Allele Frequencies Research Articles

Tumor purity as confounder for the determination of tumor mutational burden (TMB).

e14656 Background: TMB determination is a prerequisite to stratify advanced cancer patients for pembrolizumab based on the histology-agnostic FDA approval. The accuracy of TMB measurement is challenged by low tumor purity resulting in a lower number of detected somatic variants for a fixed threshold of variant allele frequency (VAF) and a lower measured TMB level as a consequence. Methods: We derived a mathematical formula describing the influence of tumor purity on the VAF of somatic variants, in which the DNA copy number of the corresponding region of the tumor genome is a parameter. We simulated the effect of tumor purity in a cohort of 4,900 tumors from the TCGA project with tumor purity of at least 80%. TMB was calculated as the number of missense mutations with VAF greater or equal than 5%. Tumors were classified as TMB-high when harboring at least 199 missense mutations. This cutpoint corresponds to 10 mut/Mb as derived in the TMB bridging study. We compared tumors with a simulated tumor purity of 70%, 60%, ..., and 10% with tumors with a tumor purity of 80%, which served as reference. Results: The median of TMB in the pan-cancer cohort was reduced by 2%, 10%, and 32% for tumor purity of 60%, 40%, and 20% compared to the reference of 80%. For the 10% tumors with the worst estimation, TMB was reduced even by 12%, 35%, and 77% or more, respectively. In the pan-cancer cohort, the sensitivity to detect high TMB was 98%, 90%, and 62% for tumor purity of 60%, 40%, and 20%, respectively. For head and neck cancer, lung adenocarcinoma, lung squamous cell carcinoma, and cutaneous melanoma, the sensitivity to detect high TMB was 80%, 89%, 92%, and 91%, respectively, for tumors of tumor purity 40%. Conclusions: High tumor purity is critical for accurate determination of the TMB and to reach a high sensitivity concerning the selection of patients for immunotherapy. As shown by the simulations, the sensitivity to detect high TMB is close to 100% for tumor purity of at least 60%, while a substantial proportion of patients that could receive immunotherapy is missed for tumors with purity of 40% or less. Potential ways out of the TMB underestimation include increasing the sequencing coverage and lowering the VAF threshold for mutation calling or using clonal TMB with an adapted cutpoint instead of total TMB as biomarker for immunotherapy guidance.

Plasma mutational burden in PIK3CA and TP53 independently predicts early progression in patients with HR+/HER2- metastatic breast cancer (MBC) enrolled in the GEICAM/2014-12 FLIPPER trial.

1029 Background: There is an unmet need for molecular diagnostics to predict therapy outcomes using blood-based biomarker monitoring to guide treatments in HR+/HER2- MBC patients. Here, we report initial results of serial ctDNA analyses in a trial of Fulvestrant (F) + CDK4/6 inhibitor (CDK4/6i) Palbociclib (Pa) vs. F + Placebo (Pl). Endocrine therapy + CDK4/6i are currently the cornerstones of treatment for HR+/HER2- MBC. However, between 10–30% of patients suffer primary resistance. Thus, early identification of HR+/HER2- MBC patients that progress during CDK4/6i treatment is required. Methods: The GEICAM FLIPPER trial (NCT02690480) is a multicenter, double-blind, randomized, phase II study comparing F+Pa vs F+Pl in postmenopausal women with HR+/HER2- MBC. Sequential plasma was collected from 187 patients at baseline, 12, 24, 36, and 48 weeks on treatment and at progression. In total, 903 samples were analyzed using the Plasma-SeqSensei BC IVD kit (Sysmex Inostics) that identifies and quantifies ctDNA mutations in six BC-related genes. The mutant allele frequency (MAF) of PIK3CA and TP53 variants was assessed in baseline samples (median value as cutoff). These variants, identified as the most prevalent, were used as surrogate markers for mutational burden. The Kaplan-Meier method was used to estimate median (m) PFS and overall survival (OS). Hazard ratio (HR) and odds ratio (OR) were calculated with 95% confidence interval (CI) using Cox proportional hazards regression model and logistic regression respectively, unadjusted or adjusted by age, site of disease, disease presentation at study entry and clinical subtype. Results: Previously we showed that F+Pa improved 1-year PFS (83.5% vs. 71.9%, p=0.064) and mPFS (31.8 vs. 22.0 months, p=0.001) vs F+Pl. Here, ctDNA analyses revealed that having ≥1 mutation in PIK3CA + TP53 was prognostic of early (≤12 months) progression (OR 2.37; 95% CI 1.1-5.12, p=0.0274) independent of treatment arm. Furthermore, having ≥2 mutations was associated with treatment resistance (not achieving objective response; OR 3.55; 95% CI 1.28-9.87, p=0.0151). Additionally, worse mPFS and mOS were seen in patients with ≥2 mutations in PIK3CA + TP53 (PFS: HR 3.6; 95% CI 2.25-5.76, p<0.0001; OS: HR 2.92; 95% CI 1.66-5.12, p=0.002) and in patients with high MAF (PFS: HR 2.43; 95% CI 1.6-3.68, p<0.0001; OS: HR 2.83; 95% CI 1.75-4.58, p<0.0001). Finally, having ≥2 mutations in PIK3CA + TP53 was predictive of early progression (OR 22.32; 95% CI 4.12-120.9, p<0.0001) and worse mOS (61.8 vs. 34.79 months) in the F+Pl arm (HR 5.91; 95% CI 2.65-13.16, p<0.0001) but not in the F+Pa arm. Conclusions: Baseline plasma mutational burden in both PIK3CA and TP53 genes was significantly associated with Fulvestrant +/- Palbociclib treatment outcome in HR+/HER2- MBC and appeared to be predictive of Palbociclib benefit. Clinical trial information: NCT02690480 .

STAC3 disorder: a common cause of congenital hypotonia in Southern African patients.

