Development and Evaluation of Perl-Based Algorithms to Classify Neoplasms From Pathology Records in Synoptic Report Format

2021 ◽  
pp. 295-303
Author(s):  
Kristen R. Rossi ◽  
Diana Echeverria ◽  
Anna Carroll ◽  
Tina Luse ◽  
Christopher Rennix
Keyword(s):  
Hodgkin Lymphoma ◽  
Malignant Neoplasm ◽  
Malignant Neoplasms ◽  
Predictive Values ◽  
Software Application ◽  
Non Hodgkin Lymphoma ◽  
Institutional Variation ◽  
Sensitivity Specificity ◽  
Synoptic Reporting

PURPOSE Synoptic reporting provides a mechanism for uniform and structured pathology diagnostics. This paper demonstrates the functionality of Perl alternation and grouping expressions to classify electronic pathology reports generated from military treatment facilities. Eight Perl-based algorithms are validated to classify malignant melanoma, Hodgkin lymphoma, non-Hodgkin lymphoma, leukemia, and malignant neoplasms of the breast, ovary, testis, and thyroid. METHODS Case finding cohorts were developed using diagnostic codes for neoplasm groups and matched by unique identifiers to obtain pathology records. Preprocessing techniques and Perl-based algorithms were applied to classify records as malignant, in situ, suspect, or nonapplicable, followed by a hand-review process to determine the accuracy of the algorithm classifications. Interrater reliability, sensitivity, specificity, positive predictive values, and negative predictive values were computed following abstractor adjudication. RESULTS The specificity of the Perl-based algorithms was consistently high, over 98%. Very few benign results were classified as malignant or in situ by the Perl-based algorithms; the leukemia algorithm classification was the only group to demonstrate a positive predictive value below 95%, at 91.9%. Three algorithm classification groups demonstrated a sensitivity of < 80%, including malignant neoplasm of the ovary (33.3%), leukemia (52.8%), and non-Hodgkin lymphoma (62.9%). The pathology records for these results included substantial linguistic variation. CONCLUSION This paper contextualizes the utility and value of an algorithm logic built around synoptic reporting to identify neoplasms from electronic pathology results. The major strength includes the application of Perl-based coding in SAS, an accessible software application, to develop highly specific algorithms across institutional variation in diagnostic documentation.

scholarly journals An assessment of chromosomal alterations detected by fluorescence in situ hybridisation in pancreatobiliary tract malignancy

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Xiaohong Pu ◽  
Hongwei Zheng ◽  
Xin Yang ◽  
Qing Ye ◽  
Zhiwen Fan ◽  
...  
Keyword(s):  
Predictive Value ◽  
In Situ Hybridisation ◽  
False Negative ◽  
Chinese Patients ◽  
Fluorescence In Situ Hybridisation ◽  
Predictive Values ◽  
Formalin Fixed Paraffin Embedded ◽  
9P21 Locus ◽  
Sensitivity Specificity

Abstract Background Using fluorescence in situ hybridisation (FISH) to detect any gain of chromosomes 3, 7, or 17 and loss of the 9p21 locus has been proven to be sensitive in the diagnosis of pancreatobiliary tumors. However, both genetic and environmental factors contribute to the pathogenesis of pancreatobiliary tumors. Therefore, it is unknown whether this method is suitable for Chinese patients with pancreatobiliary tumors. This study aims to compare the sensitivity, specificity, predictive values and accuracy of cytology, ERCP/MRCP and FISH based on Chinese patients with pancreatobiliary tumors,and to analyze differences between brushing-based and formalin-fixed paraffin-embedded (FFPE)-based FISH. Methods A total of 66 brush cytology specimens obtained during ERCP were detected by FISH and cytology test respectively to compare the sensitivity, specificity, predictive values and accuracy. Besides, FFPE-based FISH was performed on 46 corresponding paraffin sections of pancreatobiliary tumors obtained by surgical resection. Results Our findings demonstrate that FISH greatly improves diagnostic sensitivity and negative predictive value compared to ERCP/MRCP and cytology without much reduction in specificity and positive predictive value. However, our results also indicate that FFPE-based FISH could not effectively identify the false-negative of brushing-based FISH. Conclusions We believe that FISH can effectively distinguish true positive and false positive results of cytological or radiological suspicions of malignancy. However, FFPE-based FISH still does not precisely recognize the false-negative of brushing-based FISH. Both cytology-based and PPFE-based FISH had limitation in some specimens.

