Illumina Doubles Down on Newborn Sequencing: Ion Genomics Newsletter, June 23, 2026
10x teams up with Cleveland Clinic, Norway embraces nanopore-based brain cancer dx, Guardant-TwinStrand legal update, a World Cup-related correction, and more.
Illumina is taking steps to entrench its new TruPath whole-genome sequencing (WGS) assay for newborn sequencing in the intensive care setting.
Last week at the annual meeting of the European Society of Human Genetics, Illumina announced the Beyond GiICS (Genomics in the Infant Intensive Care Setting) study, which has partnered with “baby animal” sequencing projects across the region, to analyze approximately 400 unresolved cases.
Some cases will get reanalysis with Illumina-developed bioinformatics tools, including its DRAGEN pipelines and new AI variant interpretation tools; however, select cases will get re-sequenced using the TruPath assay, which provides information on larger genomic features, including repeats, structural variants, and larger insertions and deletions.
There are two ways of looking at this development. On the negative side: it’s a tacit admission that short-read genomes may be leaving out clinically important variants when diagnosing genetic disease.
In pediatric rare disease, speed and diagnostic yield are two of the most important factors and Illumina is getting squeezed on both fronts. Long-read approaches from Pacific Biosciences are getting to a point where they’re becoming first-line tests for suspected genetic diseases (outside the NICU) and researchers at Children’s Mercy Kansas City have already launched a pilot study similar to Beyond GiICS, where they’re evaluating cases that were not solved by rapid WGS.
Moreover, on the speed front, nanopore-based approaches from Oxford Nanopore Technologies and, more recently, Roche, may soon lead to same-day analysis, compared to two to three days for rapid short-read WGS.
After providing the technology that established the field of newborn sequencing, Illumina must prepare to fend off competition, something its doing across many sequencing applications.
On the positive side, if Illumina is correct in its hypothesis that TruPath can boost detection rates by an additional 10 percentage points, it could strengthen its position in the newborn sequencing market. That would translate to somewhere between 40 to 50 percent diagnostic yield, as rapid newborn sequencing studies have shown yields of around 30 to 40 percent.
This is not necessarily a big market, however, it has been a winner politically — many US states and other nations have launched “baby animal” NICU sequencing programs — and if WGS-based newborn screening ever become widespread, establishing a bulwark with TruPath could pay dividends.
Other countries participating in Beyond GiICS include Austria, Czechia, and Turkiye. Illumina is in the process of finalizing a deal to bring on another Western European country.
Illumina also added a seat to its board and appointed Daniel Skovronsky to fill it, effective immediately. He currently serves as Chief Scientific and Product Officer at Eli Lilly. Lilly acquired his company Avid Radiopharmaceuticals, in 2010. He has previously served on the board of Myriad Genetics. Skovronsky holds a MD-PhD from the University of Pennsylvania.
Other genomics news
10x Genomics, Cleveland Clinic Collaborate on Single-Cell, Spatial Diagnostics
10x Genomics and the Cleveland Clinic are collaborating on new diagnostics for bladder cancer based on 10x’s single-cell and spatial technologies.
Oxford Nanopore Expands Norwegian Collaboration on Rapid Brain Cancer Classification
Oxford Nanopore Technologies and MATRIX, Norway’s national cancer research center, are expanding their collaboration to implement rapid nanopore sequencing for central nervous system tumour classification across that country’s public healthcare system.
Guardant Health, TwinStrand Legal Battle Takes A Turn
Guardant Health was unsuccessful in a bid to overturn an $83 million jury award to TwinStrand Biosciences from a patent infringement case. Moreover, a federal judge added a 6 percent ongoing royalty.
However, in parallel legal action before the US Patent Office Patent Trial and Appeals Board (PTAB), Guardant was able to get all 23 claims of a TwinStrand patent invalidated. PTAB review of another TwinStrand patent is ongoing. Guardant will appeal the royalty, according to Guggenheim Securities Analyst Subbu Nambi. “Should appeal efforts fail, Guardant could implement workflow changes” that the company believes would allow it to avoid paying TwinStrand any royalties, she wrote.
German Brain Disease Center to Sequence 25K Genomes
This story has been updated to include additional information form DZNE.
Natera MRD Test for Bladder Cancer Nabs Top-Level US Recommendation
Natera’s Signatera minimal residual disease (MRD) test has received a Category 1 recommendation in updated National Comprehensive Cancer Network clinical practice guidelines for muscle-invasive bladder cancer (MIBC.)
