Gene-sequencing giant Illumina is laying off 96 employees from its San Diego headquarters, according to paperwork filed with the state.

This workforce reduction comes at a time when Illumina is contending with geopolitics influencing its market, increased competition and a declining stock price, which is down about 35% year to date.

The company announced the layoffs last month in a WARN (Worker Adjustment and Retraining Notification) letter it sent to the state. The layoffs impact a variety of departments in the organization including finance, many senior scientists, engineers and some directors.

The layoffs will take effect on April 14, May 16 and Aug. 15, according to the WARN letter.

A company spokesperson said in an email that the layoffs were “not a broad-based reduction across the company,” when asked about whether there were cuts at other Illumina sites.

“We have created new roles and reduced others, and for those who will be leaving Illumina, we are committed to treating all with respect and compassion,” the company spokesperson said. “As always, we are guided by the needs of our customers around the world. Illumina continues to invest in advancing our strategy while also ensuring our structure, talent, and operating costs are aligned to support it.”

The layoff announcement came a week after Illumina reported its fourth quarter and full year fiscal 2024 earnings.

Illumina, which is one of San Diego’s largest public companies, had just under 9,000 full-time employees globally as of Dec. 29, 2024. Most of these employees, or 5,250, are based in the Americas region, 1,290 are in Europe, 2,190 are in Africa/Middle East and 300 are in the greater China region, according to Illumina’s annual report.

Illumina recorded about $4.37 billion in total revenue during the 2024 fiscal year, down about 3% from the previous year. The company attributed this to a decrease in sequencing instrument revenue from fewer shipments of its machines. Illumina’s net loss increased about 5% year over year to $1.2 billion in fiscal year 2024, according to the filing.

“For 2025, we will continue our transformation, executing our refreshed strategy that prioritizes a sharp focus on customers and our own operational excellence in order to drive Illumina forward,” said CEO Jacob Thaysen in the earnings release.

Thaysen has had to deal with orchestrating Illumina’s comeback strategy and the loose ends related to unwinding the company’s failed $7.1 billion acquisition of Grail. The early stage blood testing company was officially spun off from Illumina last June.

Over the past year, the shadow of the Grail deal has hung over Illumina despite its reinvigorated leadership and launch of new partnerships or products, namely the MiSeq i100 benchtop sequencer.

The past month alone has spelled choppy waters for Illumina with some variables out of its control. At the beginning of February, Illumina was placed on China’s “unreliable entities list” which could stifle its business there. The news came one day after President Donald Trump enacted steep tariffs on China.

Then, there are other companies, including local startup Element Biosciences, who seek to challenge Illumina’s market dominance. Health care giant Roche announced its plans recently for a new kind of sequencing analysis method called “sequencing-by-expansion,” which is expected to launch in 2026.

Additionally, Illumina — alongside the rest of the biotech industry — is facing uncertainty amidst looming cuts to research funding and grants, primarily from the National Institutes of Health (NIH). Local organizations, such as UC San Diego, could lose more than $100 million in annual federal funds that support research, if the proposed cuts prevail.

For Illumina, the customer base for its gene sequencing machines includes researchers at universities and private institutions as well as clients in clinical and commercial settings.

“A reduction or delay in research and development budgets and government funding may adversely affect our business,” Illumina reported as a risk factor in its annual filing. “For example, changes in the regulatory environment affecting life sciences and pharmaceutical companies, and reduced allocations to government agencies that fund research and development activities, such as the U.S. National Institutes of Health, or NIH, or targeted cancellations by the U.S. federal government of certain grants or contracts, could adversely affect our business or results of operations.”

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