Cancer Epidemiology, Biomarkers & Prevention

BackgroundWe previously reported that >5% of the population carries pathogenic or likely pathogenic variants (P/LPVs) in key cancer susceptibility genes. However, gene-specific cancer prevalence, spectrum, burden, lifetime risk, comorbidity, and the risk associated with autosomal recessive (AR) genes among carriers remain incompletely defined. MethodsWe analyzed 72 cancer susceptibility genes in the All of Us dataset (N=633,547), including 287,076 participants with both genomic and electronic health record data. Cancer diagnoses were identified using SNOMED codes and grouped into 35 categories. Associations between P/LPVs and overall and site-specific cancer risk were evaluated using regression models adjusted for age, sex, race, and ethnicity. ResultsAmong genes with [≥]10 unique carriers, cancer prevalence was highest for MEN1 (80%), followed by TP53 (57.7%), MLH1 (48.4%), and MSH2 (47.2%). Carriers of P/LPVs in BRCA1, BRCA2, MLH1, APC, NF1, PTEN, and PALB2 had significantly earlier cancer diagnosis compared to non-carriers. Cancer prevalence was markedly higher in BRCA1 and BRCA2 carriers who are also mono-allelic MUTYH carriers (75% and 45.5%, respectively) compared with BRCA1 and BRCA2 alone (43.2% and 36.5%). Adjusted survival analysis showed increased cancer risk for MLH1 (OR=6.08), PTEN (OR=5.80), and MSH2 (OR=5.19). Novel associations included MITF with anal/perianal and prostate cancer; BLM with ovarian and soft tissue/sarcoma; WRN with gynecologic cancer (NOS); and FH with hematologic malignancy. ConclusionsThis population-based analysis defines gene-specific cancer prevalence, spectrum, and risk, including contributions from AR variants, in the U.S. population. These findings support more precise genetic testing, screening, and risk stratification for individuals carrying inherited P/LPVs.

BackgroundSubsequent primary malignancies following human papillomavirus (HPV)-related cancers represent an important survivorship concern. However, evidence remains limited regarding sociodemographic and clinical factors associated with registry-defined subsequent cancers among children, adolescents, and young adults in U.S. population-based cohorts. MethodsWe conducted a retrospective population-based analysis of 1,326 individuals diagnosed with HPV-related cancers using Surveillance, Epidemiology, and End Results (SEER) data. Registry-defined subsequent cancer was operationalized as the occurrence of additional primary HPV-related malignancies according to SEER multiple primary rules. Multivariable logistic regression models estimated associations with sex, age group, area-level socioeconomic status (Yost Index quintiles), persistent poverty census tract status, and primary cancer site. Sex-stratified analyses by cancer site were performed. ResultsRegistry-defined subsequent cancers were significantly associated with female sex and young adult age (20-29 years). Females had higher odds of subsequent cancer compared with males (OR = 1.06, 95% CI: 1.03-1.10), and individuals aged 20-29 years had higher odds than those aged 0-9 years (OR = 1.10, 95% CI: 1.05-1.16). Associations persisted after adjustment for socioeconomic indicators. No significant associations were observed with Yost Index quintiles or persistent poverty. Sex-stratified analyses showed higher odds of subsequent cancer for anal cancer among males and vulvar cancer among females relative to oropharyngeal cancer. ConclusionsSex and age are key determinants of registry-defined subsequent cancers following HPV-related malignancies, independent of area-level socioeconomic context. These findings support age- and sex-specific survivorship surveillance strategies across early life-course stages.

BackgroundMetabolomic changes related to colorectal cancer (CRC) may serve as diagnostic markers to identify patients may develop or have developed CRC. MethodsUntargeted lipidomics were performed on serum from CRC cases and clean-colon controls from the Chicago Colorectal Cancer Consortium (CCCC) and the University of Arizona Cancer Center (UACC). ResultsUntargeted lipidomics in the CCCC CRC series revealed significant alterations in sphingolipids. Targeted lipidomics revealed a signature of five sphingomyelins (SMs) were significantly decreased in CRC patients in CCCC and UACC CRC series. Circulating SMs are degraded primarily by S-SMase and serum S-SMase activity was significantly higher in UACC cases as compared to controls. Serum S-SMase activity was also measured in two series of adenoma patients to determine if S-SMase may serve as a biomarker for development of colorectal neoplasia. While S-SMase activity was significantly higher in adenoma patients compared to controls in the mostly white UACC series, S-SMase activity in samples from the Chicago Black series (CCCC) were indistinguishable from each other and significantly higher than UACC controls. ConclusionsTogether, these studies suggest the potential for S-SMase activity to serve as a biomarker for colorectal neoplasia, with potential implications in some but perhaps not all populations.

