scholarly journals CAFE MOCHA:An Integrated Platform for Discovering Clinically Relevant Molecular Changes in Cancer; an Example of Distant Metastasis and Recurrence-linked Classifiers in Head and Neck Squamous Cell Carcinoma

2017 ◽  
Author(s):  
Neeraja M Krishnan ◽  
I Mohanraj ◽  
Janani Hariharan ◽  
Binay Panda
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Squamous Cell ◽  
Distant Metastasis ◽  
Neck Squamous Cell Carcinoma ◽  
Molecular Signature ◽  
Cancer Type ◽  
Molecular Changes ◽  
Statistical Framework

AbstractBackgroundCAFE MOCHA(Clinical Association of Functionally Established MOlecular CHAnges) is an integrated GUI-driven computational and statistical framework to discover molecular signatures linked to a specific clinical attribute in a cancer type. We testedCAFE MOCHAin head and neck squamous cell carcinoma (HNSCC) for discovering a signature linked to distant metastasis and recurrence (MR) in 517 tumors from TCGA and validated the signature in 18 tumors from an independent cohort.MethodsThe platform integrates mutations and indels, gene expression, DNA methylation and copy number variations to discover a classifier first, predict an incoming tumour for the same by pulling defined class variables into a single framework that incorporates a coordinate geometry-based algorithm, called Complete Specificity Margin Based Clustering (CSMBC) with 100% specificity.CAFE MOCHAclassifies an incoming tumour sample using either a matched normal or a built-in database of normal tissues. The application is packed and deployed using theinstall4jmulti-platform installer.ResultsWe testedCAFE MOCHAto discover a signature for distant metastasis and recurrence in HNSCC. The signature MR44 in HNSCC yielded 80% sensitivity and 100% specificity in the discovery stage and 100% sensitivity and 100% specificity in the validation stage.ConclusionsCAFE MOCHAis a cancer type- and clinical attribute-agnostic computational and statistical framework to discover integrated molecular signature for a specific clinical attribute.CAFE MOCHAis available in GitHub (https://github.com/binaypanda/CAFEMOCHA).

scholarly journals CAFE MOCHA: An Integrated Platform for Discovering Clinically Relevant Molecular Changes in Cancer—An Example of Distant Metastasis– and Recurrence-Linked Classifiers in Head and Neck Squamous Cell Carcinoma

2018 ◽  
pp. 1-11
Author(s):  
Neeraja M. Krishnan ◽  
Mohanraj I ◽  
Janani Hariharan ◽  
Binay Panda
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Squamous Cell ◽  
Cancer Genome ◽  
Neck Squamous Cell Carcinoma ◽  
Cancer Type ◽  
Molecular Signatures ◽  
Molecular Changes ◽  
Statistical Framework

Purpose With large amounts of multidimensional molecular data on cancers generated and deposited into public repositories such as The Cancer Genome Atlas and International Cancer Genome Consortium, a cancer type agnostic and integrative platform will help to identify signatures with clinical relevance. We devised such a platform and showcase it by identifying a molecular signature for patients with metastatic and recurrent (MR) head and neck squamous cell carcinoma (HNSCC). Methods We devised a statistical framework accompanied by a graphical user interface–driven application, Clinical Association of Functionally Established MOlecular CHAnges ( CAFE MOCHA; https://github.com/binaypanda/CAFEMOCHA), to discover molecular signatures linked to a specific clinical attribute in a cancer type. The platform integrates mutations and indels, gene expression, DNA methylation, and copy number variations to discover a classifier first and then to predict an incoming tumor for the same by pulling defined class variables into a single framework that incorporates a coordinate geometry–based algorithm called complete specificity margin-based clustering, which ensures maximum specificity. CAFE MOCHA classifies an incoming tumor sample using either its matched normal or a built-in database of normal tissues. The application is packed and deployed using the install4j multiplatform installer. We tested CAFE MOCHA in HNSCC tumors (n = 513) followed by validation in tumors from an independent cohort (n = 18) for discovering a signature linked to distant MR. Results CAFE MOCHA identified an integrated signature, MR44, associated with distant MR HNSCC, with 80% sensitivity and 100% specificity in the discovery stage and 100% sensitivity and 100% specificity in the validation stage. Conclusion CAFE MOCHA is a cancer type and clinical attribute agnostic statistical framework to discover integrated molecular signatures.

scholarly journals Utility of a Hybrid IVIM-DKI Model to Predict the Development of Distant Metastasis in Head and Neck Squamous Cell Carcinoma Patients

2018 ◽  
Vol 17 (1) ◽  
pp. 21-27 ◽  
Author(s):  
Noriyuki Fujima ◽  
Tomohiro Sakashita ◽  
Akihiro Homma ◽  
Daisuke Yoshida ◽  
Kohsuke Kudo ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Squamous Cell ◽  
Distant Metastasis ◽  
Neck Squamous Cell Carcinoma

P-102 Dissemination patterns and chronology of distant metastasis affect survival of patients with head and neck squamous cell carcinoma

Oral Oncology ◽  
2021 ◽  
Vol 118 ◽  
pp. 14
Author(s):  
Diako Berzenji ◽  
Aniel Sewnaik ◽  
Stijn Keereweer ◽  
Dominiek A. Monserez ◽  
Gerda M. Verduijn ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Squamous Cell ◽  
Distant Metastasis ◽  
Neck Squamous Cell Carcinoma

scholarly journals Assessment Criteria and Clinical Implications of Extranodal Extension in Head and Neck Cancer

2021 ◽  
pp. 265-278
Author(s):  
Shao Hui Huang ◽  
Rebecca Chernock ◽  
Brian O’Sullivan ◽  
Carole Fakhry
Keyword(s):  
Squamous Cell Carcinoma ◽  
High Risk ◽  
Risk Stratification ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Squamous Cell ◽  
Distant Metastasis ◽  
Neck Squamous Cell Carcinoma ◽  
Extranodal Extension ◽  
Pathology Specimen

Tumor breaching the capsule of a lymph node is termed extranodal extension (ENE). It reflects aggressiveness of a tumor, creates anatomic challenges for disease clearance, and increases the risk of distant metastasis. Extranodal extension can be assessed on a pathology specimen, by radiology studies, and by clinical examination. Presence of ENE in a pathology specimen has long been considered a high-risk feature of disease progression and would ordinarily benefit from the addition of chemotherapy to adjuvant radiotherapy. Although the eighth edition of the Union for International Cancer Control/American Joint Committee on Cancer stage classification dichotomizes pathologic ENE according to its presence or absence, emerging evidence suggests that the extent of a pathologic ENE may provide additional value for risk stratification to guide adjuvant therapy. Recent data suggest that the prognostic importance of pathologic ENE is also applicable for HPV-associated head and neck squamous cell carcinoma. In addition, compelling data demonstrate that indisputable radiologic ENE is a powerful risk stratification tool to identify patients at high risk for treatment failure, especially distant metastasis, applicable for both HPV-positive and HPV-negative head and neck squamous cell carcinoma. However, the definition and taxonomy of radiologic ENE requires standardization. The goal of this review is to clarify the contemporary understanding of the prognostic implications of ENE in head and neck squamous cell carcinoma, present the nuances of what is presently known and unknown, and elucidate how to classify ENE pathologically and radiologically with an understanding of the strengths and weaknesses of each approach. Finally, with the development of several risk stratification methods, the relative role of ENE and other prognostic schema will be explored.

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