STAC3 disorder, or Native American myopathy, is characterised by congenital myopathy, hypotonia, musculoskeletal and palatal anomalies, and susceptibility to malignant hyperthermia. A STAC3 c.851 G > C (p.Trp284Ser) pathogenic variant, common in the Lumbee Native American tribe, has been identified in other populations worldwide, including patients of African ancestry. We report on the frequency of STAC3 c.851 G > C in a cohort of 127 patients presenting with congenital hypotonia that tested negative for spinal muscular atrophy and/or Prader-Willi syndrome. We present a clinical retrospective, descriptive review on 31 Southern African patients homozygous for STAC3 c.851 G > C. The frequencies of various phenotypic characteristics were calculated. In total, 25/127 (20%) laboratory-based samples were homozygous for STAC3 c.851 G > C. A carrier rate of 1/56 and a predicted birth rate of 1/12 500 was estimated from a healthy cohort. A common haplotype spanning STAC3 was identified in four patients. Of the clinical group, 93% had a palatal abnormality, 52% a spinal anomaly, 59% had talipes equinovarus deformity/deformities, 38% had arthrogryposis multiplex congenita, and 22% had a history suggestive of malignant hyperthermia. The novel finding that STAC3 disorder is a common African myopathy has important clinical implications for the diagnosis, treatment and genetic counselling of individuals, with neonatal and/or childhood hypotonia with or without arthrogryposis multiplex congenita, and their families. The spread of this variant worldwide and the allele frequency higher in the African/African-American ancestry than the Admixed Americans, strongly indicates that the STAC3 c.851 G > C variant has an African origin which may be due to anancient mutation with migration and population bottlenecks.

TBCRC 048 (olaparib expanded) expansion cohorts: Phase 2 study of olaparib monotherapy in patients (pts) with metastatic breast cancer (MBC) with germline (g) mutations in PALB2 or somatic (s) mutations in BRCA1 or BRCA2.

1021 Background: TBCRC 048 is an investigator-initiated proof of principle phase II trial that demonstrated responses with monotherapy olaparib in MBC pts with g PALB2 or s BRCA mutations. Here we report results of the expansion cohorts for additional pts with g PALB2(Cohort 1a) or s BRCA (Cohort 2a) mutations. Methods: 24 MBC pts with g PALB2m and 30 pts with s BRCAm were enrolled in the expansion cohorts from Sept 2020 to Oct 2023.Eligibility included: MBC with measurable disease; documented g PALB2m or s BRCAm (with normal g BRCA testing); progression on < 2 metastatic chemotherapy regimens. Prior PARP inhibitor or progression on platinum was not allowed. Patients received olaparib 300 mg bid until progression or unacceptable toxicity. The null hypothesis for each expansion cohort [≤ 30% objective response rate (ORR)] would be rejected if > 13 responses were seen. Secondary endpoints include clinical benefit rate (CBR) at 18 weeks, progression-free survival (PFS), duration of response (DOR) and whether the mutant allele frequency (MAF) is significantly higher in responders than in non-responders. Enrollment to the g PALB2 cohort was closed early due to slow enrollment. PFS and DOR were estimated using the Kaplan-Meier method. Association between MAF and response status was assessed using Wilcoxon rank sum test. Results: In Cohort 1a (g PALB2, n=24), median age was 52.5 years (range: 26-86). 19 pts had ER+ HER2-negative, 2 HER2-positive, and 3 triple-negative breast cancer (TNBC). There were 18 confirmed responses for ORR of 75% (80% CI: 60.2%-86.3%); CBR at 18 weeks was 83.3% (90% CI: 65.8%-94.1%). Median PFS was 9.6 months (90% CI: 8.3-12.4). Median DOR was 7.1 months (90% CI: 5.6-11.0). In Cohort 2a (s BRCA1/2, n=30) 15 pts had s BRCA1m and 15 s BRCA2m. 23 pts had ER+ HER2-negative, 3 HER2-positive, and 4 TNBC. There were 11 confirmed responses for ORR of 36.7% (80% CI: 24.8%-50%). CBR was 53.3% (90% CI: 37%-69.2%) and median PFS was 5.6 months (90% CI: 3.0-8.3). Median DOR was 12.4 months (90% CI: 4.3-not reached). One additional pt with a s BRCAm had a PR, which was not confirmed. Clinical and molecular factors associated with response to olaparib are being evaluated. MAF was available and evaluable for 33 of the 46 pts in Cohorts 2 plus 2a who had s BRCAm identification by tumor biopsy. The mean MAF was 43% in responders and 39 % in non-responders (p=0.7), which was not significantly different. Conclusions: The notable ORR (75%) with olaparib in this second cohort of women with MBC and g PALB2m was again demonstrated.Olaparib activity inMBC pts with s BRCAm was also confirmed, though identifying predictors of response for these pts is of critical importance to distinguish those more likely to respond to PARP inhibition. Clinical trial information: NCT02032823 .

Gene-environment interactions between clonal hematopoiesis of indeterminate potential and air pollution in non-small cell lung cancer among non-smokers.

10514 Background: Small particulate matter air pollution (≤ 2.5µm diameter; PM2.5) is a recognized driver of non-small cell lung cancer (NSCLC) among non-smokers. PM2.5 recruits pro-inflammatory macrophages to the lungs, which facilitate the clonal expansion of mutated epithelial cells and eventual transformation to NSCLC. Clonal hematopoiesis of indeterminate potential (CHIP) is a common age-related condition caused by the acquisition of somatic mutations in hematopoietic stem cells. CHIP and its accompanying pro-inflammatory phenotype have been linked with various age-related diseases, including incident NSCLC; however, the mechanisms underlying this relationship are unknown. In this study, we aimed to explore the interaction between CHIP and exposure to PM2.5 in the development of incident NSCLC. Methods: This study was conducted using data from participants in the UK Biobank (n = 451,095). CHIP status was determined from peripheral blood whole exome sequencing data, and defined as the presence of a somatic driver mutation in the blood at variant allele frequency (VAF) ≥2% (PMID: 36652671). Incident NSCLC was determined from UK cancer registry data, and PM2.5 exposure was determined based on ambient regional measures from 2010. Cox proportional hazard models were used to evaluate associations between CHIP, PM2.5, and NSCLC. Proteomics data was measured using OLINK proteomics in a subset of UK Biobank participants (n = 44,625). Results: CHIP was prevalent in 3.4% of UK Biobank participants (n = 15,633; never smokers: 3.0%, n = 6,916/227,133). There were 1983 incident cases of NSCLC (never smokers: n = 307). CHIP status was associated with incident NSCLC when adjusting for smoking status (HR = 1.73, 95% CI: 1.48–2.02) and analyzing exclusively non-smokers (HR = 2.01, 95% CI: 1.34-3.00). PM2.5 levels were not associated with NSCLC in non-smokers (HR = 1.00, 95% CI: 0.89–1.12 per µg/m3 increase in PM2.5); however, there was a significant interaction between PM2.5 and CHIP (HR = 1.46, 95% CI: 1.02–2.11, pint = 0.04), suggesting that it is the interplay between the two that drives incident NSCLC risk. We found no association between PM2.5 levels and increased CHIP prevalence or CHIP VAF. PM2.5 and CHIP were also found to interact to increase systemic inflammatory markers C-reactive peptide (pint = 0.01) and IL-6 (pint = 0.002). Conclusions: PM2.5 and CHIP act as a novel gene x environment interaction pair that play a key role in NSCLC etiology among non-smokers. Rather than acting in isolation to increase risk of NSCLC, PM2.5 intensifies the relationship between CHIP and NSCLC, presumably by exacerbating systemic inflammation and the hyper-inflammatory lung microenvironment. With PM2.5 levels in the UK among the lowest in the world, we posit that the CHIP x PM2.5 interaction contributes substantially to the global burden of NSCLC in non-smokers.

