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Deep Learning in Cancer Diagnostics: Predicting Outcomes from Histology and Genomics – Histology

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<main class="site-main" id="main"> <article id="post-71" class="post-71 post type-post status-publish format-standard has-post-thumbnail hentry category-cancer-diagnostics tag-ai-in-healthcare tag-cancer-diagnostics tag-cancer-prognosis tag-convolutional-neural-networks tag-deep-learning tag-genomics tag-histopathology tag-personalized-medicine tag-predictive-biomarkers" itemtype="https://schema.org/CreativeWork" itemscope> <div class="inside-article"> <div class="featured-image page-header-image-single "> <img width="1200" height="628" src="https://histology.blog/archive/wp-content/uploads/2024/10/banner-17-min-scaled-e1727786157966.jpg" class="attachment-full size-full" alt="" itemprop="image" decoding="async" fetchpriority="high" /> </div> <header class="entry-header"> <h1 class="entry-title" itemprop="headline">Deep Learning in Cancer Diagnostics: Predicting Outcomes from Histology and Genomics</h1> <div class="entry-meta"> <span class="posted-on"><time class="entry-date published" datetime="2024-10-01T18:06:06+05:30" itemprop="datePublished">October 1, 2024</time></span> <span class="byline">by <span class="author vcard" itemprop="author" itemtype="https://schema.org/Person" itemscope><a class="url fn n" href="https://histology.blog/archive/author/histology/" title="View all posts by histology" rel="author" itemprop="url"><span class="author-name" itemprop="name">histology</span></a></span></span> </div> </header> <div class="entry-content" itemprop="text"> <h3><b>Introduction</b></h3> <p><span style="font-weight: 400;">Cancer is a group of diseases with diverse characteristics that remain a daunting clinical problem in the context of diagnosis, risk estimation, and therapy. Even today, determining the prognosis in cancer patients is still a challenge owing to intratumor heterogeneity and patients’ predisposition to therapy. Deep learning, which can largely be classified under AI, has recently emerged and brought with it tools applicable to cancer diagnosis that can analyze huge amounts of data, such as histological images and genomic data. Many DL models, especially CNNs, have proven their ability to extract relevant features from histopathological images and fuse genomic data to predict cancer development, treatment efficacy, and the patient’s survival. This blog introduces deep learning in different aspects of cancer diagnosis and how these complex algorithms are revolutionizing the way cancer is diagnosed and prognosis is made.</span></p> <h3><b>The Role of Histopathology and Genomics in Cancer Diagnosis</b></h3> <p><span style="font-weight: 400;">The laboratory method of examination of tissues for disease, notably cancer, through the lens of a microscope, has been around for over a century. This helps pathologists to determine the architectural and functional changes of tissues and whether there are tumor-facilitating changes, aggressiveness, and location. Genomic profiling, on the other hand, provides an understanding of the molecular nature of cancer by defining the genes and their products, altered expression, and other characteristics that determine tumor activity. Histopathological and genomic features provide a broad understanding of cancer, but interpreting and analyzing these multilayered datasets are subjective, time-consuming, and affected by inter-observer variability.</span></p> <p><span style="font-weight: 400;">Subsequent developments in improving deep learning ML capabilities have covered such a gap through the provision of computerized, accurate, and replicable approaches to histopathology and genomics analysis. It appears that deep learning models can be trained to detect complex patterns in histological slides that cannot be discerned by humans, as well as to identify relationships between such patterns and genomic changes, which makes for a systemic approach to cancer diagnosis.