Cancer Informatics最新文献

{"title":"ExGenet, Integrating Design of Experiments and Response Surface Methodology for Cancer Gene Detection in Gene Regulatory Networks.","authors":"Mahboube Ayoubi, Babak Teimourpour, Alireza Hassanzadeh","doi":"10.1177/11769351241255645","DOIUrl":"10.1177/11769351241255645","url":null,"abstract":"<p><strong>Objective: </strong>Network analysis techniques often require tuning hyperparameters for optimal performance. For instance, the independent cascade model necessitates determining the probability of diffusion. Despite its importance, a consensus on effective parameter adjustment remains elusive.</p><p><strong>Methods: </strong>In this study, we propose a novel approach utilizing experimental design methodologies, specifically 2-Factorial Analysis for Screening, and Response Surface Methodology (RSM) for parameter adjustment. We apply this methodology to the task of detecting cancer driver genes in colorectal cancer.</p><p><strong>Result: </strong>Through experimental validation of colorectal cancer data, we demonstrate the effectiveness of our proposed methodology. Compared with existing methods, our approach offers several advantages, including reduced computational overhead, systematic parameter selection grounded in statistical theory, and improved performance in detecting cancer driver genes.</p><p><strong>Conclusion: </strong>This study presents a significant advancement in the field of network analysis by providing a practical and systematic approach to hyperparameter tuning. By optimizing parameter settings, our methodology offers promising implications for critical biomedical applications such as cancer driver gene detection.</p>","PeriodicalId":35418,"journal":{"name":"Cancer Informatics","volume":"23 ","pages":"11769351241255645"},"PeriodicalIF":2.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11159540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141296901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Alternative Polyadenylation Regulatory Factors Signature for Survival Prediction in Kidney Renal Cell Carcinoma.","authors":"Xiaoyu Wang, Yao Lin, Zheng Li, Yueqi Li, Mingcong Chen","doi":"10.1177/11769351231180789","DOIUrl":"https://doi.org/10.1177/11769351231180789","url":null,"abstract":"<p><strong>Background: </strong>Alternative polyadenylation (APA) plays a vital regulatory role in various diseases. It is widely accepted that APA is regulated by APA regulatory factors.</p><p><strong>Objective: </strong>Whether APA regulatory factors affect the prognosis of renal cell carcinoma remains unclear, and this is the main topic of this study.</p><p><strong>Methods: </strong>We downloaded the transcriptome and clinical data from The Cancer Genome Atlas (TCGA) database. We used the Lasso regression system to construct an APA model for analyzing the relationship between common APA regulatory factors and renal cell carcinoma. We also validated our APA model using independent GEO datasets (GSE29609, GSE76207).</p><p><strong>Results: </strong>It was found that the expression levels of 5 APA regulatory factors (CPSF1, CPSF2, CSTF2, PABPC1, and PABPC4) were significantly associated with tumor gene mutation burden (TMB) score in renal clear cell carcinoma, and the risk score constructed using the expression level of 5 key APA regulatory factors could be used to predict the outcome of renal clear cell carcinoma. The TMB score is associated with the remodeling of the immune microenvironment.</p><p><strong>Conclusions: </strong>By identifying key APA regulatory factors in renal cell carcinoma and constructing risk scores for key APA regulatory factors, we showed that key APA regulators affect prognosis of renal clear cell carcinoma patients. In addition, the risk score level is associated with TMB, indicating that APA may affect the efficacy of immunotherapy through immune microenvironment-related genes. This helps us better understand the mRNA processing mechanism of renal clear cell carcinoma.</p>","PeriodicalId":35418,"journal":{"name":"Cancer Informatics","volume":"23 ","pages":"11769351231180789"},"PeriodicalIF":2.0,"publicationDate":"2024-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11015750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140871150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Paradigm Shift in Non-Small-Cell Lung Cancer (NSCLC) Diagnostics: From Single Gene Tests to Comprehensive Genomic Profiling.","authors":"Ushna Zameer, Wajiha Shaikh, Abdul Moiz Khan","doi":"10.1177/11769351241243243","DOIUrl":"https://doi.org/10.1177/11769351241243243","url":null,"abstract":"<p><p>Lung cancer imposes a burden on the health care system worldwide affecting 2 million people and causing 1.8 million deaths in 2021.More than 85% of all lung cancer cases are reported under Non-small-cell lung cancer (NSCLC). It is critical to discover gene alterations to treat non-small cell lung cancer successfully. The CAP/IASLC/AMP recommendations supported use of polymerase chain reaction (PCR) and fluorescent in situ hybridization (FISH) <i>EGFR</i> (epidermal growth factor receptor) mutations and <i>ALK</i> (Anaplastic lymphoma kinase) rearrangements, respectively. A study presented in the annual meeting of the American Society of Clinical Oncology (ASCO) in Chicago emphasized the need for comprehensive genomic profiling (CGP) before single gene tests (SGTs) since it demonstrated that SGT can result in the depletion of precious biopsy samples. As a result, the efficacy of thorough genetic Profiling (CGP) is reduced, preventing patients from receiving valuable genetic information about their tumors.