Context SummaryO_ST_ABSKey ObjectiveC_ST_ABSCan polygenic hazard scores accurately predict prostate cancer disease risk and age at diagnosis in Nordic populations? Knowledge GeneratedPolygenic hazard score PHS601 stratified prostate cancer risk with a towfold increase per standard deviation increase in two Norwegian populations (N = 17,538). The top 1.7% of scores conferred 8.7-fold higher risk compared with median risk, exceeding the risk associated with pathogenic HOXB13 variants. PURPOSEMore accurate risk prediction is needed for prostate cancer (PCa) to identify individuals at greatest risk of early-onset and clinically-significant disease. Current screening paradigms, such as prostate-specific antigen screening, pose risks due to over-diagnosis and over-treatment of indolent disease. Polygenic hazard scores (PHS) can predict age-at-diagnosis of PCa and are being tested in prospective clinical screening trials. We evaluated the performance of the latest PHS model for PCa (PHS601) in two Norwegian populations. MATERIALS AND METHODSWe assessed PHS601 performance in two Norwegian cohorts (N = 14,688 and N = 2,850) for predicting age-at-diagnosis of PCa and aggressive PCa. In a subset with whole-genome sequencing (N = 526), we compared PHS601 performance to screening for rare pathogenic variants, including HOXB13. RESULTSPHS601 effectively stratified participants by risk in both cohorts (HR per SD = 1.87 [1.78, 1.96] and 2.02 [1.83, 2.23]). Among individuals with whole-genome sequencing, the top 1.7% of PHS values conferred 8.7-fold higher risk than the median (HR = 8.75 [5.02, 14.77]), exceeding the risk associated with HOXB13 pathogenic variants (HR = 3.77 [1.75, 8.11]; 1.7% carrier frequency). CONCLUSIONThese findings support the potential utility of PHS601 in a precision screening paradigm for PCa.

IntroductionBRCA1/2 alterations are increasingly recognized as biologically and clinically relevant features in prostate cancer, yet the prognostic and therapeutic significance of zygosity status remains uncertain. Understanding differences between monoallelic and biallelic inactivation may refine risk stratification and guide therapeutic decision-making. Materials and MethodsA retrospective, desk-based observational analysis was performed using publicly accessible datasets from TCGA-PRAD (primary disease) and SU2C/PCF (metastatic disease). BRCA1/2 status was categorized as wild-type, monoallelic, or biallelic based on mutation, copy-number, and loss-of-heterozygosity profiles. Overall survival was evaluated using Kaplan-Meier estimates and Cox models. Systemic therapy outcomes were assessed by treatment class, incorporating exploratory interaction tests. ResultsIn TCGA-PRAD (n=300), OS did not significantly differ by zygosity (global log-rank p=0.45), with median OS of 80.0 months (wild-type), 78.0 months (monoallelic), and 55.0 months (biallelic). In SU2C/PCF (n=200), zygosity stratified outcomes significantly (global log-rank p=0.04): median OS was 22.0 months (wild-type), 14.0 months (monoallelic), and 16.0 months (biallelic). Treatment analyses showed ARSI exposure improved OS in wild-type disease (HR 0.60; 95% CI 0.38-0.95), while interaction testing suggested potential heterogeneity without statistical confirmation (interaction p=0.092). PARP inhibitor exposure showed directionally favorable HRs in wild-type and monoallelic groups but no significant interaction (interaction p=0.757). No therapy class demonstrated consistent effect modification by zygosity. ConclusionBRCA1/2 zygosity shows prognostic relevance in metastatic prostate cancer but not clearly in primary disease. While zygosity did not consistently modify systemic therapy associations in this dataset, findings support zygosity-aware reporting as a practical tool for molecular stratification and future research design.

