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PubMed1999

Tenascin expression in gastric cancer with special emphasis on the WHO-, Lauren-, and Goseki-classifications.

Ample evidence has been provided concerning the presence of tenascin in various histological subtypes of gastric cancer. However, conflict and discussion still persist regarding the correlation with different classification systems and prognostic impact. Therefore, we studied 203 adenocarcinomas of the stomach with special emphasis to the WHO-classification, Lauren's and Goseki's subtypes as well. The immunohistochemical ABC-method was applied using a monoclonal anti-human-tenascin antibody. 30% of all tumours showed a distinct staining reaction. Tubulo-papillary carcinomas (WHO) revealed a significantly stronger reactivity than signet-ring subtypes. Adenocarcinomas of intestinal type (Lauren) were significantly more positive than the diffuse types. Mucin-poor tumours (Goseki I+III) stained positive in a much higher degree compared to mucin-rich subtypes (Goseki II+IV). However, no correlation could been demonstrated regarding TNM-stage or prognosis.

Adenocarcinoma↗

PubMed1996

Clinical analysis of 670 cases in two trials of the European Organization for the Research and Treatment of Cancer Lymphoma Cooperative Group subtyped according to the Revised European-American Classification of Lymphoid Neoplasms: a comparison with the Working Formulation.

In the Working Formulation (WF), non-Hodgkin's lymphomas (NHL) are grouped according to their clinical behavior. These disorders are listed as entities defined by morphology, phenotype, and cytogenetics in the proposed Revised European-American Classification of Lymphoid Neoplasms (REAL), the clinical relevance of which is still debated. We analyzed 670 NHL cases included in two randomized clinical trials (EORTC 20855 WF-intermediate/high-grade and 20856 WF-low-grade malignancy) with histologic material available for review. Based on hematoxylin-eosin-stained sections, 77% of cases could be subtyped. Immunophenotyping was considered to be mandatory only in diagnosing T-cell lymphoma and anaplastic large-cell lymphoma. Of 522 cases subtyped, 11% were mantle cell lymphoma (MCL), 5% were marginal zone B-cell lymphoma (MZBCL), 46% were follicle center lymphoma, and 32% were diffuse large B-cell lymphoma. Statistical analysis and comparisons between classifications were made only within each trial and treatment group. MCL and MZBCL were characterized by a shorter median survival (3.4 and 4.1 years, respectively) in comparison with low- and intermediate-grade WF groups (> 9.3 and 5.8 years, respectively). In terms of progression-free survival, MCL showed a behavior similar to the low-grade group, with frequent relapses. Follicle center cell lymphomas behaved as low-grade lymphomas as defined by the WF and diffuse large B-cell lymphomas as the WF-intermediate grade group. Because several NHL entities have a clinical behavior of their own, their recognition by the REAL classification offers clinicians additional information that is not obtained when the WF is used.

Antineoplastic Combined Chemotherapy Protocols↗

PubMed2026

Stage-Independent Real-Time Subtype Classification and Comprehensive Biopsy Profiling of Urothelial Carcinomas by the Lund Taxonomy System.

