Missense mutations have been extensively studied in tumor-suppressing antigens (TP53) to understand oncogenesis within malignant epithelial cells. Using Whole Exome Sequencing (WXS), missense mutations can be profiled into protein sequences to identify the most common variants in tumor samples. Since most mutations arise randomly, it is necessary to isolate those that produce dysfunctional proteins within large cohorts. Using threading and generative algorithms such as AlphaFold and ColabFold, large cohorts of WXS information can be converted into computationally analyzable structures. By evaluating both high- and low-confidence regions in these structures, these antigens can be studied en masse using pipelines that generate analytical inputs for quantum chemistry analysis. We created a pipeline that processed whole-exome sequencing (WXS) data and selected 28 representative TP53 missense mutants from the TCGA-BRCA cohort for quantum-chemical feasibility analysis. These structures were systematically cleaned using tools such as OpenBabel and AmberTools, and each was prepared for Natural Population Analysis (NPA), Electrostatic Potential (ESP) calculations, and Highest and Lowest Occupied Molecular Orbital (HOMO/LUMO) evaluation within Q-Chem. Using this pipeline, population genomics can be integrated with chemoinformatics to analyze electron density concentrations and generate hypothesis-generating electronic descriptors associated with protein dysfunction. By modifying the generated inputs, additional analyses such as Fukui orbitals, chemical shifts, and Raman shifts can also be performed. This provides a computational means to probe electronic properties not readily accessible at scale using experimental techniques.

Toripalimab, a PD-1 inhibitor, is approved in China as second-line therapy for metastatic urothelial carcinoma. This subgroup analysis evaluated its efficacy and safety in previously treated patients with metastatic upper tract urothelial carcinoma (mUTUC). In the phase II POLARIS-03 trial, patients with mUTUC received toripalimab (3 mg/kg Q2W) until progression or unacceptable toxicity. Tumor response was assessed by an independent review committee (IRC) per RECIST v1.1. PD-L1 expression and tumor mutational burden (TMB) were assessed by immunohistochemistry and whole-exome sequencing (WES), respectively. Between June 2017 and September 2019, 71 patients with mUTUC were enrolled. As of June 16, 2025, median follow-up of 70.5 months, the IRC-assessed objective response rate (ORR) was 26.8% (95% CI, 16.9-38.6), and disease control rate (DCR) was 46.5%. Median duration of response was 45.0 months; median progression-free survival (PFS) and overall survival (OS) were 1.9 months and 11.2 months, respectively. PD-L1-positive patients showed higher ORR (34.8% vs 20.5%) and longer PFS (2.3 vs 1.8 months; HR = 0.71). Among 63 patients with WES data, TMB-high patients (≥10 muts/Mb; n = 14) had higher ORR (42.9% vs 22.4%) and numerically longer PFS and OS. Frequent mutations included TP53, KMT2D, TERT, CDKN2A/B, and FGFR3. ORR reached 75.0% in SMARCA4-mutated tumors and 50.0% in NECTIN4-amplified cases. Toripalimab demonstrated promising activity and manageable safety in pretreated mUTUC. High TMB was associated with numerically improved outcomes, suggesting its potential role as an exploratory biomarker for response to PD-1 blockade in this population.

Carrier screening serves as an effective measure for reproductive planning. Given ancestry/regional variations in genetic spectra, this study aimed to comprehensively identify high carrier frequency genes/variants in the Chinese population, thereby providing evidence for developing tailored expanded carrier screening (ECS) strategies. In this retrospective study, 5,018 healthy participants from Eastern China who visited Peking Union Medical College Hospital between January 2013 and December 2023 underwent ECS. Whole exome sequencing (WES) was employed to detect over 3,000 monogenic disorders with autosomal recessive (AR), X-linked (XL), or X-linked recessive (XLR) inheritance patterns, followed by comprehensive analysis of the WES data. The cumulative carrier rate in the study population was 84% (4,213/5,018), with an average of 1.84 pathogenic/likely pathogenic variants per participant. The study identified 204 at-risk couples, representing an overall risk rate of 8.54%. Additionally, 62 high-frequency genes (carrier frequency ≥ 1/200) were detected, including some ACMG-recommended genes previously excluded from Chinese ECS panels due to unclear carrier frequencies. Further analysis proposed an optimized Chinese ECS strategy incorporating 200–300 key high-frequency pathogenic genes for panel size design and utilizing hybridization capture sequencing to maximize panel efficiency. This study revealed distinctive genetic characteristics of the Chinese population and provides foundation for developing population-specific ECS strategies.