</span></p> <p></div></div> <div style="background: #f7f7f7;border: 1px solid rgba(0, 0, 0, 0.07);"> <div style="padding: 30px;"><div class="Adblock-main"> <div class="Adblock-head"> <h2>Yearwise Publication Trend on <b>“<a href="https://histology.blog/publication-trends/index/cancer diagnostics" target="_blank" title="cancer diagnostics - yearwise publication trends">cancer diagnostics</a>”</b></h2> </div> </div><div class="results-container"><div class="chart-block" style="padding:15px;"> <div class="left"> <div id="results" class="results"></div> </div> <div class="right"> <div class="chart-container"><canvas id="publicationChart"></canvas></div> </div> <div class="keywordsdiv"> <div style="text-align:center;"><b>Find publication trends on relevant topics</b> </div> <span class="gp-icon icon-tags"><svg viewBox="0 0 512 512" aria-hidden="true" xmlns="http://www.w3.org/2000/svg" width="1em" height="1em"><path d="M20 39.5c-8.836 0-16 7.163-16 16v176c0 4.243 1.686 8.313 4.687 11.314l224 224c6.248 6.248 16.378 6.248 22.626 0l176-176c6.244-6.244 6.25-16.364.013-22.615l-223.5-224A15.999 15.999 0 00196.5 39.5H20zm56 96c0-13.255 10.745-24 24-24s24 10.745 24 24-10.745 24-24 24-24-10.745-24-24z"></path><path d="M259.515 43.015c4.686-4.687 12.284-4.687 16.97 0l228 228c4.686 4.686 4.686 12.284 0 16.97l-180 180c-4.686 4.687-12.284 4.687-16.97 0-4.686-4.686-4.686-12.284 0-16.97L479.029 279.5 259.515 59.985c-4.686-4.686-4.686-12.284 0-16.97z"></path></svg></span> <span id="keyword-stats"></span> </div> </div></div></div><div class="inside-article"><style> table { margin: 0 0 1.5em; 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When operated on large datasets, deep learning models can also identify features for disease progression and the consequent treatment, as well as for the probability of survival, which is more accurate than most traditional methods.</span></p> <h4><b>Predicting Survival from Histology Slides</b></h4> <p><span style="font-weight: 400;">Convolutional neural networks have been particularly deep in analyzing histology slides and the prognosis of the life span of cancer patients. Digital histopathological images teach these models to understand features related to malignancy and patient survival. For instance, research has demonstrated that CNNs accurately evaluate the tumor microenvironment and estimate the overall survival rates of patients diagnosed with colorectal cancer. Because these models were trained using thousands of images, they can accurately capture the histology of primary tumors, including the stromal content and distribution of tumor cells, which are prognostic factors.</span></p> <p><span style="font-weight: 400;">Deep learning models can also help unravel the processes that lead to cancer progression, for instance, by identifying histological features that are indicative of poor survival. For example, AI models can study and rate basic things that are hard to measure with notations, such as microvascular proliferation, necrosis, and cellular heterogeneity. Not only does this automated analysis improve the accuracy of prognostic prediction but also helps in determining the kind of care that is appropriate for a specific patient.</span></p> <h4><b>Integrating Genomics with Histopathology</b></h4> <p><span style="font-weight: 400;">In other words, histology studies the tumor&#8217;s outer structure, while genomics studies how cancer works by looking at mutations, gene expression patterns, and other changes that make up a tumor&#8217;s features. Combining these two kinds of data with deep learning models can give a better picture of the disease.</span></p> <p><span style="font-weight: 400;">Researchers have established deep learning frameworks that fuse histological and genomic data to enhance diagnostic and prognostic strength. For example, models trained on whole-slide images and genomic data can predict patients&#8217; outcomes with better accuracy than existing models. These types of multimodal models incorporate molecular changes such as mutation profiles, gene expression profiles, and CNAs alongside histopathology features to provide a comprehensive understanding of cancer.