Editors: Donna E. Hansel, MD, PhD, division head of pathology and laboratory medicine, MD Anderson Cancer Center, Houston; James Solomon, MD, PhD, assistant professor, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York; Erica Reinig, MD, assistant professor and medical director of molecular diagnostics, University of Wisconsin-Madison; Marcela Riveros Angel, MD, molecular genetic pathology fellow, Department of Pathology, Oregon Health and Science University, Portland; Maedeh Mohebnasab, MD, assistant professor of pathology, University of Pittsburgh; Alicia Dillard, MD, associate clinical laboratory director, Omniseq/Labcorp, Buffalo, NY; and Richard Wong, MD, PhD, assistant professor of pathology, University of California San Diego.
Multicenter validation of a platform for rapid molecular profiling of CNS tumors
June 2025—Comprehensive molecular profiling and DNA methylation classification have become critical for diagnosing and managing central nervous system tumors. However, workflows for molecular testing of these tumors are often limited by the cost of equipment and reagents, technical complexity, and lengthy turnaround times. The wide range of alterations that can be present, including MGMT promoter methylation, single nucleotide variants, insertions or deletions (indels), copy number variants, and fusions and structural variants, often necessitate the use of multiple assays for a complete molecular workup. All of these factors have led to a growing demand for molecular assays that are faster, more comprehensive, and more accessible. Recognizing this need, the authors had previously conducted a proof-of-concept study of an adaptive sampling-based nanopore sequencing workflow platform, called Rapid-CNS2, that they had developed. For the study featured herein, they comprehensively validated and further developed the platform for intraoperative use. Rapid-CNS2 now provides real-time methylation classification and DNA copy number assessment within a 30-minute intraoperative window and comprehensive molecular profiling within 24 hours. The authors validated the assay in a multicenter setting using 301 archived (frozen) and prospective (fresh) tissue samples, including 18 samples tested intraoperatively. Rapid-CNS2 accurately called 91.67 percent of the single nucleotide variants identified by next-generation sequencing for the 103 samples for which matched NGS data were available. MGMT promoter status was concordant with matched MGMT predictions in 227 of 251 (90.4 percent) cases. Copy number profiles were consistent with methylation array-generated counterparts in all 254 samples that had corresponding Illumina Infinium Methylation BeadChip array data available. While the Heidelberg Molecular Neuropathology methylation classifier has become a critical tool for CNS tumor diagnostics, the current model only accepts methylation array data as input. To address this limitation, the authors also developed MNP-Flex, a platform-agnostic methylation classifier that encompasses 184 tumor classes. Using clinically applicable thresholds on a multi-institutional cohort of more than 78,000 frozen and formalin-fixed, paraffin-embedded samples that had been processed using whole genome bisulfite sequencing, methylation panels, Oxford Nanopore Technologies whole genome sequencing, as well as Rapid-CNS2 data, MNP-Flex achieved 99.6 percent accuracy for methylation families and 99.2 percent accuracy for methylation classes. However, the authors acknowledged the limitations of this workflow, including a high prevalence of missing values and errors in the Rapid-CNS2 data set. In addition, their validated Rapid-CNS2 assay is limited to use on fresh or cryopreserved tissue. Despite these limitations, the workflow developed by the authors (Rapid-CNS2 combined with MNP-Flex classifier) offers several advantages, including speed and cost-effectiveness and the ability to use one assay to interrogate for multiple types of genetic abnormalities. The speed and accessibility of this approach could allow for more timely utilization of targeted therapies and molecularly informed treatment options, even in remote facilities.
Patel A, Göbel K, Ille S, et al. Prospective, multicenter validation of a platform for rapid molecular profiling of central nervous system tumors. Nat Med. 2025. doi.org/10.1038/s41591-025-03562-5
Correspondence: Dr. Martin Sill at [email protected] or Dr. Felix Sahm at [email protected]
Low-cost generation of pharmacogenetic passports using oligonucleotide arrays
Use of pharmacogenomic testing in clinical practice remains limited, despite the availability of clinical guidelines and expanding knowledge of pharmacogenes. Such testing is often confined to assays that target only a subset of haplotypes for a single gene. Cost and speed limit the ability to implement pre-emptive pharmacogenomic (PGx) testing that would cover multiple genes. The authors hypothesized that results from genomewide oligonucleotide genotyping arrays could be used to generate comprehensive information for PGx passports in a timely, cost-efficient manner. Using the Lifelines cohort study and biobank and the Lifelines Next cohort study and biobank, in the Netherlands, they developed and validated Asterix, a low-cost, clinical-grade PGx passport pipeline for 12 PGx genes. Given that the PGx gene CYP2D6 is also affected by copy number variations (CNVs), the authors developed and validated a CYP2D6 copy number variant-calling tool, omitting the need for PCR-based copy number detection. To improve patient understanding of PGx information, the authors also developed a layperson-friendly translation of Dutch Pharmacogenetics Working Group guidelines and a smartphone app for communicating PGx results to the biobank participants. A technical report for health care providers can be downloaded from the app. A total of 36,373 Lifelines samples from the University Medical Centre Groningen Genetics Lifelines Initiative (UGLI), 470 Lifelines Next samples, 2,285 validation samples from the University Medical Centre Groningen Genome Diagnostics patient cohort, and 76 validation samples with known PGx genotypes passed initial quality control. After applying more stringent diagnostic quality control measures to the data set, the authors returned 1,227 PGx passports to biobank participants who had given consent to receive their passports via the smartphone app. The authors demonstrated the feasibility of a clinical-grade PGx passport pipeline that could provide broader access to PGx information and enhance personalized health care. Their smartphone app provides a potential avenue for breaking down barriers to patient understanding and engagement with PGx information. The authors acknowledge several limitations to the production of their PGx passport. The process was unable to provide a complete passport for every person in the cohorts. In the diagnostic setting, backup molecular analysis would be necessary if array data did not yield a reliable result. CNV calling for CYP2D6 was aimed at detecting whole gene deletions and duplications, meaning that potential hybrid alleles could be missed. Furthermore, the authors were unable to evaluate the impact of the identified actionable variants on adverse events and drug efficacy given the scale of the study. Asterix was also designed and validated for the European population, specifically for the general population of the Netherlands. Consequently, the pipeline would not be as applicable to patient populations in other areas. Data regarding the efficacy and cost-effectiveness of broader, preemptive PGx testing are also limited. However, many of these limitations could be minimized or overcome with further study.
Lanting P, Warmerdam R, Slager J, et al. Low-cost generation of clinical-grade, layperson-friendly pharmacogenetic passports using oligonucleotide arrays. Am J Hum Genet. 2025. doi.org/10.1016/j.ajhg.2025.03.003
Correspondence: Dr. Jackie Dekens at [email protected] or Dr. Lude Franke at [email protected]