Despite years of experience from scientific teams around the world, diagnosing the cause of monogenic diabetes (MD) remains a challenge, mainly due to the proper definition of the patients' phenotype and the multitude of molecular causes. Our goal was to present the results of the efforts to make the molecular diagnosis of patients with suspected MD as precise as possible from the last few years of our Rare Disease Center for Children and Adolescents and Diabetogenetics using the NGS (Next Generation Sequencing) method. We used a targeted NGS panel and whole exome sequencing (WES) data. The study group consisted of 644 individuals, including 501 patients who were referred from 17 Polish diabetes centers with suspected MD and who were diagnosed between January 2020 and December 2023, as well as their 143 family members. The median age for the patients was 14 years (IQR: 9-18). Overall, MD was confirmed by identifying the causative genetic variant in 43.3% of probands. We identified causative variants in 16 genes, most commonly in GCK and HNF1A (85.7%), mainly of the SNV (single nucleotide variant) type, and CNV variants in the GCK and HNF1B genes (1.4%). Using WES data, we could also identify the 17q12 syndrome in one patient. The subgroups of MD and unresolved patients differed in regard to age of clinical and genetic diagnosis (p = 0.00714 and p = 0.00004), birth weight (p = 0.00255), BMI (p = 0.00075), and HbA1c (p = 0.00001). Analysis of WES data (44%) and targeted gene panels (43%) provided similar results in successful diagnosis of MD. However, WES data offer a more complete molecular picture for the diagnosis of MD, especially for large rearrangements, and allow for kinship and ethnicity analysis, which can expand the scope of the diagnosis.

Clonal hematopoiesis may precede the diagnosis of aplastic anemia by several years.

Primary ciliary dyskinesia (PCD) is a rare hereditary disorder characterized by defective motile cilia and impaired mucociliary clearance in the respiratory tract. In recent years, significant advances have been made in both clinical and basic research on PCD, especially regarding the identification of newly discovered pathogenic genes. However, early diagnosis and treatment of PCD in China still face considerable challenges. In response, a new expert consensus on the diagnosis and treatment of PCD in China has been developed. This consensus was initiated by the Genetic and Rare Lung Disease Group (Preparatory) of the Chinese Thoracic Society of the Chinese Medical Association and the China Bronchiectasis Clinical Diagnosis and Research Alliance. This consensus is based on extensive opinion collection, literature review, online and offline discussions, and previous expert consensus on PCD in China. The consensus addresses 9 core issues related to PCD, including its clinical presentation, diagnosis, treatment, patient management, and follow-up. Nine recommendations have been formulated to improve the diagnostic and therapeutic approaches to PCD in China.Issue 1: Which high-risk populations should undergo PCD screening?Recommendation 1: It is recommended to screen for PCD in patients with a history of bronchiectasis plus any one of the following: situs inversus; chronic sinusitis or nasal polyps; recurrent or chronic otitis media; infertility/subfertility; consanguinity, or a sibling or first-degree relative with a confirmed PCD diagnosis (1C).Issue 2: What is the value of imaging examinations in the diagnosis and management of PCD?Recommendation 2: For the high-risk PCD populations mentioned above, we recommend performing active imaging investigations-including chest high-resolution computed tomography (HRCT), sinus CT, and cardiac ultrasonography-to aid in the early detection of clinical features indicative of PCD, such as bronchiectasis, sinusitis, and situs inversus. In addition, for patients diagnosed with PCD, we recommend regular follow-up chest HRCT to monitor the progression of pulmonary lesions (1C).Issue 3: What is the value of transmission electron microscopy (TEM) in diagnosing PCD?Recommendation 3: For patients with a high clinical suspicion of PCD, we recommend transmission electron microscopy (TEM) for the assessment of ciliary ultrastructure. TEM serves as a direct diagnostic tool for suspected PCD. A definitive diagnosis of PCD can be made if a class 1 defect is identified (1B). If a class 2 defect is observed, the results should be interpreted in conjunction with other diagnostic findings.Issue 4: What is the value of genetic testing in PCD diagnosis, and which genetic testing strategy should be used?Recommendation 4: For patients with a high clinical suspicion of PCD, we recommend performing genetic testing using whole-exome sequencing (WES) at an early stage. WES serves as a direct diagnostic tool for suspected PCD. A definitive diagnosis can be made when biallelic pathogenic or likely pathogenic variants in known PCD-related genes are identified. During WES data analysis, it is essential to include the assessment of copy number variations (CNVs) (1C).Issue 5: What is the value of nasal nitric oxide (nNO) measurement in diagnosing PCD?Recommendation 5: nNO measurement is recommended as an adjunctive diagnostic test for suspected PCD. Using a threshold of 77 nl/min, patients with nNO values below this threshold should undergo further confirmatory PCD testing (2B).Issue 6: What is the value of high-speed video microscopy analysis (HSVA) in diagnosing PCD?Recommendation 6: In clinical settings with access to HSVA, HSVA is recommended as an adjunctive diagnostic test for suspected PCD. A positive HSVA result warrants further confirmatory testing (2C).Issue 7: What is the value of immunofluorescence (IF) in diagnosing PCD?Recommendation 7: In clinical settings where IF is available, it can be recommended as an adjunctive diagnostic test for suspected PCD. A positive IF result warrants further confirmatory testing (2D).Issue 8: How should PCD patients be followed up?Recommendation 8: Regular annual follow-up is recommended for adult PCD patients. Key follow-up components include assessment of pulmonary, sinus, and otologic symptoms and function. Additional assessments should include evaluation of disease severity, immune status, quality of life, and psychological status. Furthermore, infertility/subfertility assessment and follow-up are recommended for PCD patients of reproductive age (1C).Issue 9: How can genetic counseling assist PCD patient families in reproductive planning and decision-making?Recommendation 9: Providing appropriate genetic counselling to families of PCD patients can help identify carriers and assess the risk of offspring having PCD for individuals of reproductive age, thereby assisting them in making informed reproductive decisions (1D).

