Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking.

BACKGROUND: High-throughput sequencing (HTS) has become the gold standard approach for variant analysis in cancer research. However, somatic variants may occur at low fractions due to contamination from normal cells or tumor heterogeneity; this poses a significant challenge for standard HTS analysis pipelines. The problem is exacerbated in scenarios with minimal tumor DNA, such as circulating tumor DNA in plasma. Assessing sensitivity and detection of HTS approaches in such cases is paramount, but time-consuming and expensive: specialized experimental protocols and a sufficient quantity of samples are required for processing and analysis. To overcome these limitations, we propose a new computational approach specifically designed for the generation of artificial datasets suitable for this task, simulating ultra-deep targeted sequencing data with low-fraction variants and demonstrating their effectiveness in benchmarking low-fraction variant calling. RESULTS: Our approach enables the generation of artificial raw reads that mimic real data without relying on pre-existing data by using NEAT, a fine-grained read simulator that generates artificial datasets using models learned from multiple different datasets. Then, it incorporates low-fraction variants to simulate somatic mutations in samples with minimal tumor DNA content. To prove the suitability of the created artificial datasets for low-fraction variant calling benchmarking, we used them as ground truth to evaluate the performance of widely-used variant calling algorithms: they allowed us to define tuned parameter values of major variant callers, considerably improving their detection of very low-fraction variants. CONCLUSIONS: Our findings highlight both the pivotal role of our approach in creating adequate artificial datasets with low tumor fraction, facilitating rapid prototyping and benchmarking of algorithms for such dataset type, as well as the important need of advancing low-fraction variant calling techniques.

Assessing quality of hepato-pancreato-biliary surgery: nationwide benchmarking.

BACKGROUND: Clinical auditing is a powerful tool to evaluate and improve healthcare. Deviations from the expected quality of care are identified by benchmarking the results of individual hospitals using national averages. This study aimed to evaluate the use of quality indicators for benchmarking hepato-pancreato-biliary (HPB) surgery and when outlier hospitals could be identified. METHODS: A population-based study used data from two nationwide Dutch HPB audits (DHBA and DPCA) from 2014 to 2021. Sample size calculations determined the threshold (in percentage points) to identify centres as statistical outliers, based on current volume requirements (annual minimum of 20 resections) on a two-year period (2020-2021), covering mortality rate, failure to rescue (FTR), major morbidity rate and textbook/ideal outcome (TO) for minor liver resection (LR), major LR, pancreaticoduodenectomy (PD) and distal pancreatectomy (DP). RESULTS: In total, 10 963 and 7365 patients who underwent liver and pancreatic resection respectively were included. Benchmark and corresponding range of mortality rates were 0.6% (0 -3.2%) and 3.3% (0-16.7%) for minor and major LR, and 2.7% (0-7.0%) and 0.6% (0-4.2%) for PD and DP respectively. FTR rates were 5.4% (0-33.3%), 14.2% (0-100%), 7.5% (1.6%-28.5%) and 3.1% (0-14.9%). For major morbidity rate, corresponding rates were 9.8% (0-20.5%), 28.1% (0-47.1%), 36% (15.8%-58.3%) and 22.3% (5.2%-46.1%). For TO, corresponding rates were 73.6% (61.3%-94.4%), 54.1% (35.3-100), 46.8% (25.3%-59.4%) and 63.3% (30.7%-84.6%). Mortality rate thresholds indicating a significant outlier were 8.6% and 15.4% for minor and major LR and 14.2% and 8.6% for PD and DP. For FTR, these thresholds were 17.9%, 31.6%, 22.9% and 15.0%. For major morbidity rate, these thresholds were 26.1%, 49.7%, 57.9% and 52.9% respectively. For TO, lower thresholds were 52.5%, 32.5%, 25.8% and 41.4% respectively. Higher hospital volumes decrease thresholds to detect outliers. CONCLUSION: Current event rates and minimum volume requirements per hospital are too low to detect any meaningful between hospital differences in mortality rate and FTR. Major morbidity rate and TO are better candidates to use for benchmarking.

Usability of an Automated System for Real-Time Monitoring of Shared Decision-Making for Surgery: Mixed Methods Evaluation.