</span></p> <p><span style="font-weight: 400;">Molecular profiles and formalin-fixed paraffin-embedded tissue sections can find outcomes that are clinically important, like how often cancer comes back, how long people live, and how well they respond to treatment. This is because of deep learning. This method not only improves the accuracy of predictions but also helps figure out how the changes in the genome affect the tumor&#8217;s pathologic features.</span></p> <h4><b>Identifying Biomarkers and Predicting Treatment Response</b></h4> <p><span style="font-weight: 400;">Deep learning also plays a critical role in detecting biomarkers that can help in the determination of cancer treatment tests. The HDCM deep learning algorithm finds features in primary tumor images that are linked to genetic mutations, protein levels, and other factors that are important for treatment. The HDCM deep learning algorithm identifies features in primary tumor images that correlate with genetic mutations, protein levels, and other treatment-relevant factors. The algorithm makes observations in gliomas using MRI and histology images. Such models help in predicting the likelihood of occurrence of mutations such as IDH1, 1p/19q codeletion, and MGMT promoter. methylation. This information is crucial for developing effective treatment strategies. Likewise, using such deep learning techniques, it is possible to determine the response to immunotherapy in colorectal cancer, based on mismatch repair deficiencies and microsatellite instability.</span></p> <p><span style="font-weight: 400;">Deep learning models also have the potential to predict responses to targeted therapies as well as immunotherapies. Because AI models can figure out the chances of getting the best results from PD-1 blockade immunotherapy in cancers that don&#8217;t have enough mismatch repair, this is possible. This predictive capacity is especially beneficial to cancer treatment since it assists oncologists in choosing the most appropriate treatment methods for patients.</span></p> <p></div></div> <div style="background: #f7f7f7;border: 1px solid rgba(0, 0, 0, 0.07);"> <div style="padding: 30px;"><div class="Adblock-main"> <div class="Adblock-head"> <h2>Recent Publications on <b>“<a href="https://histology.blog/recent-publications/index/cancer diagnostics" target="_blank" rel="noopener" title="cancer diagnostics - yearwise publication list">cancer diagnostics</a>”</b></h2> </div> </div> <div class="pb-main"><div class="article-scroll"><div id="results_recent" class="results"></div></div><div class="keywordsdiv" style="margin: 0px 15px;margin-top:20px;"> <div style="text-align:center;"><b>Find publications on relevant topics</b> </div> <span class="gp-icon icon-tags"><svg viewBox="0 0 512 512" aria-hidden="true" xmlns="http://www.w3.org/2000/svg" width="1em" height="1em"><path d="M20 39.5c-8.836 0-16 7.163-16 16v176c0 4.243 1.686 8.313 4.687 11.314l224 224c6.248 6.248 16.378 6.248 22.626 0l176-176c6.244-6.244 6.25-16.364.013-22.615l-223.5-224A15.999 15.999 0 00196.5 39.5H20zm56 96c0-13.255 10.745-24 24-24s24 10.745 24 24-10.745 24-24 24-24-10.745-24-24z"></path><path d="M259.515 43.015c4.686-4.687 12.284-4.687 16.97 0l228 228c4.686 4.686 4.686 12.284 0 16.97l-180 180c-4.686 4.687-12.284 4.687-16.97 0-4.686-4.686-4.686-12.284 0-16.97L479.029 279.5 259.515 59.985c-4.686-4.686-4.686-12.284 0-16.97z"></path></svg></span> <span id="keyword-papers"></span> </div></div></div><div class="inside-article"> <style> .pb-main{ border: solid 1px #ccc; border-top: none; margin-bottom: 20px; padding-bottom: 25px; background:#fff; } .author-main { border: solid 1px #ccc; border-top: none; margin-bottom: 20px; padding-bottom: 25px; background:#fff; } .publication-block { padding: 10px; margin-bottom: 10px; background-color: #f9f9f9; text-align: left; background: #FFF; border-bottom: solid 1px #ccc; margin-left: 15px; margin-right: 15px; } .publication-block h3 { margin: 0 0 10px; color: #000!important; } .publication-block a { font-size: 16px !important; line-height: 1em; font-weight: 600; text-transform: none; color: #000; padding: 0px; } .publication-block a:hover{ color: #227cdc; text-decoration:underline; } .article-scroll { max-height: 445px; overflow-y: auto; overflow-x: hidden; } ::-webkit-scrollbar-track { -webkit-box-shadow: inset 0 0 6px rgba(0,0,0,0.3); background-color: #efefef; border-radius:30px; } ::-webkit-scrollbar { width: 6px; background-color: #efefef; border-radius:30px; } ::-webkit-scrollbar-thumb { background-color: #ababab; 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publicationBlock.innerHTML = publicationHTML; resultsContainer.appendChild(publicationBlock); }); } function displayKeywordPapers(keywords) { var resultsContainer = document.getElementById('keyword-papers'); resultsContainer.innerHTML = ''; if (!keywords || keywords.length === 0) { resultsContainer.innerHTML = '<p>No data found.