Natera, Germany’s Pirche Partner on Testing for Kidney Transplant Risk and Monitoring
German bioinformatics company Pirche and Natera will collaborate to integrate pre-transplant immunological risk assessment with post-transplant molecular monitoring in kidney transplant care.
Swedish Entrepreneur Gifts Millions to Support Prostate Research
The Karolinska Institute (KI) said it has received SEK 80 million ($8.3 million) from entrepreneur Björn Gysell to support prostate cancer research. In a statement, KI said it will use the funding to develop diagnostics and therapies. The donation will also finance the application of AI and advanced genetic analysis to better understand patients’ response to treatment.
In April, Gysell committed SEK 30 million over three years to support prostate cancer-related research at Uppsala University.
Elsewhere on Substack
Journalist William Herkewitz explores whether aid cuts have exacerbated the current Ebola epidemic in the Democratic Republic of Congo. There are technological challenges, such as a lack of effective vaccines for this particular strain, but many of the issues are human problems.
“It’s hard to pinpoint what isn’t going wrong,” he writes. (Full disclosure: Will is a dear friend of mine.)
Testing is nowhere near keeping pace with the epidemic. Treatment centers are being overwhelmed. Patients are fleeing care. Responders tasked with burying highly-infectious bodies are being attacked. And in some places, as one Congolese public health official has leaked, “people continue to die in communities without ever coming to the attention of health authorities.”
Erratum
In my podcast last week with Jen Dionne, a researcher at Stanford University and CEO and Cofounder of Pumpkinseed, I said that the US Men’s National Team failed to qualify for the 2022 World Cup. This was incorrect; the US had actually failed to qualify for the 2018 World Cup.
I’ll chalk this one up to the 2018 World Cup qualifying failure still looming large in my mind. I watched (on TV) the US lose 2-1 against Trinidad and Tobago to seal their fate and it seems like we’ve been clawing our way back to relevance since then.
And relevant we are again! The USMNT’s two wins to start this tournament has jolted me awake. I told Jen that on the eve of the World Cup, my enthusiasm was muted. I’d like to state for the record that I’m fully aboard the hype train. The team is playing a visually and emotionally attractive style. We have a modern coach using modern tactics and we finally have a striker who can finish in front of goal. I don’t care if this comes off as American naïveté (I’m usually more measured in my expectations) but I think they could make it all the way to the semifinals.
Elsewhere on the Internet (and also on Substack)
Would you believe ChatGPT if it tells you ‘I know how you feel?’, if instead of a chat pane it is a bunch of goats in Age of Empires II?
A Microsoft computer scientist has tackled questions of AI sentience in a delightfully absurd way: by showing how one could theoretically build a large language model (LLM) — the kind powering your favorite AI chatbot du jour — inside the classic computer strategy game Age of Empires II.
In a preprint titled “If AI is sentient, then so is Age of Empires II” (AOE2), Adrian de Wynter, also of the University of York, argued that the representation of an LLM affects its perceived properties.
It’s an interesting point, but let’s not lose sight of the real contribution here: making logic gates and “perceptrons” using goats, an in-game unit that provides food resources to players as they take their civilizations out from the dark ages and into more advanced states of conquest. (Not sure why he specifically went with goats, when it could have also been sheep, or even turkeys.)
Also, this is a sentence you don’t often see in academic papers:
Corollary 1 (AoE II is Turing-Complete). Let I be an instance of AoE II with two players p0,p1. Assume p0 has a market, a monk, a monastery, a relic, six villagers, and five farms; while p1 has a scout unit and only attacks p0’s buildings. Then if I has no time or size limits and the terrain allows for buildings everywhere, the game session in I is Turing-complete.
De Wynter goes into more detail about his paper and digital goatherding on his Substack. Unfortunately, I was unable to find any explanation as to why he chose AoE2 to make his point, rather than any other game with a custom map editor.
If it’s not clear by now, AoE2 is a personal favorite of mine. My brother and I used to play against each other all the time when we were teenagers and we rekindled our rivalry during the COVID-19 pandemic thanks to the remastered version. Like many players and real-life would-be conquerors, I never quite managed how to sustain a military campaign without letting my home base and economy fall to pieces. The in-game AI (not to be confused with De Wynter’s goat-gate features) on the hardest settings always seemed to get the better of me.
That’s all for this week, I have to go practice my build orders.