Response Assessment Using Early and End-of-Treatment 18F-FLT PET Can Predict Outcome in Patients with Non-Hodgkin Lymphoma,

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 3679-3679
Author(s):  
Hyewon Lee ◽  
Seok-Ki Kim ◽  
Tae Sung Kim ◽  
Se Hun Kang ◽  
Weon Seo Park ◽  
...  
Keyword(s):  
Treatment Outcome ◽  
Hodgkin Lymphoma ◽  
Predictive Factor ◽  
Response Assessment ◽  
Early Response ◽  
Independent Predictive Factor ◽  
Predictive Values ◽  
Non Hodgkin Lymphoma ◽  
Flt Pet ◽  
End Of Treatment

Abstract Abstract 3679 Background Fluorine-18-fluorodeoxyglucose (FDG) positron emission tomography (PET) scan has been known as a useful modality for response assessment in malignant lymphoma. However, FDG is not tumor-specific and can be false positive in inflammatory lesions. To overcome these limitations, a new PET tracer, thymidine analog 3'-deoxy-3'-18F-fluorothymidine (FLT), was introduced recently. Preliminary data showed close correlation between FLT uptake and tumor cell proliferation in lymphoma, suggesting the possibility of noninvasive tumor grading and early response assessment. Therefore, we performed a prospective trial to evaluate the feasibility of FLT-PET in risk stratification and prediction for treatment outcome, especially in early interim analysis, in patients with non-Hodgkin lymphoma (NHL). Methods Seventy-five patients newly diagnosed with NHL were prospectively enrolled at National Cancer Center, Korea, from Oct 2005 to Oct 2008. All received standard chemotherapy for their pathologic classifications. Patients were evaluated with FLT-PET at baseline (FLT0), after 1 cycle of chemotherapy (FLT1, early), and after completion of the 1st line chemotherapy (FLTE, end-of-treatment). FLT-PET results were assessed according to the International Workshop Criteria (IWC). Maximum standardized uptake values (SUVmax) of each FLT-PET were calculated to evaluate its correlation with the clinical characteristics and treatment outcome. Treatment outcome was estimated using 3-year progression-free survival (3yr-PFS) and overall survival (3yr-OS). Results Of the 75 enrolled patients, 63 (84%) had diffuse large B-cell lymphoma. Median age at diagnosis was 57 years (range, 29–87). Twenty-eight (37.3%) presented with stage III or IV diseases and 20 (26.7%) showed more than 3 IPI scores. Median follow up duration was 4.5 years (range, 3.5–5.8). Five (6.7%) patients underwent hematopoietic stem cell transplantation at last. Three-year PFS and OS rates for all enrolled patients were 68% and 78.7%. Seventy-three (97.3%) had their FLT-PET at baseline, 69 (92%) after 1 cycle of chemotherapy, and 66 (88%) at the end of the 1st line treatment. By IWC, 50 (66.7%) patients achieved complete remission (CR) on FLT1 and 56 (74.7%) had CR on FLTE. Positive predictive values (PPV) of residual uptake on FLT1 and FLTE for relapse or disease progression were 83.3% (95%CI 57.7–95.6) and 80% (95%CI 44.2–96.5), respectively. Negative predictive values (NPV) of them were 88% (95%CI 75.0–95.0) and 82.1% (95%CI 69.2–90.7). Sensitivity and specificity were 71.4% (47.7–87.8) and 93.6% (81.4–98.3) for FLT1 and 44.4% (22.4–67.8) and 95.8% (84.6–99.3) for FLTE, respectively. Complete disappearance of uptake on FLT1 was significantly associated with better PFS compared to residual uptake on FLT1 (3yr-PFS rates, 87.5% and 12.2%, p<0.001). Three-year OS rates according to CR achievement on FLT1 were 96.0% and 27.8%, significantly lower in patients with residual disease after 1 cycle of chemotherapy (p<0.001). SUVmax of FLT0 correlated with LDH level significantly (p=0.044), but not with age (p=0.214), Ki-67 index (p=0.073), IPI score (p=0.270), and Ann Arbor stage (p=0.089). SUVmax of FLT0 were not associated with survival outcomes, however, residual SUVmax of FLT1 reflecting early response to treatment was significantly associated with poor survival outcome (PFS, HR 1.29, 95%CI 1.14–1.47; OS, HR 1.27, 95%CI 1.08–1.49). In multivariate analysis, SUVmax of FLT1 remained as an independent predictive factor for PFS (HR 1.63, 95%CI 1.25–2.13) and for OS (HR 1.89, 95%CI 1.38–2.58). Residual SUVmax of FLTE also revealed to be significantly associated with PFS (HR 1.43, 95%CI 1.05–1.94) and OS (HR 1.59, 95%CI 1.12–2.26) in the same multivariate model. Conclusion Response assessment in cooperation with FLT-PET provided accurate prediction for clinical outcome including PFS and OS in patients with NHL. Especially, early FLT-PET result after 1 cycle of chemotherapy was an independent predictive factor for survival as well as relapse or disease progression, with comparable performance with end-of-treatment FLT-PET. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Detección del Virus de Epstein-Barr en linfoma mediante qPCR //Detection of Epstein-Barr Virus (EBV) in lymphoma through qPCR