Bladder cancer is a heterogeneous malignancy with diverse clinical outcomes, and conventional pathological assessment alone is insufficient to capture its underlying biology. Gene expression profiling can stratify tumors into molecular subtypes with prognostic and predictive potential, but the reliability of transcriptomic classification and its clinical utility remains to be established. The translational/observational UROSCANSEQ study (ISRCTN15459149) prospectively evaluates RNA-based Lund Taxonomy (LundTax) molecular subtype classification in a clinical setting. Among 784 consecutive biopsies collected between 2018 and 2022, RNA sequencing was successful for 90% of all biopsies, encompassing 662 bladder cancer patients with a stage distribution of 48% Ta, 27% T1, 24% ≥T2, and 1% CIS. We demonstrate that the LundTax subtype classification algorithm, applied to individual samples, accurately identifies cancer cell phenotypes with characteristic gene and protein expression patterns in a manner robust to RNA quality, data preprocessing strategies, and batch effects, supporting its clinical feasibility across both non-muscle-invasive and muscle-invasive disease. We further extend the LundTax framework by incorporating single-sample molecular risk scores reflecting tumor grade, proliferation, and progression risk, as well as tumor microenvironment signatures. Both risk scores and overall immune and stromal content in biopsies were significantly associated with an increased risk of clinical progression in noninvasive disease. In a separate analysis of the relative cellular composition of the tumor microenvironment, however, only the fraction of natural killer cells remained significant. Together, the expanded LundTax system provides a comprehensive molecular portrait of individual tumor biopsies. By explicitly separating cancer cell-intrinsic phenotypes, prognostic indexes, and microenvironmental signals, the framework minimizes biological confounding and establishes a strong foundation for future studies evaluating clinical outcomes and treatment responses.

Humans↗

PubMed2001

A prospective correlation of Laurén's histological classification of stomach cancer with clinicopathological findings including DNA flow cytometry.

Between November 1990 and December 1992, 217 patients with stomach cancer were enrolled in a prospective study evaluating the prognostic value of DNA flow cytometry. Laurén's histological type was evaluated in 216 cases, of which 102 (47%) were of the diffuse type, 74 (34%) were of the intestinal type, and 40 (19%) were mixed type tumors. Laurén's histological type showed a significant correlation with age (p = 0.028), sex (p = 0.004), tumor size (p = 0.002), T stage (p = 0.006), overall TNM stage (p = 0.008), histological grade (p < 0.001), and tumor ploidy (p < 0.001). Intestinal type stomach cancer showed a significantly higher proportion of aneuploidy [diffuse vs. intestinal type; 41/102 (40%) vs. 52/74 (70%)]. After a median follow-up of 66.1 months (range, 29.6-78.1), 110 of 216 patients (51%) survived. Patients with intestinal type stomach cancer had a significantly better survival than did those with diffuse type stomach cancer (64% vs. 42% of patients surviving, p = 0.020). Our study suggests that there are biological differences between the two subtypes of Laurén's classification of stomach cancer in addition to the morphological differences. Laurén's classification should remain valid in future studies investigating the pathogenetic and clinical aspects of stomach cancer.

Adult↗

PubMed1984

The prognostic significance of histologic subtyping in small cell carcinoma of the lung.

Previously untreated patients with small cell carcinoma of the lung (SCCL), who were treated at the Medical College of Wisconsin with combined chemotherapy and radiation therapy, were retrospectively subtyped according to the 1981 World Health Organization Lung Cancer Classification. Of 54 evaluated patients, 27 (50%) had "oat cell" subtype, 22 (41%) "intermediate cell" variety, and five (9%) were classified as "combined" type. There was no significant difference in response to therapy or median survival between the subtypes. In addition to the absence of prognostic significance among the subtypes, there were many technical factors affecting accuracy of subtyping, including tissue-crushing artifacts, size of biopsy materials, fixation of tissue samples, and variation of subtypes within the same biopsy. We conclude that subtyping of SCCL should not be construed as a prognostic tool or guideline to therapy. However, the recognition that SCCL may manifest in a variety of histologic patterns, some of which may be misinterpreted as a histology other than SCCL, is probably more important for choice of therapy and prognosis than the individual subtypes.

Carcinoma, Small Cell↗

PubMedDate not supplied

Fine needle aspiration cytology of palpable breast lesions. Histologic subtype in false negative cases.

