Neogen Europe (United Kingdom)

3052 Background: Tumor-informed circulating tumor DNA (ctDNA) assays, designed to track patient (pt) specific variants identified by tumor sequencing, offer enhanced sensitivity compared to traditional assays focused on driver genes. This approach enables precise ctDNA quantification, facilitating early detection of molecular progression and innovative strategies in metastatic breast cancer (mBC). Methods: HR+/HER2- mBC pts receiving standard endocrine therapy + CDK4/6 inhibitors (CDKi) were enrolled in a prospective observational cohort (2018–2023). Plasma samples were collected at baseline (BL), within 30 days (d) and ~q3 months with restaging scans. Archival tumor WES was used to design personalized panels for ctDNA monitoring. The primary endpoint was time to treatment failure (TTF). Results: Of 51 pts analyzed (median age 60 years [range 38-88], 1/2L [75/20%], visceral disease 63%, palbo-/ribo-/abemaciclib 76/22/2%), tumor-informed panels were successfully designed for 43 (1 failed WES, 7 failed QC), detecting BL ctDNA in 39 (91%). The median BL estimated variant allele fraction (eVAF) was 0.5% (0.006–17.9) and was associated with liver metastases but no other covariates (e.g. bone-only disease, history of 1ry endocrine resistance [ER]). Higher BL eVAF predicted shorter TTF (HR 1.14 CI 95% 1.05–1.23, p<0.01). Most pts had eVAF decreases below BL in the first 30 d (78%) and before the first scan (89%; median 90 d, 23–158). Early increases above BL did not significantly predict TTF, with 3/8 cases showing prolonged responses. ctDNA clearance was observed in 11/39 (28%) pts at a median of 172 d (14–410) and predicted longer TTF (HR 0.06, CI 95% 0.01–0.45, p<0.01; median TTF not reached vs 14.5 mo for pts with and without clearance), with treatment failure (TF) rates of 0% vs 40%, and 8% vs 80%, at the 1- and 2-year landmarks, respectively. Clearance was not associated with any clinical covariate (i.e. disease sites, therapy line, CDKi, history of 1ry ER). For any sample irrespective of the trajectory, higher eVAF ratios to BL predicted shorter lead times to TF, though with poor correlation (r2 0.08, p=0.01). eVAF ratios to BL >1, >0.5 and <0.5 at any timepoint had median lead times to TF of 76 d (Q1–Q3 25–135), 133 d (41–360), and 326 d (174–471). A complete analysis of ctDNA dynamics and operating parameters will be presented along with RECIST 1.1 evaluation and WES-based genomic subgroups. Conclusions: ctDNA levels and changes on therapy are prognostic and high sensitivity tumor-informed assays expand the proportion of pts who can be monitored. ctDNA clearance identified pts with better outcome and might inform pt follow up and interventional strategies. Reappraisal of existing early response cutoffs, with limited precision for individual decision making, may be necessary with more sensitive assays.

6051 Background: Immune checkpoint blockade (ICB) is the standard of care for recurrent/metastatic head and neck squamous cell carcinoma (R/M HNSCC) yet, response rates are poor. Currently there are no real-time, non-invasive biomarkers of treatment response. Circulating tumor DNA (ctDNA) has shown promising results as a non-invasive response prediction tool in several solid malignancies. In this retrospective study we applied a tumor-informed next-generation sequencing liquid biopsy assay (RaDaR, NeoGenomics Laboratories, Inc.) to track the dynamics of ctDNA in HNSCC patients treated with ICB to test the primary hypothesis that ctDNA detection across treatment predicts disease progression and the secondary hypothesis that ctDNA clearance during treatment positively impacts clinical outcomes in HNSCC. Methods: Whole exome sequencing was performed on pre-ICB archival tumor sections from 16 R/M HNSCC patients. A median sequencing coverage of 306x was obtained. Personalized assays targeting a median of 48 tumor-derived somatic variants were used in serial plasma samples for the detection and monitoring of ctDNA during ICB. Response was assessed using RECIST 1.1 or clinical assessment when imaging was unavailable. Multivariable logistic regression was performed to measure the effect of clinicopathologic features on achieving ctDNA-clearance. Multivariate Cox regression was performed to measure the effect of achieving ctDNA-clearance on survival. Results: 137 plasma samples were collected from 16 patients with a median of 6.5 samples per patient. 14/16 patients had a pre-ICB plasma sample available and ctDNA was detected in 12 (85.7%) (median estimated variant allele frequency: 0.28%, range: 0.004%-1.8%). In the cohort there were 2 patients with complete response (CR), 4 patients with partial response (PR), 2 patients with stable disease (SD), 7 patents with progressive disease (PD), and 1 patient whose response could not be assessed. In patients who cleared ctDNA (n=9) during ICB, there were 2 CR, 4 PR, 1 SD, and 1 PD. In patients who did not clear ctDNA (n =7) there was 1 SD and 6 PDs. ctDNA-clearance at any point after ICB start, including beyond PD on ICB, was associated with 33-fold increased odds of achieving CR, PR, or SD (OR 33.6, 95% CI 2.4-1400.6, p=0.022) independent of PD-L1 status, ICB regimen, and if ICB was administered as first or later line. Achieving ctDNA-clearance was associated with improved overall survival (OS) (HR 0.052, 95% CI 0.005-0.493, p=0.0101) after controlling for ICB regimen, virus status, and PD-L1 status. Median OS from start of ICB was 7.1 months in patients who remained ctDNA-positive and 28.5 months in those who became ctDNA-negative at any point after starting ICB. Conclusions: Undetectable levels of ctDNA at any point during ICB treatment were strongly predictive of achieving CR, PR, or SD in patients with R/M HNSCC.

The aging of bone marrow (BM) remains a very imperative and alluring subject, with an ever-increasing interest among fellow scientists. A considerable amount of progress has been made in this field with the established ‘hallmarks of aging’ and continued efforts to investigate the age-related changes observed within the BM. Inflammaging is considered as a low-grade state of inflammation associated with aging, and whilst the possible mechanisms by which aging occurs are now largely understood, the processes leading to the underlying changes within aged BM remain elusive. The ability to identify these changes and detect such alterations at the genetic level are key to broadening the knowledgebase of aging BM. Next-generation sequencing (NGS) is an important molecular-level application presenting the ability to not only determine genomic base changes but provide transcriptional profiling (RNA-seq), as well as a high-throughput analysis of DNA–protein interactions (ChIP-seq). Utilising NGS to explore the genetic alterations occurring over the aging process within alterative cell types facilitates the comprehension of the molecular and cellular changes influencing the dynamics of aging BM. Thus, this review prospects the current landscape of BM aging and explores how NGS technology is currently being applied within this ever-expanding field of research.

Summary "Crosshole seismic (CS) survey is a reliable and informative method of investigation of geological media, being a leading and sometimes unique geophysical method in geological-engineering researches. However, there is a pitfall in processing of CS data: correctness of result model urgently depends on the correctness of input data. Examples of CS engineering researches are considered. The main aim is to investigate dependence of the results of first breaks tomography on the initial model choice. Use of homogeneous velocity model is shown to lead often to artifact results. It is necessary to consider all a priory information, including velocities, calculated for the pairs of sources and receivers at the nearly same depths, and different wave types. Presence of contrast velocity boundaries in the lower part of investigated media and, as a rule, the first break of the head waves is shown to result in incorrect definition of velocities in the upper part. To solve this problem, the 2-stage processing is suggested. First, it is carried out only for the upper part, dealing with direct waves. Then, inversion for the whole volume is performed, using in the initial model the result of the first stage. The approach is verified by numerical modeling."