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Stetson D, Labrousse P, Russell H, Shera D, Abbosh C, Dougherty B, Barrett JC, Hodgson D, Hadfield J. Next-Generation Molecular Residual Disease Assays: Do We Have the Tools to Evaluate Them Properly? J Clin Oncol 2024; 42:2736-2740. [PMID: 38754043 DOI: 10.1200/jco.23.02301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/27/2024] [Accepted: 03/05/2024] [Indexed: 05/18/2024] Open
Affiliation(s)
- Dan Stetson
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - Paul Labrousse
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - Hugh Russell
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - David Shera
- Oncology Biometrics, AstraZeneca, Gaithersburg, MD
| | - Chris Abbosh
- Cancer Biomarker Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Brian Dougherty
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - J Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - Darren Hodgson
- Cancer Biomarker Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - James Hadfield
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
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Iurca I, Isakescu E, Pop LA, Budisan L, Pirlog R, Harangus A, Ciuleanu TE, Braicu C, Berindan-Neagoe I. Next-generation sequencing as a valuable tool for mutational spectrum in advanced-stage NSCLC patients. Med Pharm Rep 2024; 97:298-307. [PMID: 39234458 PMCID: PMC11370849 DOI: 10.15386/mpr-2763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/16/2024] [Accepted: 07/05/2024] [Indexed: 09/06/2024] Open
Abstract
Background and aim Lung cancer remains one of the most threatening malignancies, ranking as the second most diagnosed cancer, and it continues to be the leading cause of cancer-related deaths worldwide. Challenges persist with late diagnosis and the high mutational burden characteristic of lung cancer. Methods Our study focuses on identifying the mutational spectrum of a cohort of advanced-stage non-small cell lung cancer (NSCLC) patients using a minimally invasive method through blood collection. To analyze the mutational landscape of these patients, we employed plasma DNA for the next-generation sequencing (NGS) cancer panel Ion Torrent, which contains 50 of the most mutated genes in lung cancer. All protocols for extraction, quality and quantity control, and library preparation follow the manufacturer's rules. Bioinformatics analysis was performed to select pathogenic mutations versus non-pathogenic-benign ones. Results This approach is particularly valuable for patients in advanced stages (III and IV, n=10) of lung adenocarcinoma and lung squamous cell carcinoma, who lack surgical options and limited therapeutic avenues. The comprehensive sequencing analysis revealed that nine of the ten lung cancer patients carried a TP53 mutation. Also, several other mutations exist in various cases, showing heterogeneous profiling. Conclusions Our findings demonstrate the potential of liquid biopsies in providing crucial genetic insights that can guide personalized treatment strategies, improving the management and outcomes for patients with advanced lung cancer.
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Affiliation(s)
- Ioana Iurca
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- County Hospital Baia-Mare, Baia -Mare, Romania
| | - Ecaterina Isakescu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Laura Ancuta Pop
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Liviuta Budisan
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Radu Pirlog
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | | | | | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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Morrison T, Lo B, Deharvengt SJ, Lazaridis N, Tsongalis GJ. Internal Standards for Limit Controls and Absolute Abundance Measurement of Oncogenic Fusions and Mutations. J Appl Lab Med 2024; 9:175-179. [PMID: 38167771 DOI: 10.1093/jalm/jfad108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/30/2023] [Indexed: 01/05/2024]
Affiliation(s)
| | - Bryan Lo
- Molecular Oncology Diagnostics Laboratory, Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Eastern Ontario Laboratory Association, Ottawa, ON, Canada
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Sophie J Deharvengt
- Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Health System, Lebanon, NH, United States
- The Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | | | - Gregory J Tsongalis
- Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Health System, Lebanon, NH, United States
- The Geisel School of Medicine at Dartmouth, Hanover, NH, United States
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Hernandez KM, Bramlett KS, Agius P, Baden J, Cao R, Clement O, Corner AS, Craft J, Dean DA, Dry JR, Grigaityte K, Grossman RL, Hicks J, Higa N, Holzer TR, Jensen J, Johann DJ, Katz S, Kolatkar A, Keynton JL, Lee JSH, Maar D, Martini JF, Meyer CG, Roberts PC, Ryder M, Salvatore L, Schageman JJ, Somiari S, Stetson D, Stern M, Xu L, Leiman LC. Contrived Materials and a Data Set for the Evaluation of Liquid Biopsy Tests: A Blood Profiling Atlas in Cancer (BLOODPAC) Community Study. J Mol Diagn 2023; 25:143-155. [PMID: 36828596 DOI: 10.1016/j.jmoldx.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/21/2022] [Accepted: 12/02/2022] [Indexed: 02/24/2023] Open
Abstract
The Blood Profiling Atlas in Cancer (BLOODPAC) Consortium is a collaborative effort involving stakeholders from the public, industry, academia, and regulatory agencies focused on developing shared best practices on liquid biopsy. This report describes the results from the JFDI (Just Freaking Do It) study, a BLOODPAC initiative to develop standards on the use of contrived materials mimicking cell-free circulating tumor DNA, to comparatively evaluate clinical laboratory testing procedures. Nine independent laboratories tested the concordance, sensitivity, and specificity of commercially available contrived materials with known variant-allele frequencies (VAFs) ranging from 0.1% to 5.0%. Each participating laboratory utilized its own proprietary evaluation procedures. The results demonstrated high levels of concordance and sensitivity at VAFs of >0.1%, but reduced concordance and sensitivity at a VAF of 0.1%; these findings were similar to those from previous studies, suggesting that commercially available contrived materials can support the evaluation of testing procedures across multiple technologies. Such materials may enable more objective comparisons of results on materials formulated in-house at each center in multicenter trials. A unique goal of the collaborative effort was to develop a data resource, the BLOODPAC Data Commons, now available to the liquid-biopsy community for further study. This resource can be used to support independent evaluations of results, data extension through data integration and new studies, and retrospective evaluation of data collection.
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Affiliation(s)
- Kyle M Hernandez
- Department of Medicine, University of Chicago, Chicago, Illinois; Center for Translational Data Science, University of Chicago, Chicago, Illinois
| | | | | | | | - Ru Cao
- Thermo Fisher Scientific, Austin, Texas
| | | | - Adam S Corner
- Digital Biology Group, Bio-Rad Laboratories Inc., Pleasanton, California
| | | | | | | | | | - Robert L Grossman
- Department of Medicine, University of Chicago, Chicago, Illinois; Open Commons Consortium, Chicago, Illinois; Pfizer, San Diego, California
| | - James Hicks
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | - Nikki Higa
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | | | | | - Donald J Johann
- Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Anand Kolatkar
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | | | - Jerry S H Lee
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA; Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, California
| | - Dianna Maar
- Digital Biology Group, Bio-Rad Laboratories Inc., Pleasanton, California
| | | | - Christopher G Meyer
- Center for Translational Data Science, University of Chicago, Chicago, Illinois
| | | | | | | | | | | | | | - Mark Stern
- Bristol Myers Squibb, Newton, New Jersey
| | - Liya Xu
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
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