ImportancePersistent racial and ethnic disparities in breast and prostate cancer mortality are well documented. Most prior studies emphasize between-group differences and rely on population averages or single composite measures of social disadvantage, which can obscure high-need communities within groups. How socio-behavioral determinants of health vary within groups across local gradients of cancer mortality remains incompletely characterized. A framework that combines race- and cancer-specific mortality with local, domain-level socio-behavioral profiles may help identify where burden is greatest and which specific barriers warrant prioritization. ObjectiveTo determine how socio-behavioral risk relates to breast and prostate cancer mortality within racial and ethnic groups and to characterize domain-specific behavioral profiles across low-, moderate- and high-mortality counties to inform targeted, equity-oriented cancer control strategies. DesignCross-sectional study of U.S. counties. Setting United States, county-level analysis. Participants3,141 U.S. counties, stratified within Non-Hispanic White, Non-Hispanic Black, and Hispanic populations. ExposuresCounty-level socio-behavioral determinants of health measured using a composite index comprising seven domains: community solidarity; education, health literacy, and digital connectivity; quality of care; housing and environmental risk; economic livelihoods; lifestyle behaviors; and touchpoints with care. Main outcomes and measuresRace/ethnicity-specific, age-adjusted breast and prostate cancer mortality rates (2018-2022) and county-level socio-behavioral risk scores. Counties were grouped into mortality tertiles within each race/ethnicity-by-cancer-stratum. ResultsAcross groups, higher socio-behavioral risk was associated with higher breast and prostate cancer mortality. For breast cancer, socio-behavioral risk increased monotonically across mortality tertiles for all groups, with the largest within-group increases among Hispanic and Non-Hispanic Black women. For prostate cancer, risk generally increased across mortality tertiles for all groups. Although Hispanic populations had lower population-average mortality, high-mortality Hispanic counties exhibited pronounced risk in lifestyle behaviors, economic livelihoods, and touchpoints with care. Domain patterns associated with high mortality varied by race, ethnicity, and cancer type, with touchpoints with care and economic livelihoods consistently prominent. Conclusions and relevanceWithin-group heterogeneity in socio-behavioral risk is substantial across U.S. counties. Linking population-specific, domain-level socio-behavioral profiles to cancer mortality may support more precise and equity-oriented cancer control strategies than reliance on group averages or composite indices. Key pointsO_ST_ABSQuestionC_ST_ABSWithin racial and ethnic groups, how do socio-behavioral determinants of health vary across US counties with low, moderate, and high breast and prostate cancer mortality? FindingsIn this cross-sectional study, higher county-level socio-behavioral risk was associated with higher breast and prostate cancer mortality across racial and ethnic groups. Race/ethnicity-specific, domain-level profiles revealed within-group heterogeneity, including persistently elevated risk among Non-Hispanic Black populations and pronounced domain-specific gaps in high-mortality Hispanic counties. MeaningLinking population-specific socio-behavioral profiles to local cancer mortality can guide more precise and equity-oriented prioritization of intervention domains and geographies than reliance on group averages or composite indices.

IntroductionSporadic colorectal cancer (CRC) remains a significant driver of worldwide morbidity and mortality. Environmental factors associated with CRC are increasingly well-described and now include generalized colonic dysbiosis and individual enteric bacteria. Clostridioides difficile is one such species, with recent mouse model work suggesting prolonged exposure to C. difficile toxin B is conducive to colonic tumorigenesis. However, there is a dearth of real-world human evidence linking C. difficile infection and CRC. MethodsHerein, we analyzed a multicenter, longitudinal, Electronic Health Record (EHR)-based dataset to test the association between C. difficile test positivity and the risk for incident CRC utilizing unadjusted and multivariable (controlled for clinical conditions independently associated with CRC development) Cox proportional hazard modeling to compare C. difficile exposed and non-exposed cohorts ResultsWe found that individuals who tested recurrently positive for C. difficile had a significantly increased risk for incident CRC (aHR 2.05 [95% CI 1.27-3.29]) compared with those who tested positive only once (aHR 0.70 [0.45-1.10]) or never. Furthermore, we found potential trends that the effect of C. difficile test positivity on the risk for incident CRC was stronger amongst females compared with males. ImportanceThese findings help translate emerging mouse model work on C. difficile-influenced colorectal tumorigenesis and lay groundwork for more substantial human investigations into this connection. These findings also may begin to help guide the personalized deployment of novel fecal microbiota-based therapies designed to interrupt the life cycle of C. difficile within the gut of human hosts and, potentially, prevent long-term health sequelae of chronic C. difficile infection.

