Search bioRxiv⌕ Search

Biology subjects

Schulte, J. J.

Publications and source records attributed to Schulte, J. J..

2 recordsLinked to original sources

Validating a low-cost, open-source, locally manufactured workstation and computational pipeline for automated histopathology evaluation using deep learning

Deployment and access to state-of-the-art diagnostic technologies remains a fundamental challenge in providing equitable global cancer care to low-resource settings. The expansion of digital pathology in recent years and its interface with computational biomarkers provides an opportunity to democratize access to personalized medicine. Here we describe a low-cost platform for digital side capture and computational analysis composed of open-source components. The platform provides low-cost ($200) digital image capture from glass slides and is capable of real-time computational image analysis using an open-source deep learning (DL) algorithm and Raspberry Pi ($35) computer. We validate the performance of deep learning models performance using images captured from the open-source workstation and show similar model performance when compared against significantly more expensive standard institutional hardware.

pathology↗

Pan-cancer image-based detection of clinically actionable genetic alterations

Precision treatment of cancer relies on genetic alterations which are diagnosed by molecular biology assays.1 These tests can be a bottleneck in oncology workflows because of high turnaround time, tissue usage and costs.2 Here, we show that deep learning can predict point mutations, molecular tumor subtypes and immune-related gene expression signatures3,4 directly from routine histological images of tumor tissue. We developed and systematically optimized a one-stop-shop workflow and applied it to more than 4000 patients with breast5, colon and rectal6, head and neck7, lung8,9, pancreatic10, prostate11 cancer, melanoma12 and gastric13 cancer. Together, our findings show that a single deep learning algorithm can predict clinically actionable alterations from routine histology data. Our method can be implemented on mobile hardware14, potentially enabling point-of-care diagnostics for personalized cancer treatment in individual patients.

genetics↗