Aug 2026· Virchows Archiv· 0 citations· 53 references
Medicine
TL;DR
Screening tumor types for which a first-line, integrated DNA-RNA NGS strategy provides a valuable advantage for rapid therapeutic decisions demonstrates that integrated DNA-RNA high-throughput NGS enables timely, precise molecular profiling for personalized therapy in solid tumors.
Next-generation sequencing (NGS) has become a cornerstone of precision oncology in colorectal cancer (CRC), although its role in routine patient stratification remains incompletely defined. This retrospective single-centre study characterised the molecular landscape of clinically selected CRC patients undergoing routine NGS and explored associations between genomic alterations and clinicopathological features. 97 eligible patients who underwent targeted NGS using two validated sequencing platforms were selected. Demographic, clinicopathological, and molecular data were integrated, and associations were evaluated using descriptive statistics, exploratory association testing, principal component analysis, and multiple correspondence analysis. At least one reportable genetic alteration was identified in 91 patients (93.8%), comprising 198 alteration events across multiple cancer-related genes. The most frequently altered genes with pathogenic or likely pathogenic variants were TP53 (55.7%), KRAS (40.2%), PIK3CA (18.6%), and BRAF (11.5%), while microsatellite instability was detected in 19.1% of evaluable tumours. Exploratory analyses identified associations between selected molecular alterations and clinicopathological characteristics. However, these were generally modest, frequently limited by small subgroup sizes, and none survived Benjamini–Hochberg correction. Principal component analysis demonstrated substantial molecular heterogeneity without defining distinct clinicopathological subgroups. Routine targeted NGS provides detailed molecular characterisation of CRC and generates information relevant to biomarker-informed clinical decision-making in real-world practice. However, targeted panels alone were insufficient to establish robust molecular subgroups in this retrospective cohort. These findings highlight the biological complexity of CRC and support larger prospective studies incorporating broader molecular profiling to improve precision patient stratification and optimise personalised therapeutic strategies.
Afonso Cunha, C. Robalo, C. Lemos et al.· International Journal of Mol...· 0 citations
Due to the rapidly evolving landscape of targeted therapies, there is an unmet need for comprehensive molecular profiling to guide treatment decisions for patients with large B-cell lymphoma (LBCL). Therefore, we designed a pilot study to assess the feasibility and turnaround time (TAT) of a comprehensive whole exome sequencing (WES) and transcriptome sequencing (RNA-seq) assay in patients with LBCL (NCT05464823). Patients aged ≥18 years with LBCL were eligible. Formalin-fixed paraffin-embedded tissues at diagnosis or recurrence underwent WES, RNA-seq, and copy number analysis with concomitant germline DNA sequencing. Genomic and transcriptomic data were profiled to define various LBCL signatures such as cell-of-origin (COO), dark zone signature (DZsig), LymphGen and lymphoma microenvironment (LME) classification. Among 100 patients enrolled, samples from 71 patients (48 with newly diagnosed and 23 with relapsed/refractory disease) passed pathology quality control and underwent WES and RNA-seq analysis and reporting. The median TAT was 8 days for individual patient reports (range: 6-22 days), with 73% of reports delivered ≤10 days. Applying molecular risk classification, high risk event-free survival within 24 months (EFS24) signature was associated with DZsig and LME, but not with COO or LymphGen indicating the complex heterogeneity of the disease. We demonstrated the clinical utility and acceptable TAT of a comprehensive WES and RNA-seq assay for LBCL managed in routine clinical practice. These findings support the real-world feasibility of using integrated WES and RNA-seq to define molecular subgroups, guide clinical decision-making at the time of a new line of therapy, and enable biology based subtype-driven clinical trials.