Ciencia Unemi ◽  
2018 ◽  
Vol 11 (26) ◽  
pp. 126 ◽  
Author(s):  
Sunny Sánchez-Giler ◽  
Alan Herrera-Vásquez ◽  
Claudia Castillo-Zambrano ◽  
Luis Solórzano-Alava ◽  
Dolores Zambrano-Castro ◽  
...  
Keyword(s):  
Hodgkin Lymphoma ◽  
Malignant Tumors ◽  
Tissue Samples ◽  
Virus Identification ◽  
Barr Virus ◽  
Non Hodgkin Lymphoma ◽  
Latently Infected ◽  
Infected Cells ◽  
Epstein Barr

Virus Epstein Barr (VEB) ha sido relacionado con una serie de tumores malignos de origen epitelial y linfoide. Existe una clara correlación entre este virus y enfermedades linfoproliferativas como Linfoma de Burkitt (LB), Linfoma Hodgkin (LH), Linfoma no Hodgkin (LNH) y carcinoma gástrico. Se han desarrollado diversas técnicas para la detección de VEB en células tumorales: hibridación in situ (RISH) que detecta RNAs (ácido ribonucleico) pequeños codificados para VEB (EBERs) en las células con infección latente, considerado el estándar de oro para la identificación del virus; la reacción en cadena de la polimerasa (PCR) que permite la detección de la cepa viral y representa un ensayo importarte en el diagnóstico del virus. Se realizó un estudio retrospectivo a partir de muestras de tejidos en parafina de pacientes con linfoma y se buscó al virus mediante PCR y RISH. La prevalencia del virus fue de 58,82%, el género más afectado fue el masculino y el grupo más afectado fue el de 31/40 años. La presencia del virus fue similar en ambos tipos de linfoma: Hodking y No Hodking. La técnica de RISH se mostró más eficiente para detectar la presencia del virus. AbstractEpstein Barr Virus (EBV) is linked to a number of malignant tumors of epithelial and lymphoid origin. There is a strong correlation between this virus and lymphoproliferative diseases such as Burkitt's lymphoma (BL), Hodgkin lymphoma (HL), non-Hodgkin lymphoma (NHL) and gastric carcinoma. There are various techniques developed to detect EBV in tumor cells: in situ hybridization (ISH) detects small coded RNAs (ribonucleic acid) to VEB (EBERs) in latently infected cells. This is considered the gold standard for virus identification. The polymerase chain reaction (PCR) allows the detection of the viral strain and represents an important fact in the virus diagnose. We conducted a retrospective study in paraffin from tissue samples of patients with lymphoma and we sought the virus through PCR and RISH. The virus prevalence was 58.82%, the most affected gender was male and the most affected group was 31/40 years. The virus was similar in both types of lymphoma: Hodgkin and non-Hodgkin. RISH technique seemed to be more efficient to detect the virus.

scholarly journals Application of the Paris Reporting System for Urine Cytology: The Three-Year Experience of a Single Tertiary Care Institute in Thailand

2022 ◽  
pp. 1-8
Author(s):  
Bantita Phruttinarakorn ◽  
Sirithep Plumworasawat ◽  
Jitchai Kayankarnnavee ◽  
Jirasit Lualon ◽  
Atcharaporn Pongtippan
Keyword(s):  
Urothelial Carcinoma ◽  
Predictive Value ◽  
Diagnostic Category ◽  
Malignant Neoplasm ◽  
Urine Cytology ◽  
Malignant Neoplasms ◽  
Low Grade ◽  
High Grade ◽  
Sensitivity Specificity