Introduction: We recently identified variants in 10 genes that are members of either the p53 pathway or Fanconi Anemia Complex (FAC), regulators of DNA repair (DNA damage response [DDR]) in 17 cases with pediatric acute-onset neuropsychiatric syndrome (PANS) or regression in autism spectrum disorder and other neurodevelopmental disorders (NDD). We aimed to identify additional cases with genetic vulnerabilities in DDR and related pathways. Methods: Whole-exome sequencing (WES) and whole-genome sequencing (WGS) data from 32 individuals were filtered and analyzed to identify ultrarare pathogenic or likely pathogenic variants. Results: Variants affecting DDR were found in 14 cases diagnosed with PANS or regression (CUX1, USP45, PARP14, UVSSA, EP300, TREX1, SAMHD1, STK19, MYTl1, TEP1, PIDD1, ADNP, FANCD2, and RAD54L). The CUX1 variant is de novo, as are two cases that had mutations in genes that affect mitochondrial functions that are connected directly or indirectly to mitophagy (PRKN and POLG), which can trigger the same innate immune pathways when disrupted as abnormal DDR. We also found pathogenic or likely pathogenic secondary mutations in several genes that are primarily expressed in the gut that have been implicated in gut microbiome homeostasis (e.g., LGALS4, DUOX2, CCR9). Conclusion: These findings align with previous genetic findings and strengthen the hypothesis that abnormal DDR and mitochondrial dysfunction underlie pathogenic processes in at least some cases of neuropsychiatric decompensation. The potential involvement of genetic variants in gut microbiome homeostasis is a novel aspect of our study. Functional characterization of the downstream impact of DDR deficits may point to novel treatment strategies.

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is traditionally recognized as a risk factor for drug- or infection-induced hemolytic anemia. Emerging evidence implicates potential roles of G6PD in neurodevelopment, yet its association with rare neurological disorders remains underexplored in population-based genetic studies, especially within the Chinese population. We conducted a retrospective case-control study utilizing whole-exome sequencing (WES) data from a Chinese cohort. Six most prevalent pathogenic G6PD variants in China were screended in children with rare neurological disorders (n = 211) and in controls without neurological involvement (n = 202). Genotype and carrier frequency comparisons were performed. Stratified analyses were performed based on diagnostic certainty and the presence of de novo mutations. Multivariable logistic regression was employed to calculate sex-adjusted odds ratios (ORs) to control for potential sex-related confounding. After adjusting for sex, the overall carrier rate of pathogenic G6PD variants was significantly higher in patients with neurological disorders than in controls (adjusted OR = 2.44, 95% CI: 1.18-5.06, p = 0.014). Further comparisons across specific groups revealed distinct patterns: affected male patients had a higher carrier rate than their own unaffected fathers (OR = 2.30, 95% CI: 1.08-4.91, p = 0.043), and mothers of case patients showed a higher carrier rate than mothers of controls (OR = 2.03, 95% CI: 1.09-3.78, p = 0.030). The variants NM_001042351.3: c.1376G>T (G6PD Canton) and NM_001042351.3:c.1388G>A (G6PD Kaiping) were the most prevalent across all groups. This population-based genetic analysis provides preliminary evidence that G6PD deficiency may be a underrecognized genetic risk factor for rare neurological disorders in Chinese children. The findings suggest a potential maternal genetic contribution and indicate that the phenotypic spectrum of G6PD deficiency may extend beyond hematological manifestations to include neurodevelopmental vulnerability. Important limitations include the lack of functional validation and the use of a clinical control group. Further prospective studies incorporating G6PD enzyme activity assessment and functional investigations are warranted to elucidate the underlying mechanisms.

