Multiomics, rooted in research, is increasingly closing in on clinical practice, to the point that institutions should be at least be ready. This was the consensus at CAP TODAY’s roundtable panel on “NGS and Cancer Biomarkers.” Looking at multiple layers of molecular data from the same sample to render all the important interactions visible, that’s an approach that could line up with demanding new therapies and a “get more from less sample” philosophy in cancer.
CAPTODAY’s full roundtable is at: (https://www.captodayonline.com/ngs-and-the-cancer-biomarker-balancing-act/)
No longer academic, it could be economical. Indeed, it may reach the point where it would be a waste of time not to employ multiomic approaches to maximize a limited sample, or to assist with effective use of one of the newer “targeted payload” cancer-killing drugs.
“…every research project is one paper away from being clinically actionable, and then people start knocking on your door and asking when you can do x, y, and z.”
There were several comments from participants related to the future of multiomics:
- Robert Yamulla, PhD, MBA, research applications marketing lead at Illumina said that: “Getting to the right answer as quickly as possible involves getting additional layers of information, which you might miss by looking at one layer… especially in a limited funding environment.”
- José Luis Costa, PhD, global director of scientific affairs, clinical next-generation sequencing and oncology, Thermo Fisher Scientific said: “Companies need to differentiate what is clinical and provide the best clinical solutions but still leave bandwidth to bring in innovation, research, translational aspects, and multiomics.”
- Jeremy Segal, University of Chicago: “every research project is one paper away from being clinically actionable, and then people start knocking on your door and asking when you can do x, y, and z. It’s not a question of trying to set up a spatial genomics clinical test today. It’s more about how we make sure we’re ready for it when it needs to be done.”
It’s not all future: Biomarkers like NTRK and TMB right now guide pan- cancer drug usage, NTRK fusions led to the pan-tumor FDA approval of larotrectinib in 2018 for any solid tumor with an NTRK fusion, regardless of the cancer’s location or type.
In a NTRK case, You need to find an abnormal joining of the NTRK gene with another gene—a fusion that causes the cell to make a TRK protein that stays “switched on” and drives cancer growth. You target it, so the drug can block it.
OK, but identifying them often requires multiple types of tests—sometimes even a multiomics approach—to improve diagnostic accuracy and ensure the patient is a good match for therapy.
Similarly, TMB-high enabled Keytruda to receive pan-tumor approval in 2020. For a tumor mutational burden (TMB) case, TMB is derived from whole-exome or large-panel sequencing to get a view of the tumor’s mutational landscape.
But TMB plays nicely with others—MSI status, PD-L1 protein expression, and even transcriptomic or epigenomic signals. It works best when combined with other signals, helping doctors see a fuller picture of the tumor and choose the treatment that’s most likely to work.
CAP TODAY’s discussion was by no means all about multiomics. It also got into other topics: In-house vs. outsourcing, the use of “gateway” tech like PCR prior to NGS investment, and other trends. https://www.captodayonline.com/ngs-and-the-cancer-biomarker-balancing-act/)
Roche Highlights LumiraDx POC System
At the recent Roche investor presentation in London, many have focused on the naming of the Roche SBX sequencer. But we note that Roche Diagnostics also showcased the LumiraDx point of care handheld instrument. The instrument requires only a small amount of blood and uses assays that do not need refrigeration, making it especially suitable for clinics or remote locations. Theoretically home care. Roche executives described it as a potential “game changer.”
Currently, the LumiraDx system supports tests such as NT-proBNP, D-dimer, HbA1c, C-reactive protein, INR, and a respiratory panel covering COVID-19, flu, and RSV.
In July 2024, Roche completed the acquisition of LumiraDx’s Point of Care (POC) technology platform. The deal was valued at up to $350 million.
