix was launched along with Warburg Pincus and Sutter Hill Ventures to focus on genetic sequencing for consumers interested in what their DNA indicates about their ancestry and health.

Flatley underscored the importance of both GRAIL and Helix to Illumina's future success. He referred to both start-up companies as "important investments" that will "catalyze significant long-term revenue growth for the company."

5. Cautious first-quarter outlook
Despite plenty of positive points, Illumina's management team sounded cautious about the first quarter of 2016. Part of the challenge will be in comparing the quarter against the same period in 2015. Illumina had a much larger backlog for HiSeq X units headed into first quarter of 2015 than it did at the beginning of this year.

The impact of the large customer moving NIPT in-house mentioned earlier stands as another factor that could dampen first-quarter results. And while Illumina doesn't expect too much cannibalization of MiSeq by MiniSeq, Flatley acknowledged that "sometimes customers take a little bit of time to make a decision" between potentially competing products. This could hold down orders for both systems at least temporarily.

Japan also continues to be an area of concern. Illumina isn't very optimistic that the funding situation in Japan will improve significantly enough to help in the first quarter.