BACKGROUND: Improving shared decision-making (SDM) for patients has become a health policy priority in many countries. Achieving high-quality SDM is particularly important for approximately 313 million surgical treatment decisions patients make globally every year. Large-scale monitoring of surgical patients' experience of SDM in real time is needed to identify the failings of SDM before surgery is performed. We developed a novel approach to automating real-time data collection using an electronic measurement system to address this. Examining usability will facilitate its optimization and wider implementation to inform interventions aimed at improving SDM. OBJECTIVE: This study examined the usability of an electronic real-time measurement system to monitor surgical patients' experience of SDM. We aimed to evaluate the metrics and indicators relevant to system effectiveness, system efficiency, and user satisfaction. METHODS: We performed a mixed methods usability evaluation using multiple participant cohorts. The measurement system was implemented in a large UK hospital to measure patients' experience of SDM electronically before surgery using 2 validated measures (CollaboRATE and SDM-Q-9). Quantitative data (collected between April 1 and December 31, 2021) provided measurement system metrics to assess system effectiveness and efficiency. We included adult patients booked for urgent and elective surgery across 7 specialties and excluded patients without the capacity to consent for medical procedures, those without access to an internet-enabled device, and those undergoing emergency or endoscopic procedures. Additional groups of service users (group 1: public members who had not engaged with the system; group 2: a subset of patients who completed the measurement system) completed user-testing sessions and semistructured interviews to assess system effectiveness and user satisfaction. We conducted quantitative data analysis using descriptive statistics and calculated the task completion rate and survey response rate (system effectiveness) as well as the task completion time, task efficiency, and relative efficiency (system efficiency). Qualitative thematic analysis identified indicators of and barriers to good usability (user satisfaction). RESULTS: A total of 2254 completed surveys were returned to the measurement system. A total of 25 service users (group 1: n=9; group 2: n=16) participated in user-testing sessions and interviews. The task completion rate was high (169/171, 98.8%) and the survey response rate was good (2254/5794, 38.9%). The median task completion time was 3 (IQR 2-13) minutes, suggesting good system efficiency and effectiveness. The qualitative findings emphasized good user satisfaction. The identified themes suggested that the measurement system is acceptable, easy to use, and easy to access. Service users identified potential barriers and solutions to acceptability and ease of access. CONCLUSIONS: A mixed methods evaluation of an electronic measurement system for automated, real-time monitoring of patients' experience of SDM showed that usability among patients was high. Future pilot work will optimize the system for wider implementation to ultimately inform intervention development to improve SDM. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.1136/bmjopen-2023-079155.

Cataract-1K Dataset for Deep-Learning-Assisted Analysis of Cataract Surgery Videos.

In recent years, the landscape of computer-assisted interventions and post-operative surgical video analysis has been dramatically reshaped by deep-learning techniques, resulting in significant advancements in surgeons' skills, operation room management, and overall surgical outcomes. However, the progression of deep-learning-powered surgical technologies is profoundly reliant on large-scale datasets and annotations. In particular, surgical scene understanding and phase recognition stand as pivotal pillars within the realm of computer-assisted surgery and post-operative assessment of cataract surgery videos. In this context, we present the largest cataract surgery video dataset that addresses diverse requisites for constructing computerized surgical workflow analysis and detecting post-operative irregularities in cataract surgery. We validate the quality of annotations by benchmarking the performance of several state-of-the-art neural network architectures for phase recognition and surgical scene segmentation. Besides, we initiate the research on domain adaptation for instrument segmentation in cataract surgery by evaluating cross-domain instrument segmentation performance in cataract surgery videos. The dataset and annotations are publicly available in Synapse.

Benchmarking multi-ancestry prostate cancer polygenic risk scores in a real-world cohort.

Prostate cancer is a heritable disease with ancestry-biased incidence and mortality. Polygenic risk scores (PRSs) offer promising advancements in predicting disease risk, including prostate cancer. While their accuracy continues to improve, research aimed at enhancing their effectiveness within African and Asian populations remains key for equitable use. Recent algorithmic developments for PRS derivation have resulted in improved pan-ancestral risk prediction for several diseases. In this study, we benchmark the predictive power of six widely used PRS derivation algorithms, including four of which adjust for ancestry, against prostate cancer cases and controls from the UK Biobank and All of Us cohorts. We find modest improvement in discriminatory ability when compared with a simple method that prioritizes variants, clumping, and published polygenic risk scores. Our findings underscore the importance of improving upon risk prediction algorithms and the sampling of diverse cohorts.

Attention-guided variational graph autoencoders reveal heterogeneity in spatial transcriptomics.