OBJECTIVE: To evaluate the use of fine needle aspiration cytology (FNAC) in the management of benign and malignant breast disease in an outpatient breast clinic and to determine the guidelines for reporting on FNAC of breast lesions, we evaluated the test results in correlation with the histologic diagnosis. STUDY DESIGN: We evaluate the test results of 669 cases of FNAC of the breast in 17 months in our outpatient breast clinic in correlation with the histologic diagnosis, histologic subtype according to the Japan Mammary Cancer Society classification and mammography results in false negative cases. RESULTS: Among 669 cases, 25.3% were inadequate for cytologic diagnosis. An analysis of the results using the two-by-four contingency table, including cases with inadequate cytologic diagnosis, showed that 10.6% and 1.0% had false negative and false positive cytologic diagnoses, respectively; sensitivity and specificity were 76.9% and 91.6%, respectively. The false negative rate of 10.6% was higher than expected, and those belonged mostly to the "inadequate" cytologic diagnosis category even though they were discrete, obviously malignant masses clinically. To try to explain this, we compared the cytologic results and histologic subtype according to the Japan Mammary Cancer Society classification and the mammography results. Of 73 cases of infiltrating ductal carcinoma in which retrospective reexamination of the histology slide was possible, 27 (37.0%) were papillo-tubular type, 11 (15.1%) were solid-tubular type and 35 cases (47.9%) were scirrhous type. Although the scirrhous subtype was only 37.0% in the group in which a cytologic diagnosis of carcinoma was possible, more than two-thirds of the cases of false negative cytology were scirrhous type and had malignant mammographic findings. This finding was statistically significant. CONCLUSION: In cases of ductal carcinoma of scirrhous subtype, the FNAC tended to be inadequate and false negative, but mammography showed better discrimination in such cases.

Biopsy, Needle↗

PubMed2003

Loss of E-cadherin expression correlates with poor differentiation and invasion into adjacent organs in gastric adenocarcinomas.

Perturbation in E-cadherin expression leads to loss of cellular adhesion with possible consequence of cellular transformation and tumor progression. The aims of this study were to determine E-cadherin expression in each subtype of gastric cancer classified by different classification systems, and to investigate the role of E-cadherin in cell differentiation, cancer invasion and metastasis. Expression of E-cadherin was analyzed in 84 patients with gastric adenocarcinoma by immunohistochemistry and correlated with clinicopahotlogical parameters. Our results showed loss of E-cadherin expression in 0% (0/3), 20.0% (9/45), 48% (15/31), 100% (3/3) and 100% (2/2) of papillary, tubular, poorly differentiated, signet-ring cell, and mucinous adenocarcinoma by Japanese histological classification. The reduction of E-cadherin expression was inversely correlated with the grade of differentiation. According to the histological classification of Lauren and Ming, the frequency of lost E-cadherin expression was higher in diffuse type (65%) and infiltrative type (64%) gastric cancer than in intestinal type (20%, P<0.001) and expanding type cancer (22%, P<0.001), respectively. The loss of E-cadherin expression was significantly associated with tumor invasion (P<0.05). Furthermore, there was a borderline association between the loss of E-cadherin expression and poor survival (P=0.109). These data demonstrated a striking correlation between E-cadherin expression and the differentiation of gastric carcinoma. The loss of E-cadherin expression may contribute to gastric cancer invasion to adjacent organs.

Adenocarcinoma↗

PubMed2005

An entropy-based gene selection method for cancer classification using microarray data.

BACKGROUND: Accurate diagnosis of cancer subtypes remains a challenging problem. Building classifiers based on gene expression data is a promising approach; yet the selection of non-redundant but relevant genes is difficult. The selected gene set should be small enough to allow diagnosis even in regular clinical laboratories and ideally identify genes involved in cancer-specific regulatory pathways. Here an entropy-based method is proposed that selects genes related to the different cancer classes while at the same time reducing the redundancy among the genes. RESULTS: The present study identifies a subset of features by maximizing the relevance and minimizing the redundancy of the selected genes. A merit called normalized mutual information is employed to measure the relevance and the redundancy of the genes. In order to find a more representative subset of features, an iterative procedure is adopted that incorporates an initial clustering followed by data partitioning and the application of the algorithm to each of the partitions. A leave-one-out approach then selects the most commonly selected genes across all the different runs and the gene selection algorithm is applied again to pare down the list of selected genes until a minimal subset is obtained that gives a satisfactory accuracy of classification. The algorithm was applied to three different data sets and the results obtained were compared to work done by others using the same data sets. CONCLUSION: This study presents an entropy-based iterative algorithm for selecting genes from microarray data that are able to classify various cancer sub-types with high accuracy. In addition, the feature set obtained is very compact, that is, the redundancy between genes is reduced to a large extent. This implies that classifiers can be built with a smaller subset of genes.

