52 research outputs found
Deep-Learning for Classification of Colorectal Polyps on Whole-Slide Images
Histopathological characterization of colorectal polyps is an important
principle for determining the risk of colorectal cancer and future rates of
surveillance for patients. This characterization is time-intensive, requires
years of specialized training, and suffers from significant inter-observer and
intra-observer variability. In this work, we built an automatic
image-understanding method that can accurately classify different types of
colorectal polyps in whole-slide histology images to help pathologists with
histopathological characterization and diagnosis of colorectal polyps. The
proposed image-understanding method is based on deep-learning techniques, which
rely on numerous levels of abstraction for data representation and have shown
state-of-the-art results for various image analysis tasks. Our
image-understanding method covers all five polyp types (hyperplastic polyp,
sessile serrated polyp, traditional serrated adenoma, tubular adenoma, and
tubulovillous/villous adenoma) that are included in the US multi-society task
force guidelines for colorectal cancer risk assessment and surveillance, and
encompasses the most common occurrences of colorectal polyps. Our evaluation on
239 independent test samples shows our proposed method can identify the types
of colorectal polyps in whole-slide images with a high efficacy (accuracy:
93.0%, precision: 89.7%, recall: 88.3%, F1 score: 88.8%). The presented method
in this paper can reduce the cognitive burden on pathologists and improve their
accuracy and efficiency in histopathological characterization of colorectal
polyps, and in subsequent risk assessment and follow-up recommendations
Association of IgG4 response and autoimmune pancreatitis with intraductal papillary-mucinous neoplasms
Objectives: Concurrent intraductal papillary-mucinous neoplasm (IPMN) and autoimmune pancreatitis (AIP) was observed in a patient (index case) at our institution. Cases of coincidental IPMN and type 1 AIP and concurrent ductal adenocarcinoma (PDAC) and AIP have been previously reported. In this study we evaluate the hypothesis that IPMN elicits an IgG4 response. Methods: Twenty-one pancreases (including the index case) with IPMN resected at our institution were studied. H&E stained slides were reviewed and blocks of peritumoral pancreas were immunostained with IgG4 to look for IgG4-positive plasma cells. Results: We found evidence of variable IgG4 overexpression in 4/21 (19%) of IPMN. These included the index case and three others without stigmata of AIP. Conclusion: A small subset of pancreatic neoplasms including intraductal papillary-mucinous neoplasms (IPMN) is associated with an IgG4 autoimmune response that sometimes progresses to peritumoral type 1 AIP and less often to diffuse AIP and IgG4-related systemic disease
Automated detection of celiac disease on duodenal biopsy slides: a deep learning approach
Celiac disease prevalence and diagnosis have increased substantially in
recent years. The current gold standard for celiac disease confirmation is
visual examination of duodenal mucosal biopsies. An accurate computer-aided
biopsy analysis system using deep learning can help pathologists diagnose
celiac disease more efficiently. In this study, we trained a deep learning
model to detect celiac disease on duodenal biopsy images. Our model uses a
state-of-the-art residual convolutional neural network to evaluate patches of
duodenal tissue and then aggregates those predictions for whole-slide
classification. We tested the model on an independent set of 212 images and
evaluated its classification results against reference standards established by
pathologists. Our model identified celiac disease, normal tissue, and
nonspecific duodenitis with accuracies of 95.3%, 91.0%, and 89.2%,
respectively. The area under the receiver operating characteristic curve was
greater than 0.95 for all classes. We have developed an automated biopsy
analysis system that achieves high performance in detecting celiac disease on
biopsy slides. Our system can highlight areas of interest and provide
preliminary classification of duodenal biopsies prior to review by
pathologists. This technology has great potential for improving the accuracy
and efficiency of celiac disease diagnosis.Comment: Accepted in Journal of Pathology Informatic
Hyper-Methylated Loci Persisting from Sessile Serrated Polyps to Serrated Cancers
Although serrated polyps were historically considered to pose little risk, it is now understood that progression down the serrated pathway could account for as many as 15%–35% of colorectal cancers. The sessile serrated adenoma/polyp (SSA/P) is the most prevalent pre-invasive serrated lesion. Our objective was to identify the CpG loci that are persistently hyper-methylated during serrated carcinogenesis, from the early SSA/P lesion through the later cancer phases of neoplasia development. We queried the loci hyper-methylated in serrated cancers within our rightsided SSA/Ps from the New Hampshire Colonoscopy Registry, using the Illumina Infinium Human Methylation 450 k panel to comprehensively assess the DNA methylation status. We identified CpG loci and regions consistently hyper-methylated throughout the serrated carcinogenesis spectrum, in both our SSA/P specimens and in serrated cancers. Hyper-methylated CpG loci included the known the tumor suppressor gene RET (p = 5.72 x 10−10), as well as loci in differentially methylated regions for GSG1L, MIR4493, NTNG1, MCIDAS, ZNF568, and RERG. The hyper-methylated loci that we identified help characterize the biology of SSA/P development, and could be useful as therapeutic targets, or for future identification of patients who may benefit from shorter surveillance intervals
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