Agilent’s PD-L1 Companion Diagnostic Assay Expands IVDR Certification
Keytruda is a $27 billion-dollar product directly connected to an IVD for its success. In most indications, PD-L1 expression must be confirmed via an FDA- or IVDR-approved companion diagnostic. The key test is Agilent’s. In April, the company announced the expansion of its IVDR certification for the PD-L1 companion diagnostic assay. This assay is utilized to identify patients eligible for treatment with Keytruda (pembrolizumab), supporting personalized oncology care.
Holding on to gold-standard status as Keytruda companion and certified in the EU for seven cancers.
Agilent’s PD-L1 IHC 22C3 pharmDx assay plays a crucial role in the assessment of PD-L1 expression, which is a key biomarker for determining patient eligibility for immunotherapy treatments like Keytruda. Agilent’s PD-L1 IHC 22C3 pharmDx assay (Code SK006) received European In Vitro Diagnostic Regulation (IVDR) certification as a companion diagnostic (CDx) for identifying patients with gastric or gastroesophageal junction (GEJ) adenocarcinoma eligible for treatment with KEYTRUDA.
This certification expands the assay’s approved indications under IVDR to seven cancer types, including non-small cell lung cancer (NSCLC), urothelial carcinoma, esophageal cancer, head and neck squamous cell carcinoma (HNSCC), triple-negative breast cancer (TNBC), cervical cancer, and now gastric or GEJ adenocarcinoma.
The PD-L1 IHC 22C3 pharmDx assay is approved for exclusive use with the Agilent Autostainer Link 48 advanced staining solution. It was developed by Agilent in partnership with Merck (known as MSD outside the United States and Canada).
In addition to Agilent’s PD-L1 companion diagnostic, several other companies offer or develop assays used to guide Keytruda (pembrolizumab) treatment. Roche’s Ventana Medical Systems provides PD-L1 assays, such as SP263 and SP142, which are approved in certain cancer types. Labcorp and Foundation Medicine (a Roche subsidiary) include PD-L1 testing within broader tumor profiling services, though not all are formally approved as companion diagnostics. Promega also offers an approved assay for Keytruda that targets a different biomarker—microsatellite instability (MSI)—used to identify patients with tumors exhibiting deficient mismatch repair.
Keytruda (pembrolizumab), developed by Merck & Co. (MSD outside the U.S. and Canada), is one of the world’s top-selling drugs at $27.5 billion globally It accounted for over 40% of Merck’s pharmaceutical sales , making it their single largest product.
Need For Routine Fungal Culture?
Fungal infections are a nationwide issue but cultures for fungal infection on a routine basis might be questionable, per a hospital study. Fungal blood cultures may still be used as a baseline tool, but targeted molecular or antigen-based tests are now generally superior in speed and diagnostic yield. For patients with suspected invasive candidiasis, sepsis, or immunocompromised status, using a β-D-glucan test or molecular panel often improves early detection and treatment.
“Even when fungal organisms were detected, they were often also caught by standard blood cultures.”
A retrospective study from University of Florida Health Shands Hospital examining over 2,000 inpatient sepsis evaluations. The study found that routine fungal blood cultures provided minimal added diagnostic value compared to standard blood cultures. Only 12.5% of fungal cultures were uniquely positive, while nearly half of fungal detections were already caught by standard cultures. Additionally, fungal cultures had a slower median turnaround time (48 vs. 33 hours).
Logan Brock, PharmD made the presentation atMAD-ID 2025, the 27th Annual Meeting of Making a Difference in Infectious Diseases, which took place May 28–31, 2025, in Orlando, Florida. The Antimicrobial Stewardship Meeting brought together healthcare professionals focused on infectious disease management and stewardship strategies.
Though fungal blood cultures may help in select high-risk cases—such as one patient with Candida glabrata requiring treatment adjustment—the authors concluded that routine use offers minimal benefit. Logan Brock, a PGY-2 infectious diseases pharmacy resident, noted that the study was prompted by rising concerns among ICU pharmacists about the increasing volume of fungal blood culture orders. Preliminary reviews showed that even when fungal organisms were detected, they were often also caught by standard blood cultures. This overlap, coupled with longer turnaround times for fungal culture.