</p>","PeriodicalId":35418,"journal":{"name":"Cancer Informatics","volume":"23 ","pages":"11769351241243243"},"PeriodicalIF":2.0,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10998481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140852584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An Intelligent Search & Retrieval System (IRIS) and Clinical and Research Repository for Decision Support Based on Machine Learning and Joint Kernel-based Supervised Hashing.","authors":"David J Foran, Wenjin Chen, Tahsin Kurc, Rajarshi Gupta, Jakub Roman Kaczmarzyk, Luke Austin Torre-Healy, Erich Bremer, Samuel Ajjarapu, Nhan Do, Gerald Harris, Antoinette Stroup, Eric Durbin, Joel H Saltz","doi":"10.1177/11769351231223806","DOIUrl":"10.1177/11769351231223806","url":null,"abstract":"<p><p>Large-scale, multi-site collaboration is becoming indispensable for a wide range of research and clinical activities in oncology. To facilitate the next generation of advances in cancer biology, precision oncology and the population sciences it will be necessary to develop and implement data management and analytic tools that empower investigators to reliably and objectively detect, characterize and chronicle the phenotypic and genomic changes that occur during the transformation from the benign to cancerous state and throughout the course of disease progression. To facilitate these efforts it is incumbent upon the informatics community to establish the workflows and architectures that automate the aggregation and organization of a growing range and number of clinical data types and modalities ranging from new molecular and laboratory tests to sophisticated diagnostic imaging studies. In an attempt to meet those challenges, leading health care centers across the country are making steep investments to establish enterprise-wide, data warehouses. A significant limitation of many data warehouses, however, is that they are designed to support only alphanumeric information. In contrast to those traditional designs, the system that we have developed supports automated collection and mining of multimodal data including genomics, digital pathology and radiology images. In this paper, our team describes the design, development and implementation of a multi-modal, Clinical & Research Data Warehouse (CRDW) that is tightly integrated with a suite of computational and machine-learning tools to provide actionable insight into the underlying characteristics of the tumor environment that would not be revealed using standard methods and tools. The System features a flexible Extract, Transform and Load (ETL) interface that enables it to adapt to aggregate data originating from different clinical and research sources depending on the specific EHR and other data sources utilized at a given deployment site.</p>","PeriodicalId":35418,"journal":{"name":"Cancer Informatics","volume":"23 ","pages":"11769351231223806"},"PeriodicalIF":2.0,"publicationDate":"2024-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10840403/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139698512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Designing a Deep Learning-Driven Resource-Efficient Diagnostic System for Metastatic Breast Cancer: Reducing Long Delays of Clinical Diagnosis and Improving Patient Survival in Developing Countries.","authors":"William Gao, Dayong Wang, Yi Huang","doi":"10.1177/11769351231214446","DOIUrl":"10.1177/11769351231214446","url":null,"abstract":"<p><p>Breast cancer is one of the leading causes of cancer mortality. Breast cancer patients in developing countries, especially sub-Saharan Africa, South Asia, and South America, suffer from the highest mortality rate in the world. One crucial factor contributing to the global disparity in mortality rate is long delay of diagnosis due to a severe shortage of trained pathologists, which consequently has led to a large proportion of late-stage presentation at diagnosis. To tackle this critical healthcare disparity, we have developed a deep learning-based diagnosis system for metastatic breast cancer that can achieve high diagnostic accuracy as well as computational efficiency and mobile readiness suitable for an under-resourced environment. We evaluated 4 Convolutional Neural Network (CNN) architectures: MobileNetV2, VGG16, ResNet50 and ResNet101. The MobileNetV2-based diagnostic model outperformed the more complex VGG16, ResNet50 and ResNet101 models in diagnostic accuracy, model generalization, and model training efficiency. The ROC AUC of MobilenetV2 (0.933, 95% CI: 0.930, 0.936) was higher than VGG16 (0.911, 95% CI: 0.908, 0.915), ResNet50 (0.869, 95% CI: 0.866, 0.873), and ResNet101 (0.873, 95% CI: 0.869, 0.876). The time per inference step for the MobileNetV2 model (15 ms/step) was substantially lower than that of VGG16 (48 ms/step), ResNet50 (37 ms/step), and ResNet110 (56 ms/step). The visual comparisons between the model prediction and ground truth have demonstrated that the MobileNetV2 diagnostic models can identify very small cancerous nodes embedded in a large area of normal cells which is challenging for manual image analysis. Equally Important, the light weight MobleNetV2 models were computationally efficient and ready for mobile devices or devices of low computational power. These advances empower the development of a resource-efficient and high performing AI-based metastatic breast cancer diagnostic system that can adapt to under-resourced healthcare facilities in developing countries.