Algorithms↗

PubMed1987

A morphologic study of childhood lymphoma of the diffuse "histiocytic" type. The Pediatric Oncology Group experience.

Of 227 cases of pediatric non-Hodgkin's lymphoma with adequate histopathologic material for review, 72 (32%) were classified as diffuse "histiocytic" lymphoma (DHL). These cases were further divided into different morphologic subtypes according to the Lukes-Collins classification, and the National Cancer Institute Working Formulation, to ascertain whether there were any significant prognostic differences among the different subtypes. The results of our study showed that 40 patients were classified as immunoblastic lymphomas, and 32 were called large follicular center cell (FCC) tumors. Of the 40 patients with immunoblastic histology, 19 had morphologic features of the clear cell type and were interpreted as consistent with T-immunoblastic lymphomas; an additional two had polymorphous features also consistent with T-cell type: 17 had plasmacytoid features, and were morphologically classified as B-immunoblastic lymphomas; two could not be subtyped. Of the 32 patients with morphologic features of FCC lymphomas, 29 were classified as large noncleaved type, and three as large cleaved type. A clinicopathologic analysis showed that 90% of the patients obtained complete remission, and there were no significant differences in complete remission rate among the different morphologic subtypes of DHL. The estimated five year disease-free survival for all patients was over 70%, with no failure after the second year; and there were no significant differences in the disease-free survival among the different subtypes. The only clinical differences that we found, were that patients with lymphomas of FCC (large noncleaved) type were younger (P = 0.01); had less nodal involvement (P = 0.03); and had more organ involvement (P less than 0.01). We conclude that the morphologic subclassification of DHL in children currently has limited clinical prognostic significance.

Adolescent↗

PubMed1997

Detection and classification of early squamous cell esophageal cancer.

The authors analyzed 230 cases of T1 cancer of the thoracic esophagus resected in our surgical department between 1985 and 1996. This study showed that mucosal cancer was superior to submucosal cancer with respect to the 5-year survival rate (84% vs 64%), the incidence of lymph node metastasis (2% vs 42%) and the incidence of vascular invasion (8% vs 79%); therefore, the true early cancer of the esophagus can be defined as mucosal cancer of the esophagus. As for endoscopic classification, 93% of the 0-IIb subtype lesion and 80% of the 0-IIc subtype were mucosal cancer. Endoscopic staining with Lugol's solution can produce more precise information in the diagnosis of such flat lesions. Important points in screening for the detection of mucosal cancer of the esophagus include: (i) esophagoscopy for patients with only slight esophageal symptoms; (ii) annual endoscopic examination for high-risk populations; and (iii) endoscopic staining with Lugol's solution for abnormal findings on conventional endoscopy.

Carcinoma, Squamous Cell↗

PubMed2002

Relationship between biologic behavior and phenotypic expression in intramucosal gastric carcinomas.

