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Shannon NB, Tan LLY, Tan QX, Tan JWS, Hendrikson J, Ng WH, Ng G, Liu Y, Ong XYS, Nadarajah R, Wong JSM, Tan GHC, Soo KC, Teo MCC, Chia CS, Ong CAJ. A machine learning approach to identify predictive molecular markers for cisplatin chemosensitivity following surgical resection in ovarian cancer. Sci Rep 2021; 11:16829. [PMID: 34413360 PMCID: PMC8377048 DOI: 10.1038/s41598-021-96072-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/31/2021] [Indexed: 12/27/2022] Open
Abstract
Ovarian cancer is associated with poor prognosis. Platinum resistance contributes significantly to the high rate of tumour recurrence. We aimed to identify a set of molecular markers for predicting platinum sensitivity. A signature predicting cisplatin sensitivity was generated using the Genomics of Drug Sensitivity in Cancer and The Cancer Genome Atlas databases. Four potential biomarkers (CYTH3, GALNT3, S100A14, and ERI1) were identified and optimized for immunohistochemistry (IHC). Validation was performed on a cohort of patients (n = 50) treated with surgical resection followed by adjuvant carboplatin. Predictive models were established to predict chemosensitivity. The four biomarkers were also assessed for their ability to prognosticate overall survival in three ovarian cancer microarray expression datasets from The Gene Expression Omnibus. The extreme gradient boosting (XGBoost) algorithm was selected for the final model to validate the accuracy in an independent validation dataset (n = 10). CYTH3 and S100A14, followed by nodal stage, were the features with the greatest importance. The four gene signature had comparable prognostication as clinical information for two-year survival. Assessment of tumour biology by means of gene expression can serve as an adjunct for prediction of chemosensitivity and prognostication. Potentially, the assessment of molecular markers alongside clinical information offers a chance to further optimise therapeutic decision making.
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Affiliation(s)
- Nicholas Brian Shannon
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Laura Ling Ying Tan
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Qiu Xuan Tan
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Joey Wee-Shan Tan
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Josephine Hendrikson
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Wai Har Ng
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Gillian Ng
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Ying Liu
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Xing-Yi Sarah Ong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Ravichandran Nadarajah
- Department of Obstetrics and Gynaecology, Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore
| | - Jolene Si Min Wong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore
| | - Grace Hwei Ching Tan
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore
| | - Khee Chee Soo
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Melissa Ching Ching Teo
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Claramae Shulyn Chia
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Chin-Ann Johnny Ong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore. .,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore. .,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore. .,SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore. .,Institute of Molecular and Cell Biology, A*STAR Research Entities, 61 Biopolis Drive, Singapore, 138673, Singapore.
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4
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Kilgore MR, McIlwain CA, Schmidt RA, Norquist BM, Swisher EM, Garcia RL, Rendi MH. Reflex test reminders in required cancer synoptic templates decrease order entry error: An analysis of mismatch repair immunohistochemical orders to screen for Lynch syndrome. J Pathol Inform 2016; 7:48. [PMID: 27994940 PMCID: PMC5139450 DOI: 10.4103/2153-3539.194840] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/28/2016] [Indexed: 12/03/2022] Open
Abstract
Background: Endometrial carcinoma (EC) is the most common extracolonic malignant neoplasm associated with Lynch syndrome (LS). LS is caused by autosomal dominant germline mutations in DNA mismatch repair (MMR) genes. Screening for LS in EC is often evaluated by loss of immunohistochemical (IHC) expression of DNA MMR enzymes MLH1, MSH2, MSH6, and PMS2 (MMR IHC). In July 2013, our clinicians asked that we screen all EC in patients ≤60 for loss of MMR IHC expression. Despite this policy, several cases were not screened or screening was delayed. We implemented an informatics-based approach to ensure that all women who met criteria would have timely screening. Subjects and Methods: Reports are created in PowerPath (Sunquest Information Systems, Tucson, AZ) with custom synoptic templates. We implemented an algorithm on March 6, 2014 requiring pathologists to address MMR IHC in patients ≤60 with EC before sign out (S/O). Pathologists must answer these questions: is patient ≤60 (yes/no), if yes, follow-up questions (IHC done previously, ordered with addendum to follow, results included in report, N/A, or not ordered), if not ordered, one must explain. We analyzed cases from July 18, 2013 to August 31, 2016 preimplementation (PreImp) and postimplementation (PostImp) that met criteria. Data analysis was performed using the standard data package included with GraphPad Prism® 7.00 (GraphPad Software, Inc., La Jolla, CA, USA). Results: There were 147 patients who met criteria (29 PreImp and 118 PostImp). IHC was ordered in a more complete and timely fashion PostImp than PreImp. PreImp, 4/29 (13.8%) cases did not get any IHC, but PostImp, only 4/118 (3.39%) were missed (P = 0.0448). Of cases with IHC ordered, 60.0% (15/25) were ordered before or at S/O PreImp versus 91.2% (104/114) PostImp (P = 0.0004). Relative to day of S/O, the mean days of order delay were longer and more variable PreImp versus PostImp (12.9 ± 40.7 vs. -0.660 ± 1.15; P = 0.0227), with the average being before S/O PostImp. Conclusion: This algorithm ensures MMR IHC ordering in women ≤60 with EC and can be applied to similar scenarios. Ancillary tests for management are increasing, especially genetic and molecular-based methods. The burden of managing orders and results remains with the pathologist and relying on human intervention alone is ineffective. Ordering IHC before or at S/O prevents oversight and the additional work of retrospective ordering and reporting.
