San Diego’s biggest biotech company, whose systems can sequence a human genome for under $1,000, reported a record fourth quarter with double-digit increases in revenue and profit.

Illumina, with headquarters in University City, on Tuesday announced fourth fiscal quarter net income of $153.3 million, or $1.03 per share, a 90 percent increase from the same quarter a year ago. Revenue grew by 32 percent to $512 million compared to a year ago.

The results “greatly exceeded our expectations,” CEO Jay Flatley said in a statement. “Our focus on technology innovation, as evidenced by the launch of HiSeq XTM Ten, which enables the $1,000 genome, and the NextSeq® 500, were major contributors to our outperformance.”

In July 2014, U-T San Diego reported Illumina had a market value exceeding $20 billion, making it easily the most valuable biotech company in San Diego County.

Illumina is getting a San Diego sales and use tax rebate of up to $1.5 million over 10 years under an Economic Development Incentive Agreement approved by the San Diego City Council. It’s meant to keep hundreds of biotech manufacturing jobs in San Diego.

The company recently announced that its HiSeq X Five, HiSeq 3000/4000 and NextSeq 550 instruments “will position us for continued long-term growth as we develop and address the large and nascent market opportunities ahead of us.”

Gross margin in the fourth quarter was 75.1 percent compared with 66.9 percent in the prior-year period.

Research and development expenses for the fourth quarter totaled $142.9 million compared with $76.7 million in the prior-year period.

Results for the company’s entire 2014 fiscal year included:

  • Revenue of $1.86 billion for the year, a 31 percent increase compared to $1.42 billion in the prior year.
  • Net income of $353 million, or $2.37 per share, for the year, compared to $125 million, or $0.90 per share, the previous year.
  • Cash flow from operations of $501 million and free cash flow of $395 million for the year.
  • Research and development expenses for the year of $388.1 million compared to $276.7 million in the prior year.

Illumina has emerged as the global leader in gene sequencing and DNA array technologies. Last March, the editors of the MIT Technology Review named Illumina the “smartest company in the world.”