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Samsom KG, Bosch LJW, Schipper LJ, Schout D, Roepman P, Boelens MC, Lalezari F, Klompenhouwer EG, de Langen AJ, Buffart TE, van Linder BMH, van Deventer K, van den Burg K, Unmehopa U, Rosenberg EH, Koster R, Hogervorst FBL, van den Berg JG, Riethorst I, Schoenmaker L, van Beek D, de Bruijn E, van der Hoeven JJM, van Snellenberg H, van der Kolk LE, Cuppen E, Voest EE, Meijer GA, Monkhorst K. Optimized whole-genome sequencing workflow for tumor diagnostics in routine pathology practice. Nat Protoc 2024; 19:700-726. [PMID: 38092944 DOI: 10.1038/s41596-023-00933-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/19/2023] [Indexed: 03/10/2024]
Abstract
Two decades after the genomics revolution, oncology is rapidly transforming into a genome-driven discipline, yet routine cancer diagnostics is still mainly microscopy based, except for tumor type-specific predictive molecular tests. Pathology laboratories struggle to quickly validate and adopt biomarkers identified by genomics studies of new targeted therapies. Consequently, clinical implementation of newly approved biomarkers suffers substantial delays, leading to unequal patient access to these therapies. Whole-genome sequencing (WGS) can successfully address these challenges by providing a stable molecular diagnostic platform that allows detection of a multitude of genomic alterations in a single cost-efficient assay and facilitating rapid implementation, as well as by the development of new genomic biomarkers. Recently, the Whole-genome sequencing Implementation in standard Diagnostics for Every cancer patient (WIDE) study demonstrated that WGS is a feasible and clinically valid technique in routine clinical practice with a turnaround time of 11 workdays. As a result, WGS was successfully implemented at the Netherlands Cancer Institute as part of routine diagnostics in January 2021. The success of implementing WGS has relied on adhering to a comprehensive protocol including recording patient information, sample collection, shipment and storage logistics, sequencing data interpretation and reporting, integration into clinical decision-making and data usage. This protocol describes the use of fresh-frozen samples that are necessary for WGS but can be challenging to implement in pathology laboratories accustomed to using formalin-fixed paraffin-embedded samples. In addition, the protocol outlines key considerations to guide uptake of WGS in routine clinical care in hospitals worldwide.
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Affiliation(s)
- Kris G Samsom
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Linda J W Bosch
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Luuk J Schipper
- Department of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Office Jaarbeurs Innovation Mile (JIM), Utrecht, the Netherlands
| | - Daoin Schout
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Paul Roepman
- Hartwig Medical Foundation, Science Park, Amsterdam, the Netherlands
| | - Mirjam C Boelens
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ferry Lalezari
- Department of Radiology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Adrianus J de Langen
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Tineke E Buffart
- Department of Medical Oncology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Berit M H van Linder
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Kelly van Deventer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Kay van den Burg
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Unga Unmehopa
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Efraim H Rosenberg
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roelof Koster
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Frans B L Hogervorst
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - José G van den Berg
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Immy Riethorst
- Hartwig Medical Foundation, Science Park, Amsterdam, the Netherlands
| | - Lieke Schoenmaker
- Hartwig Medical Foundation, Science Park, Amsterdam, the Netherlands
| | - Daphne van Beek
- Hartwig Medical Foundation, Science Park, Amsterdam, the Netherlands
| | - Ewart de Bruijn
- Hartwig Medical Foundation, Science Park, Amsterdam, the Netherlands
| | | | | | | | - Edwin Cuppen
- Oncode Institute, Office Jaarbeurs Innovation Mile (JIM), Utrecht, the Netherlands
- Hartwig Medical Foundation, Science Park, Amsterdam, the Netherlands
- Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Emile E Voest
- Department of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Office Jaarbeurs Innovation Mile (JIM), Utrecht, the Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Kim Monkhorst
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
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Govas P, Ha MV, Wessel CB, Hurst A, Gordon BR, Carroll BT. Reported Outcome Measures in Mohs Micrographic Surgery in Studies With Defined Techniques for Embedding and Processing of Tissue: A Systematic Review. Dermatol Surg 2023; 49:1116-1121. [PMID: 37962132 DOI: 10.1097/dss.0000000000004013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
BACKGROUND Mohs micrographic surgery (MMS) is a technique that combines surgical excision and histologic evaluation to achieve higher cure rates for skin cancer than traditional surgical excision. Competing performance measures have fostered numerous histologic techniques for MMS. OBJECTIVE To analyze differences in primary outcomes in the published literature regarding the technique of tissue processing and embedding during the MMS process. METHODS A systematic review was performed of the published literature in MEDLINE, PubMed, Embase, and Cochrane library that included a description of the manipulation of tissue during the grossing and embedding steps of MMS. RESULTS Inclusion criteria were met by 61 articles. Of these studies, the cure/recurrence rate was assessed in 1 article (1.6%), tissue conservation was assessed in 47 (77%), time-saving was assessed in 35 (57%), cost-saving was assessed in 6 (10%), and decreased artifact were assessed in 20 (33%). CONCLUSION There is a lack of standardization for assessing clinical outcomes in the published literature regarding MMS process techniques. Cure is a critical outcome in studies comparing MMS processing methodologies.