We investigated the biologic behavior of gastric phenotype carcinoma of the stomach, especially in association with degradation of the extracellular matrix. One hundred fourteen lesions of intramucosal gastric carcinoma (IMGC) of differentiated type were studied. IMGCs were classified into 4 phenotypic categories--complete intestinal type (C type), incomplete intestinal type (I type), gastric type (G type), and unclassified type--through a combination of the expression of CD10, MUC2, HGM, and Con A. The expression of MMP-2, MMP-9, TIMP-2, and type IV collagen was investigated by immunohistochemical staining. The incidence of C-type IMGC, I-type IMGC, and G-type IMGC was 7.9%, 55.3%, and 36.8%, respectively. The incidence of positive MMP-9 expression in G-type IMGCs (57%) was significantly higher than that in C-type IMGCs (11%) or I-type IMGCs (35%) (P < .01). There was no significant correlation between phenotypes and expression of MMP-2, TIMP-2, or type IV collagen. There was a reverse correlation between the expression of type IV collagen and the expression of type IV collagenase (P < .001). In conclusion, gastric phenotype carcinomas have been shown to be highly invasive and metastatic, However, although they can potentially degrade the extracellular matrix via overexpression of MMPs compared with intestinal phenotype carcinoma, our data show no statistically significant separation of subtypes of intramucosal gastric cancer based on gross classification, histologic type, lymphatic or venous invasion, or lymph node metastases.

Aged↗

PubMed2004

Applications of biochips: from diagnostics to personalized medicine.

This review examines the role of advances in biochip and microarray technologies in the development of personalized medicine. Biochips (eg, GeneChip, CYP450, electrochemical biochips, protein biochips, microfluidic biochips and nanotechnology-based biochips) are assuming an important role in molecular diagnostics, and their application in point-of-care diagnosis is expected to facilitate the development of personalized medicine. Gene expression profiling by microarrays should advance the progress of personalized cancer treatment based on the molecular classification of subtypes. Refinements in biochip miniaturization with the advent of nanotechnology will further contribute to molecular diagnostics and the development of personalized medicine.

Gene Expression Profiling↗

PubMed2006

Pathology and molecular biology of gastric cancer.

Several attempts to classify gastric cancer (GCA) have been made over the past decades. Most successful, and widely used, is the classification by Laurén, which distinguishes, by microscopical morphology alone, two main cancer pathogeneses, diffuse (DGCA) and intestinal (IGCA) subtypes, which appear clearly as dissimilar clinical and epidemiological entities. Here we review the main differences in epidemiology, histopathology, and molecular pathology of the two main subtypes of gastric carcinomas based on Laurén classification. In clinical practice, however, clinical staging, particularly in predicting the survival, still remains superior to all classifications of gastric cancer independent of cancer type. The existence of local precursor lesions or conditions of IGCA tumours, i.e. Helicobacter pylori gastritis, atrophic gastritis (AG), intestinal metaplasia (IM), adenoma, dysplasia, and intramucosal neoplasia, is firmly established. The links of DGCA with intestinal-type epithelium, AG or IM are poor, or do not exist. So far, H. pylori gastritis is the only universal precursor condition for DGCA. It implies that AG and achlorhydria are of minor significance and infrequent in the development of DGCA but are important steps in that of IGCA. Despite an increasing body of data, the overall view on molecular pathology of GCA remains fragmentary. No consistent differences in the molecular pathology of GCA subtypes to meet the Laurén classification have been established. With the exception of TP53, no gene mutation occurring regularly in both histological types of GCA has been reported. Chromosomal aberrations and loss of heterozygosity seem to be non-specific and do not follow any consistent route in the progression of GCA. Microsatellite instability is more commonly found in IGCA than in DGCA. The present epigenetic data suggest that most of the decrease (or loss) of gene expression may be explained by promoter hypermethylation which is more often found in IGCA. In DGCA specific genes such as CDH1 are more often hypermethylated. Compared with GCA, in premalignant condition lesions gene mutations and chromosomal aberrations are infrequent. Epigenetic dysregulation might also represent a major mechanism for altered gene expression in premalignant stages in gastric carcinogenesis.

Biomarkers, Tumor↗

PubMed2025

MO-GCAN: multi-omics integration based on graph convolutional and attention networks.

