Pretreatment tumor sampling and prognostic factors in patients with soft-tissue sarcoma of the head and neck

Background Insufficient preoperative work-up and consequent intralesional or marginal resection of soft-tissue sarcomas of the head and neck (STSHNs) is common. Methods This retrospective cohort study comprised 63 patients with STSHN treated at the Helsinki University Hospital between 2005 and 2017. We assessed the effect of pretreatment tumor sampling on surgical margin status and need for supplemental surgery, as well as prognostic factors and survival. Results The lack of representative pretreatment biopsy specimen was associated with unfavorable margin status. Primary surgery at a non-academic center was associated with need for supplemental surgery. The 3-year overall survival (OS) was 68%, disease-specific survival (DSS) 71%, and recurrence-free survival (RFS) 61%. Higher tumor grade and primary tumor size over 5 cm were associated with reduced DSS. Conclusions Diagnosis and management of STSHNs should be centralized to experienced academic centers. Decision-making between needle biopsy, open biopsy, or upfront radical surgery depends on tumor location and size.

Contribution of the IdyllaTM System to Improving the Therapeutic Care of Patients with NSCLC through Early Screening of EGFR Mutations

Epidermal growth factor receptor (EGFR) genotyping, a critical examen for the treatment decisions of patients with non-small cell lung cancer (NSCLC), is commonly assayed by next-generation sequencing (NGS), but this global approach takes time. To determine whether rapid EGFR genotyping tests by the IdyllaTM system guides earlier therapy decisions, EGFR mutations were assayed by both the IdyllaTM system and NGS in 223 patients with NSCLC in a bicentric prospective study. IdyllaTM demonstrated agreement with the NGS method in 187/194 cases (96.4%) and recovered 20 of the 26 (77%) EGFR mutations detected using NGS. Regarding the seven missed EGFR mutations, five were not detected by the IdyllaTM system, one was assayed in a sample with insufficient tumoral cells, and the last was in a sample not validated by the IdyllaTM system (a bone metastasis). IdyllaTM did not detect any false positives. The average time between EGFR genotyping results from IdyllaTM and the NGS method was 9.2 ± 2.2 working days (wd) (12.6 ± 4.0 calendar days (cd)). Subsequently, based on the IdyllaTM method, the timeframe from tumor sampling to the initiation of EGFR-TKI was 7.7 ± 1.2 wd (11.4 ± 3.1 cd), while it was 20.4 ± 6.7 wd (27.5 ± 7.7 cd) with the NGS method (p < 0.001). We thus demonstrated here that the IdyllaTM system contributes to improving the therapeutic care of patients with NSCLC by the early screening of EGFR mutations.

Novel non-terminal tumor sampling procedure using fine needle aspiration supports immuno-oncology biomarker discovery in preclinical mouse models

BackgroundImmuno-oncology therapies are now part of the standard of care for cancer in many indications. However, durable objective responses remain limited to a subset of patients. As such, there is a critical need to identify biomarkers that can predict or enrich for treatment response. So far, the majority of putative biomarkers consist of features of the tumor microenvironment (TME). However, in preclinical mouse models, the collection of tumor tissue for this type of analysis is a terminal procedure, obviating the ability to directly link potential biomarkers to long-term treatment outcomes.MethodsTo address this, we developed and validated a novel non-terminal tumor sampling method to enable biopsy of the TME in mouse models based on fine needle aspiration.ResultsWe show that this technique enables repeated in-life sampling of subcutaneous flank tumors and yields sufficient material to support downstream analyses of tumor-infiltrating immune cells using methods such as flow cytometry and single-cell transcriptomics. Moreover, using this technique we demonstrate that we can link TME biomarkers to treatment response outcomes, which is not possible using the current method of terminal tumor sampling.ConclusionThus, this minimally invasive technique is an important refinement for the pharmacodynamic analysis of the TME facilitating paired evaluation of treatment response biomarkers with outcomes and reducing the number of animals used in preclinical research.

OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations

Background DNA sequencing has unveiled extensive tumor heterogeneity in several different cancer types, with many exhibiting diverse subclonal populations. Identifying and tracing mutations throughout the expansion and progression of a tumor represents a significant challenge. Furthermore, prioritizing the subset of such mutations most likely to contribute to tumor evolution or that could serve as potential therapeutic targets represents an ongoing problem. Results Here, we describe OncoGEMINI, a new tool designed for exploring the complex patterns and trajectory of somatic and inherited variation observed in heterogeneous tumors biopsied over the course of treatment. This is accomplished by creating a searchable database of variants that includes tumor sampling time points and allows for filtering methods that reflect specific changes in variant allele frequencies over time. Additionally, by incorporating existing annotations and resources that facilitate the interpretation of cancer mutations (e.g., CIViC, DGIdb), OncoGEMINI enables rapid searches for, and potential identification of, mutations that may be driving subclonal evolution. Conclusions By combining relevant genomic annotations alongside specific filtering tools, OncoGEMINI provides powerful and customizable approaches that enable the quick identification of individual tumor variants that meet specified criteria. It can be applied to a wide range of tumor-derived sequence data, but is especially designed for studies with multiple samples, including longitudinal datasets. It is available under an MIT license at github.com/fakedrtom/oncogemini.