Association of germline HSD3B1 (c.1100) genotype with tumoral and clinical outcomes in breast and endometrial cancers.

10587 Background: A germline single-nucleotide polymorphism in HSD3B1 results in adrenal-permissive (c.1100 C) and adrenal-restrictive (c.1100 A) phenotypes with respect to androgen synthesis. In pre- and post-menopausal patients with breast cancer (n=3548 and 7871) and endometrial cancer (n=1588 and 8439), we annotated samples as adrenal permissive (CC/AC) or restrictive (AA) based on HSD3B1 variant status and then examined tumoral characteristics and clinical outcomes. Methods: We utilized tumors from the Caris Life Sciences Precision Oncology Alliance database and inferred germline HSD3B1 c.1100 genotype using variant allele frequencies (VAFs): c.1100 C VAF of 0% defined the AA genotype, VAF of 40-60% defined the AC genotype, and VAF of 100% defined the CC genotype. We explored associations of each HSD3B1genotypes with other genomic (WES) and transcriptomic (RNA-seq) features, as well as with survival outcomes. To performed consider menopausal status we used the patient’s age at the time of biopsy (>55 indicating post-menopausal). Results: In breast cancer (BC) and endometrial cancer (EC), the permissive HSD3B1genotype had greater mRNA expression of the estrogen receptor ( ESR1) and co-alterations of the TP53 (p<0.0001). In post-menopausal ECs, the permissive genotype was associated with increased alterations in the PI-3-kinase pathway ( PTEN, PIK3CA, PIK3R1, p<0.0001). In pre-menopausal HER2+ BCs, the restrictive genotype was associated with worse survival (HR=1.40, 95% CI = 1.05-1.85, p=0.027) and exhibited increases in hallmark GSEA signatures including epithelial-to-mesenchymal transition. Post-menopausal basal BCs with the permissive genotype had numerically higher PD-L1 protein expression (50% vs 13%) and less PI-3-kinase alterations ( PTEN, PIK3R1, p<0.01). Post-menopausal clear cell ECs with the restrictive genotype exhibited worse survival (HR=1.60, 95% CI=1.07-2.38, p=0.03) and were 3-fold more likely to be TMB-high or MSI-high (p<0.05). Distinctly, post-menopausal endometrioid ECs of the restrictive genotype were less likely to be TMB- or MSI-high (p<0.05). Conclusions: Breast and endometrial cancers can be classified as adrenal-permissive or -restrictive based on HSD3B1 c.1100 genotype. This classification distinguishes clinical outcomes and tumoral features, particularly when stratifying by menopausal status. Importantly, these genotypes are differentially associated with druggable pathways (PI-3-kinase) and markers of immune sensitivity (PD-L1, TMB, MSI). [Table: see text]

Updates on Rare Genetic Variants, Genetic Testing, and Gene Therapy in Individuals With Obesity.

The goal of this paper is to aggregate information on monogenic contributions to obesity in the past five years and to provide guidance for genetic testing in clinical care. Advances in sequencing technologies, increasing awareness, access to testing, and new treatments have increased the utilization of genetics in clinical care. There is increasing recognition of the prevalence of rare genetic obesity from variants with mean allele frequency < 5% -new variants in known genes as well as identification of novel genes- causing monogenic obesity. While most of these genes are in the leptin melanocortin pathway, those in adipocytes may also contribute. Common variants may contribute either to higher lifetime tendency for weight gain or provide protection from monogenic obesity. While specific genetic mutations are rare, these segregate in individuals with early-onset severe obesity; thus, collectively genetic etiologies are not as rare. Some genetic conditions are amenable to targeted treatment. Research into the discovery of novel genetic causes as well as targeted treatment is growing over time. The utility of therapeutic strategies based on the genetic risk of obesity is an advancing frontier.

Multi-cancer early detection (MCED) in circulating tumor DNA (ctDNA) using an ultrasensitive mutation-based amplicon next-generation sequencing (NGS) assay.