PurposeTumor comprehensive genomic profiling (CGP) has revolutionized cancer care and identifies patients for biomarker-specific therapy. In metastatic hormone-sensitive prostate cancer (mHSPC), CGP is not currently prognostic and no DNA-based genomic classification exists that accounts for combinations of alterations. We developed a DNA-based CGP classification that is prognostic for overall survival (OS) and could inform treatment. MethodsRetrospective cross-sectional study using multivariable models to develop a clinico-genomic prognostic risk classification in U.S. Veterans diagnosed with synchronous mHSPC. Primary outcome was overall survival (OS) from time of metastatic diagnosis. Results7201 Veterans with metastatic prostate cancer who underwent CGP were identified. There were 2484 Veterans (median [IQR] age 72 [67-77] years) with synchronous mHSPC and tissue CGP, which were divided into training and testing datasets. 16 genes associated with survival were identified and favorable, intermediate, and unfavorable genomic prognostication groups were created based upon mortality risk to generate the STRATOS-P classification. In a multivariable model, classification into intermediate and unfavorable groups was associated with increased mortality relative to the favorable group (aHR 1.54 [95% CI 1.33-1.78]; aHR 2.37 [95% CI 1.97-2.485], respectively), demonstrating an average AUC of 0.83. In an external validation cohort of non-Veterans, intermediate and unfavorable classifications were associated with increased mortality (aHR 2.45 [95% CI 1.87-3.21]; aHR 4.37 [95% CI 3.06-6.22], respectively) with an AUC of 0.79. The intermediate and unfavorable genomic prognostication groups were also associated with increased mortality across multiple disease states including synchronous and metachronous diagnoses, castration-resistance, and analyte type. ConclusionsIn metastatic prostate cancer, tumor DNA genomic alterations are prognostic for OS. The STRATOS-P classification is a validated prognostic tool that has the potential to guide decision-making in mHSPC.

BackgroundHelicobacter pylori infection accounts for 98% of gastric cancer (GC) cases in Japan. Since 2013, the nationwide expansion of H. pylori eradication therapy to chronic gastritis patients has created a unique opportunity to evaluate its population-level impact on GC primary prevention. However, short-term reductions in GC deaths are difficult to interpret given the long natural history of gastric carcinogenesis. This study aimed to assess the early impact of population-level eradication on GC deaths. MethodsWe applied a two-layer analytic framework consisting of a counterfactual analysis comparing observed GC deaths during 2013-2021 with expected GC deaths had eradication uptake remained at pre-2013 levels. This was combined with a structured, time-dependent, multilayer state-transition model to estimate GC deaths prevented by eradication using GC incidence integrated with age-dependent H. pylori prevalence. ResultsObserved GC deaths declined from 48,632 in 2013 to 41,624 in 2021, whereas counterfactual GC deaths declined more modestly, from 49,794 to 45,654. The divergence between observed and counterfactual GC deaths widened steadily from 1,162 in 2013 to 4,030 in 2021. Model-based estimates indicated that eradication prevented 1,427 GC deaths during 2013-2021, with annual GC deaths prevented increasing from 17 in 2015 to 417 in 2021, particularly among adults aged 50-79. ConclusionsThis study demonstrates that H. pylori eradication has already contributed to a 10.4% reduction in GC deaths in Japan by 2021, with annual expansion of primary prevention effects. This framework supports evidence-based evaluation of short-term reductions in GC deaths attributable to H. pylori eradication in high-prevalence settings.

BackgroundThe province of Quebec has progressively implemented paired tumour-germline sequencing in paediatric oncology through two coordinated precision research programs, preceding a province-wide mainstream clinical genomics initiative. We report the prevalence, spectrum, and clinical relevance of germline findings (GFs) in children with primary extracranial cancers, integrating molecular, phenotypic, and pathological data. MethodsPatients enrolled between 2014 and 2022 underwent germline whole-exome sequencing (WES) using a virtual 352-cancer gene panel. Sequencing, bioinformatics and variant interpretation followed best practices standards based on GATK, ACMG/AMP and ClinGen recommendations. Somatic WES and transcriptomic data were integrated when available. GFs were categorised as diagnostic findings (DFs; established or suspicious association with the cancer phenotype) or as other findings further subcategorised according to actionability and age of disease onset. FindingsAmong 484 children, 130 (26.9%) carried 149 GFs, including 49 (10.1%) with a DF (42 with well-established associations with cancer phenotypes). DFs involved 21 genes related to childhood cancer predisposition, trisomy 21 and one clinical Beckwith-Wiedemann syndrome. Six DFs were initially missed by standard exome pipelines, and mosaic constitutional cancer predisposition syndrome (CPS) was confirmed in 4/49 children, underscoring the value of integrative analyses. A CPS was known at the time of primary cancer in 10/49 children. Among those diagnosed with a CPS after cancer onset, suggestive phenotypic features were present in 36/39. Other non-diagnostic findings were identified in 92 children; 21 (4.3% of the cohort) with actionable implications in childhood (n=7) or adulthood (n=14). Somatic sequencing was informative for refining causality, as somatic second hit alterations were identified in 29/33 (87.9%) DFs involving monoallelic tumour suppressor genes, whereas no such alterations were observed in non-DFs counterparts (0/57; p<0.0001). Interpretation: This provincial research experience highlights the analytical and practical challenges of germline evaluation in paediatric oncology and supports a shift toward integrative interpretation frameworks combining complementary germline, somatic, pathology, and phenotypic data. Flexibility in investigative strategies and nuanced categorisation of findings are warranted, guided by a child-centred interpretative framework. This approach underpins Quebecs paediatric oncology genomics mainstreaming initiative.