Dai Chihara, Kumudha Balakrishnan, G. Masand et al.· Blood Advances· 0 citations
Comprehensive genomic profiling (CGP) using circulating tumor DNA (ctDNA) has recently become available in Japan, but its clinical utility in daily practice remains unclear. We retrospectively evaluated 19 patients with metastatic colorectal cancer (mCRC) who underwent plasma-based CGP (Guardant360 CDx) between November 2023 and May 2025. ctDNA was detected in 18 of 19 patients (95%) with previously treated mCRC. The median turnaround time from blood collection to result was 11 days (range: 7–15). The median number of gene alterations was 5 (range: 1–29), and pathogenic/likely pathogenic alterations were identified in 15 patients (79%). ctDNA was preferentially selected over tissue CGP in patients with small tumor burden, lack of contemporary tumor sample, or double cancer (considering spatial and temporal heterogeneity). Three patients initially identified with RAS mutant tumors by tissue were subsequently identified as RAS wild-type by plasma CGP. Those were treated with anti-epidermal growth factor receptor (EGFR) therapy, resulting in partial response or stable disease. These observations suggest that plasma-based CGP may provide additional molecular information that could be clinically informative in mCRC in a real-world setting. Although the findings should be interpreted as exploratory, re-evaluation of molecular profiles using ctDNA enabled the exploratory identification of NeoRAS wild-type patients, who could potentially benefit from anti-EGFR therapy.
K. Ito, K. Kataoka, Yoshiko Muroi et al.· Journal of the Anus Rectum a...· 0 citations
Soft tissue sarcomas (STSs) are a heterogeneous group of rare mesenchymal malignancies with overlapping morphological and immunohistochemical features, often making definitive diagnosis challenging. Recent advances in next-generation sequencing (NGS) have enabled the identification of recurrent molecular alterations that contribute to tumor classification, prognostic stratification, and precision oncology approaches. This retrospective study aimed to evaluate the diagnostic and clinical impact of molecular profiling in pediatric soft tissue sarcomas using the Oncomine Childhood Cancer Research Assay (OCCRA) panel. Fifty-five frozen tumor samples representing 24 distinct soft tissue sarcoma subtypes were obtained from the Pediatric Oncology Institute -IOP/GRAACC/UNIFESP Biobank (B-053). Molecular analysis was performed using NGS to identify gene fusions, single nucleotide variants (SNVs), copy number variations (CNVs), and insertions/deletions (InDels). Clinically relevant molecular alterations were identified in 70% (37/55) of cases, including 18 fusion transcripts, 13 SNVs, 8 CNVs, and 6 InDels. Recurrent and diagnostically relevant alterations included BCOR::CCNB3, ASPSCR1::TFE3, NFR1::BRAF, FUS::DDIT3, EML4::NTRK3, ETV6::NTRK3, CIC::DUX4, NAB2::STAT6 and SS18::SSX1/2 fusions, as well as amplifications involving PDGFRA, FGFR1, GLI1, CDK4, ERBB3, and KIT. Pathogenic variants affecting genes involved in tumor suppression and chromatin remodeling, including TP53, NF1, DICER1, SMARCA4, PTEN, and PIK3CA, were also detected. Importantly, molecular profiling had significant diagnostic impact in several histologically ambiguous tumors, enabling molecular reclassification and refinement of previously inconclusive or inaccurate pathological diagnoses. In multiple cases, NGS transformed descriptive histopathological interpretations into genetically defined sarcoma entities, including NTRK-rearranged spindle cell neoplasms, CIC-rearranged sarcomas, synovial sarcoma, low-grade fibromyxoid sarcoma, and clear cell sarcoma. Furthermore, the identification of actionable alterations highlighted potential opportunities for targeted therapies and precision medicine approaches. Our findings demonstrate that comprehensive molecular profiling significantly enhances diagnostic accuracy in pediatric soft tissue sarcomas, particularly in morphologically challenging cases. The integration of NGS into routine sarcoma diagnostics enables biologically informed tumor classification and supports personalized therapeutic strategies.
