Newsletter, July 8: Illumina Tech Chosen by Spatial Perturb-Seq Spinout
A $47M 23andMe data breach settlement, a genome reanalysis study, CE certification for WGS Dx software, marathoners hitting the wall, and more.
Illumina has signed a deal to make it the official sequencing chemistry for a company commercializing one of the hottest classes of genomic technology: optical pooled screening.
Under a supply agreement announced July 8, Bifrost Biosystems will integrate Illumina’s sequencing-by-synthesis chemistry into its optical pooled screening (OPS) platform. Illumina’s reagents will be packaged and distributed as part of Bifrost’s OPS-optimized reagent kits, supporting in situ genotyping workflows on Bifrost’s system.
The deal locks in commercial access to Illumina’s sequencing chemistry, clearing one of the last technical hurdles standing between its cell-screening platform and a planned 2027 launch.
OPS is a technology that links complex cellular phenotypes, determined by imaging, to the genetic perturbations responsible for them, allowing researchers to study large numbers of genetic changes at once. It is immediately adjacent to spatial perturbation screening approaches, as discussed in the Ion Genomics podcast from June 5, 2026.
Bifrost, a Berkeley, California-based company with approximately 10 employees, licensed its core technology from the Broad Institute in 2024. On its website, Bifrost says it is a spinout from Johan Paulsson’s Harvard lab, but notes that Broad’s Paul Blainey and Harvard University’s George Church are also cofounders.
Blainey has also done key work in optical pooled screening, publishing a preprint on the method OttoSeq in April. Sami Farhi, a Broad researcher who also runs the spatial core lab there, told Ion Genomics that while his lab developed their own method for spatial perturb-seq “we use Paul [Blainey]’s method right now.” He’s using the approach to investigate how neuron morphology is affected by different psychiatric genes.
Genentech’s Aviv Regev and Eric Lubeck have also developed an OPS method, published a year ago in Nature Biotechnology.
The Illumina agreement is the company’s latest step toward commercializing the platform, which it said will support upcoming early-access collaborations with research institutions and other partners.
“This agreement represents an important validation of the maturity of the Bifrost platform,” Bifrost CEO Jonas Jarvius said in a statement.
Ion Genomics Updates
AI lab agents — software that can autonomously plan and execute complex scientific tasks — are moving from concept to reality in the life sciences. From Anthropic’s Claude Science to homegrown tools at startups like Tahoe Bio, researchers are turning to these software intermediators to get work done. This Friday’s podcast breaks down what that means for genomics.
To help break it all down, I’ve turned to Johnny Yu, chief scientific officer of Tahoe Bio, a startup that has been building huge datasets to train AI models with the aim of improving drug discovery and development. His company recently came up with their own agent-based approach to modeling biology.
We’re also just over a week away from another happy hour on Friday, July 17, this time with the wonderful Molly Zeller, who runs a DNA sequencing core lab at the University of Wisconsin. Our first happy hour also had a Madison, Wisconsin connection, so maybe there’s something to draw on.
Make sure to sign up for a Substack account before the happy hour at 6 p.m. Eastern / 5 p.m. Central / 3 p.m. Pacific on the 17th to get access to the live broadcast, or catch it later on the usual podcast channels.
Other genomics news
23andMe Data Breach $47M Settlement Approved
A Missouri-based US bankruptcy judge has approved a $46.8 million settlement for victims of a 2023 data breach at the genetic testing company 23andMe, as reported by Reuters on July 7. Approximately $14.3 million has already been disbursed.
The breach exposed genetic and other personal information of an estimated 6.9 million customers. California’s Attorney General has also filed a lawsuit related to the data breach.
World’s First CE-Certification for Whole-Genome Cancer Dx Software
Netherlands-based Hartwig Medical Foundation has received CE certification under the European In Vitro Diagnostic Regulation (IVDR) for OncoAct, its whole-genome sequencing.
Automated Genome Reanalysis Adds 5 Percent Yield
An automated process for continuous genome reanalysis developed by Australian researchers has been put into production, as reported by Yaakov Zinberg of GenomeWeb. I reported on the pipeline in 2024 before it had a name; now called Talos, the software made 241 diagnoses after being presented with 4,735 cases of unsolved rare disease, an additional yield of just over 5 percent.
In a paper published June 24 in Nature Medicine, researchers led by Zornitza Stark of the Murdoch Children’s Research Institute in Melbourne, Australia, suggested that nearly half were due to “improved analysis strategies. About a third stemmed from newly established gene-disease relationships and roughly one in five from new variant-level evidence.
Readers may recall that Illumina recently launched a study to apply both genome reanalysis and its new TruPath whole-genome assay to unresolved cases of childhood rare disease. It seeks an additional yield of more than 10 percent.
Simplify Genomics, a Human Longevity spinout, has signed a deal with SimonMed to integrate genome interpretation with whole-body MRI. Financial and other details were not disclosed.
What I’m Reading
Male runners may be twice as likely as female runners to “hit the wall” and slow down deep into a marathon, according to a recent study published in Scientific Reports.
The researchers analyzed 873,334 Berlin Marathon race times between 1999 and 2025. They found that while male runners tended to finish the marathon faster than female runners, the men were twice as likely to hit the wall and slow down by more than 20 percent. Only about a third of male runners did not slow down, while more than half of female runners were able to maintain an even pace.
The authors suggested that men may be going out too hard. Though I haven’t (yet) run a marathon, based on my college 8K races, this is a decent bet as to what’s happening. In fact, the faster a guy is, the more likely he is to hit the wall: among runners who finished in under three hours (or just under 7:00 per mile pace), “male runners were approximately six times more likely to experience catastrophic deceleration than their female counterparts,” the authors wrote.
My takeaway is that it’s a good idea to go out slightly slower than your goal pace for the first five or so minutes of a race. If you’re doing well you can make it up later and if you can’t, well, you probably got your pacing wrong to begin with.
Elsewhere on the Internet
The US Men’s National Team crapped the bed in their Round of 16 match against Belgium. I had previously said I thought the team could make the semifinals based on the way they were playing in early games. Unfortunately for me, they looked nothing like the swashbuckling team they started the tournament as.
Still, I’ll always have midfielder Malik Tillman’s magical free kick, the only US goal in the match. Belgium would retake the lead just over a minute later, so the joy was short lived, but what joy!