Aim and ObjectivesThe study aimed to evaluate the effectiveness of titanium inserts for interdental papilla reconstruction, comparing it with the Han and Takei technique using subepithelial connective tissue grafts. The objectives included assessing the black triangle height, papilla height and papilla presence index (PPI) at baseline, 1 month and 3 months postoperatively along with the evaluation of Early Wound Healing Score (EHS) during the first week of post operative healing period. Patients and MethodsThis single-blind randomized clinical trial included systemically healthy individuals aged 18-35 years with Nordland and Tarnows Class I-III papillary loss. A total of 18 participants were randomly assigned to either test group or control group. Clinical parameters were measured pre- and post-operatively at specified intervals. Both groups received standard presurgical care and postoperative follow-up. The surgical protocol for the test group involved titanium insert placement in the interdental bone, while the control group received a connective tissue graft using the Han and Takei method. ResultsBoth groups showed significant intragroup improvements in all parameters from baseline to 1 and 3 months (p<0.05). However, intergroup comparisons showed no significant differences at most time points, except at 3 months for PPI, where the control group showed significantly better results (p=0.04). EHS scores were not significant between the groups. ConclusionTitanium inserts and CTG both demonstrated clinical effectiveness in enhancing interdental papilla dimensions. These findings support the titanium insert as a viable, less invasive alternative, offering clinicians a practical option for esthetic papilla reconstruction.

Between 10 and 20% of cervical cancers are adenocarcinomas with poorer five-year survival and higher recurrence. To identify somatic alterations driving cervical cancer, we performed whole-exome sequencing of 308 subjects with invasive disease from Guatemala and Venezuela. Consistent with other studies, there is a higher rate of TP53 mutations in adenocarcinomas versus squamous cell carcinomas (SCC), especially in HPV-negative tumors. We identified a higher rate of mutations and deletions (23%) in the STK11 tumor suppressor gene in adenocarcinomas versus SCC. This result was confirmed in the AACR Project Genie and Caris cohorts. Whole-genome sequencing and SNP-array data identified significant numbers of focal deletions on chr19p that disrupt STK11, undetected by exome sequencing. In one tumor, HPV integration disrupts STK11. Chr19p is commonly deleted in cervical cancer, and we document a high rate of independent inversions, chromosomal translocations, and breakage-fusion-bridge events that provide the second hit to STK11. Significantly, STK11 alterations are associated with a younger age of onset and poorer overall survival and survival on immunotherapy. Apart from STK11, PIK3CA mutations and YAP1 amplification are prevalent cervical cancer drivers. STK11 mutations and deletions co-occur significantly with YAP1 amplifications, suggesting an interaction between these pathways. In contrast, STK11 alterations are mutually exclusive to PIK3CA mutation, suggesting redundancy. Cervical adenocarcinomas exhibit significantly lower CD274 (PD-L1) expression and a poorer response to immune checkpoint inhibitors (ICIs). STK11 mutations are associated with poor responses to ICI in other cancers, and elucidating the role of STK11 in cervical cancer may improve targeted and immunotherapies. SignificanceCharacterized one of the largest cohorts of fresh-frozen, invasive cervical cancer cohorts and documented that STK11 mutations and deletions are more prevalent in adenocarcinoma, and defined an early-onset, more aggressive subtype.