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Affiliation(s)
- Mark R Kilgore
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Carrie A McIlwain
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Rodney A Schmidt
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Barbara M Norquist
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Washington, Seattle, WA, USA
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Washington, Seattle, WA, USA
| | | | - Mara H Rendi
- Department of Pathology, University of Washington, Seattle, WA, USA
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9
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Mohanty SK, Mistry AT, Amin W, Parwani AV, Pople AK, Schmandt L, Winters SB, Milliken E, Kim P, Whelan NB, Farhat G, Melamed J, Taioli E, Dhir R, Pass HI, Becich MJ. The development and deployment of Common Data Elements for tissue banks for translational research in cancer - an emerging standard based approach for the Mesothelioma Virtual Tissue Bank. BMC Cancer 2008; 8:91. [PMID: 18397527 PMCID: PMC2329649 DOI: 10.1186/1471-2407-8-91] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2007] [Accepted: 04/08/2008] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Recent advances in genomics, proteomics, and the increasing demands for biomarker validation studies have catalyzed changes in the landscape of cancer research, fueling the development of tissue banks for translational research. A result of this transformation is the need for sufficient quantities of clinically annotated and well-characterized biospecimens to support the growing needs of the cancer research community. Clinical annotation allows samples to be better matched to the research question at hand and ensures that experimental results are better understood and can be verified. To facilitate and standardize such annotation in bio-repositories, we have combined three accepted and complementary sets of data standards: the College of American Pathologists (CAP) Cancer Checklists, the protocols recommended by the Association of Directors of Anatomic and Surgical Pathology (ADASP) for pathology data, and the North American Association of Central Cancer Registry (NAACCR) elements for epidemiology, therapy and follow-up data. Combining these approaches creates a set of International Standards Organization (ISO) - compliant Common Data Elements (CDEs) for the mesothelioma tissue banking initiative supported by the National Institute for Occupational Safety and Health (NIOSH) of the Center for Disease Control and Prevention (CDC). METHODS The purpose of the project is to develop a core set of data elements for annotating mesothelioma specimens, following standards established by the CAP checklist, ADASP cancer protocols, and the NAACCR elements. We have associated these elements with modeling architecture to enhance both syntactic and semantic interoperability. The system has a Java-based multi-tiered architecture based on Unified Modeling Language (UML). RESULTS Common Data Elements were developed using controlled vocabulary, ontology and semantic modeling methodology. The CDEs for each case are of different types: demographic, epidemiologic data, clinical history, pathology data including block level annotation, and follow-up data including treatment, recurrence and vital status. The end result of such an effort would eventually provide an increased sample set to the researchers, and makes the system interoperable between institutions. CONCLUSION The CAP, ADASP and the NAACCR elements represent widely established data elements that are utilized in many cancer centers. Herein, we have shown these representations can be combined and formalized to create a core set of annotations for banked mesothelioma specimens. Because these data elements are collected as part of the normal workflow of a medical center, data sets developed on the basis of these elements can be easily implemented and maintained.
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Affiliation(s)
- Sambit K Mohanty
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amita T Mistry
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Waqas Amin
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anil V Parwani
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Andrew K Pople
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Linda Schmandt
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sharon B Winters
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Paula Kim
- Translating Research Across Communities, USA
| | - Nancy B Whelan
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ghada Farhat
- Department of Epidemiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jonathan Melamed
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Emanuela Taioli
- Department of Epidemiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rajiv Dhir
- Translating Research Across Communities, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, Division of Thoracic Surgery and Thoracic Oncology, New York University School of Medicine, New York, NY, USA
| | - Michael J Becich
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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