Illumina Inc. reported that its third-quarter revenues increased 14 percent from the same quarter last year, consistent with the company's preliminary report earlier this month that revenues would not be as high as anticipated.

The sequencing company reported total Q3 revenues of $550.3 million, up from $480.6 million in Q3 2014, but missed analysts' average estimate of $556.1 million.

"The fundamentals of our business remain strong, despite a 3 percent miss to revenue expectations," Illumina CEO Jay Flatley said in a statement. "Our competitive position and product development pipeline are as robust as ever, which we believe will enable our continued penetration of the enormous market opportunities ahead."

Following Illumina's pre-announcement of lower than expected revenues earlier this month, several investment banks downgraded Illumina, while others cut revenue estimates.

Despite lower than anticipated overall revenue, Illumina's sequencing revenues grew 21 percent year over year with an uptick in shipments to clinical and translational customers, which grew 40 percent. Shipments to both research and clinical customers in the oncology field now represent around 20 percent of revenues, Flatley said in an earnings call.

The company finished the quarter with $551.5 million in cash and cash equivalents and $887.9 million in short-term investments.

For fiscal year 2015, Illumina said it expects approximately 18 percent total revenue growth and fourth quarter revenues of around $570 million.