Head and neck cancer (HNC) is highly prevalent in South-Asia, driven by additional region-specific exposures such as chewing tobacco and betel nut. Despite therapeutic advances, five-year survival rate remains around 50-60%, underscoring urgent need to identify novel therapeutic targets and improve disease-free survival. This study was designed to identify both somatic and germline drivers contributing to HNC pathogenesis. Through whole-exome sequencing of 103 patients, we detected mutations in known HNC drivers (TP53, CDKN2A, NOTCH1) as well as novel hotspots in several genes, including TRIM48, MAP3K19, and CDC20. A recurrent hotspot mutation (p.A187T) in POLQ gene was identified in patients with high tumor mutation burden and was absent in both TCGA and ICGC cohorts. Among known hotspots, the MYC p.T73A mutation was highly prevalent, occurring in over 50% of patients. As MYC is considered an "undruggable" target, alternative strategies targeting upstream regulators such as BRD4 with specific inhibitors may hold promise for South-Asian HNSCC patients harboring the p.T73A mutation. Copy-number variation analysis further revealed EGFR amplification and TP73 deletion in the majority of patients, highlighting additional layers of genomic dysregulation. Comparative genomic analyses showed no recurrent mutations in epigenetic regulators (ARID2, EP300, KMT2B/MLL2, KMT2D/MLL4, NSD1, and TET1). We report p.S456L germline variant in SDHA consistently among South-Asian cohorts. Patients with p.S456L mutation were younger than those without it, reflecting typical epidemiological signature of a genetic variant that increases susceptibility. Systematic molecular characterization of recurrent mutations is required to elucidate mechanism of action of these variants and to find actionable therapeutic targets.

BackgroundPancreatic ductal adenocarcinoma is one of the most aggressive and lethal malignancies of the gastrointestinal tract. The poor prognosis is largely attributed to late-stage diagnosis, pronounced tumor heterogeneity, and limited therapeutic efficacy. These challenges underscore the urgent need for the identification of robust molecular biomarkers and novel therapeutic targets. MethodsGene expression data from a total of 146 pancreatic tissue samples, comprising 72 normal and 74 tumor specimens obtained from the Pan-Cancer Atlas(TCGA) were analyzed. Differential gene expression analysis was conducted using the DESeq2 package, followed by functional enrichment analysis based on GO and KEGG. A classification model was developed using the XGBoost algorithm and evaluated through 500 bootstrapping iterations and 5-fold cross-validation to ensure robustness and generalizability. Model interpretability was assessed using SHAP (SHapley Additive exPlanations) values to identify genes with the highest predictive contribution. ResultsA comprehensive transcriptomic analysis revealed significant dysregulation of multiple genes between normal and tumor pancreatic tissues. Genes such as GJB3, S100A2, MSLN, and SLC2A1 were notably overexpressed, whereas DEFA6, APOB, and RBP2 exhibited marked downregulation, indicative of impaired exocrine function and aberrant epithelial reprogramming. The XGBoost classification model achieved an average area under the curve (AUC) of 0.9868 and an overall accuracy of 98.6%. SHAP (SHapley Additive exPlanations) analysis identified GJB3, LINC02086, and TSPAN1 as key predictive features. Six genes were concurrently identified as differentially expressed and highly influential within the model, supporting their potential utility as robust biomarkers for pancreatic tumor characterization. ConclusionsPancreatic ductal adenocarcinoma is marked by extensive transcriptomic reprogramming. The integration of differential gene expression analysis with interpretable machine learning enabled the identification of a molecular signature with potential diagnostic and therapeutic relevance.

PurposeGermline deletions affecting the Y-chromosomal gr/gr region were reported in 2005 as associated with susceptibility to testicular germ cell tumor (TGCT), a highly heritable tumor type that is the most common cancer type affecting adult men under the age of 45. Attempts to replicate this association have been equivocal, primarily due to limited power. MethodsHere, we compare and validate two computational approaches to gr/gr deletion calling in high-, low- and ultra-low-coverage whole genome sequencing data, applying these to two datasets from UK Biobank and the TECAC consortium. We generate dataset-specific effect size estimates for the gr/gr deletion-TGCT association using Firths bias-reduced logistic regression across a total of 198,306 men of European-like ancestry (2231 with and 196,075 without TGCT). ResultsUpon random-effects meta-analysis of estimated effect sizes in the two datasets, we found no significant association between gr/gr deletion status and TGCT risk (combined odds ratio=1.24, 95% CI=0.74-2.07, p=0.42), nor upon stratification of seminoma and non-seminoma/mixed histological subtypes. ConclusionOur analysis suggests gr/gr deletion status alone is likely not predictive of TGCT risk in population-scale analyses of European-like individuals; however, the importance of other proposed determinants of gr/gr deletion impact, including Y-haplogroups and semen phenotype, remains unexplored at scale.