The latest breakthroughs in spatially resolved transcriptomics technology offer comprehensive opportunities to delve into gene expression patterns within the tissue microenvironment. However, the precise identification of spatial domains within tissues remains challenging. In this study, we introduce AttentionVGAE (AVGN), which integrates slice images, spatial information and raw gene expression while calibrating low-quality gene expression. By combining the variational graph autoencoder with multi-head attention blocks (MHA blocks), AVGN captures spatial relationships in tissue gene expression, adaptively focusing on key features and alleviating the need for prior knowledge of cluster numbers, thereby achieving superior clustering performance. Particularly, AVGN attempts to balance the model's attention focus on local and global structures by utilizing MHA blocks, an aspect that current graph neural networks have not extensively addressed. Benchmark testing demonstrates its significant efficacy in elucidating tissue anatomy and interpreting tumor heterogeneity, indicating its potential in advancing spatial transcriptomics research and understanding complex biological phenomena.

ProDiv: Prototype-driven consistent pseudo-bag division for whole-slide image classification.

BACKGROUND AND OBJECTIVE: Pathology image classification is one of the most essential auxiliary processes in cancer diagnosis. To overcome the problem of inadequate Whole-Slide Image (WSI) samples with weak labels, pseudo-bag-based multiple instance learning (MIL) methods have attracted wide attention in pathology image classification. In this type of method, the division scheme of pseudo-bags is usually a primary factor affecting classification performance. In order to improve the division of WSI pseudo-bags on existing random/clustering approaches, this paper proposes a new Prototype-driven Division (ProDiv) scheme for the pseudo-bag-based MIL classification framework on pathology images. METHODS: This scheme first designs an attention-based method to generate a bag prototype for each slide. On this basis, it further groups WSI patch instances into a series of instance clusters according to the feature similarities between the prototype and patches. Finally, pseudo-bags are obtained by randomly combining the non-overlapping patch instances of different instance clusters. Moreover, the design scheme of our ProDiv considers practicality, and it could be smoothly assembled with almost all the MIL-based WSI classification methods in recent years. RESULTS: Empirical results show that our ProDiv, when integrated with several existing methods, can deliver classification AUC improvements of up to 7.3% and 10.3%, respectively on two public WSI datasets. CONCLUSIONS: ProDiv could almost always bring obvious performance improvements to compared MIL models on typical metrics, which suggests the effectiveness of our scheme. Experimental visualization also visually interprets the correctness of the proposed ProDiv.

PMFFNet: A hybrid network based on feature pyramid for ovarian tumor segmentation.

Ovarian cancer is a highly lethal malignancy in the field of oncology. Generally speaking, the segmentation of ovarian medical images is a necessary prerequisite for the diagnosis and treatment planning. Therefore, accurately segmenting ovarian tumors is of utmost importance. In this work, we propose a hybrid network called PMFFNet to improve the segmentation accuracy of ovarian tumors. The PMFFNet utilizes an encoder-decoder architecture. Specifically, the encoder incorporates the ViTAEv2 model to extract inter-layer multi-scale features from the feature pyramid. To address the limitation of fixed window size that hinders sufficient interaction of information, we introduce Varied-Size Window Attention (VSA) to the ViTAEv2 model to capture rich contextual information. Additionally, recognizing the significance of multi-scale features, we introduce the Multi-scale Feature Fusion Block (MFB) module. The MFB module enhances the network's capacity to learn intricate features by capturing both local and multi-scale information, thereby enabling more precise segmentation of ovarian tumors. Finally, in conjunction with our designed decoder, our model achieves outstanding performance on the MMOTU dataset. The results are highly promising, with the model achieving scores of 97.24%, 91.15%, and 87.25% in mACC, mIoU, and mDice metrics, respectively. When compared to several Unet-based and advanced models, our approach demonstrates the best segmentation performance.

MFSynDCP: multi-source feature collaborative interactive learning for drug combination synergy prediction.

Drug combination therapy is generally more effective than monotherapy in the field of cancer treatment. However, screening for effective synergistic combinations from a wide range of drug combinations is particularly important given the increase in the number of available drug classes and potential drug-drug interactions. Existing methods for predicting the synergistic effects of drug combinations primarily focus on extracting structural features of drug molecules and cell lines, but neglect the interaction mechanisms between cell lines and drug combinations. Consequently, there is a deficiency in comprehensive understanding of the synergistic effects of drug combinations. To address this issue, we propose a drug combination synergy prediction model based on multi-source feature interaction learning, named MFSynDCP, aiming to predict the synergistic effects of anti-tumor drug combinations. This model includes a graph aggregation module with an adaptive attention mechanism for learning drug interactions and a multi-source feature interaction learning controller for managing information transfer between different data sources, accommodating both drug and cell line features. Comparative studies with benchmark datasets demonstrate MFSynDCP's superiority over existing methods. Additionally, its adaptive attention mechanism graph aggregation module identifies drug chemical substructures crucial to the synergy mechanism. Overall, MFSynDCP is a robust tool for predicting synergistic drug combinations. The source code is available from GitHub at https://github.com/kkioplkg/MFSynDCP .