ObjectivesCongenital insensitivity to pain (CIP) is a rare sensory neuropathy marked by absent nociception that predisposes patients to injuries and complications. Variants in genes, particularly PRDM12, underlie the condition. We investigated the molecular basis of CIP in 2 unrelated families.MethodsTrio whole-exome sequencing was performed for 3 CIP patients from 2 unrelated families and their parents; 1 family with negative results subsequently underwent whole genome sequencing. Sanger sequencing and fluorescent PCR confirmed and sized a GCC repeat expansion.ResultsPRDM12 variants explained CIP in both families, each manifesting infantile-onset neuropathic keratopathy and self-mutilation. In Family 1, 2 siblings born to consanguineous parents were homozygous for a 19-GCC repeat expansion in the last exon, resulting in a polyalanine tract of 20 alanines—the largest PRDM12 polyalanine expansion reported to date. In Family 2, the proband carried 2 compound-heterozygous variants c.570+2T > G and c.796A > C (p.Thr266Pro) classified as pathogenic and likely pathogenic, respectively, and both previously undescribed.DiscussionThese data broaden the genetic spectrum of CIP and reinforce PRDM12 as a key gene in pain perception. They also emphasize that diagnostic analysis should target both single-nucleotide variants and polyalanine expansions, which are often underrepresented in whole-exome or whole-genome sequencing data.

BackgroundThis study aimed to identify novel mutations associated with the progression of gastric cancer by establishing patient-derived xenograft (PDX) models and performing comprehensive genomic characterization of these PDX models and their corresponding primary tumors.MethodsFresh gastric cancer tissue samples were collected from 20 patients who underwent surgical resection at Shanxi Cancer Hospital and were subsequently implanted into NOD-SCID mice to establish PDX models. Histopathological features were evaluated using hematoxylin and eosin (H&E) staining. Whole-exome sequencing (WES) was performed on both primary tumors and their corresponding F1-PDX and F3-PDX tumors, focusing on mutations within 559 cancer-related genes. Predictive tools, including SIFT, Polyphen2_HVAR, Polyphen2_HDIV, and Mutation Taster, were utilized to identify potentially deleterious mutations, while I-Mutant and MUpro were employed to assess protein stability.ResultsNine gastric cancer PDX models were successfully established, with seven models propagated to the third generation (F3-PDX), achieving an initial engraftment success rate of 45%. The latency of tumor establishment significantly decreased with each successive generation. The histological characteristics of the primary tumors were well preserved in the PDX models. WES of the three selected models revealed key mutated genes in primary tumors (F0), including IRS2, BLM, PDE4DIP, NUMA1, MYH9, TP53, PIK3CD, ERCC5, and ASXL1. A total of 28 somatic mutations were conserved across all three generations (F0, F1-PDX, and F3-PDX) in these models, representing a conservation rate of 43.75% (28/64). Among these conserved mutations, 10 were identified as potentially deleterious by multiple bioinformatics algorithms. Mutations in PTPRK (p.L988S), PIK3CB (p.F934L), LRP1B (p.A1912T), and IGF2R (p.G2052R) were predicted to significantly decrease protein stability.ConclusionThis study demonstrated that PDX models effectively preserve the biological and genetic characteristics of primary gastric tumors, underscoring their utility in studying tumor heterogeneity. The integrated analysis of longitudinal WES data from primary tumors and matched PDXs enabled the identification of a core set of conserved, potentially deleterious mutations. The four prioritized mutations (PTPRK, PIK3CB, LRP1B, and IGF2R) provide new insights into the genetic landscape of gastric cancer and represent promising candidates for the development of targeted therapeutic strategies.

