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Almost 25 years after the Human Genome Project launched, and a little over a decade after it reached its goal of reading all three billion base pairs in human DNA, genome sequencing for the masses is finally arriving. It will no longer be just a research tool; reading all of your DNA (rather than looking at just certain genes) will soon be cheap enough to be used regularly for pinpointing medical problems and identifying treatments. This will be an enormous business, and one company dominates it: Illumina. The San Diego–based company sells everything from sequencing machines that identify each nucleotide in DNA to software and services that analyze the data. In the coming age of genomic medicine, Illumina is poised to be what Intel was to the PC era—the dominant supplier of the fundamental technology.

Illumina already held 70 percent of the market for genome-sequencing machines when it made a landmark announcement in January: using 10 of its latest machines in parallel makes it feasible to read a person’s genome for $1,000, long considered a crucial threshold for moving sequencing into clinical applications. Medical research stands to benefit as well. More researchers will have the ability to do large-scale studies that could lead to more precise understanding of diseases and help usher in truly personalized medicine.

Illumina was relentless in getting to this point. When CEO Jay Flatley joined the company in 1999, it was a 25–person startup that sold microarray chips, which were useful in examining specific spots on the genome for important variations. But while the market grew relatively fast, competition was tough. In 2003, for example, Illumina had $28 million in revenue and a net loss of $27 million. Making matters tougher, the potential for microarrays seemed limited once more comprehensive sequencing technology began to improve quickly. In 2006, when a company called 454 Life Sciences was months away from the first rapid readout of an individual human genome (that of DNA scientist James D. Watson), Flatley knew Illumina had to have a sequencing technology of its own, and he had a choice: build it or buy it. “We had an internal development program, but we were also looking at anyone in the market that already had a sequencing technology,” he says now. Ultimately he settled on buying a company called Solexa.

Solexa took advantage of a novel way of sequencing, known as sequencing by synthesis, that was 100 times faster than other technologies and correspondingly cheaper, says Flatley. But it was a small business, with just $2.5 million in revenue in 2006. After Illumina provided the global distribution Solexa needed, “we built it into a $100 million business in one year,” he says. “It was an inflection point for us. We began this super-rapid growth.”

The deal also turned out to be a turning point for Illumina’s competitors, which quickly fell behind technologically. Roche, which bought 454 Life Sciences in 2007, announced last October that it would shutter the company and phase out its sequencers. Complete Genomics, another competitor, cut jobs and began looking for a buyer in 2012; last year the Chinese company BGI-Shenzhen bought it, although Illumina made a failed bid for it as well.

The Solexa deal was far from the last time that Flatley transformed Illumina by buying the technology he thought it needed. Another pivotal point came last year, when the company bought Verinata Health, maker of a noninvasive prenatal sequencing test to identify fetal abnormalities. That gave Illumina a service that consumers can buy (through their doctors), in a market that could be worth billions of dollars in revenue.

Since 2005 Illumina has spent more than $1.2 billion on acquisitions. But it would be a mistake to dismiss the company as just a deep pocket. Illumina has a knack for improving the technology of companies it buys, says Doug Schenkel, managing director for medical technology equity research at Cowen and Company. When Illumina bought Solexa’s sequencing technology, Schenkel says, it was considered inflexible and was thought likely to hit a “ceiling”—after which it could probably not be improved further—within three years. “Illumina took that technology and, with innovation and investment, has made it flexible enough to not only dominate existing markets but open up multiple new opportunities,” he adds. “Even today—six years later—the ceiling is still at least three years away.”

Illumina’s soup-to-nuts strategy—of providing fundamental sequencing technologies as well as services that mine genomic insights—appears to be a winner as genomic information begins to touch the practice of medicine and enter everyday life. Illumina already has an iPad app that lets you review your genome if it has been analyzed. “One of the biggest challenges now is increasing the clinical knowledge of what the genome means,” Flatley says. “It’s one thing to say, ‘Here’s the genetic variation.’ It’s another to say, ‘Here’s what the variation means.’” Demand for that understanding will only increase as millions of people get sequenced. “We want to be at the apex of that effort,” he says.

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