Comparison of lifetime mortality risk, incidence risk, and DALYs of baseline cancer rates among countries as a benchmark for radiation-related cancer risk.

Statistical benchmark data are necessary when considering the basis for radiation protection criteria based on calculated risks. We herein focused on baseline mortality and incidence cancer rates as benchmark data collected from 33 countries. Furthermore, we calculated the lifetime mortality and incidence risks and disability-adjusted life years (DALYs) for all solid cancers, colon cancer, lung cancer, breast cancer, thyroid cancer, and leukemia using the baseline cancer rates and compared them among the countries. The results showed that the lifetime mortality and incidence risks and DALYs for all solid cancers differed among the countries by a factor of 2-4 for males and 2-3 for females; these were low in less-developed countries. Our study proposed that health risk based on baseline cancer rates should be the benchmark for comparing radiation cancer risks.

Benchmarking of BMDC assay and related QSAR study for identifying sensitizing chemicals.

The Bone-Marrow derived Dendritic Cell (BMDC) test is a promising assay for identifying sensitizing chemicals based on the 3Rs (Replace, Reduce, Refine) principle. This study expanded the BMDC benchmarking to various in vitro, in chemico, and in silico assays targeting different key events (KE) in the skin sensitization pathway, using common substances datasets. Additionally, a Quantitative Structure-Activity Relationship (QSAR) model was developed to predict the BMDC test outcomes for sensitizing or non-sensitizing chemicals. The modeling workflow involved ISIDA (In Silico Design and Data Analysis) molecular fragment descriptors and the SVM (Support Vector Machine) machine-learning method. The BMDC model's performance was at least comparable to that of all ECVAM-validated models regardless of the KE considered. Compared with other tests targeting KE3, related to dendritic cell activation, BMDC assay was shown to have higher balanced accuracy and sensitivity concerning both the Local Lymph Node Assay (LLNA) and human labels, providing additional evidence for its reliability. The consensus QSAR model exhibits promising results, correlating well with observed sensitization potential. Integrated into a publicly available web service, the BMDC-based QSAR model may serve as a cost-effective and rapid alternative to lab experiments, providing preliminary screening for sensitization potential, compound prioritization, optimization and risk assessment.

Development and validation of metrics for a new RAPN training model.

Robot-assisted partial nephrectomy (RAPN) is a complex and index procedure that urologists need to learn how to perform safely. No validated performance metrics specifically developed for a RAPN training model (TM) exist. A Core Metrics Group specifically adapted human RAPN metrics to be used in a newly developed RAPN TM, explicitly defining phases, steps, errors, and critical errors. A modified Delphi meeting concurred on the face and content validation of the new metrics. One hundred percent consensus was achieved by the Delphi panel on 8 Phases, 32 Steps, 136 Errors and 64 Critical Errors. Two trained assessors evaluated recorded video performances of novice and expert RAPN surgeons executing an emulated RAPN in the newly developed TM. There were no differences in procedure Steps completed by the two groups. Experienced RAPN surgeons made 34% fewer Total Errors than the Novice group. Performance score for both groups was divided at the median score using Total Error scores, into HiError and LoError subgroups. The LowErrs Expert RAPN surgeons group made 118% fewer Total Errors than the Novice HiErrs group. Furthermore, the LowErrs Expert RAPN surgeons made 77% fewer Total Errors than the HiErrs Expert RAPN surgeons. These results established construct and discriminative validity of the metrics. The authors described a novel RAPN TM and its associated performance metrics with evidence supporting their face, content, construct, and discriminative validation. This report and evidence support the implementation of a simulation-based proficiency-based progression (PBP) training program for RAPN.

Projected Time for the Elimination of Cervical Cancer Under Various Intervention Scenarios: Age-Period-Cohort Macrosimulation Study.

