Illumina's New Low-Cost Genome Machine Will Change Health Care Forever

Dr. Bradley Patay, who is tanned and handsome, with a constant smile that pushes the limits of cheek physics, has an office at the Scripps Clinic, next to the Torrey Pines Golf Course and the Pacific Ocean. An internal medicine specialist, he also happens to be very well versed in genetics. If, like me, you’ve had your entire genome sequenced, Dr. Patay can tell you what the results mean. He’ll pull your data up on a computer and show you how to explore your own genetic makeup. Having this genome decoding skill makes him a rarity for the moment. “I want to be prepared when people come in with their data and explain it to them in a competent manner,” he says. Soon, your doctor may work this way, too.

Quietly and dramatically, genetics-based medicine has taken off in just the last couple of years. For about a decade, biotech companies had been haunted by their own hype. The promise of sequencing technology was that the mysterious triggers of disease would be uncovered and cataloged. The cures for cancer, Alzheimer’s disease, and strokes would then follow. Instead, extracting information from DNA proved more costly, time consuming, and difficult than backers of the science either believed or let on from the outset.

Now children with rare diseases that previously went undiagnosed routinely get answers about the causes of their conditions—and sometimes therapies that ease their pain. Inexpensive consumer DNA tests offer insight into resistance to certain medicines. Two companies—Foundation Medicine (FMI) and Genomic Health(GHDX)—have changed the way cancer gets treated for adults. Instead of viewing all colon cancers as uniform things, for example, Foundation sequences a patient’s tumor and compares its properties with a database of past specimens. The company then helps pinpoint a treatment that’s proven to be effective against that particular type of tumor.

Scientists and entrepreneurs encouraged by these results have turned giddy once again: A long-awaited breakthrough in sequencing—an affordable test—is at hand. As of last year, the going rate to get your genome sequenced was about $10,000. Now it will be closer to $1,000. At the center of the excitement is Illumina (ILMN), a publicly traded biotech company based in San Diego with a market capitalization of $15 billion. Founded in 1998, the company invented and acquired its way to the top of the gene-sequencing-machine market. It’s estimated that about 90 percent of all human genomes ever sequenced have been done on Illumina’s machines. This year the company should report sales of more than $1.6 billion, according to Wall Street forecasts compiled by Bloomberg.

On Jan. 14, Illumina reduced the cost of sequencing by a factor of 10 when it unveiled the HiSeq X (pronounced “high seek ten”). The machine, about the size of a large photocopier, is basically the first DNA-crunching supercomputer. It can knock out 20,000 human genomes per year. Assuming it’s running at full capacity and including all costs—the purchase price, plus labor and materials (the reagents and other chemicals)—the machine can sequence an entire genome for $1,000.

HiSeq Xs, which cost $1 million each and must be purchased 10 at a time, are designed to meet the growing ambitions of hospitals, medical research centers, and entire countries. England, for example, plans to sequence 100,000 people and thousands of cancer tumors over the next couple of years in a bid to make genomic data part of the mainstream health service. Illumina also just released the NextSeq 500: a much smaller machine that costs about $250,000 and can fit on a lab bench. Where the HiSeq X is designed for research centers that need to crunch hundreds of whole genomes simultaneously, the NextSeq 500, which handles one genome at a time, is meant to be cheap enough for a hospital or other commercial customer.

The $1,000 genome has long been considered a milestone—the price at which sequencing can finally go mainstream. Researchers can sequence thousands of people, creating much richer data sets that can in turn be used to pinpoint the causes of illness. Children with rare diseases can expect to be analyzed and treated much more quickly, and adults with cancer can afford to have their tumors analyzed. Unlike other companies that declared victory in the $1,000 genome race only to stumble, Illumina has its product in customers’ hands. “This isn’t hocus-pocus,” says Jay Flatley, the company’s silver-haired, longtime chief executive officer. “We are shipping the machine.”

The first human genome required $3 billion and 13 years to sequence. Ten years later, with the HiSeq X, that time has fallen to about 24 hours. It’s now possible to take a blood test and meet with your doctor a week or two later to go over your inherited strengths and weaknesses on an iPad. With the flick of a finger across the screen, you might learn, as I did, of a resistance to the drug Warfarin, which is used to prevent blood clots. The process can be nerve-racking, particularly as your doctor hunts for genes that can indicate a susceptibility to breast and colon cancer. “Well, you’re clear,” Dr. Patay tells me. “I probably shouldn’t have saved that for the end of our hour, because we might have been having a very different and more difficult conversation.” He’s still learning, too.


Last November, Illumina took over the Estancia La Jolla Hotel and Spa, an elegant Mexican-villa-style resort just north of San Diego, to run one of a series of events it calls Understand Your Genome, or UYG. About 60 people paid $5,000 each to have their genome sequenced. The attendees, a mix of doctors, scientists, genetic counselors, and the curious, gathered for two days of lectures and personal DNA exploration. They got white gift bags that contained an iPad tied with a gold bow, a framed glass slide of their DNA sample, a hard drive holding their entire DNA sequence, and a binder with a clinical report disclosing which markers are tied to which conditions. In my case, there were no direct genetic links to anything scary. I am, however, a carrier for five rare diseases—none of which my children have, fortunately—plus there’s the resistance to Warfarin.