</p>","PeriodicalId":35418,"journal":{"name":"Cancer Informatics","volume":"22 ","pages":"11769351231214446"},"PeriodicalIF":2.0,"publicationDate":"2023-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10683375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138463028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Applying a Gene Reversal Rate Computational Methodology to Identify Drugs for a Rare Cancer: Inflammatory Breast Cancer.","authors":"Xiaojia Ji, Kevin P Williams, Weifan Zheng","doi":"10.1177/11769351231202588","DOIUrl":"10.1177/11769351231202588","url":null,"abstract":"<p><p>The aim of this study was to utilize a computational methodology based on Gene Reversal Rate (GRR) scoring to repurpose existing drugs for a rare and understudied cancer: inflammatory breast cancer (IBC). This method uses IBC-related gene expression signatures (GES) and drug-induced gene expression profiles from the LINCS database to calculate a GRR score for each candidate drug, and is based on the idea that a compound that can counteract gene expression changes of a disease may have potential therapeutic applications for that disease. Genes related to IBC with associated differential expression data (265 up-regulated and 122 down-regulated) were collated from PubMed-indexed publications. Drug-induced gene expression profiles were downloaded from the LINCS database and candidate drugs to treat IBC were predicted using their GRR scores. Thirty-two (32) drug perturbations that could potentially reverse the pre-compiled list of 297 IBC genes were obtained using the LINCS Canvas Browser (LCB) analysis. Binary combinations of the 32 perturbations were assessed computationally to identify combined perturbations with the highest GRR scores, and resulted in 131 combinations with GRR greater than 80%, that reverse up to 264 of the 297 genes in the IBC-GES. The top 35 combinations involve 20 unique individual drug perturbations, and 19 potential drug candidates. A comprehensive literature search confirmed 17 of the 19 known drugs as having either anti-cancer or anti-inflammatory activities. AZD-7545, BMS-754807, and nimesulide target known IBC relevant genes: PDK, Met, and COX, respectively. AG-14361, butalbital, and clobenpropit are known to be functionally relevant in DNA damage, cell cycle, and apoptosis, respectively. These findings support the use of the GRR approach to identify drug candidates and potential combination therapies that could be used to treat rare diseases such as IBC.</p>","PeriodicalId":35418,"journal":{"name":"Cancer Informatics","volume":"22 ","pages":"11769351231202588"},"PeriodicalIF":2.0,"publicationDate":"2023-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/0e/64/10.1177_11769351231202588.PMC10576937.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41239386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to \"The Role of DNA Viruses in Human Cancer\".","authors":"","doi":"10.1177/11769351231208757","DOIUrl":"10.1177/11769351231208757","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1177/11769351231154186.].</p>","PeriodicalId":35418,"journal":{"name":"Cancer Informatics","volume":"22 ","pages":"11769351231208757"},"PeriodicalIF":2.0,"publicationDate":"2023-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ca/46/10.1177_11769351231208757.PMC10576910.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41239387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparing Individualized Survival Predictions From Random Survival Forests and Multistate Models in the Presence of Missing Data: A Case Study of Patients With Oropharyngeal Cancer.","authors":"Madeline R Abbott, Lauren J Beesley, Emily L Bellile, Andrew G Shuman, Laura S Rozek, Jeremy M G Taylor","doi":"10.1177/11769351231183847","DOIUrl":"10.1177/11769351231183847","url":null,"abstract":"<p><strong>Background: </strong>In recent years, interest in prognostic calculators for predicting patient health outcomes has grown with the popularity of personalized medicine. These calculators, which can inform treatment decisions, employ many different methods, each of which has advantages and disadvantages.</p><p><strong>Methods: </strong>We present a comparison of a multistate model (MSM) and a random survival forest (RSF) through a case study of prognostic predictions for patients with oropharyngeal squamous cell carcinoma. The MSM is highly structured and takes into account some aspects of the clinical context and knowledge about oropharyngeal cancer, while the RSF can be thought of as a black-box non-parametric approach. Key in this comparison are the high rate of missing values within these data and the different approaches used by the MSM and RSF to handle missingness.