Changes in hepatocellular carcinoma aggressiveness characteristics with an increase in tumor diameter

Background: Hepatocellular carcinoma prognosis depends on both liver and tumor determinants, especially on maximum tumor diameter, multifocality, and presence of portal vein thrombosis, despite apparently complete tumor removal by resection or liver transplantation. Aims: To examine parameters of hepatocellular carcinoma aggressiveness as tumor size increases. Methods: A large hepatocellular carcinoma database was examined for trends in serum alpha-fetoprotein and the percentage of patients with macroscopic portal vein thrombosis or tumor multifocality. Results: A total of 13,016 hepatocellular carcinoma patients were identified having full tumor and survival data. Of these, 76.56% were male and 23.44% were female, with a median age of 64.4 years. We found that as the maximum tumor diameter increased, there was a significant trend for increased alpha-fetoprotein levels ( P<0.001) and an increased percentage of patients with either portal vein thrombosis or tumor multifocality, each P<0.0001. Furthermore, the increases of both alpha-fetoprotein and portal vein thrombosis were proportionately greater than the related maximum tumor diameter increases. These trends of increased alpha-fetoprotein, portal vein thrombosis, and multifocality with increasing maximum tumor diameter had non-linear patterns. Within alpha-fetoprotein and multifocality trends, there were identifiable sub-trends associated with specific maximum tumor diameter ranges. Conclusions: The greater fold-increases in alpha-fetoprotein and portal vein thrombosis compared with increases in maximum tumor diameter imply that hepatocellular carcinoma characteristics may change with increasing size to a more aggressive phenotype, suggesting that follow-up tumor sampling might be useful, in addition to baseline tumor sampling, for optimal therapeutic choices to be made.

ctDNA from ascites as an alternative to tumor sampling for HRD (homologous recombination deficiency) testing in ovarian cancer (OC).

6066 Background: Knowledge regarding HRD status is becoming crucial to guide maintenance strategies for patients with newly diagnosed OC. Unfortunately, for patients (pts) treated with neoadjuvant chemotherapy (NACT), HRD testing on small biopsies from diagnostic laparoscopies (Dx Lap) or interval debulking has a high failure rate. At relapse, biopsies may not be feasible. Aim: Evaluate the feasibility and usefulness of HRD testing on cfDNA from ascites Methods: Pts enrolled in a prospective biological study (OvBIOMark) consented to analysis of biological samples obtained as part of routine diagnosis. cfDNA was extracted from 1-2ml of double-centrifuged fresh ascites and subjected to 1) targeted NGS including the most common somatic mutations in high grade ovarian cancer ( TP53) to confirm presence of tumor cfDNA and 2) SNParray for copy number (CN) analyses to calculate a genomic instability score (GIS) for HRD. Results: Thirty four ascites samples were collected from 25 pts with suspected or confirmed OC. For 15/25 pts samples were obtained at Dx Lap, and for 10 pts samples were obtained at relapse. Seven pts underwent repeat ascitic drains during treatment or at relapse. 97% (33/34) of ascitic samples had detectable cfDNA (median = 980ng, range:80-5730ng) even when obtained during chemotherapy. A deleterious mutation was identified in 87% (29/33) of samples with high allelic frequencies (median allelic frequency, AF = 60%; 3.3-87%), confirming that most of detected cfDNA was tumoral. The most common mutation was a TP53m (86%; 25/29). We have performed CN analysis on cfDNA from ascites on 17 of these patients to evaluate their HRD status. Ten pts had a high GIS (HRD+), and 7 pts a low GIS (HRD-). The 4 pts with confirmed BRCAm included in this study had a high GIS on ascites. When available from the same patient, the CN profiles derived from ascites cfDNA and tumor sampling were superimposable. Conclusions: Ascites yields large amounts of cfDNA, which can be confirmed as tumoral based on TP53 mutation detection. CN analysis on ascitic cfDNA is feasible and can be used to detect the same HRD scar as tumor testing. Ascites is frequent at diagnosis, especially in pts with inoperable disease planned for NACT and could provide a useful alternative to tumor for HRD and BRCA testing.