HLA-G encodes an immune checkpoint molecule with restricted expression in immune-privileged tissues and pathological conditions. It exhibits limited coding diversity but substantial regulatory-region variation influencing expression levels. Strong linkage disequilibrium across HLA-G creates a structured genetic architecture in which regulatory and coding variants co-segregate into well-defined haplotypes, enabling the imputation of complete HLA-G haplotypes from partial genomic data. We developed imputation models to predict HLA-G 4-field alleles, promoter, and 3'UTR haplotypes from whole-exome sequencing and SNP array data using HIBAG. Multi-ethnic reference panels were constructed from 5,347 individuals from three diverse cohorts (1000 Genomes, Human Genome Diversity Project, and Brazilian SABE cohort). Models were validated through cross-validation and independent datasets. Exome-based imputation achieved high accuracy (>99%) for common alleles (frequency>1%), with mean posterior probabilities exceeding 0.95. SNP array-based models showed slightly lower but still robust performance (>95% accuracy). Our approach enables simultaneous prediction of coding and regulatory sequences, providing comprehensive functional information from datasets that do not capture the complete HLA-G diversity. These models facilitate HLA-G analysis in widely available genomic datasets lacking introns and regulatory regions (tumor exomes, SNP arrays), enabling investigation of HLA-G's role in immune regulation, transplantation, cancer, and pregnancy complications without full-gene sequencing.

Colon cancer is genetically heterogeneous, necessitating standardized genomic analyses for cross-cohort comparisons. While The Cancer Genome Atlas (TCGA)-colon adenocarcinoma (COAD) is a widely used dataset, its comparability to other ethnically different populations remains unclear. This study systematically compares the genomic characteristics of TCGA-COAD and ChangKang, a Chinese colon cancer cohort, using an identical data-processing pipeline to minimize methodological biases. Whole-exome sequencing data from both cohorts were uniformly processed to analyze five key genomic features: tumor mutation burden (TMB), microsatellite instability (MSI), significantly mutated genes, mutational signatures, and copy number variation (CNV). Samples were classified into hypermutated and non-hypermutated subgroups for further comparisons. The TCGA-COAD cohort exhibited a higher overall TMB, driven by a greater proportion of hypermutated samples. However, the hypermutated subgroup of the ChangKang cohort included more ultramutated cases with POLE exonuclease domain mutations, leading to a higher subgroup TMB. MSI was more prevalent in TCGA-COAD, while significantly mutated gene frequencies varied, with lower APC and ACVR2A mutation rates in the ChangKang cohort. CNV patterns were largely similar, though CNV frequencies were higher in TCGA-COAD. Despite differences in subgroup distributions and mutation frequencies, the overall genomic characteristics of colon cancer remain consistent between these ethnically different cohorts. This suggests that cross-population analyses are feasible when standardized processing methods are applied. This study provides a systematic, unbiased comparison of TCGA-COAD and the Chinese ChangKang cohort, demonstrating that the genomic characteristics remain largely consistent across ethnically distinct populations.

Copy number variants (CNVs) have been shown to play a significant role in the pathogenesis of various human diseases. Although several tools have been developed for detecting CNVs based on whole-exome sequencing (WES) data, their performance remains suboptimal for small exon-level CNVs (exCNVs). This is primarily due to multiple technical variabilities, including probe capture efficiency, mappability, exon size, batch effects, experimental background noise bias, and control sample selection, all of which can lead to false negatives and false positives in exCNV detection. To address these challenges, we developed ML-ExonCNV, which innovatively integrates the XGBoost machine learning model with a multi-expert ensemble approach. The model was trained using 14 features derived from 22 364 real-world, quantitative polymerase chain reaction-validated rare exCNVs. Evaluation on a test set of 492 real WES and the NA12878 gold-standard dataset demonstrated that ML-ExonCNV outperformed widely used tools such as GATK-gCNV, ExomeDepth, and CNVkit. Notably, ML-ExonCNV can detect large segmental CNVs, mosaic CNVs, and breakpoint CNVs on exon region. Furthermore, our analysis revealed recurrent exCNV-associated genes and their phenotypic correlations. Neurodevelopmental and musculoskeletal abnormalities were identified as the most frequently associated phenotypes with high-recurrence exCNVs.