To evaluate the diagnostic yield of whole-exome sequencing (WES) vs targeted gene panel (TGP) testing in patients evaluated for autoinflammation at the Great Ormond Street Hospital Autoinflammation Centre of Excellence. We retrospectively analysed 476 patients who underwent TGP testing between 2015 and 2022, and 210 patients who underwent WES between 2022 and 2025. Analysis of WES data combined: (i) a virtual gene panel of genes (germline and somatic) associated with inflammation; (ii) agnostic filtering according to ClinVar classification of pathogenicity; (iii) copy number variant analysis using ExomeDepth; and (iv) phenotype-driven prioritization using Exomiser. TGP testing identified molecular diagnoses in 71/476 patients (14.9%). WES increased the molecular diagnostic yield to 41/210 patients (19.5%). WES also enabled the discovery of novel genotype-phenotype associations. Significant incidental findings were identified in 29/210 (13.8%) of the cases, including variants predisposing to cancer or cardiomyopathy. In patients with suspected autoinflammation, WES increased diagnostic yield compared with TGP testing, while providing additional clinical value through novel gene discovery and capacity for future systematic reanalysis of unsolved cases. Incidental findings required careful and explicit a priori patient counselling and informed consent before offering WES. While there will be an inevitable shift from WES to whole-genome sequencing in the future, significant challenges remain for WGS, including costly large-data handling and storage, and uncertainty about the interpretation of variants in non-exonic regions. Our findings, therefore, demonstrate the significant clinical impact of WES for the work-up of autoinflammation, with pragmatic utility for timely return of results.

BackgroundBladder cancer (BLCA) is a malignant tumor originating from the urothelial lining, characterized by a complex tumor microenvironment (TME) and heterogeneous tumor mutation burden (TMB). Cancer-associated epithelial cells (EpiCs) exhibit substantial heterogeneity during BLCA initiation and progression. Therefore, elucidating the diversity and functional states of EpiCs is essential for improving future diagnostic and therapeutic strategies.MethodsWe integrated multi-omics datasets, including 13 single-cell RNA-seq samples, 514 bulk transcriptome profiles, and 30 whole-exome sequencing (WES) samples, to comprehensively characterize EpiC subtypes. Nonlinear dimensional reduction (UMAP) and clustering analyses were performed to identify major epithelial subsets, followed by secondary clustering. TMB values calculated from self-generated WES data were incorporated into scAB and Ro/e algorithms to determine the TMB-associated epithelial subset, ultimately identifying the key cluster Epi14. Differentially expressed genes (DEGs) of Epi14 were analyzed, and CellChat was used to infer intercellular communication networks. CytoTRACE and Monocle2 were applied to assess stemness potential and differentiation trajectories. Random survival forest (RSF) combined with DEG analysis was used to identify hub genes. Immune infiltration, drug sensitivity, and functional pathway analyses were subsequently conducted. Spatial transcriptomics were deconvoluted using spacexr, CellChat, and PROGENy to map cellular composition, signaling activity, and pathway nodes. Finally, qPCR and Western blot assays were performed to validate hub gene expression in tumor versus adjacent tissues.ResultsA total of 77,263 cells and 3,000 highly variable genes were included, yielding 32 annotated cell clusters. Secondary clustering combined with WES-derived TMB identified 14 epithelial subpopulations, among which Epi14 was confirmed as the key TMB-associated subset using the Ro/e algorithm. Integration of DEGs, RSF, and multi-cohort datasets revealed ABRACL and ARPC3 as the pivotal hub genes, from which a risk-score model was constructed. Notably, ABRACL expression showed a strong positive association with tumor TMB and exhibited pronounced enrichment in spatial transcriptomic tumor regions.ConclusionBy integrating multi-omics and spatial datasets, this study reveals the epithelial heterogeneity of BLCA and identifies ABRACL and ARPC3 as key TMB-associated hub genes within EpiCs. The established risk-score model and validated functional markers provide valuable insights for future mechanistic studies and potential clinical translation in BLCA.