BACKGROUND: The World Health Organization aims for the global elimination of cervical cancer, necessitating modeling studies to forecast long-term outcomes. OBJECTIVE: This paper introduces a macrosimulation framework using age-period-cohort modeling and population attributable fractions to predict the timeline for eliminating cervical cancer in Taiwan. METHODS: Data for cervical cancer cases from 1997 to 2016 were obtained from the Taiwan Cancer Registry. Future incidence rates under the current approach and various intervention strategies, such as scaled-up screening (cytology based or human papillomavirus [HPV] based) and HPV vaccination, were projected. RESULTS: Our projections indicate that Taiwan could eliminate cervical cancer by 2050 with either 70% compliance in cytology-based or HPV-based screening or 90% HPV vaccination coverage. The years projected for elimination are 2047 and 2035 for cytology-based and HPV-based screening, respectively; 2050 for vaccination alone; and 2038 and 2033 for combined screening and vaccination approaches. CONCLUSIONS: The age-period-cohort macrosimulation framework offers a valuable policy analysis tool for cervical cancer control. Our findings can inform strategies in other high-incidence countries, serving as a benchmark for global efforts to eliminate the disease.

ACR benchmark testing of a novel high-speed ring-gantry linac kV-CBCT system.

A new generation cone-beam computed tomography (CBCT) system with new hardware design and advanced image reconstruction algorithms is available for radiation treatment simulation or adaptive radiotherapy (HyperSight CBCT imaging solution, Varian Medical Systems-a Siemens Healthineers company). This study assesses the CBCT image quality metrics using the criteria routinely used for diagnostic CT scanner accreditation as a first step towards the future use of HyperSight CBCT images for treatment planning and target/organ delineations. Image performance was evaluated using American College of Radiology (ACR) Program accreditation phantom tests for diagnostic computed tomography systems (CTs) and compared HyperSight images with a standard treatment planning diagnostic CT scanner (Siemens SOMATOM Edge) and with existing CBCT systems (Varian TrueBeam version 2.7 and Varian Halcyon version 2.0).  Image quality performance for all Varian HyperSight CBCT vendor-provided imaging protocols were assessed using ACR head and body ring CT phantoms, then compared to existing imaging modalities. Image quality analysis metrics included contrast-to-noise (CNR), spatial resolution, Hounsfield number (HU) accuracy, image scaling, and uniformity. All image quality assessments were made following the recommendations and passing criteria provided by the ACR. The Varian HyperSight CBCT imaging system demonstrated excellent image quality, with the majority of vendor-provided imaging protocols capable of passing all ACR CT accreditation standards. Nearly all (8/11) vendor-provided protocols passed ACR criteria using the ACR head phantom, with the Abdomen Large, Pelvis Large, and H&N vendor-provided protocols produced HU uniformity values slightly exceeding passing criteria but remained within the allowable minor deviation levels (5-7 HU maximum differences). Compared to other existing CT and CBCT imaging modalities, both HyperSight Head and Pelvis imaging protocols matched the performance of the SOMATOM CT scanner, and both the HyperSight and SOMATOM CT substantially surpassed the performance of the Halcyon 2.0 and TrueBeam version 2.7 systems. Varian HyperSight CBCT imaging system could pass almost all tests for all vendor-provided protocols using ACR accreditation criteria, with image quality similar to those produced by diagnostic CT scanners and significantly better than existing linac-based CBCT imaging systems.

Benchmarking enrichment analysis methods with the disease pathway network.

Enrichment analysis (EA) is a common approach to gain functional insights from genome-scale experiments. As a consequence, a large number of EA methods have been developed, yet it is unclear from previous studies which method is the best for a given dataset. The main issues with previous benchmarks include the complexity of correctly assigning true pathways to a test dataset, and lack of generality of the evaluation metrics, for which the rank of a single target pathway is commonly used. We here provide a generalized EA benchmark and apply it to the most widely used EA methods, representing all four categories of current approaches. The benchmark employs a new set of 82 curated gene expression datasets from DNA microarray and RNA-Seq experiments for 26 diseases, of which only 13 are cancers. In order to address the shortcomings of the single target pathway approach and to enhance the sensitivity evaluation, we present the Disease Pathway Network, in which related Kyoto Encyclopedia of Genes and Genomes pathways are linked. We introduce a novel approach to evaluate pathway EA by combining sensitivity and specificity to provide a balanced evaluation of EA methods. This approach identifies Network Enrichment Analysis methods as the overall top performers compared with overlap-based methods. By using randomized gene expression datasets, we explore the null hypothesis bias of each method, revealing that most of them produce skewed P-values.

Enhancing TCR specificity predictions by combined pan- and peptide-specific training, loss-scaling, and sequence similarity integration.