Cancer is among the leading causes of death worldwide; however, with incidence rising, there is a requirement to identify novel risk factors and biomarkers to prevent and diagnose cancer earlier. Previous work has implicated a role of the gut microbiome in cancer aetiology; however, its causal relevance is not clear. Whilst Mendelian randomisation (MR) is increasingly being applied to assess the causal role of the gut microbiome on several health outcomes, the complexities and limitations of the method are not fully addressed in much of the current literature. Here, we aimed to appropriately apply MR to understand the role of the gut microbiome in cancer aetiology, whilst demonstrating the range of sensitivity analyses required to provide appropriate causal inference. Whilst findings initially suggested that there were several bacterial genera, families and phyla that may alter cancer risk, further sensitivity analyses indicated that these results were unlikely to reflect causality given violations of core MR assumptions. This study highlights the need for a rigorous MR analysis pipeline, incorporating sensitivity analyses evaluating the plausibility of MR-derived effect estimates, to avoid incorrect conclusions around causality, where estimates likely reflect more complex relationships.

Importance: Recurrence rates for locally advanced HPV-independent (HPV-) head and neck squamous cell carcinoma (HNSCC) are high. Circulating tumor DNA (ctDNA)-based minimal residual disease (MRD) assays have shown promise to improve management and surveillance in several tumor types, but their clinical utility in HPV- HNSCC remains understudied. Objective: To evaluate the performance of a tumor-informed ctDNA-based MRD assay (PredicineBEACON) in patients with newly diagnosed, locally advanced HNSCC (LA-HNSCC). Design: Between 12/2020 and 3/2022 ctDNA was assessed before surgery, before the start of adjuvant treatment (MRD-E), within six weeks of completion of treatment (MRD-TC), and during surveillance (MRD-S). Patients were followed for at least 12 months after treatment completion. We used Kaplan-Meier survival analyses to compare recurrence-free survival (RFS) and overall survival (OS) between patients who were MRD positive those who were MRD negative during each time window. Multivariable Cox hazard regressions were used to assess the association between MRD status and outcomes while controlling for established risk factors. Setting: This was a prospective cohort study of patients treated at a large referral center specializing in treatment of HNSCC. Participants: Forty patients with newly diagnosed, LA-HNSCC treated with surgery followed by risk-adjusted adjuvant treatment Intervention: Tumor-informed ctDNA-based MRD testing Main Outcomes and Measures: Recurrence-free survival (RFS) and overall survival (OS) Results: We processed 142 samples from 40 patients. The median age was 63, 27% were female, 87% were Caucasian, and 95% had HPV- disease. Fifty percent (20/40) of patients experienced recurrence. The pre-surgery ctDNA detection rate was 97% (35/36). MRD-TC positivity was associated with worse OS (HR= 7.15; 95% CI: 1.44-35.3) and RFS (HR= 5.39; 95% CI: 1.98-21.07). MRD-S positivity was associated with worse RFS (HR=8.2; 95% CI: 2.06-33.6). The median time from first MRD detection to clinical detection of recurrence was 5 months (range 0.2-21.6). In multivariable analyses, MRD positivity was associated with worse RFS (HR 13.8; 95% CI 2.92-65.7) and worse OS (HR 18.9; 95% CI 2.27-158). Conclusions and Relevance: Tumor-informed ctDNA MRD positivity was associated with worse RFS and OS in patients with HNSCC. MRD testing could serve as a non-invasive, prognostic biomarker in HPV- HNSCC patients. Key PointsQuestion: Among patients with locally advanced HNSCC (LA-HNSCC) treated with curative-intent surgery, is minimal residual disease (MRD) detection using a tumor-informed ctDNA-based assay prognostic for recurrence free survival (RFS) or overall survival (OS)? Findings: In this prospective cohort study of 40 patients with LA-HNSCC, nearly all of whom had HPV-independent disease, MRD positivity during the first 6 weeks after completing treatment and during surveillance was associated with worse OS and RFS. Meaning: Tumor-informed ctDNA MRD detection after treatment completion could serve as a non-invasive, prognostic biomarker in HPV-independent HNSCC patients. Social Media PostFindings by @FadenLab and colleagues show that detection of MRD using a tumor-informed ctDNA-based after treatment completion is associated with worse recurrence free survival and overall survival in HPV-independent HNSCC.