Abstract Purpose/Objectives: Radiotherapy (RT) +/- androgen deprivation therapy (ADT) plays a key role in salvage therapy of prostate cancer (PC) recurrent after radical prostatectomy. However, not all patients benefit, and there is an unmet need for biomarkers to distinguish responders from non-responders (defined as those with second biochemical failure after salvage). We hypothesized that somatic mutations in primary PC are correlated with response to salvage RT+ADT. Materials/Methods: We retrospectively identified 718 consecutive PC patients treated with post-operative RT at a single institution from 1992-2013, of whom 40 were treated with salvage RT+ADT and had formalin-fixed, paraffin-embedded prostatectomy and matched normal tissues available for DNA extraction. The indication for salvage therapy was biochemical failure after an undetectable post-operative PSA in 72%, gross local recurrence in 17%, and persistently elevated PSA after surgery in 11%. Median RT dose was 64.8 Gy, and all patients received concurrent ADT. Whole exome sequencing (WES) was performed to an average depth of 162X (r, 70.7-219). We tested for association between somatic mutations and clinical outcomes using the log-rank test and Cox proportional hazards model. Results: Median age at salvage was 64.5 yrs. High-quality WES data were available in 39 patients. With a median follow-up of 122 months (range, 29-248), 21 experienced second biochemical failure after salvage, while 18 did not. Median time to second biochemical failure was 82.3 months (range, 1.2-140). Overall tumor mutational burden (TMB) was 2.72 mutations/Mb (range, 1.4-12.8). TMB among those with second biochemical failure was 3.9 vs. 3.1 among those without (p=0.29). The most common mutations detected in the overall cohort were PLEC and TTN (n=7). The presence of mutations in BRCA2 (n = 1, p < 0.01, HR = 37 (95% CI: 2.3-600)), CASZ1 (n = 3, p < 0.01, HR = 10 (95% CI: 2.4-44)), XRCC4 (n = 1, p = 0.017, HR = 9.0 (95% CI: 1.0-8.)), ATR (n = 2, p < 0.01, HR = 7.8 (95% CI: 1.6-39)), WDR26 (n = 3, p < 0.01, HR = 6.5 (95% CI: 1.7-24)) and MYT1 (n = 3, p < 0.01, HR = 6.4 (95% CI: 1.5-20)) was significantly correlated with second biochemical failure after salvage RT+ADT. In contrast, none of the patients with mutations in FOXA1 (n=4, p = 0.046, HR: not calculable) experienced second biochemical failure during follow-up. Conclusions: In this cohort of PC patients with >10 years median follow-up after post-prostatectomy salvage RT+ADT, WES revealed that mutations in BRCA2, CASZ1, XRCC4, and ATR were associated with second biochemical failure after salvage therapy, while FOXA1 mutation was associated with favorable outcomes. These findings require validation in larger cohorts, but suggest that somatic mutations may serve as biomarkers to identify patients at greatest risk for recurrence after post-prostatectomy salvage therapy. Citation Format: Keisuke Otani, David J. Konieczkowski, Yukako Otani, Grace Cerrato, Shulin Wu, Philip J. Saylor, Douglas M. Dahl, Chin-Lee Wu, Sophia C. Kamran, Jason A. Efstathiou, David T. Miyamoto. Somatic mutations and outcomes of salvage radiation and hormonal therapy for prostate cancer recurrence after prostatectomy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Prostate Cancer Research and Treatment; 2026 Jan 20-22; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86(2_Suppl):Abstract nr A053.

Abstract Background: MicroRNAs (miRNAs) are central regulators of gene expression, and rare pathogenic mutations in miRNA genes can cause Mendelian disease. However, the contribution of germline miRNA variants to prostate cancer (PCa) risk and clinical outcomes remains unclear, in part due to limited coverage of miRNA genes in previous exome, GWAS, and population sequencing datasets. Methods: We performed ultra-deep, targeted germline sequencing and rigorous variant calling of over 500 miRNA genes (including flanking regions) in 1,502 PCa patients from hereditary and sporadic cohorts, representing both high- and low-grade disease. Variants were systematically annotated for functional region (stem, seed, mature, loop) and predicted impact on pre-miRNA folding (ΔG). Frequencies of recurrent variants (>2 carriers) were compared to gnomAD whole-genome sequencing (WGS) and whole-exome sequencing (WES) populations using Fisher’s exact test within ancestry-matched groups. Results were cross-referenced with miRNASNP-v4, miRNA-seq data from prostate cancer cell lines, and TCGA-PRAD expression/outcome data. Per-gene miRNA burdens and individual variants were assessed for association with clinical features (family history, age, grade, metastasis, progression, PSA, cause of death). Results: We generated a comprehensive, high-confidence annotation resource of miRNA gene variants in germline DNA from prostate cancer patients, identifying 48 recurrent miRNA gene variants significantly enriched in PCa cases versus gnomAD (p < 1×10^−8), including both known and novel polymorphisms. A subset displayed significant pre-miRNA folding change (ΔG > 2 or > 5 kcal/mol) and/or mapped to seed or mature regions. Several variants overlapped miRNA genes robustly detected in PCa cell lines and differentially expressed in TCGA-PRAD, with recurrent hits in known risk regions such as 8q24 (notably enriched among African/African American patients). Conclusions: This study establishes the deepest and most extensive annotation of miRNA gene variants in prostate cancer to date, integrating germline miRNA variation, functional prediction, and population ancestry. We observed significant discrepancies in miRNA variant allele frequencies when comparing gnomAD WGS to WES data, underscoring the critical need to use WGS datasets for reliable estimation of miRNA gene variant frequencies. Our results identify multiple miRNA gene variants that are enriched in our PCa cohort compared to gnomAD WGS reference populations and are predicted to impact miRNA biogenesis, function, and/or PCa cell biology. While these findings are novel and present strong candidates for further study, they remain preliminary and should be validated in independent cohorts for association with PCa risk and biological effects. Citation Format: Shawn E. Lupold, Jun Wei, Siqun Zheng, Jun Luo, William Isaacs, Jianfeng Xu. Comprehensive Evaluation of Recurrent microRNA Gene Variants in Prostate Cancer: Integrative Association with Risk, Predicted Function, and Clinical Outcome [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Prostate Cancer Research and Treatment; 2026 Jan 20-22; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86(2_Suppl):Abstract nr A041.