</p>'; return; } var keywordHTML = ''; keywords.forEach((key, index) => { let key_replace = key.replace(/ /g, '-'); key_replace = key_replace.toLowerCase(); keywordHTML += `<a href="https://histology.blog/recent-publications/index/${key_replace}" target="_blank" title="${key} - publication list">${key}</a>`; if (index < keywords.length - 1) { keywordHTML += ', '; } }); resultsContainer.innerHTML = keywordHTML; } // Call the function with the PHP data var recent_papers = [ { "title": "A self-immobilizing near-infrared fluorogenic probe for in vivo imaging of fibroblast activation protein-\u03b1.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38944939", "publishedDate": "2024" }, { "title": "A critical appraisal of the role of metabolomics in breast cancer research and diagnostics.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38944408", "publishedDate": "2024" }, { "title": "From Genotype to Phenotype: Raman Spectroscopy and Machine Learning for Label-Free Single-Cell Analysis.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38950145", "publishedDate": "2024" }, { "title": "Electrolyte-gated amorphous IGZO transistors with extended gates for prostate-specific antigen detection.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38847194", "publishedDate": "2024" }, { "title": "A Kernelized Classification Approach for Cancer Recognition Using Markovian Analysis of DNA Structure Patterns as Feature Mining.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38847942", "publishedDate": "2024" }, { "title": "Identifying miRNA as biomarker for breast cancer subtyping using association rule.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38850957", "publishedDate": "2024" }, { "title": "Is Automatic Tumor Segmentation on Whole-Body F-FDG PET Images a Clinical Reality?", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38844359", "publishedDate": "2024" }, { "title": "Amonafide-based HO-responsive theranostic prodrugs: Exploring the correlation between HO level and anticancer efficacy.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38878752", "publishedDate": "2024" }, { "title": "Assessment of Biological Damage Induced during Multidetector Computed Tomography (MDCT) Examination.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38858307", "publishedDate": "2024" }, { "title": "Urinary PSA-ZINC biomarker outperforms standard of care in early detection of prostate cancer.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38864687", "publishedDate": "2024" }, { "title": "Clinical application of targeted tumour sequencing tests for detecting ERBB2 amplification and optimizing anti-HER2 therapy in gastric cancer.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38862927", "publishedDate": "2024" }, { "title": "CoHIT: a one-pot ultrasensitive ERA-CRISPR system for detecting multiple same-site indels.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38866774", "publishedDate": "2024" }, { "title": "Efficacy of blood plasma spectroscopy for early liver cancer diagnostics in obese patients.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38866366", "publishedDate": "2024" }, { "title": "Infectious complications in the paediatric immunocompromised host: a narrative review.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38851426", "publishedDate": "2024" }, { "title": "Biocompatibility characterisation of CMOS-based Lab-on-Chip electrochemical sensors for in vitro cancer cell culture applications.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38941688", "publishedDate": "2024" }, { "title": "HPV, HBV, and HIV-1 Viral Integration Site Mapping: A Streamlined Workflow from NGS to Genomic Insights of Carcinogenesis.