<b><i>Introduction:</i></b> Urothelial carcinoma is one of the most common human cancers, both in Thailand and worldwide. Urine cytology is a screening tool used to detect urothelial carcinoma. The Paris System for Reporting Urinary Cytology (TPSRUC) was first published in 2016 to standardize the procedures, reporting, and management of urothelial carcinoma. Diagnostic categories include negative for high-grade urothelial carcinoma (NHGUC), atypical urothelial cells (AUCs), suspicious for HGUC (SHGUC), HGUC, low-grade urothelial neoplasm, and other malignancies. <b><i>Material and Methods:</i></b> In a retrospective review, urine cytology specimens from 2016 to 2019 were reevaluated using the TPSRUC. The risk of high-grade malignant neoplasm (ROHM) for each diagnostic category was calculated. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of prediction of high-grade malignant neoplasms were evaluated for cases with histological follow-up specimens. <b><i>Results:</i></b> In total, 2,178 urine cytology specimens were evaluated, of which 456 cases had follow-up histological specimens. The ROHM in each diagnostic category was as follows: NHGUC, 17.4%; AUC, 49.9%; SHGUC, 81.2%; HGUC, 91.3%; and other malignant neoplasms, 87.5%. The sensitivity, specificity, PPV, NPV, and accuracy for high-grade malignant neoplasm prediction were 63%, 92.8%, 89%, 73.1%, and 78.5% when AUC was included as malignant in the comparison and 82.6%, 74.7%, 75.1%, 82.3%, and 78.5% when AUC was not considered malignant. <b><i>Conclusions:</i></b> TPSRUC provides reliable results that are reproducible by different interpreters and is a helpful tool for the detection of HGUC.

The Accuracy of Intraoperative Frozen Sections in Epithelial Ovarian Tumor

2021 ◽  
Vol 104 (2) ◽  
pp. 214-218
Keyword(s):  
Ovarian Tumor ◽  
Frozen Section ◽  
High Accuracy ◽  
Malignant Neoplasms ◽  
Frozen Sections ◽  
Predictive Values ◽  
Intraoperative Frozen Section ◽  
Epithelial Ovarian Tumor ◽  
Sensitivity Specificity ◽  
Epithelial Neoplasm

Objective: To evaluate the accuracy of the intraoperative frozen section in the diagnosis of epithelial ovarian tumor. Materials and Methods: An observational study of epithelial ovarian tumor reports from patients that underwent surgery with intraoperative consultation at Ramathibodi Hospital, Thailand between 2013 and 2017 was done. The frozen section diagnoses were compared with the final surgical diagnoses and the overall accuracy, sensitivity, specificity, positive predictive values (PPV), negative predictive values (NPV) were studied. Results: One hundred sixteen ovarian specimen reports were reviewed, comprised of 74 (63.8%) benign, 21 (18.1%) borderline, and 21 (18.1%) malignant neoplasms. Nine cases (7.7%) were discordant diagnoses. The overall accuracy was 92.2%. The sensitivity and specificity for benign, borderline, and malignant neoplasms were 100%, 80.9%, and 76.2%, and 88.1%, 95.8%, and 100%, respectively. The PPV and NPV for benign, borderline, and malignant neoplasms were 93.7%, 80.9%, and 100%, and 100%, 95.8%, and 95.0%, respectively. Conclusion: The intraoperative frozen section has high accuracy in the diagnosis of ovarian epithelial neoplasm. The results can be used in guidance on the extent and type of surgical management. Keywords: Frozen section, Accuracy, Epithelial ovarian tumor

Response of a non-Hodgkin lymphoma to 60Co therapy monitored by 31P MRS in situ

1987 ◽  
Vol 13 (10) ◽  
pp. 1545-1551 ◽  
Author(s):  
Thian C. Ng ◽  
Srinivasan Vijayakumar ◽  
Anthony W. Majors ◽  
Frank J. Thomas ◽  
Thomas F. Meaney ◽  
...  
Keyword(s):  
Hodgkin Lymphoma ◽  
31P Mrs ◽  
Non Hodgkin Lymphoma

scholarly journals Non-Hodgkin lymphoma of bone of the femur and humerus: a case report and review of the literature

2021 ◽  
Vol 2021 (4) ◽  
Author(s):  
Alex Mremi ◽  
Jeremia J Pyuza ◽  
Bilal Ahmad ◽  
Alice A Andongolile ◽  
Adnan Sadiq ◽  
...  
Keyword(s):  
Hodgkin Lymphoma ◽  
Lymphoid Cells ◽  
Diagnosis Delay ◽  
Delay In Diagnosis ◽  
Non Hodgkin Lymphoma ◽  
Radiological Images ◽  
Soft Tissue Masses ◽  
The Right