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Affiliation(s)
- Panayiota Govas
- Department of Dermatology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Megan V Ha
- Department of Dermatology, Case Western Reserve University School of Medicine, Cleveland, Ohio
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Charles B Wessel
- University of Pittsburgh, Health Sciences Library System, Pittsburgh, Pennsylvania
| | - Anne Hurst
- Atlantic Skin Cancer Surgery, Virginia Beach, Virginia
| | - Beth R Gordon
- Department of Internal Medicine, NYU Langone Health, New York, New York
| | - Bryan T Carroll
- Department of Dermatology, Case Western Reserve University School of Medicine, Cleveland, Ohio
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, Ohio
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Girolami I, Neri S, Eccher A, Brunelli M, Hanna M, Pantanowitz L, Hanspeter E, Mazzoleni G. Frozen section telepathology service: Efficiency and benefits of an e-health policy in South Tyrol. Digit Health 2022; 8:20552076221116776. [PMID: 35923756 PMCID: PMC9340333 DOI: 10.1177/20552076221116776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/13/2022] [Indexed: 12/03/2022] Open
Abstract
Objective/Background Telepathology has been widely adopted to allow intraoperative pathology
examinations to be performed remotely and for obtaining second opinion
teleconsultation. In the Italian northern region of South Tyrol, the
widespread geographical distances and consequent cost for the health system
of having a travelling pathologist cover intraoperative consultations in
peripheral hospitals was a key driver for the implementation of a
telepathology system. Methods In 2010, four Menarini D-Sight whole slide scanners to digitize entire
pathology slides were placed in the peripheral hospitals of Merano,
Bressanone, Brunico, and in the hub hospital of Bolzano. Digital
workstations were also installed to allow pathologists to remotely perform
intraoperative consultations with digital slides. This study reviews the
outcome after 12 years of telepathology for this intended clinical use. Results After an initial validation phase with 100 cases which yielded a sensitivity
of 65% (CI 43–84%) and specificity of 100% (CI 95–100%), there were 2058
intraoperative consultations handled by telepathology. The cases evaluated
were mainly breast sentinel lymph nodes, followed by urological,
gynecological and general surgical pathology frozen section specimens. There
were no false-positive cases and 165 (8%) false-negative cases, yielding an
overall sensitivity and specificity of 65% (CI 61–69%) and 100% (CI
99–100%), respectively. Conclusion Telepathology is reliable for remote intraoperative diagnosis and, despite
technical issues and initial acquaintance issues, proved beneficial for
patient care in satellite hospitals, improved standardization, promoted
innovation, and resulted in cost savings for the health system.
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Affiliation(s)
- Ilaria Girolami
- Department of Pathology, Provincial Hospital of Bolzano (SABES-ASDAA), Bolzano-Bozen, Italy
| | - Stefania Neri
- Department of Pathology, Provincial Hospital of Bolzano (SABES-ASDAA), Bolzano-Bozen, Italy
| | - Albino Eccher
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Matteo Brunelli
- Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy
| | - Mattew Hanna
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Liron Pantanowitz
- Department of Pathology & Clinical Labs, University of Michigan, Ann Arbor, MI, USA
| | - Esther Hanspeter
- Department of Pathology, Provincial Hospital of Bolzano (SABES-ASDAA), Bolzano-Bozen, Italy
| | - Guido Mazzoleni
- Department of Pathology, Provincial Hospital of Bolzano (SABES-ASDAA), Bolzano-Bozen, Italy
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Renne SL, Redaelli S, Paolini B. Cryoembedder, automatic processor/stainer, liquid nitrogen freezing, and manual staining for frozen section examination: A comparative study. Acta Histochem 2019; 121:761-764. [PMID: 31078257 DOI: 10.1016/j.acthis.2019.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/03/2019] [Accepted: 05/05/2019] [Indexed: 10/26/2022]
Abstract
Frozen section examination (FSE) reshaped surgical pathology and is characterized by a high accuracy. Nonetheless pathologists can experience artefacts that can compromise or defer the diagnosis. We compared a commercial system, composed by a cryoembedder and a processor/stainer, to our FSE protocol. Feasibility of diagnosis as well as overall architecture, cytology, and staining, were scored under the following conditions: Traditional (liquid nitrogen freezing and manual staining), Only-Presto (liquid nitrogen freezing and commercial processor/stainer), Only-PrestoCHILL (cryoembedder and manual staining), and PrestoSystem (cryoembedder and processor/stainer). Scores were compared across the different experimental conditions. PrestoSystem had significantly higher scores than Traditional, Only-Presto or Only-PrestoCHILL in all categories (Wilcoxon test; all P-value <.001); similarly, also Only-Presto and Only-PrestoChill had significantly higher scores than Traditional in all categories. Only-PrestoCHILL had significantly higher scores than Only-Presto in Cytology and Architecture. In conclusion the control of pre-analytical variables provided reproducible results, of a higher quality.
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