Background/Objectives: Whole exome sequencing (WES) is an effective method for detecting disease-causing variants. However, copy number variation (CNV) detection using WES data often has limited sensitivity and high false-positive rates. Methods: In this study, we constructed a reference CNV set using chromosomal microarray analysis (CMA) data from 44 of 180 individuals who underwent WES and CMA and evaluated four WES-based CNV callers (CNVkit, CoNIFER, ExomeDepth, and cn.MOPS) against this benchmark. For each tool, we first defined software-specific problematic genomic regions across the full WES cohort and filtered out the CNVs that overlapped these regions. Results: The four algorithms showed low mutual concordance and distinct distributions in the problematic regions. On average, 2210 sequencing target baits (1.23%) were classified as problematic; these baits had lower mappability scores and higher coefficients of variation in RPKM than the remaining probes. After the supplementary filtration step, all tools demonstrated improved performance. Notably, ExomeDepth achieved gains of 14.4% in sensitivity and 7.9% in positive predictive value. Conclusions: We delineated software-specific problematic regions and demonstrated that targeted filtration markedly reduced false positives in WES-based CNV detection.

Crohn's disease (CD) is a chronic inflammatory bowel disease with a complex etiology involving genetic, immune, microbial, and environmental factors. Despite advances in understanding its pathogenesis, accurately predicting CD risk remains challenging, particularly in East Asian populations. In this study, we evaluated the performance of a polygenic risk score (PRS) model to predict CD risk in a Chinese cohort comprising whole-exome sequencing data of 76 CD patients and 552 healthy controls. We calculated PRS by applying causal genetic effect estimated from summary statistics of a public large-scale multi-ethnic genome-wide association study. Our results demonstrated that the PRS model effectively distinguished CD patients from healthy controls, achieving an area under the receiver opperating characteristiccurve of 0.75 and an odds ratio of 13 for individuals with a PRS above 2.3. The model also showed consistent performance in independent control data sets of Chinese, East Asian, European, and American ancestries. These findings highlight the potential of PRS derived from multi-ethnic causal effect as a non-invasive tool for CD risk prediction in East Asian populations. However, the moderate predictive accuracy and unexplained variance emphasize the need for larger studies and the integration of additional genetic and environmental factors to refine PRS model further.

IntroductionPrevious studies have illuminated a significant genetic component in motor neuron disease (MND) pathogenesis, with several causative genes identified. However, a substantial proportion of MND cases remain genetically unexplained, particularly regarding the comprehensive contribution of rare, high-impact variants across the exome.MethodsLeveraging whole-exome sequencing data from nearly half a million UK Biobank participants, we systematically investigated the association between high-confidence protein-truncating variants (HC PTVs) and MND risk in a Caucasian subset. Our large-scale gene-based association analysis utilized REGENIE software and LOFTEE-defined HC PTVs.ResultsWe identified significant preliminary associations between HC PTVs in 14 genes and an increased risk of MND. Notably, while NEK1 has been previously implicated in ALS, the remaining 13 genes (BLVRB, KLHL32, RIMS2, DYDC2, DCBLD1, ANXA4, COMP, TRIM42, ANO4, NFX1, CFAP206, CKAP2L, and ANGPTL4) show preliminary associations as novel candidate loci for the disease. Functional enrichment analyses further indicated that these genes are significantly involved in critical biological pathways, including collagen-containing extracellular matrix organization and ciliary function. Furthermore, tissue specificity analysis highlighted a strong enrichment of these genes’ expression in brain regions, with the hypothalamus showing the highest specificity.DiscussionThese findings suggest a potential expansion of the known genetic landscape of MND, and highlight novel biological pathways implicated in its pathogenesis. This study underscores the power of large-scale population genetics in uncovering critical disease mechanisms and offers new avenues for mechanistic research and therapeutic development for MND, pending independent validation.