ABSTRACT Lymphoma of bone is a rare neoplasm composed of malignant lymphoid cells, producing a tumefactive lesion within bone. We report a 13-year-old male who presented with progressively increasing swellings at the right shoulder and right mid-thigh for one month. Radiological images revealed lytic destructive lesions associated with soft tissue masses in both sites and a pathological fracture on the right humerus. The patient had no significant medical history. Histological, immunohistochemical and fluorescent in-situ hybridization assessment of biopsies from the lesions confirmed the diagnosis of primary non-Hodgkin lymphoma of bone. Unfortunately, due to coronavirus disease 2019 outbreak, the patient was unable to follow-up treatment and died shortly after establishment of the diagnosis. Delay in diagnosis and treatment is of serious concern when it comes to improve the prognosis of patients with this disease.

scholarly journals Melanocytic lesions ≤ 6mm: Prospective series of 481 melanocytic trunk and limb lesions in Brazil

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252162
Author(s):  
Gabriella Campos-do-Carmo ◽  
Aretha Brito Nobre ◽  
Tullia Cuzzi ◽  
Giuseppe Argenziano ◽  
Carlos Gil Ferreira ◽  
...  
Keyword(s):  
Excisional Biopsy ◽  
Benign Lesions ◽  
Cutaneous Lesions ◽  
Predictive Values ◽  
Mortality And Morbidity ◽  
Melanocytic Lesions ◽  
Sensitivity Specificity ◽  
Breslow Index

Early diagnosis when melanoma is still small and thin is essential for improving mortality and morbidity. However, the diagnosis of small size melanoma might be particularly difficult, not only clinically but also dermoscopically. This study aimed to define clinical and dermatoscopic parameters in the diagnosis of suspicious pigmented cutaneous lesions with a diameter of ≤ 6mm and determine the sensitivity, specificity, positive and negative predictive values as well as the accuracy of each clinical and dermatoscopic criterion. This is a transversal, descriptive and analytical study of dermatoscopic analysis with the gold standard being the pathologic examination obtained from the excisional biopsy of suspicious melanocytic lesions with a diameter of ≤ 6mm. Trunk and limb lesion data from a public health service and a private clinic were prospectively collected from 2011 to 2017 by a unique observer. In total, 481 melanocytic lesions were included, with 73.8% being ≤ 4mm in diameter. Overall, 123 were diagnosed as melanoma, 56.0% in situ and 22.0% as thin melanomas (Breslow index 0.1 to 1.0mm). Melanoma presented symmetry in 53.7% of cases, regular borders in 54.5% and a single color in 60.2%. Regarding evolution, 13.8% of melanomas versus 10.9% of benign lesions (p = 0.116) were new by comparing photos from baseline with photos from the follow-up. The majority of melanomas (65%) were found on the limbs compared to 37.2% of the benign lesions at this location (p<0.001). A multiple logistic regression model adjusted for age, gender and location was created. The independent variables associated with the diagnosis of melanoma ≤ 6mm, adjusted for age, gender and location, were: streaks (adjusted Odds Ratio [aOR] 2.5; 95% CI 1.3–4.7; p = 0.006), and the presence of a structureless area (aOR 2.2, 95% CI 1.2–4.0, p = 0.011). Conversely, a symmetric typical pigment network was a protection variable (aOR 0.4, 95% 0.7–0.9, p = 0.040). In conclusion, dermatoscopic criteria have been identified which help to diagnose cases of small size melanoma. These include streaks and structureless areas that can be taken, particularly in consideration for the diagnosis of this subset of small difficult melanomas.

Fluorescence in situ hybridization assessment of the telomeric regions of jumping translocations in a case of aggressive B-cell non-Hodgkin lymphoma

1997 ◽  
Vol 98 (1) ◽  
pp. 20-27 ◽  
Author(s):  
Brian A. Gray ◽  
Angela Bent-Williams ◽  
Julie Wadsworth ◽  
Russell L. Maiese ◽  
Andres Bhatia ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
B Cell ◽  
Fluorescence In Situ Hybridization ◽  
Hodgkin Lymphoma ◽  
Non Hodgkin Lymphoma

Interphase Detection of BCL6/IgH Fusion Gene in Non-Hodgkin Lymphoma by Fluorescence In Situ Hybridization

1997 ◽  
Vol 99 (2) ◽  
pp. 102-107 ◽  
Author(s):  
Yutaka Ueda ◽  
Kazuhiro Nishida ◽  
Tohru Miki ◽  
Shigeo Horiike ◽  
Hiroto Kaneko ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Hodgkin Lymphoma ◽  
Fusion Gene ◽  
Non Hodgkin Lymphoma
Sign in / Sign up

Export Citation Format

Share Document