e15042 Background: Cancer remains a leading cause of mortality globally. For most cancers, routine screening options are still unavailable. Blood-based MCED has emerged as a promising strategy to bridge this gap. Mutation-based NGS in ctDNA detects highly specific cancer signals, an attribute critical for MCED assays. We developed an ultrasensitive mutation-based NGS assay optimized to detect cancer signals in 50 cancers and predict tissue-of-origin (TOO) for up to 21 cancer classes. Methods: An amplicon-based NGS assay incorporating mirror barcodes for error correction was designed to detect cancer-associated alterations (CAAs), including single nucleotide variants (SNVs), insertion-deletion mutations (indels), and viral DNA (EBV and 20 genotypes of HPV), in 50 cancers. Analytical validation was performed using reference standards and clinical validation was performed in a retrospective case-control cohort of 601 subjects comprising cell-free DNA (cfDNA) from 313 self-declared healthy donors and 288 cancer patients (30.9% early-stage, 50.3% late-stage and 9.4% hematolymphoid cancers). Tissue-of-origin (TOO) was predicted for 21 cancer classes using a weighted sum model. Where relevant, matched buffy coat genomic DNA (gDNA) was analyzed to rule out clonal hematopoiesis. Results: Analytical validation demonstrated a limit of detection (LoD) of 0.05% variant allele frequency (VAF) for indels and 0.07% VAF for SNVs in cfDNA. LoD was matched in gDNA (0.04% and 0.05% VAF for indels and SNVs respectively). In clinical validation, the assay demonstrated a specificity of 99.0% (310/313) and an overall sensitivity of 80.9% (233/288), with sensitivities of 64.0%, 91.7%, and 85.2% in early-stage, late-stage, and hematolymphoid cancers respectively. The mean number of CAAs detected in early-stage, late-stage, and hematolymphoid CAA-positive cancers was 2.1, 3.1, and 4.6. Inclusion of viral targets aided the detection of nasopharyngeal (NPC), cervical, and p16+ oropharyngeal (oPSCC) cancers. EBV DNA was detected in 91.7% of NPC cases. In cervical cancer and p16+ oPSCC, HPV DNA (genotypes 16, 18, 33 and 39) was detected in 71.4% and 90.9% of cases respectively. Conversely, none of the p16- oPSCC cancers had detectable HPV DNA. Across the 21 TOO classes, a high confidence prediction could be made in 62.4% (mean 73.6%, range 26.7%-100%) of cases with an overall accuracy of 87.7% (mean 84.9%, range 33.3%-100%). Overall TOO prediction performance was modeled in a simulated cohort based on cancer incidence in Singapore and Hong Kong, giving an accuracy of 87.3% and 88.7% respectively. Conclusions: The mutation-based NGS assay sensitively detects cancer signals and accurately predicts the tumor origin for early-stage, late-stage, and hematolymphoid cancers. Inclusion of viral targets additionally enables early detection of virus-associated cancers.

An analysis of likely germline events by tumor tissue testing on large somatic panels.

e22524 Background: The increase in large panel testing has facilitated the detection of numerous events, including those in genes associated with inherited cancer. Further, large panel sequencing may uncover variants in these genes in non-inherited cancers. Hence the frequency of pathogenic/likely pathogenic (P/LP) events in some common germline genes was studied across cancers in the Indian population. Methods: A statistical model was used to derive a method to label variants as likely germline. Variants in hereditary breast and ovarian cancer (HBOC) and mismatch repair (MMR) genes from 1553 cases sequenced at our referral laboratory on the TruSight Oncology 500 panel (TSO500) were analyzed for their variant allele frequency (VAF) distribution. A 3 component Gaussian mixture model (intended to separate somatic, germline heterozygous, homozygous variants) was fit to this VAF distribution and a cutoff was determined such that the area under the curve of the somatic component above the cutoff was below 0.01. This gave a threshold value of 40% VAF for determining likely germline variants (LGVs). Data from 1713 TSO500 cases was then analyzed to identify LGVs. Results: The dataset of 1713 cases comprised 20.67% NSCLC, 12.61% breast, 12.49% ovarian and 10.5% colorectal cancer and &lt; 10% of other cancer types including 2.39% pancreatic and 2.04% prostate cancer. 23.8% of ovarian, 17.14% of prostate, 12.5% of breast and 12.2% of pancreatic cancer cases had variants in BRCA1/BRCA2. Among these, 18.69% of ovarian, 17.14% of prostate, 8.33% of breast and 7.32% of pancreatic cancers had LGVs. LGVs in BRCA1/2 were also found in 3.33% of colorectal and 1.13% of NSCLC. The BRCA1/BRCA2 LGV ratio was found to be 3.0 in ovarian, 1.0 in breast and 2.0 in pancreatic but 0.2 in prostate and colorectal and 0.33 in NSCLC cancer. Adding other HBOC genes (ATM, BRCA1/2, BRIP1, CHEK2, PALB2, RAD51C, RAD51D) increased the LGV frequency to 22.43% of ovarian, 22.86% of prostate, 11.11% of breast, 9.76% of pancreatic, 4.44% of colorectal and 2.26% of NSCLC. MMR gene LGVs were seen in 1.23% of all cancers mainly in 10.71% of endometrial and 4.44% of colorectal cancers. Unlike the HBOC genes, MMR gene variants were not observed across multiple cancers and did not show a predominantly germline distribution (somatic/LGV 1:1). In contrast, the background P/LP frequency calculated from gnomAD v4 South Asian data (excluding those with conflicting labels) was 0.74% for BRCA1/2, 1.82% for the extended HBOC list and 0.5% for the MMR genes. Conclusions: Somatic testing was used to identify LGVs and determine the frequencies of HBOC and MMR genes in cancers in the Indian population. Somatic testing also identified LGVs in multiple tissues at frequencies above the background P/LP frequency for this population, suggesting a possible role for these genes in other cancers. This information underscores the need for further study and may be useful to define a clinically relevant subset of patients.

Association between CH mutation in TET2and solid cancer in elderly Asian women.

