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Thangavelu T, Wirta V, Orsmark-Pietras C, Cavelier L, Fioretos T, Barbany G, Olsson-Arvidsson L, Pandzic T, Staffas A, Rosenquist R, Levin LÅ. Micro-costing of genetic diagnostics in acute leukemia in Sweden: from standard-of-care to whole-genome sequencing. J Med Econ 2024; 27:1053-1060. [PMID: 39101813 DOI: 10.1080/13696998.2024.2387515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/06/2024]
Abstract
AIMS AND BACKGROUND Whole-genome sequencing (WGS) is increasingly applied in clinical practice and expected to replace standard-of-care (SoC) genetic diagnostics in hematological malignancies. This study aims to assess and compare the fully burdened cost ('micro-costing') per patient for Swedish laboratories using WGS and SoC, respectively, in pediatric and adult patients with acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). METHODS The resource use and cost details associated with SoC, e.g. chromosome banding analysis, fluorescent in situ hybridization, and targeted sequencing analysis, were collected via activity-based costing methods from four diagnostic laboratories. For WGS, corresponding data was collected from two of the centers. A simulation-based scenario model was developed for analyzing the WGS cost based on different annual sample throughput to evaluate economy of scale. RESULTS The average SoC total cost per patient was €2,465 for pediatric AML and €2,201 for pediatric ALL, while in adults, the corresponding cost was €2,458 for AML and €1,207 for ALL. The average WGS cost (90x tumor/30x normal; sequenced on the Illumina NovaSeq 6000 platform) was estimated to €3,472 based on an annual throughput of 2,500 analyses, however, with an annual volume of 7,500 analyses the average cost would decrease by 23% to €2,671. CONCLUSION In summary, WGS is currently more costly than SoC, however the cost can be reduced by utilizing laboratories with higher throughput and by the expected decline in cost of reagents. Our data provides guidance to decision-makers for the resource allocation needed when implementing WGS in diagnostics of hematological malignancies.
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Affiliation(s)
- Tharshini Thangavelu
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
- Department of Register and Statistics, The National Board of Health and Welfare, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH Royal Instititute of Technology, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Christina Orsmark-Pietras
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Lund, Sweden
| | - Lucia Cavelier
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Lund, Sweden
| | - Gisela Barbany
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Linda Olsson-Arvidsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Lund, Sweden
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anna Staffas
- Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Richard Rosenquist
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Lars-Åke Levin
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
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Souza da Silva R, Pinto R, Cirnes L, Schmitt F. Tissue management in precision medicine: What the pathologist needs to know in the molecular era. Front Mol Biosci 2022; 9:983102. [DOI: 10.3389/fmolb.2022.983102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
Precision medicine is “an emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person.” Among many medical specialists involved in precision medicine, the pathologists play an important and key role in the implementation and development of molecular tests that are in the center of decision of many therapeutic choices. Besides many laboratory procedures directly involved in the molecular tests, is fundamental to guarantee that tissues and cells collected for analysis be managed correctly before the DNA/RNA extraction. In this paper we explore the pivotal and interconnected points that can influence molecular studies, such as pre-analytical issues (fixation and decalcification); diagnosis and material selection, including the calculation of nuclei neoplastic fraction. The standardization of sample processing and morphological control ensures the accuracy of the diagnosis. Tissue or cytological samples constitutes the main foundation for the determination of biomarkers and development of druggable targets. Pathology and precision oncology still have a long way to go in terms of research and clinical practice: improving the accuracy and dissemination of molecular tests, learning in molecular tumor boards for advanced disease, and knowledge about early disease. Precision medicine needs pathology to be precise.
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Validation of HER2 Status in Whole Genome Sequencing Data of Breast Cancers with the Ploidy-Corrected Copy Number Approach. Mol Diagn Ther 2021; 26:105-116. [PMID: 34932189 PMCID: PMC8766398 DOI: 10.1007/s40291-021-00571-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2021] [Indexed: 11/02/2022]
Abstract
BACKGROUND AND OBJECTIVE Human epidermal growth factor receptor 2 (HER2) protein overexpression is one of the most significant biomarkers for breast cancer diagnostics, treatment prediction, and prognostics. The high accessibility of HER2 inhibitors in routine clinical practice directly translates into the diagnostic need for precise and robust marker identification. Even though multigene next-generation sequencing methodologies have slowly taken over the field of single-biomarker molecular tests, the copy number alterations such as amplification of the HER2-coding ERBB2 gene are hard to validate on next-generation sequencing platforms as they are characterized by chromosomal structural heterogeneity, polysomy, and genomic context of ploidy. In our study, we tested the approach of using whole genome sequencing instead of next-generation sequencing panels to determine HER2 status in the clinical set-up. METHODS We used a large dataset of 876 patients with breast cancer whole genomes with curated clinical data and an additional set of 551 patients' external genomic data. We used the decision-tree-based algorithm for optimization of the diagnostic tool for HER2 status assessment by whole genome sequencing. RESULTS The most efficient approach to assess HER2 status in whole genome sequencing data was the ploidy-corrected copy number, utilizing ERBB2 copy number and mean tumor ploidy. The classifier achieved sensitivity of 91.18% and specificity of 98.69% on the internal validation dataset and 89.86% and 96.06% on the external data, which is similar to other next-generation sequencing methods, currently tested in the clinic. CONCLUSIONS We provide evidence that the HER2 status may be reliably determined by whole genome sequencing and is applicable across different laboratory protocols and pipelines. We suggest using the ploidy-corrected copy number for diagnostic purposes.
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Fridland S, Choi J, Nam M, Schellenberg SJ, Kim E, Lee G, Yoon N, Chae YK. Assessing tumor heterogeneity: integrating tissue and circulating tumor DNA (ctDNA) analysis in the era of immuno-oncology - blood TMB is not the same as tissue TMB. J Immunother Cancer 2021; 9:jitc-2021-002551. [PMID: 34462324 PMCID: PMC8407207 DOI: 10.1136/jitc-2021-002551] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2021] [Indexed: 12/29/2022] Open
Abstract
Tissue tumor mutational burden (tTMB) is calculated to aid in cancer treatment selection. High tTMB predicts a favorable response to immunotherapy in patients with non-small cell lung cancer. Blood TMB (bTMB) from circulating tumor DNA is reported to have similar predictive power and has been proposed as an alternative to tTMB. Across many studies not only are tTMB and bTMB not concordant but also as reported previously by our group predict conflicting outcomes. This implies that bTMB is not a substitute for tTMB, but rather a composite index that may encompass tumor heterogeneity. Here, we provide a thorough overview of the predictive power of TMB, discuss the use of tumor heterogeneity alongside TMB to predict treatment response and review several methods of tumor heterogeneity assessment. Furthermore, we propose a hypothetical method of estimating tumor heterogeneity and touch on its clinical implications.
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Affiliation(s)
- Stanislav Fridland
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jaeyoun Choi
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Myungwoo Nam
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | | | - Eugene Kim
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Grace Lee
- Northwestern University, Evanston, Illinois, USA
| | | | - Young Kwang Chae
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA .,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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