F. Tesser-Gamba, T. B. Mendes, Fernanda Teresa de Lima et al.· International Journal of Mol...· 0 citations
Background: Sensitive detection of EGFR mutations in liquid biopsies of advanced non-small-cell lung cancer (aNSCLC) is vital for guiding targeted treatments. Real-time PCR offers a quick turnaround time but relatively low sensitivity while Next-Generation Sequencing (NGS) offers broader EGFR coverage, co-mutation evaluation and high sensitivity. Methods: This study evaluated the amplicon-based NGS Plasma-SeqSensei™ Solid Cancer In Vitro Diagnostics (IVD) Kit (Sysmex) against the real-time PCR-based cobas® EGFR Mutation Test v2 (Roche), the current routine standard at the Veneto Institute of Oncology IOV-IRCCS. We enrolled 130 patients with aNSCLC in the RARE Study between April 2022 and August 2025 who were referred to our institute. Liquid biopsies were taken at diagnosis or at progression and analyzed using two methods with the primary objective of assessing diagnostic concordance for EGFR profiling. Sysmex NGS libraries were sequenced on a NextSeq 550 sequencer (Illumina), with the NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles) in single-end mode. Results: Among 129 evaluable samples, the NGS assay demonstrated a marginally higher EGFR mutation detection rate, identifying mutations in 31/129 cases (24.0%, 95% CI: 17–33), versus 28/129 (21.7%, 95% CI: 15–30) by cobas, specifically for variants covered by both assays. Overall concordance was almost perfect (Cohen’s Kappa = 0.89, 95% CI: 0.80–0.98), confirming the high reliability of both methods. Furthermore, we identified a cfDNA input threshold of at least 20 ng as critical for ensuring optimal assay sensitivity and reliable mutation detection (Odds Ratio = 4.41 for inputs ≥ 20 ng, p = 0.006). Conclusions: Ultimately, the Sysmex NGS proved to be a robust and highly sensitive assay. It delivers performance comparable to that of standard RT-PCR while providing the clinical advantage of concurrently detecting a broader spectrum of EGFR variants and actionable mutations in other genes.
A. Boscolo Bragadin, Valeria Tosello, S. Longo et al.· Diagnostics· 0 citations
Patient-derived organoids (PDOs) have transformed translational cancer research, allowing tractable models that better represent clinical features than traditional immortalized cell lines. Here we describe two PDOs with differential responses to carboplatin derived from sequential ascites fluid collections from a patient with high-grade müllerian carcinoma, that could not be further subclassified on the omental biopsy. Uterine origin was clinically excluded by pelvic imaging/CT scan of the uterus and absence of vaginal bleeding. Successful derivation from independent collections enabled comparison of intra-patient heterogeneity across sequential ascites samples and demonstrates that PDO efficiency rate is at least partly patient-specific or tumor-dependent. We performed long-read whole genome sequencing on the two PDOs, OC104 and OC109, to better characterize the structural variant landscape while also obtaining information on single nucleotide variants and DNA methylation. In addition to confirming single nucleotide variants noted in clinical sequencing (TP53, KRAS, SPOP, PPP2R1A, KMT2D), we identified additional variants in TSC2, NCOR2, and CTNNA2 that are predicted to be likely pathogenic. The spectrum of mutations, particularly the coincident KRAS and TP53, highlighted unexpected overlap with ovarian mucinous carcinoma. We also identified larger insertions and deletions that result in non-synonymous variants in MUC5AC, TPRX1, and BMX, as well as four translocation events, including two that could not have been resolved with short-read sequencing. Differentially methylated promoters between the two PDOs include 201 oncogenes and tumor suppressor genes, with HNF1A, MSI2, and SETBP1 having methylation directions consistent with these genes’ roles in platinum response differences observed between the PDOs. Notably, the clonal nature of PDOs produced from two samples taken one week apart is important for the field to appreciate, particularly since they have clonal differences in platinum response. The temporal differences in clonality may indicate a limitation of low volume sampling, however may provide opportunity to longitudinally predict clinical outcomes. We also demonstrate the ability of long-read sequencing to add detail into the genomics and epigenetics of ovarian cancer.
J. Wendt, Kristin M. Adams, Ryan Moreno et al.· bioRxiv· 0 citations