10585 Background: Clonal hematopoiesis (CH), defined by the expansion of mutated hematopoietic cells due to somatic mutations acquired during aging, is associated with increased age and inflammatory conditions. CH serves as a predictor for the risks of cancer and cardiovascular events, highlighting the importance of early detection of genetic alterations for proactive intervention. As Asian societies are experiencing rapid aging alongside genetic and environmental variations distinct from Western cohorts, we aimed to evaluate the predictive significance of CH in solid cancer in an Asian cohort. Methods: We conducted a nested case-control study within Singapore Longitudinal Ageing Study 1 (SLAS1; NCT03405675). Chinese females (aged 55.0-83.9), comprising 31 patients with solid cancers (breast, lung, colon) who developed cancer during the follow-up, and 29 controls, were randomly selected from the SLAS1. SLAS1 is a community-based longitudinal aging cohort study. Subjects aged 55 years or older, capable of self-ambulation, were recruited between 2003 and 2005 (n=2804) and were followed up in 2005-2007, 2008-2009, and 2018-2020. We linked SLAS1 with records from the Singapore National Death Registry to identify subjects with cancers as cause of death during this period (median follow-up period 17 years). Buffy coat samples taken at baseline were sequenced using the 42-gene target HemeMark panel (Lucence, Singapore) with a reported 0.1% limit of detection. Chi-square test and t-test were performed to compare the frequency of CH variants and the mean number of mutations per person in the case and control group. We evaluated multiple variant allele frequency (VAF) thresholds on an exploratory basis (0.1% to 2%). The relationship between CH mutations and the likelihood of developing cancer was investigated through a logistic regression model, considering CH mutation defined at various cutoff points. Results: CH was found in 29.0% (9/31) of cases and 37.9% (11/29) of controls, with common mutated genes being TET2 (8/31, 25.8%), ASXL1 (4/31, 12.9%), and DNMT3A (2/31, 6.5%) in case group (VAF threshold=0.5%). Multi-gene CH did not predict cancer at any threshold (with the lowest P value of 0.5858 corresponding to VAF 0.5), Genes correlating with increased cancer risk included TET2 with adjusting for age, which was notably significant at thresholds of 0.3% and above (VAF 0.3%, adjusted OR=2.25, 95% CI: 1.14-4.47, p=0.0201; 0.5%, adjusted OR=4.12, 95% CI: 2.00-8.88, p=0.0002). Conclusions: CH determined through multi-genes was not associated with solid cancers, but TET2 mutations at 0.3-0.5% VAF thresholds were more prevalent in cancer cases, as compared to the current 2% threshold used for calling CHIP. The finding in this nested case-control study, conducted within a cohort with a 17-year follow-up, implies a potential association between TET2 mutation and solid cancer. Further study is warranted on a larger cohort.

Integration of circulating tumor DNA and metabolic parameters for outcome prediction in unresectable locally advanced non-small cell lung cancer.

8080 Background: An effective biomarker to direct precise consolidation treatment after CRT is still lacking. Circulating tumor DNA (ctDNA) molecular residual disease (MRD) following curative-intent treatment strongly predicts recurrence in multiple tumor types, but whether further treatment can improve outcomes in patients with MRD remains unclear. Hereby, we applied CAPP-Seq ctDNA analysis to plasma samples collected before and after definitive chemoradiotherapy (CRT) or radiotherapy (RT) in unresectable LA-NSCLC. Methods: A total of 62 unresectable LA-NSCLC patients were prospectively enrolled, providing 62 baseline and 49 post-definitive CRT/RT plasma samples. All patients underwent a PET/CT scan at baseline and 33 patients received a mid-treatment PET/CT scan upon reaching a RT dose of 40Gy/20f during therapy. These 33 patients were randomly assigned to either receive or not receive adaptive dose-escalated RT. A group of patients who received immune checkpoint inhibitor (ICI) consolidation after CRT/RT was compared with patients who were ctDNA-/high △TMTV post-treatment. Results: ctDNA was detected at baseline in 44 (71.0%) patients. Pre-treatment ctDNA concentration was significantly correlated with TMTV (p = 0.004) and TLG (p = 0.010). Baseline ctDNA detection and concentration were not able to differentiate patients with varying treatment responses or predict survival. However, patients with undetectable ctDNA and low TMTV exhibited significantly better PFS (p = 0.024). One month after completing CRT or RT, ctDNA was detected in 25 (47.2%) patients. While the concentration of circulating free DNA (cfDNA) remained relatively stable (p = 0.652), both the mean ctDNA Variant Allele Frequency (VAF) (p = 0.002) and ctDNA concentration (p = 0.043) showed a significant decrease. Patients with undetectable ctDNA post-treatment exhibited significantly longer PFS and OS. A lower ∆TMTV was significantly associated with longer PFS and OS. Compared to the non-response group, the response group exhibited significantly lower change in △SUVmax (p = 0.024), with a trend towards lower change in TMTV, although not significant (p = 0.064). Compared with the matched 30 patient receiving ICI consolidation, those with negative ctDNA and high △TMTV after CRT demonstrated significantly better PFS (p = 0.042) and OS (p = 0.039). Conclusions: Baseline ctDNA combined with TMTV can enhance the predictive ability for survival. Post-CRT ctDNA and △TMTV possess strong prognostic capabilities. Patients who are ctDNA- and with high △TMTV may be exempt from ICI consolidation therapy.

Clinical validation of the Ion Torrent Oncomine Myeloid Assay GX v2 on the Genexus Integrated Sequencer as a stand-alone assay for single-nucleotide variants, insertions/deletions, and fusion genes: Challenges, performance, and perspectives.

Myeloid neoplasms require comprehensive characterization of genetic abnormalities, including single-nucleotide variants, small insertions and deletions, and fusions and translocations for management. The Oncomine Myeloid Assay GX v2 (Thermo Fisher Scientific) analyzes 17 full genes, 28 hotspot genes, 30 fusion driver genes, and 5 expression genes. The validation set included 192 DNA samples, 28 RNA samples, and 9 cell lines and contrived controls. The DNA and RNA were extracted from both peripheral blood and bone marrow. Library preparation, templating, and sequencing was performed on the fully automated Genexus Integrated Sequencer (Thermo Fisher Scientific). The sequencing data were analyzed by manual curation, default Oncomine filters and the Oncomine Reporter (Thermo Fisher Scientific). Of the 600 reference pathogenic DNA variants targeted by the assay, concordance was seen in 98.3% of unfiltered variant call format files. Precision and reproducibility were 100%, and the lower limit of detection was 2% variant allele frequency for DNA. Inability to detect variants in long homopolymer regions intrinsic to the Ion Torrent chemistry led to 7 missed variants; 100% concordance was seen with reference RNA samples. This extensive clinical validation of the Oncomine Myeloid Assay GX v2 on the Genexus Integrated Sequencer with its built-in bioinformatics pipeline and Ion Torrent Oncomine Reporter shows robust performance in terms of variant calling accuracy, precision, and reproducibility, with the advantage of a rapid turnaround time of 2 days. The greatest limitation is the inability to detect variants in long homopolymer regions.

Comprehensive clinical characteristics and ctDNA mutational profile analysis of endocrine resistance/sensitivity to adjuvant ET therapy in luminal breast cancer from the GEICAM/2014-03_RegistEM registry.