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38932267", "publishedDate": "2024" }, { "title": "Findings and Challenges in Replacing Traditional Uterine Cervical Cancer Diagnosis with Molecular Tools in Private Gynecological Practice in Mexico.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38932179", "publishedDate": "2024" }, { "title": "Determinants of Chromatin Organization in Aging and Cancer-Emerging Opportunities for Epigenetic Therapies and AI Technology.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38927646", "publishedDate": "2024" }, { "title": "Novel Semi-Nested Real-Time PCR Assay Leveraging Extendable Blocking Probes for Improved Methylation Analysis in Lung Cancer.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38927132", "publishedDate": "2024" }, { "title": "Pan-cancer proteogenomics expands the landscape of therapeutic targets.", "url": "https:\/\/pubmed.ncbi.nlm.nih.gov\/38917788", "publishedDate": "2024" } ]; var keywordsArray = ["Deep learning","cancer diagnostics","histopathology","genomics","convolutional neural networks","predictive biomarkers","cancer prognosis","personalized medicine","AI in healthcare"]; displayResults_recent(recent_papers); displayKeywordPapers(keywordsArray); // function stripslashes(str) { // if (typeof str === 'string') { // return str.replace(/\/g, ''); // } // } </script></p> <h4><b>Enhancing Diagnostic Accuracy and Reducing Variability</b></h4> <p><span style="font-weight: 400;">The application of deep learning in cancer diagnostics addresses a critical challenge in pathology: it will help to reduce the problem of inter-observer variability. The main problem with traditional histopathological analysis is that it relies on the opinions of pathologists, which means that different observers can make different diagnoses and give different grades. Deep-learning tissue segmentation models set a new standard for tissue analysis by reducing variation and increasing the possibility of making a diagnosis.</span></p> <p><span style="font-weight: 400;">Pathologists find the use of wise diagnostic tools, which include several parameters such as tumor grading, mitosis detection, and quantification of histological features, tiresome. These tools not only save time but also reduce the likelihood of errors during sample diagnosis by conducting equally rigorous tests on all obtained samples.</span></p> <p><span style="font-weight: 400;">Furthermore, we can train deep learning models on specific histopathological features associated with different cancer subtypes to aid in precise classification and diagnosis. For example, scientists have taught CNNs to correctly identify different types of breast cancer from histological images. They can do this by guessing the status of hormonal receptors and other markers without having to do expensive molecular testing on the samples.</span></p> <h3><b>Challenges and Future Directions</b></h3> <p><span style="font-weight: 400;">However, there are some challenges in the implementation of deep learning in clinical practices, although the studies have produced promising results. The availability of large datasets, tagged and curated to prepare ideal models, poses a major challenge. These limitations, which include differences in staining, image quality, and even the slides used in different institutions, pose a significant challenge to models that should come with standardized protocols.</span></p> <p><span style="font-weight: 400;">Furthermore, the rationale behind deep learning models is difficult to understand due to their &#8216;black box&#8217; characteristics, which makes clinical implementation difficult. Current work is in progress, to build explainable artificial intelligence systems, whereby clinicians can understand the way in which the predictions are being arrived at, increasing clinician trust in these models.</span></p> <p><span style="font-weight: 400;">Future deep-learning models will continue to use cancers diagnosed with histology, genomics, and other clinical data. </span><span style="font-weight: 400;">With these models, it is possible to obtain patient-individualized risk estimation, make the right decisions concerning treatment, and, as a result, achieve better outcomes.