The Testicular Cancer Consortium (TECAC) was established in 2012 and is comprised of researchers from over 25 centers in Europe and North America. TECAC's overarching goal is to investigate the genetic susceptibility of testicular germ cell tumors (TGCT) to better understand their biology, impact prevention strategies, and inform treatment decisions. To provide an overview of TECAC genetic and phenotypic holdings. TECAC has composed by-laws describing the consortium structure and governance, codified the processes for manuscript development and data transfer, and developed guidance for the transfer of biological samples and access to data. TECAC has assembled a vast amount of genetic information on males with TGCT-including SNP-array data on over 13,500 cases, whole-exome sequencing data on over 4500 cases, and low-pass whole-genome sequence data on over 2700 cases. Genetic information on males without TGCT (controls) is derived from studies designed to assess risk factors for TGCT and from publicly available resources. When available, corresponding phenotypic information is collected and harmonized. Fifteen publications have resulted from genetic and phenotypic information curated by TECAC. The sharing of genetic and phenotypic data by TECAC centers to inform large studies of TGCT susceptibility has led to novel insights into the genetic architecture of this cancer, including the roles of genes involved in male germ cell development, sex determination, chromosomal segregation, and RNA transcription. These findings would not have been achievable by individual centers or smaller collaborative efforts. We invite investigators from any discipline who have access to collections of germline DNA, somatic cell DNA, or genomic information on males with TGCT to consider joining TECAC to further strengthen our efforts to reduce the global burden of TGCT.

Hepatolithiasis (HL) is a prevalent condition in hepatobiliary surgery, often complicated by hepatatrophia. This study aimed to identify gene mutations in HL specimens with hepatatrophia and construct a mutation landscape using whole-exome sequencing (WES). Genetic variants and copy number variations (CNVs) were compared between HL (n = 10) and normal control (NC, n = 10) specimens, encompassing 20 participants in total, using WES data. Hub genes within HL specimens were identified via the GeneCards database. The mutation frequencies and interaction patterns of these hub genes were explored, and their potential molecular mechanisms were assessed. A competing endogenous RNA (ceRNA) network and a transcription factor (TF)-mRNA network were established to clarify the regulatory mechanisms of hub genes. Therapeutic drugs targeting these hub genes were predicted using the DrugBank database, and molecular docking assessed the binding energies. Finally, hub gene expression was validated through reverse-transcription quantitative PCR (RT-qPCR). Seven hub genes (TMEM150B, TNIP1, ATRN, FAAH, FBXW4, RAX, and WNT8B) were identified as uniquely mutated in HL specimens, with TMEM150B exhibiting the highest mutation frequency. The concurrent mutations of these genes are likely associated with the pathogenesis of HL combined with hepatatrophia. Functional enrichment analysis indicated that these hub genes are involved in the inflammatory response and Wnt signaling pathway. The ceRNA-TF network revealed that 296 lncRNAs (e.g., C1RL-AS1) regulate six miRNAs (e.g., hsa-miR-195-5p) targeting four hub genes, while 19 TFs (e.g., NFYA, HINFP) also regulate these genes. Furthermore, fostamatinib exhibited the strongest binding affinity with FAAH, with a binding energy of -9.2 kcal/mol, suggesting that it is a promising candidate for further investigation. RT-qPCR confirmed that TMEM150B and FAAH expression levels were reduced in HL samples, while TNIP1, ATRN, FBXW4, and WNT8B were upregulated. Expression of RAX was not reliably detectable. This study identified TMEM150B, TNIP1, ATRN, FAAH, FBXW4 and WNT8B as key genes in the development of HL through inflammatory response and Wnt signaling pathways, providing new theoretical insights into therapeutic mechanisms.

DNA Methylation Profiling Classifies and Reveals Origin of Gynecologic Central Nervous System-Like Tumors.