1011 Background: Patients (pts) with hormone receptor-positive (HR) early breast cancer (BC) may develop resistance to adjuvant endocrine therapies (ET), with relapse occurring months (m) to decades after surgery. Our study explores clinical characteristics, prognosis, and oncogenic drivers in circulating tumor DNA (ctDNA) at relapse in HR+ BC pts, based on their sensitivity to adjuvant ET. Methods: In the REGISTEM study, we identified 805 primary HR-positive BC pts who developed metastatic relapse. These cases were classified based on their sensitivity to adjuvant ET, according to the 5th ESO-ESMO ABC Guidelines: 1ET-resistance (1ET-R, relapse within the first 2 years of adj ET; n=138), 2ET-resistance (2ET-R, relapse after the first 2 years or &lt;12 m after completing adj ET; n=284), and ET-sensitive (ET-S, relapse after &gt;12 m of completing adj ET; n=383). Out of this cohort, 139 individuals had plasma samples obtained prior to the initiation of the first-line treatment for advanced disease, and these samples were analyzed using the AVENIO ctDNA assay. Results: Pts with 1ET-R were significantly more likely to have grade 3, stage III, and highly proliferative tumors (Ki67&gt;20%). The median time to distant relapse was 24 m for 1ET-R, 52.8 m for 2ET-R, and 124 m for ET-S cases. For first-line treatment, the median PFS was 8.1 m for 1ET-R, 13 m for 2ET-R, and 21.2 m for ET-S relapse (p&lt;0.0001). With a median follow-up in the advanced setting of 34 m, median OS was 28 m for 1ET-R, 46 m for 2ET-R, and 55 m for ET-S relapses (p&lt;0.0001). Pts with ET resistance had more mutations (mut) and higher mut allele frequency than ET-sensitive relapse. Pts with ET resistance showed higher incidence of mut in TP53, ESR1, PTEN, andhigh copy number in EGFRand ERBB2 than ET-sensitive, but similar incidence of mut in PIK3CA.Mut in ESR1 and high copy number in EGFR were correlated with poorer PFS, while ESR1 mut were additionally associated with worse OS, although these associations were not independent of the ET relapse groups (Table). Furthermore, mut in PIK3CA were associated to worse PFS only in ET-R pts. Conclusions: In HR-positive BC, both primary and secondary resistance to adjuvant ET represents a highly aggressive disease with enriched actionable genetic alterations detected at the time of diagnosis of metastatic relapse. Addressing these alterations has the potential to mitigate the unfavorable prognosis associated with these cases. Clinical trial information: NCT02819882 .[Table: see text]

Retrospective study of BRAF inhibitor-based therapy in patients with BRAF mutated advanced solid tumors (RBAST study).

e23265 Background: BRAF mutations are frequently found in melanoma, non-small cell lung cancer (NSCLC), thyroid cancer, to a lesser degree in other tumor types. These mutations constantly activate the kinase domain and result in MAPK pathway hyperactivation. Successful inhibition of this pathway with BRAF/MEK inhibitors (BRAFi/MEKi) results in a clinically meaningful benefit for some patients. The RBAST study, to assess the efficacy and survival outcomes of BRAF inhibitor-based therapy were investigated in patients with solid tumors harboring BRAF mutations. Methods: Data was collected on a total of 697 cases of solid tumor throughout China between Sep 2018 and Dec 2023. Next Generation Sequencing (NGS) is based on the sequencing of tissue samples. Among the samples, the primary endpoints of this study were objective response rate (ORR), disease control rate (DCR), progress-free survival (PFS) and overall survival (OS). The impact of co-mutations with other genes and BRAF variant allele frequency on treatment efficacy was also assessed in this study. Results: BRAF mutations were detected in 36 cases and 15 patients received BRAFi based therapy were identified. For patients who received BRAFi therapy, the best ORR was 26.7% with 4 patients recorded partial response (PR). There were 2 patients with progressive disease giving a DCR of 86.7%. Responses were observed in 4 types of tumors. PR was observed in patients with colorectal cancer (CRC) and melanoma. Median PFS (mPFS) and median OS (mOS) of these patients were 6.0 months (95% CI: 2.3-7.0) and 17.1 months (95% CI: 4.4-NA), respectively. The co-occurring mutation rates of TP53, PTEN, FAT2 and NF1 were 40% (6/15), 20% (3/15), 20% (3/15) and 13.3% (2/15), respectively. No significant difference (p&gt;0.05) in PFS and OS was observed in any co-occurrence of mutations. BRAF mutation variant allele frequency is not an independent prognostic factor for survival with patients received BRAF inhibitor treatment (p&gt;0.05). Conclusions: To the best of our knowledge, this is the first retrospective study exploring BRAFi treatment effectiveness to BRAF mutated solid tumors for Chinese patients. Treatment with BRAF inhibitors is effective for BRAF mutated advanced solid tumors with DCR of 86.7%, mPFS of 6.0 months and mOS of 17.1 months. Co-mutations with other genes and BRAF variant allele frequency did not impact survival outcomes.

Application of a Newly Constructed NGS Panel with 45 X-linked Microhaplotypes Demonstrates the Unique Value of X-MH for Kinship Testing and Mixture Analysis

X-linked microhaplotypes (X-MHs) have the potential to be a valuable supplementary tool in complex kinship identification or the resolution of DNA mixtures, because they bring together the distinctive genetic pattern of X chromosomal markers and the benefits of microhaplotypes (MHs). In this study, we used the 1000 Genome database to screen and select 63 X-MHs; 18 MHs were filtered out though a batch sequencing assessment of the DNA samples collected from 112 unrelated Chinese Han individuals. The resulting 45-plex panel performed well in comprehensive assessments including repeatability, sensitivity, species specificity, resistance to PCR inhibitors or degradation, mutation rate, and accuracy in detecting DNA mixture samples. The minimum amount of DNA template that can be tested with this panel is 0.5ng. Additionally, the alleles of the minor contributor can be accurately detected when the mixture rate is larger than 1:9 in female-male mixture or 1:19 in male-male mixture. Then, we calculated population parameters on each MH based on the allele frequency data obtained from the sequence results of the aforementioned 112 unrelated samples. Combining these parameters on each MH, it can be calculated that TDPm, TDPf, CPET, CPEDFM, CPEDFF and CNCEP3 of the 45-plex system were 1-8.99×10-13, 1-1.62×10-19, 0.9999999995, 0.9999981, 0.9955, 0.9999971 and 0.99940, respectively, indicating that the panel is capable in personal identification and parentage testing. To reveal the unique advantage of X-MHs in the analyses of complex kinship and male DNA mixture, further assessments were made. For complex kinship identification, 22 types of individual pairs with different second-degree kinship were simulated and different types of likelihood ratios (LR) were calculated for each. The results revealed that the panel can achieve accuracy of approximately 70%~80% when dividing each of the three types of second-degree kinships into three or four groups. Theoretically, such sub-division cannot be done by using independent autosomal markers. For male DNA mixture analysis without suspects, the maximum likelihood ratio strategy was derived and employed in the estimation of the number of male contributors (NOMC). Simulations were conducted to verify the efficacy of the 45-plex panel in the field and to compare it with autosomal markers by assuming the 45 MHs as autosomal ones. The results showed that X-MHs can achieve higher accuracy in the estimation of NOMC than autosomal ones when the mixed males were unrelated. The results highlighted the unique value of X-linked MHs in complex kinship and male mixture analyses.