</p><p><strong>Results: </strong>We compare the accuracy (discrimination and calibration) of survival probabilities predicted by both approaches and use simulation studies to better understand how predictive accuracy is influenced by the approach to (1) handling missing data and (2) modeling structural/disease progression information present in the data. We conclude that both approaches have similar predictive accuracy, with a slight advantage going to the MSM.</p><p><strong>Conclusions: </strong>Although the MSM shows slightly better predictive ability than the RSF, consideration of other differences are key when selecting the best approach for addressing a specific research question. These key differences include the methods' ability to incorporate domain knowledge, and their ability to handle missing data as well as their interpretability, and ease of implementation. Ultimately, selecting the statistical method that has the most potential to aid in clinical decisions requires thoughtful consideration of the specific goals.</p>","PeriodicalId":35418,"journal":{"name":"Cancer Informatics","volume":"22 ","pages":"11769351231183847"},"PeriodicalIF":2.0,"publicationDate":"2023-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/7d/d9/10.1177_11769351231183847.PMC10328055.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10647910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Role of DNA Viruses in Human Cancer.","authors":"Zohreh-Al-Sadat Ghoreshi, Hamid Reza Molaei, Nasir Arefinia","doi":"10.1177/11769351231154186","DOIUrl":"10.1177/11769351231154186","url":null,"abstract":"<p><p>This review discusses the possible involvement of infections-associated cancers in humans, with virus infections contributing 15% to 20% of total cancer cases in humans. DNA virus encoded proteins interact with host cellular signaling pathways and control proliferation, cell death and genomic integrity viral oncoproteins are known to bind cellular Deubiquitinates (DUBs) such as cyclindromatosis tumor suppressor, ubiquitin-specific proteases 7, 11, 15 and 20, and A-20 to improve their intracellular stability and cellular signaling pathways and finally transformation. Human papillomaviruses (cervical carcinoma, oral cancer and laryngeal cancer); human polyomaviruses (mesotheliomas, brain tumors); Epstein-Barr virus (B-cell lymphoproliferative diseases and nasopharyngeal carcinoma); Kaposi's Sarcoma Herpesvirus (Kaposi's Sarcoma and primary effusion lymphomas); hepatitis B (hepatocellular carcinoma (HCC)) cause up to 20% of malignancies around the world.</p>","PeriodicalId":35418,"journal":{"name":"Cancer Informatics","volume":"22 ","pages":"11769351231154186"},"PeriodicalIF":2.0,"publicationDate":"2023-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/42/1d/10.1177_11769351231154186.PMC10286548.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9715574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantifying the Contributions of Environmental Factors to Prostate Cancer and Detecting Risk-Related Diet Metrics and Racial Disparities.","authors":"Wensheng Zhang, Kun Zhang","doi":"10.1177/11769351231168006","DOIUrl":"10.1177/11769351231168006","url":null,"abstract":"<p><p>The relevance of nongenetic factors to prostate cancer (PCa) has been elusive. We aimed to quantify the contributions of environmental factors to PCa and identify risk-related diet metrics and relevant racial disparities. We performed a unique analysis of the Diet History Questionnaire data of 41 830 European Americans (EAs) and 1282 African Americans (AAs) in the PLCO project. The independent variables in the regression models consisted of age at trial entry, race, family history of prostate cancer (PCa-fh), diabetes history, body mass index (BMI), lifestyle (smoking and coffee consumption), marital status, and a specific nutrient/food factor (X). <i>P</i> < .05 and a 95% confidence interval excluding zero were adopted as the criteria for determining a significant difference (effect). We established a priority ranking among PCa risk-related genetic and environmental factors according to the deviances explained by them in the multivariate Cox-PH regression analysis: age > PCa-fh > diabetes ⩾ race > lifestyle ⩾marital-status ⩾BMI > X. We confirmed previous studies showing that (1) high protein and saturated fat levels in diet were related to increased PCa risk, (2) high-level supplementary selenium intake was harmful rather than beneficial for preventing PCa, and (3) supplementary vitamin B6 was beneficial for preventing benign PCa. We obtained the following novel findings: high-level organ meat intake was an independent predictor for increased aggressive PCa risk; supplementary iron, copper and magnesium increased benign PCa risk; and the AA diet was \"healthy\" in terms of the relatively lower protein and fat levels and was \"unhealthy\" in that it more commonly contained organ meat. In conclusion, we established a priority ranking among the contributing factors for PCa and identified several risk-related diet metrics and the racial disparities. Our findings suggested some new approaches to prevent PCa such as restriction of organ meat intake and supplementary microminerals.</p>","PeriodicalId":35418,"journal":{"name":"Cancer Informatics","volume":"22 ","pages":"11769351231168006"},"PeriodicalIF":2.0,"publicationDate":"2023-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/7e/22/10.1177_11769351231168006.PMC10150431.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9416305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}