</span></p> <h3><b>Conclusion</b></h3> <p><span style="font-weight: 400;">Deep learning is revolutionizing cancer diagnostics and replacing traditional approaches with histopathology and genomics. From predicting if a patient is likely to survive or not beyond five years to the identification of patient subgroups, that may respond positively to treatment, such AI models are opening up new horizons in cancer care management. Future developments in these technologies promise to improve diagnostic accuracy, decrease inter-observer variability, and ultimately contribute to cancer fights and better patient care.</span></p> <p></p> <h3><b>References</b></h3> <ol> <li>Lakkis, J., Wang, D., Zhang, Y., Hu, G., Wang, K., Pan, H., Ungar, L., Reilly, M.P., Li, X. and Li, M., 2021. <a href="https://genome.cshlp.org/content/31/10/1753.short">A joint deep learning model enables simultaneous batch effect correction, denoising, and clustering in single-cell transcriptomics.</a> <i>Genome research</i>, <i>31</i>(10), pp.1753-1766.</li> <li>Kather, J.N., Krisam, J., Charoentong, P., Luedde, T., Herpel, E., Weis, C.A., Gaiser, T., Marx, A., Valous, N.A., Ferber, D. and Jansen, L., 2019. <a href="https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1002730">Predicting survival from colorectal cancer histology slides using deep learning: A retrospective multicenter study.</a> <i>PLoS medicine</i>, <i>16</i>(1), p.e1002730.</li> <li>Chang, P., Grinband, J., Weinberg, B.D., Bardis, M., Khy, M., Cadena, G., Su, M.Y., Cha, S., Filippi, C.G., Bota, D. and Baldi, P., 2018. <a href="https://www.ajnr.org/content/39/7/1201.short">Deep-learning convolutional neural networks accurately classify genetic mutations in gliomas.</a> <i>American Journal of Neuroradiology</i>, <i>39</i>(7), pp.1201-1207.</li> <li>Chen, R.J., Lu, M.Y., Wang, J., Williamson, D.F., Rodig, S.J., Lindeman, N.I. and Mahmood, F., 2020. <a href="https://ieeexplore.ieee.org/abstract/document/9186053">Pathomic fusion: an integrated framework for fusing histopathology and genomic features for cancer diagnosis and prognosis.</a> <i>IEEE Transactions on Medical Imaging</i>, <i>41</i>(4), pp.757-770.</li> <li>Kather, J.N., Schulte, J., Grabsch, H.I., Loeffler, C., Muti, H., Dolezal, J., Srisuwananukorn, A., Agrawal, N., Kochanny, S., Stillfried, S.V. and Boor, P., 2019. <a href="https://www.biorxiv.org/content/10.1101/690206v1.abstract">Deep learning detects virus presence in cancer histology.</a> <i>BioRxiv</i>, p.690206.</li> <li>Mobadersany, P., Yousefi, S., Amgad, M., Gutman, D.A., Barnholtz-Sloan, J.S., Velázquez Vega, J.E., Brat, D.J. and Cooper, L.A., 2018. <a href="https://www.pnas.org/doi/abs/10.1073/pnas.1717139115">Predicting cancer outcomes from histology and genomics using convolutional networks.</a> <i>Proceedings of the National Academy of Sciences</i>, <i>115</i>(13), pp.E2970-E2979.</li> <li>Chen, K.H., Boettiger, A.N., Moffitt, J.R., Wang, S. and Zhuang, X., 2015. <a href="https://www.science.org/doi/full/10.1126/science.aaa6090">Spatially resolved, highly multiplexed RNA profiling in single cells.</a> <i>Science</i>, <i>348</i>(6233), p.aaa6090.</li> <li>Lee, J., Lee, J. and Kim, J.H., 2019. <a href="https://ar.iiarjournals.org/content/39/11/5963.short">Identification of matrix metalloproteinase 11 as a prognostic biomarker in pancreatic cancer.</a> <i>Anticancer Research</i>, <i>39</i>(11), pp.5963-5971.</li> </ol> <p></div></div> <div style="background: #f7f7f7;border: 1px solid rgba(0, 0, 0, 0.07);"> <div style="padding: 30px;"><div class="Adblock-main"> <div class="Adblock-head"> <h2>Top Experts on “<b style="color:#000;font-size:22px;">cancer diagnostics</b>“</h2> </div> </div><div class="author-main"><div id="results_author"></div><div style="text-align: center;"><a class="register-button" href="https://histology.blog/expert-search" target="_blank" rel="noopener">Find experts on any field</a></div></div><div class="inside-article" style="background: none;border: none;box-shadow: none;margin-top: -70px;"> <style> .author-block { padding: 15px; 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