MOTIVATION: Cancer subtypes play a critical role in disease progression, prognosis, and treatment, making their detection essential for tailoring precision medicine. Studies have shown that multi-omics integration outperforms single-omics approaches in cancer subtyping tasks. However, due to the high-dimensionality of multi-omics data, many existing studies either fail to capture the correlation between true labels and learned features, or lack sufficient capacity to model complex biological representations. These limitations hinder the full potential of leveraging the rich and complementary information embedded in multi-omics datasets. RESULT: We propose a framework that leverages supervised feature learning and classification based on a graph-based learning approach with attention mechanism for cancer subtyping. More specifically, we train graph convolutional network models on each omics dataset to extract latent representations, which are then concatenated to form a comprehensive multi-omics feature embedding. We further develop sample fusion network based on the omics-specific graphs, incorporating the derived features and feeding them into a graph attention model for subtype classification. This two-stage multi-omics framework is applied to eight cancer types, with performance evaluated in terms of test accuracy, training time, macro-averaged precision, recall, and F-score. Experimental results show that the proposed method outperforms state-of-the-art approaches across various cancer types. Additionally, we provide empirical evidence supporting the hypothesis that retaining a limited number of high-confidence edges and utilizing enriched embeddings from intermediate graph neural network layers can improve predictive performance. AVAILABILITY AND IMPLEMENTATION: Data and the code are available at https://github.com/YD-00/MO-GCAN-Updated.git.

Neoplasms↗

PubMed2000

Prognostic utility of the recently recommended histologic classification and revised TNM staging system of renal cell carcinoma: a Swiss experience with 588 tumors.

BACKGROUND: A new, internationally accepted histologic classification of renal cell carcinoma (RCC) and a new edition of the TNM staging system were introduced in 1997. In the latter, there was a dramatic change in the pT classification of organ-confined renal cancer in which the break point between category pT1 and pT2 was increased from 2.5 cm to 7 cm. METHODS: To study the significance of the new pT classification and the new recommendations for histologic classification, 588 nephrectomy specimens were reevaluated to define morphologic prognostic parameters in RCC. pT classification (TNM 1997), histologic subtype, histologic tumor grade, presence of necrosis, and sarcomatoid differentiation were assessed. RESULTS: The histopathologic review according to the new classification revealed 487 conventional (clear cell) (83%), 64 papillary (11%), 31 chromophobe (5%), and 6 collecting duct (1%) RCCs. Clinical follow-up was available for 470 RCCs. The new pT classification (1997) was strongly correlated with patient survival (P < 0.0001). Histologic grade, presence of necrosis, and sarcomatoid differentiation provided independent prognostic information on the clear cell subtype of renal cancer. Sarcomatoid differentiation, but not tumor necrosis, portended a dismal prognosis for patients with papillary RCC. Chromophobe RCC was associated with a significantly better prognosis than clear cell RCC (P = 0.05). Papillary RCC with scanty cytoplasm and small cells (type 1) behaved less aggressively than papillary tumors with eosinophilic cytoplasm and large cells (type 2; P < 0.001). CONCLUSIONS: Accurate histologic classification according to the new recommendations has implications because the prognostic importance of other histologic features that are of independent significance varies with tumor subtype. The data suggest that the new pT classification allows good separation of prognostic groups of patients with renal cancer.

Carcinoma, Renal Cell↗

PubMed2000

Numerical aberrations of chromosomes 1 and 17 correlate with tumor site in human gastric carcinoma of the diffuse and intestinal types. Fluorescence in situ hybridization analysis on gastric biopsies.