Predicting the interaction between Major Histocompatibility Complex (MHC) class I-presented peptides and T-cell receptors (TCR) holds significant implications for vaccine development, cancer treatment, and autoimmune disease therapies. However, limited paired-chain TCR data, skewed towards well-studied epitopes, hampers the development of pan-specific machine-learning (ML) models. Leveraging a larger peptide-TCR dataset, we explore various alterations to the ML architectures and training strategies to address data imbalance. This leads to an overall improved performance, particularly for peptides with scant TCR data. However, challenges persist for unseen peptides, especially those distant from training examples. We demonstrate that such ML models can be used to detect potential outliers, which when removed from training, leads to augmented performance. Integrating pan-specific and peptide-specific models alongside with similarity-based predictions, further improves the overall performance, especially when a low false positive rate is desirable. In the context of the IMMREP22 benchmark, this modeling framework attained state-of-the-art performance. Moreover, combining these strategies results in acceptable predictive accuracy for peptides characterized with as little as 15 positive TCRs. This observation places great promise on rapidly expanding the peptide covering of the current models for predicting TCR specificity. The NetTCR 2.2 model incorporating these advances is available on GitHub (https://github.com/mnielLab/NetTCR-2.2) and as a web server at https://services.healthtech.dtu.dk/services/NetTCR-2.2/.

Postmenopausal endometrial non-benign lesion risk classification through a clinical parameter-based machine learning model.

OBJECTIVE: This study aimed to develop and evaluate a machine learning model utilizing non-invasive clinical parameters for the classification of endometrial non-benign lesions, specifically atypical hyperplasia (AH) and endometrioid carcinoma (EC), in postmenopausal women. METHODS: Our study collected clinical parameters from a cohort of 999 patients with postmenopausal endometrial lesions and conducted preprocessing to identify 57 relevant characteristics from these irregular clinical data. To predict the presence of postmenopausal endometrial non-benign lesions, including atypical hyperplasia and endometrial cancer, we employed various models such as eXtreme Gradient Boosting (XGBoost), Random Forest (RF), Logistic Regression (LR), Support Vector Machine (SVM), Back Propagation Neural Network (BPNN), as well as two ensemble models. Additionally, a test set was performed on an independent dataset consisting of 152 patients. The performance evaluation of all models was based on metrics including the area under the receiver operating characteristic curve (AUC), sensitivity, specificity, precision, and F1 score. RESULTS: The RF model demonstrated superior recognition capabilities for patients with non-benign lesions compared to other models. In the test set, it attained a sensitivity of 88.1% and an AUC of 0.93, surpassing all alternative models evaluated in this study. Furthermore, we have integrated this model into our hospital's Clinical Decision Support System (CDSS) and implemented it within the outpatient electronic medical record system to continuously validate and optimize its performance. CONCLUSIONS: We have trained a model and deployed a system with high discriminatory power that may provide a novel approach to identify patients at higher risk of postmenopausal endometrial non-benign lesions who may benefit from more tailored screening and clinical intervention.

Sparse Dynamic Volume TransUNet with multi-level edge fusion for brain tumor segmentation.

3D MRI Brain Tumor Segmentation is of great significance in clinical diagnosis and treatment. Accurate segmentation results are critical for localization and spatial distribution of brain tumors using 3D MRI. However, most existing methods mainly focus on extracting global semantic features from the spatial and depth dimensions of a 3D volume, while ignoring voxel information, inter-layer connections, and detailed features. A 3D brain tumor segmentation network SDV-TUNet (Sparse Dynamic Volume TransUNet) based on an encoder-decoder architecture is proposed to achieve accurate segmentation by effectively combining voxel information, inter-layer feature connections, and intra-axis information. Volumetric data is fed into a 3D network consisting of extended depth modeling for dense prediction by using two modules: sparse dynamic (SD) encoder-decoder module and multi-level edge feature fusion (MEFF) module. The SD encoder-decoder module is utilized to extract global spatial semantic features for brain tumor segmentation, which employs multi-head self-attention and sparse dynamic adaptive fusion in a 3D extended shifted window strategy. In the encoding stage, dynamic perception of regional connections and multi-axis information interactions are realized through local tight correlations and long-range sparse correlations. The MEFF module achieves the fusion of multi-level local edge information in a layer-by-layer incremental manner and connects the fusion to the decoder module through skip connections to enhance the propagation ability of spatial edge information. The proposed method is applied to the BraTS2020 and BraTS2021 benchmarks, and the experimental results show its superior performance compared with state-of-the-art brain tumor segmentation methods. The source codes of the proposed method are available at https://github.com/SunMengw/SDV-TUNet.