Intellectual disability (ID) is a genetically heterogeneous neurodevelopmental disorder, with etiological diagnosis remaining challenging due to clinical phenotypes and genetic diversity. To investigate the diagnostic value of whole exome sequencing (WES) combined with copy number variation (CNV) analysis in unexplained ID through a large cohort analysis, and to analyze the genetic etiology of intellectual disability. Performed WES on 1052 individuals with unexplained ID, analyzing single nucleotide variants (SNVs), small insertions/deletions (InDels), and CNVs. Variants were classified as pathogenic or likely pathogenic based on clinical guidelines. Four hundred eighty-five pathogenic or likely pathogenic variants that could explain the clinical indication were identified in 458 individuals, with an overall diagnostic rate of 43.54% (458/1052). Three hundred thirty-three SNVs were detected, distributed in 178 genes, of which 222 cases were novel. Inheritance pattern analysis showed that autosomal dominant inheritance was the most prevalent (242/333, 72.67%), followed by recessive inheritance (41/333, 12.31%) and sex-linked inheritance (50/333, 15.02%), which aligns with the established role of new dominant variants in developmental disorders. By CNV analysis, we further identified 152 structural variant events with sizes ranging from 103.54bp to 67.34 Mbp. WES with CNV analysis significantly improves molecular diagnosis in ID, particularly in cases of unclear etiology. This integrated approach elucidates diverse variantal mechanisms and enhances genotype-phenotype correlations, supporting clinical management and genetic counseling. WES combined with CNV analysis provides a powerful and economical approach for ID diagnosis. This study offers valuable insights for precision diagnosis and genetic counseling in Chinese ID populations. KEY MESSAGES: 1. Whole-Exome Sequencing (WES) Significantly Enhances Diagnostic Yield in Intellectual Disability (ID) 2. WES analysis of 1052 Chinese ID patients achieved a diagnostic yield of43.54%, surpassing chromosomal microarray analysis (CMA, 15-20%) and aligning with prior WES studies in neurodevelopmental disorders (NDDs). By integrating detection of single nucleotide variants (SNVs), insertions/deletions (Indels), and exon-level copy number variations (CNVs), WES overcomes limitations of traditional methods, particularly for patients with complex phenotypes or genetic heterogeneity. 3. SNVs Dominate the Genetic Etiology of ID 4. SNVs accounted for68.7%(333/485) of pathogenic or likely pathogenic variants, reinforcing their critical role in ID pathogenesis. 5. CNV Analysis from WES Data Improves Diagnostic Efficiency 6. A total of152 pathogenic or likely pathogenic CNVs(31.3% of all variants) were identified, including150 patients diagnosed solely through CNV analysis, increasing the overall diagnostic yield by14.3%. Advanced algorithms (e.g., XHMM, HMZDelFinder) enabled precise detection of small CNVs (down to single-exon deletions/duplications), positioning WES as a cost-effective clinical screening tool. 7. High-Frequency Mutated Genes Highlight Molecular Pathogenesis 8. Top five mutated genes (DUOX2,SCN2A,SHANK3,KDM5C,DDX3X) are strongly linked to neurodevelopmental dysfunction: • SCN2A(voltage-gated sodium channel) associates with epilepsy and autism spectrum disorder (ASD); • SHANK3(synaptic scaffolding protein) is mutated in ~2% of ASD patients with comorbid ID; • KDM5Cis a common X-linked ID gene. 9. Incidental Findings: Clinical and Ethical Implications 10. 4.09%(12/1052) harbored actionable incidental variants unrelated to ID (e.g., hereditary cancer or metabolic disorders). Balancing clinical actionability with psychological burden requires standardized reporting frameworks to maximize patient benefit while minimizing harm.

Evaluation of CNV detection tools for prenatal diagnosis using amniotic fluid clinical whole-exome sequencing data.