Recent studies predict that tumor aneuploidy plays a direct role in tumor instability. The relationship between interphase cytogenetics, histology, grade, and tumor site was analyzed in 20 primary gastric carcinomas. Using fluorescence in-situ hybridization, the numerical changes of centromeric sequences of chromosomes 1, 3, 10, and 17 were directly analyzed in gastric biopsies. Polysomic copy numbers of chromosomes 1 and 17 were discovered in 63% (10 of 16) and 59% (10 of 17), respectively, of informative cancer cases. Chromosome 3 and 10 signal number changes were found in only 6% (1 of 16) and 13% (1 of 8), respectively, of informative cancer cases. There was a positive correlation between the appearance of polysomic nuclear target sites of chromosomes 1 and 17 (correlation coefficient r = 0.72; p < 0.005). Copy number changes were not significantly related to histologic subtypes of either the Laurén or WHO classifications. However, incidence of cancers having dual polysomic signal number abnormalities for both chromosomes 1 and 17 was significantly correlated to tumor location at the cardia. The data suggests that (i) human gastric cancer appears in two genomic groups that can be reliably diagnosed by fluorescence in-situ hybridization on routine biopsy sections, (ii) numerical aberrations of chromosomes 1, 3, 10, and 17 are largely independent of histologic subtypes, and (iii) polysomic copy number abnormalities of chromosomes 1 and 17 correlate to intragastric tumor site and are highest in cardia cancers, suggesting high tumor instability at this particular location.

Aged↗

PubMed2006

Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.

BACKGROUND: The histopathologic heterogeneity of lung cancer remains a significant confounding factor in its diagnosis and prognosis-spurring numerous recent efforts to find a molecular classification of the disease that has clinical relevance. METHODS AND FINDINGS: Molecular profiles of tumors from 186 patients representing four different lung cancer subtypes (and 17 normal lung tissue samples) were compared with a mouse lung development model using principal component analysis in both temporal and genomic domains. An algorithm for the classification of lung cancers using a multi-scale developmental framework was developed. Kaplan-Meier survival analysis was conducted for lung adenocarcinoma patient subgroups identified via their developmental association. We found multi-scale genomic similarities between four human lung cancer subtypes and the developing mouse lung that are prognostically meaningful. Significant association was observed between the localization of human lung cancer cases along the principal mouse lung development trajectory and the corresponding patient survival rate at three distinct levels of classical histopathologic resolution: among different lung cancer subtypes, among patients within the adenocarcinoma subtype, and within the stage I adenocarcinoma subclass. The earlier the genomic association between a human tumor profile and the mouse lung development sequence, the poorer the patient's prognosis. Furthermore, decomposing this principal lung development trajectory identified a gene set that was significantly enriched for pyrimidine metabolism and cell-adhesion functions specific to lung development and oncogenesis. CONCLUSIONS: From a multi-scale disease modeling perspective, the molecular dynamics of murine lung development provide an effective framework that is not only data driven but also informed by the biology of development for elucidating the mechanisms of human lung cancer biology and its clinical outcome.

Adenocarcinoma↗

PubMed2021

Automated Extraction of Tumor Staging and Diagnosis Information From Surgical Pathology Reports.

PURPOSE: Typically stored as unstructured notes, surgical pathology reports contain data elements valuable to cancer research that require labor-intensive manual extraction. Although studies have described natural language processing (NLP) of surgical pathology reports to automate information extraction, efforts have focused on specific cancer subtypes rather than across multiple oncologic domains. To address this gap, we developed and evaluated an NLP method to extract tumor staging and diagnosis information across multiple cancer subtypes. METHODS: The NLP pipeline was implemented on an open-source framework called Leo. We used a total of 555,681 surgical pathology reports of 329,076 patients to develop the pipeline and evaluated our approach on subsets of reports from patients with breast, prostate, colorectal, and randomly selected cancer subtypes. RESULTS: Averaged across all four cancer subtypes, the NLP pipeline achieved an accuracy of 1.00 for International Classification of Diseases, Tenth Revision codes, 0.89 for T staging, 0.90 for N staging, and 0.97 for M staging. It achieved an F1 score of 1.00 for International Classification of Diseases, Tenth Revision codes, 0.88 for T staging, 0.90 for N staging, and 0.24 for M staging. CONCLUSION: The NLP pipeline was developed to extract tumor staging and diagnosis information across multiple cancer subtypes to support the research enterprise in our institution. Although it was not possible to demonstrate generalizability of our NLP pipeline to other institutions, other institutions may find value in adopting a similar NLP approach-and reusing code available at GitHub-to support the oncology research enterprise with elements extracted from surgical pathology reports.

Humans↗