BackgroundThe genetic architecture of Breast Cancer (BC) in Arab populations remains largely understudied, limiting the precision of current prevention and screening programs. The Emirati Genome Program (EGP), one of the worlds first nation-wide sequencing initiatives, offers an unprecedented opportunity to delineate inherited BC risk across an entire population. MethodsWe analyzed 436,780 EGP individuals, including 229,309 women, integrating whole-genome sequencing (WGS) with electronic health records (EHRs). We quantified the prevalence and penetrance of pathogenic and likely pathogenic (P/LP) variants across 13 NCCN-recommended BC genes, evaluated the performance of established polygenic risk scores (PRS), and reconstructed >48,000 pedigrees to measure familial aggregation. ResultsP/LP variants were identified in 0.84% of women, accounting for 5.2% of BC cases (mean age of 45.9{+/-}11.1 years). Highly penetrant BRCA1 c.4065_4068del (p.Asn1355fs) and BRCA2 c.2808_2811del (p.Ala938Profs) variants showed age-specific cumulative risks of 37.6% and 31% by age 60, respectively, and allele frequencies up to tenfold higher in the Emirati population than in global reference datasets. The European-derived PRS model (PGS000004) demonstrated strong performance, advancing 10-year BC risk onset by a decade for women in the top decile. Family-based PRS discriminated affected from unaffected individuals, revealing higher polygenic risk even within sister pairs. Integration of monogenic, polygenic, and familial data defined a national framework for risk stratification, identifying disease-free women potentially eligible for targeted prevention. ConclusionsNation-scale genome sequencing reveals, for the first time, the comprehensive landscape of inherited BC susceptibility within a Middle Eastern population. The integration of monogenic, polygenic, and familial data establishes a national framework for genomic risk stratification--transforming population genomics into a foundation for precision prevention and early detection in the UAE and beyond.

Chromosome 5p15.33 harbors several independent association signals which demonstrate antagonistic pleiotropy across cancer types, with causal mechanisms largely unresolved. To identify functional variants and enhancer elements at this locus, we performed statistical fine-mapping followed by massively parallel reporter assays (MPRA) and proliferation based CRISPRi screens. This approach identified eight multi-cancer functional variants (MCFVs) across three GWAS signals. Targeting rs421629 (part of the CLPTM1L signal marked by rs465498) with CRISPRi revealed opposing effects on TERT expression in pancreatic versus lung cancer cells, consistent with the antagonistic pleiotropy observed for this signal. Furthermore, CRISPRi nominated an intronic CLPTM1L variable number tandem repeat (VNTR) as a potent enhancer. Long-read sequencing established VNTR polymorphisms as potential causal variants for the rs465498 signal. We showed that Hippo-pathway transcription factors mediate VNTR enhancer activity in lung and pancreatic cancer cells. Together, these findings indicate that cancer susceptibility at 5p15.33 may be mediated by both SNPs and VNTRs and provide an integrated framework for resolving complex pleiotropic loci.

ObjectiveTumor transformation is accompanied by widespread methylation changes, in the form of cytosine modifications, in transposable elements (TEs). The purpose of this study was to investigate whether changes in methylation and hydroxymethylation in the form of 5mC and 5hmC within transposable elements in circulating cell-free DNA (cfDNA) can serve as predictive markers of ovarian malignancy. MethodsHealthy women as well as women undergoing surgery for various benign, borderline, or malignant adnexal masses and gynecologic conditions were selected for this study. 5hmC-Seal or LABS-seq were performed on cfDNA isolated from prospectively collected serum and plasma samples. We built two models using either differentially hydroxymethylated (5hmC) or methylated (5mC) features within TEs to establish models predictive of ovarian malignancy in women with adnexal masses. ResultsWe isolated cfDNA and analyzed a total of 522 samples (plasma, n = 363; serum, n = 159) from women receiving care at the University of Chicago Medical Center. Multivariate modelling using age, cell deconvolution and the top 38 differentially hydroxymethylated (5hmC) transposable elements was able to accurately predict malignancy in women with an area under the curve (AUC) of 0.854 and a 95% confidence interval: 0.746- 0.962 (95% CI) in plasma and an AUC of 0.893 (95% CI: 0.806- 0.98%) in serum. 5mC-based modelling using the top 25 positive and negatively correlated features, based on differentially methylated transposable element promoters, was able to accurately predict malignancy with an AUC of 0.970 (accuracy of 0.936). ConclusionsWe developed two multivariate models based on cfDNA-derived 5hmC or 5mC modified transposable elements to accurately predict ovarian malignancy in women. Furthermore, we show that our 5hmC-based model applies to plasma (EDTA) and serum samples, which are commonly collected in clinical practice. The results of our study warrant further investigation of the predictive performance of our models in large-scale cohorts in the future.