Effect of ctDNA whole-exome sequencing in pancreatic adenocarcinoma on prognostic value, actionable alterations, and organ tropisms in metastatic disease.

4149 Background: The dismal prognosis associated with pancreatic ductal adenocarcinoma (PDAC) needs a deeper understanding of progression mechanisms and personalized treatment. While the prognostic value of ctDNA has already been established, this study purposes to apply plasma whole-exome sequencing (WES) to identify molecular alterations beyond KRAS. This approach aims to predict survival, uncover progression mechanisms, and identify therapeutic targets. Methods: Eighty metastatic PDAC patients were prospectively recruited and divided into two consecutive cohorts: discovery (n=37) and validation (n=43). Tumor and plasma obtained at diagnosis were analyzed using WES. The variant allele frequency (VAF) of KRASmutations was quantified by ddPCR in plasma at baseline and at response from all patients (n=80). Results: Plasma WES identified at least one pathogenic variant across all individuals, which can be categorized into four pathways: oncogenic mechanisms, DNA repair, microsatellite instability and TGFb pathway alterations. 7 unique druggable mutations were detected in tissue and 11 in plasma. Other targetable mutations ( CDK12, NF1, BRCA2, and TSC2), were prevalent in plasma but absent in tissue. Patients with survival less than 11 months showed enrichment in cellular organization pathways and exclusive targetable CDK12 mutations. Longer survival cases exhibited exclusive mutations in DNA regulation and repair genes. Patients with liver metastasis displayed unique mutations not just in KRAS but also in the adaptive immune response pathway genes. Baseline plasma KRAS mutations detected by ddPCR was associated with worse progression-free survival. (HR=2.315, CI 95%= 1.027-5.217, p = 0.038; and HR= 3.022, CI 95% = 1.299 - 7.030, p= 0.007 in the discovery and validation cohort, respectively). A significant risk of progression (p = 0.006) was observed if KRAS VAF at response assessment did not decrease, at least, 84.75% in both cohorts. Conclusions: ctDNA WES unveils molecular signatures of rapid progression, potential actionable alterations, and liver metastasis-specific mutations in the adaptive immune response pathway. KRAS detection at baseline and its evolution during treatment emerge as prognostic biomarkers. [Table: see text]

The combination of tumor mutational burden and T-cell receptor repertoire predicts the response to immunotherapy in patients with advanced non-small cell lung cancer.

Tumor mutational burden (TMB) and T-cell receptor (TCR) might predict the response to immunotherapy in patients with non-small cell lung cancer (NSCLC). However, the predictive value of the combination of TMB and TCR was not clear. Targeted DNA and TCR sequencing were performed on tumor biopsy specimens. We combined TMB and TCR diversity into a TMB-and-TCR (TMR) score using logistic regression. In total, 38 patients with advanced NSCLC were divided into a discovery set (n=17) and validation set (n=21). A higher TMR score was associated with better response and longer progression-free survival to immunotherapy in both the discovery set and validation set. The performance of TMR score was confirmed in the two external validation cohorts of 225 NSCLC patients and 306 NSCLC patients. Tumors with higher TMR scores were more likely to combine with LRP1B gene mutation (p=0.027) and top 1% CDR3 sequences (p=0.001). Furthermore, LRP1B allele frequency was negatively correlated with the top 1% CDR3 sequences (r=-0.55, p=0.033) and positively correlated with tumor shrinkage (r=0.68, p=0.007). The TMR score could serve as a potential predictive biomarker for the response to immunotherapy in advanced NSCLC.

Candidate molecular alterations associated with potential resistance in KRAS G12D gastrointestinal cancers.

3519 Background: KRAS G12D commonly occurs in pancreatic (PDAC) and colorectal (CRC) cancers. Though developing KRAS G12D inhibitors is pertinent, it is expected that primary and acquired resistance will limit efficacy, similar to those seen with KRAS G12C inhibitors. Here, we assessed the prevalence and outcomes of candidate mutations co-occurring with KRAS G12D in PDAC and CRC using liquid biopsy data. Methods: Patients with advanced CRC and PDAC tested with Guardant360 genomic profiling from 2020 to 2023 (~2500 &amp; 3500 samples) were included. Candidate resistance mutations were determined based on mutations reported following KRAS G12C inhibition. Patients with advanced CRC and PDAC tested with Guardant360 at Mayo Clinic (2016-2023) (1158 &amp; 904 samples) were assessed for overall survival (OS). Patients were divided into three groups: KRAS G12D alone, KRAS G12D with candidate resistance alterations, and KRAS G12D not detected (ND). OS was estimated using Kaplan-Meier method. Cox regression was used for multivariable survival analyses. Results: The Guardant360 database reported KRAS G12D in 16.5% of CRC and 40.2% of PDAC samples. The Table below summarizes the most frequent candidate resistance alterations co-occurring with KRAS G12Dincluding point mutations of KRASand PIK3CAand amplifications of EGFR, KRAS, BRAFand MYC. In the Mayo cohort, 8.9% of CRC and 23.5% of PDAC patients had KRAS G12D. In CRC, those with KRAS G12Dand ≥1 candidate resistance alteration had a significantly lower OS (mOS 18.7m) than KRAS G12D alone (30.9m), and ND (37.3m) ( p=0.004). The presence of concurrent candidate resistance alterations with KRAS G12D remained a poor prognostic factor with HR 2.1 (95% CI: 1.3 – 3.2, p=0.001) after adjusting for age and other patient characteristics. Similarly, in PDAC, those with KRAS G12D and ≥1 resistance mutation had significantly lower OS (mOS 8.1m) than KRAS G12D alone (10.5m) and ND (16.1m) (p&lt;0.0001). In multivariable analyses, both KRAS G12D with candidate resistance alterations (HR 2.1, 95% CI: 1.4-3.3, p&lt;0.001) and G12Dalone (HR 1.6; 1.3–2.0, p&lt;0.001) were poor prognostic factors. Among patients with serial Guardant360, treatment response trended with KRAS G12D variant allele frequency. Conclusions: Circulating tumor DNA testing is a useful tool to reveal candidate molecular alterations linked to potential resistance to KRAS G12D targeting in patients with KRAS G12D gastrointestinal cancers. KRAS G12D with these concurrent molecular alterations is a poor prognostic factor in both PDAC and CRC. [Table: see text]

