SAN FRANCISCO—Illumina said Monday it will join with Nashville Biosciences and Amgen’s deCODE Genetics subsidiary on a collaboration to whole-genome sequence the largest-ever dataset of genomes from African-Americans—approximately 35,000 DNA samples.
deCODE has agreed to carry out whole-genome sequencing on the 35,000 samples using Illumina sequencing technologies, and will upload the data to the Illumina Connected Analytics platform.
In their announcement, Illumina and partners emphasized that the project would help diversify genomic data, which to date has largely been drawn from patients of European ancestry—and thus, the partners hope to improve understanding of the underlying genetic causes of disease among African-Americans, and promote more equitable access to precision health therapies.
“The whole-genome sequencing of these 35,000 samples will work toward greater diversity of genomic data to ultimately enable improved access to precision therapies for all people,” Joydeep Goswami, chief strategy and corporate development officer and interim chief financial officer of Illumina, said in a statement.
The project will be the first undertaken by Illumina and Nashville Biosciences—a wholly-owned subsidiary of Vanderbilt University Medical Center (VUMC)—through their Alliance for Genomic Discovery (AGD), a multiyear agreement designed to establish a preeminent clinico-genomic data set, and more broadly accelerate therapeutic development through large-scale genomics.
The AGD, launched last year, aims to whole-genome sequence at least 250,000 de-identified human DNA samples from VUMC’s BioVU biobank over two and a half years, in collaboration with several biopharma companies. The BioVU samples, which were extracted from blood collected during routine clinical testing, are linked to de-identified clinical data derived from VUMC’s electronic medical records. Patients who provided the samples consented to their use in research.
“Once complete, this data set will provide a wealth of new information about the human genome and accelerate the study of disease in—and discovery of new therapeutics for—populations less well represented in prior large-scale sequencing efforts,” stated Leeland Ekstrom, chief executive officer of Nashville Biosciences. “The opportunity to sequence this diverse set of samples will help broaden our understanding for individuals who have been underrepresented in genetic research and continue to experience health disparities.”
Pharma and biotech collaboration partners planning to participate in the AGD, and in further sequencing, are expected to be announced soon, Illumina, Nashville, and Amgen said. Researchers will analyze the data for drug discovery and therapy development, with the data to be returned to BioVU in order to be made available for academic research within the Vanderbilt community.
Shares fall on earnings forecast
The collaboration with Amgen capped a flurry of announcements by Illumina during its presentation at the JP Morgan 41st Healthcare Conference, held here at the Westin St. Francis Hotel—the first in-person conference since 2020, just days before COVID-19 became a global pandemic.
Illumina CEO Francis deSouza told conference attendees that Illumina will finish the fourth quarter of 2022 with $1.075 billion in revenue—down 10% from $1.193 billion in Q4 2021—and all of last year with $4.576 billion in revenue, up 1% from $4.526 in 2021.
deSouza projected a much brighter 2023 for Illumina with revenue expected range from $4.9 billion to $5.03 billion, for 7 to 10% revenue growth, and earnings per share set to range from $1.25 to $1.50. The EPS forecast fell short of the $2.99 that analysts surveyed by Bloomberg News expected Illumina to project.
That appeared to explain why Illumina shares fell 16% Monday in after-hours trading, after climbing about three percent during the day.
During his presentation and in a Q&A session afterward, deSouza asserted that Illumina expects to reap the reward of shipping the first of its new NovaSeq X sequencing systems later this quarter. According to Illumina, more than 140 orders have been placed for NovaSeq Xs—about half the 300 that the company expects to ship to customers this year.
About 35% of those orders were placed by clinical customers—an unexpectedly large share, deSouza said, of the company’s customer base, whose academic and industry users typically account for the bulk of sequencing system orders.
Illumina also projected a sizable increase in revenue for Grail, the cancer blood test developer that it agreed to acquire for $7 billion in 2020. From about $55 million in 2022—including $23 million generated in Q4—Illumina guided investors to expect between $90 million and $110 million in revenue for Grail this year. De Souza said 80% of that growth will come from Grail accelerating adoption of its Grail Galleri® test.
In 2022, Grail sold more than 60,000 tests ordered by more than 4,500 physicians—a feat Illumina trumpets as the fastest first-year revenue ramp in the history of cancer screening tests.
Illumina’s acquisition of Grail was completed in 2021—but blocked in Europe in September 2022, after the European Commission concluded the purchase would stifle innovation and reduce choice in the emerging market for blood-based early cancer detection tests.
Illumina’s acquisition of Grail has fared better in the U.S., where as administrative law judge ruled in its favor against the U.S. Federal Trade Commission (FTC)’s challenge to the Grail acquisition. The FTC is appealing the ruling, just as Illumina is appealing the EC decision.
Illumina’s presentation follows a year of announcements by competitors clearly taking aim at the sequencing giant, often by name.
Among notable rivals, Singular Genomics has launched its G4 platform, positioned between Illumina’s NextSeq and NovaSeq sequencing systems. And this week at JPM itself, Complete Genomics—a subsidiary of China’s MGI—announced the arrival of its full sequencing platform in the U.S., while Pacific Biosciences (PacBio) said it received orders for 76 Revio systems during the fourth quarter of 2022, making it the most successful product announcement in PacBio’s history.
Illumina maintains that it can still maintain leadership in sequencing even as would-be rivals step up their activity in the space, potentially shrinking its market share as more rivals emerge over time.
“We’ve always had competition,” deSouza said—starting with when the company entered the next-generation sequencing market in 2007. “We always take competition seriously.”
“We continue to monitor the market, and we want to make sure that from a customer perspective, we’re continuing to provide the best value proposition to our customers across the dimensions that they care about,” deSouza added. “Performance is certainly one. Cost effectiveness is another. Ease of use, the clinical infrastructure that we deliver. So, we will continue to take competition seriously.”
deSouza said Illumina is well-served by its “fantastic” commercial organization, given the company’s more than 9,500 customers in over 155 countries. He said the company’s customer focus was reflected most recently in its creation of 15 new thermostable reagents designed to support ambient-temperature shipping, which will eliminate the need for dry ice as well as reduce waste.
“We have a front-row seat into what our customers not only want today, but will want in the future,” deSouza declared.