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EmTech: Illumina Says 228,000 Human Genomes Will Be Sequenced This Year

Record number of genomes being decoded, but cost of DNA sequencing might not fall much further, says Illumina president.
September 24, 2014

Henry Ford kept lowering the price of cars, and more people kept buying them. The San Diego–based gene sequencing company Illumina has been doing something similar with the tools needed to interpret the human genetic code.

Francis de Souza, president of Illumina
Francis de Souza, president of Illumina

As of this year, an estimated 228,000 human genomes have been completely sequenced by researchers around the globe, said Francis de Souza, president of Illumina, the maker of machines for DNA sequencing, during MIT Technology Review’s EmTech conference in Cambridge, Massachusetts.

De Souza said Illumina’s estimates suggest that the number will double about every 12 months, reaching 1.6 million genomes by 2017, as the technology shifts from a phase of collapsing prices to expanding use in medicine.

The price of sequencing a single genome has dropped from the $3 billion spent by the original Human Genome Project 13 years ago to as little as $1,000, he said.

During an interview, De Souza questioned whether the price would keep falling at that rate. “It’s not clear you can get another order of magnitude out of this,” he said. Instead, he said, his company’s focus is now on making DNA studies more widespread in hospitals, police labs, and other industries.

“The bottleneck now is not the cost—it’s going from a sample to an answer,” De Souza said. “People are saying the price is not the issue.”

Illumina’s sequencing machines, which cost as much as $1 million each, are unmatched in their speed and accuracy. But the company’s growth has rested sometimes precariously on two curves. One has been the collapsing price of sequencing. The other is the soaring demand from genome scientists and funding agencies.

During the EmTech conference, De Souza said Illumina’s success was due to a “hard pivot” the company made in 2006, when it got into the DNA sequencing business by acquiring Solexa, a U.K. startup, and bet its fortunes “on a technology with no sales, that no one knew if it would work.”

That bet succeeded spectacularly, with Illumina machines now accounting for more than 90 percent of all DNA data produced. Last year, Illumina sold $1.4 billion worth of equipment, chemicals, and tests, about 25 percent more than the year before.

But De Souza says Illumina is now pivoting again. This time, its big bet is that DNA sequencing will become routine in medicine, not just in research labs. To make sure that happens, he said, the company is investing in simplifying its technology, winning FDA approval for more diagnostic tests doctors could order directly, developing ways to store DNA data in the cloud, and even launching a DNA app store. “The big pivot now is to the clinic. Getting there will change everything that we do,” he said.

For now, most DNA sequencing is still done by science labs. Of the 228,000 genomes Illumina estimates have been sequenced so far, more than 80 percent are part of scientific research projects, De Souza said. Those include a plan that the U.K.’s government is undertaking to decode 100,000 genomes over several years.

But Illumina’s future business will look different, De Souza said. Sequencing is becoming common in hospitals, particularly for guiding the treatment of cancer patients. Illumina has said it thinks the total possible market for high-speed DNA studies is about $20 billion a year, of which half is connected to studying the DNA of people fighting malignancies like melanoma, lung cancer, or brain tumors, the company estimates.

Recently, many smaller companies and labs have launched DNA tests to scan tumor tissue for mutations. These tests, which largely use Illumina machines, are designed to detect the “driver mutations” of a person’s cancer and help doctors pick the drug that could work best. However, the tests are only lightly regulated, and scientific findings have been rushed into commercial use. Often, doctors are picking drugs on the strength of slim evidence.

“There is a cacophony that is not serving patients well,” Rick Klausner, Illumina’s chief medical officer, said earlier this year. “We think these tests need to be regulated.”

In cancer clinics, Illumina thinks its job is to reduce confusion and offer simplified, and standardized, tests. This year it announced collaborations with several drug companies and academic centers to develop “panels” that would decode the 100 or so most important cancer genes. Those panels would be sold as FDA-approved kits.

De Souza said such cancer diagnostics would be a test of Illumina’s effort to transform itself from a seller of complex instruments to an everyday brand in hospitals. “Researchers can roll their own, but a lot of customers just want the answer,” he said. “For a lot of uses, the technology needs to be pre-packaged to be accessible.”

An earlier version of this article incorrectly described an estimate by the DNA sequencing company Illumina. It estimates that 228,000 human genomes have been sequenced through 2014, including all previous years, not in 2014 alone.

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