Monitoring ctDNA dynamics in early breast cancer using a novel ultra-sensitive tumor-informed structural variant approach combining whole-genome sequencing and multiplex dPCR.

568 Background: Persistent circulating cell-free tumor DNA (ctDNA) detection during neoadjuvant treatment of early-breast cancer (EBC) indicates high-risk disease. Detection of ctDNA post-resection of EBC (molecular residual disease, MRD) indicates occult metastatic disease and impending disease relapse. For ctDNA to be integrated into EBC management, accessible and scalable diagnostic tools are required. Here, we apply a highly sensitive, personalized tumor-informed approach to ctDNA evaluation predicated on analyses of structural variants (SVs) using a novel digital PCR (dPCR) SV technology. Methods: 170 patients with EBC and eligible for neoadjuvant therapy (NAT) were recruited through the prospective SCAN-B study (NCT02306096) between Dec 2014 and Mar 2019 (25.8% TNBC, 47.1% HR+/HER2- and 24.1% HER2+). Interim results are presented for the first 46 consecutive patients (comprising 567 plasma samples) where minimum QC criteria were met (10% tumor content and 10x sequencing depth). Whole genome sequencing (WGS) was performed on tumor material and personalized multiplex dPCR assays designed tracking up to 8 SVs for use in ctDNA analyses. Plasma samples were collected at baseline, during NAT, pre- and post-surgery and at 6-monthly intervals during follow up. Clinical characteristics and recurrence outcomes were recorded. Results: ctDNA was detected at one or more timepoints prior to surgery in 43/46 (93%) patients across all breast cancer subtypes, at a median variant allele frequency (VAF) of 0.14% (range 0.0002% - 27.6%). ctDNA levels remained detectable at the end of NAT in 24% patients (11/46); 5/11 (45%) ctDNA positive patients experienced disease relapse versus 1/35 (3%) ctDNA negative patients (P=0.002, Fisher’s exact test). At one or more post-operative timepoints, ctDNA was detected in 6/6 (100%) patients who experienced clinical recurrence, with lead times up to 52 months (median 11.8 months, range 3.5 to 52 months). In 40 patients without presentation of clinical recurrence to date, ctDNA was undetectable across 285/287 (99.3%) plasma timepoints collected post-surgery. Post-operative detection of ctDNA associated with poor overall survival (OS) compared to absence of ctDNA (log-rank P&lt;0.0001). Conclusions: In this interim analysis of an ongoing prospective study in patients with EBC receiving NAT, we analyzed plasma for ctDNA using a novel tumor-informed dPCR assay tracking patient-specific SVs. ctDNA detection post-neoadjuvant therapy, prior to surgery associated with high-risk of disease relapse. Postoperative ctDNA detection was observed in 100% patients with clinical recurrence, and associated with poorer OS and long lead-times. Our data demonstrate the feasibility of SVs as an MRD analyte and provide evidence for high levels of clinical sensitivity achievable with this approach in EBC. Clinical trial information: NCT02306096 .

Clonal hematopoiesis of indeterminate potential (CHIP): Outcomes and adverse events in patients with solid tumors.

3521 Background: CHIP is the clonal expansion of hematopoietic stem cells following acquisition of somatic mutations. It is a common incidental finding in cell-free DNA (cfDNA). We investigated the incidence of CHIP in cfDNA from patients with solid tumors and explored its association with outcomes and adverse events (AEs). Methods: We reviewed cfDNA results from a local prospective solid tumor cohort (PREDICT-L) and two randomized trials: CCTG CO.26 (durvalumab + tremelimumab [D+T] or best supportive care [BSC] in metastatic colorectal cancer [mCRC]) and CCTG PA.7 (gemcitabine and nab-paclitaxel [GN] +/- D+T in metastatic pancreatic adenocarcinoma [mPDAC]). CHIP+ was defined as any mutation in DNMT3A, TET2, ASXL1or ATM with a variant allele frequency (VAF) 2% or higher. Variants were considered germline if the VAF was &gt;40%, or were annotated as germline by respective assays. The first line of treatment after cfDNA was reviewed for grade 3 or higher and dose-limiting AEs. Results: The prevalence of CHIP was 10%-21% and was more common in older patients (p=0.003). There was no association between CHIP and sex (p=0.80) or ECOG status (p=0.31). The VAF of CHIP variants was similar across all panels, and DNMT3A was the gene most frequently mutated in all cohorts. Patients with CHIP in PA.7 treated with immunotherapy (IO) had improved progression-free survival (PFS) versus patients without CHIP (p=0.036, p-interaction=0.061 [multivariable]). However, patients with CHIP treated with chemotherapy (Chemo) showed a trend towards worse overall survival (OS) in the PREDICT-L cohort (p=0.057). There was no significant difference in the rates of AEs between the CHIP+ versus CHIP- groups for those treated with Chemo or IO. Conclusions: CHIP is common in patients with solid tumors. Although not appearing to impact rates of AEs, CHIP may impact outcomes from Chemo or IO. [Table: see text]