Radiation to the hypothalamic-pituitary (HP) region (HP-RT) is a strong risk factor for HP deficiency among childhood cancer survivors (survivors). However, there is inter-individual variability in developing HP deficiency after similar HP-RT dose exposures. To assess the genetic contribution to developing deficiencies of GH (GHD), LH/FSH (LH/FSHD), TSH (TSHD), and ACTH (ACTHD) among survivors exposed to HP-RT. Eligible participants included five-year survivors exposed to HP-RT (n=809; median follow-up 31.9 years) from the St. Jude Lifetime Cohort. We assessed the association between rare variants from whole-exome sequencing data [minor allele frequency (MAF)<0.01, predicted to be pathogenic by functional prediction tools] and HP deficiency rate (total counts/person-year) among 801 survivors by the exact Poisson test. Genome-wide association analysis (GWAS) was conducted among 606 survivors of European ancestry with available whole-genome sequence data, targeting variants with MAF≥0.01. The replication population was 1,328 survivors from the Childhood Cancer Survivor Study (CCSS). Carriers of rare variants in TNS2, a ubiquitously expressed protein-coding gene including in brain, had significantly higher rates of HP deficiencies [rate ratio 2.72 (95% confidence interval 1.81-4.09), p=1.5×10-5] compared to non-carriers, which was replicated in the CCSS. This was also observed in individual HP deficiencies: LH/FSHD [3.31 (1.28-7.99)], TSHD [5.29 (2.42-11.34)], and ACTHD [3.97 (1.05-12.31)]. There were no statistically significant variants in GWAS. TNS2 may contribute to radiation-induced HP deficiencies. With further validation, screening for TNS2 variants has potential to help identify individuals who would benefit from surveillance and intervention following HP-RT.

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.

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).

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 &amp;lt; 0.01, HR = 37 (95% CI: 2.3-600)), CASZ1 (n = 3, p &amp;lt; 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 &amp;lt; 0.01, HR = 7.8 (95% CI: 1.6-39)), WDR26 (n = 3, p &amp;lt; 0.01, HR = 6.5 (95% CI: 1.7-24)) and MYT1 (n = 3, p &amp;lt; 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 &amp;gt;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 (&amp;gt;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 &amp;lt; 1×10^−8), including both known and novel polymorphisms. A subset displayed significant pre-miRNA folding change (ΔG &amp;gt; 2 or &amp;gt; 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.

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.

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

Despite advances in understanding genetic causes of DSD (differences of sex development), the molecular cause remains unknown for over half of affected individuals. Next-generation sequencing (NGS) has improved diagnosis, but interpreting results can be challenging, especially when no known DSD gene mutations are found, or only variants of unknown significance appear. Identifying new genes involved in sex development from whole exome sequencing (WES) alone is difficult. To overcome this, we introduce "GONAD-ResNet," a residual convolutional neural network designed to predict novel DSD-associated genes by learning complex patterns in time-dependent single-cell gene expression data. When applied to WES data from six patients (three XX, three XY) with DSD, GONAD-ResNet prioritized genes with expression profiles similar to known DSD genes while disregarding ubiquitous or irrelevant genes. This narrowed the list of potential candidates from around 1000 to a few promising novel genes per patient. This innovative approach accelerates the discovery of new DSD-related genes, opening new research avenues and potentially improving patient outcomes.

ABSTRACTBackgroundPharmacogenomics (PGx) enables precision medicine by improving efficacy and reducing adverse drug reactions, but implementation is limited by testing burden and ethnic variability. With whole‐exome sequencing (WES) increasingly applied in Taiwan, we evaluated its feasibility for PGx analysis.MethodsWe analyzed WES data from 3562 individuals at a tertiary medical center. PGx calling was performed on 17 pharmacogenomic loci using Aldy, and HLA typing was inferred using the high‐quality dictionary (HLA‐HD). Phenotypes were annotated using the Pharmacogenomics Clinical Annotation Tool (PharmCAT).ResultsAfter comparison with WGS and sequencing‐based HLA typing data, 14 pharmacogenomic loci were found to be suitable for PGx calling from WES. On average, each individual carried approximately 2.4 actionable phenotypes across 14 genes. Compared with East Asian and European populations, the Taiwanese population has a greater frequency of actionable pharmacogenomic phenotypes for G6PD deficiency (2%) and HLA‐B*58:01 (21%). Additionally, the CYP2C19, CYP3A5, NUDT15, and HLA‐B*15:02 actionable phenotypes occur at frequencies similar to those of East Asians but are more frequent than those in Europeans. Our WES findings are generally consistent with previous Taiwanese WGS and array data.ConclusionsEthnic differences in PGx variants underscore the need for population‐specific data. The high prevalence of actionable phenotypes in Taiwanese individuals supports the use of WES, which effectively captures certain key pharmacogenes for routine PGx testing.