1
|
Peters AL, Hall PS, Jordan LB, Soh FY, Hannington L, Makaranka S, Urquhart G, Vallet M, Cartwright D, Marashi H, Elsberger B. Enhancing clinical decision support with genomic tools in breast cancer: A Scottish perspective. Breast 2024; 75:103728. [PMID: 38657322 PMCID: PMC11061332 DOI: 10.1016/j.breast.2024.103728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 03/12/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
INTRODUCTION The Oncotype DX Breast RS test has been adopted in Scotland and has been the subject of a large population-based study by a Scottish Consensus Group to assess the uptake of the recurrence score (RS), evaluate co-variates associated with the RS and to analyse the effect it may have had on clinical practice. MATERIALS & METHODS Pan-Scotland study between August 2018-August 2021 evaluating 833 patients who had a RS test performed as part of their diagnostic pathway. Data was extracted retrospectively from electronic records and analysis conducted to describe change in chemotherapy administration (by direct comparison with conventional risk assessment tools), and univariate/multivariate analysis to assess relationship between covariates and the RS. RESULTS Chemotherapy treatment was strongly influenced by the RS (p < 0.001). Only 30 % of patients received chemotherapy treatment in the intermediate and high risk PREDICT groups, where chemotherapy is considered. Additionally, 55.5 % of patients with a high risk PREDICT had a low RS and did not receive chemotherapy. There were 17 % of patients with a low risk PREDICT but high RS who received chemotherapy. Multivariate regression analysis showed the progesterone receptor Allred score (PR score) to be a strong independent predictor of the RS, with a negative PR score being associated with high RS (OR 4.49, p < 0.001). Increasing grade was also associated with high RS (OR 3.81, p < 0.001). Classic lobular pathology was associated with a low RS in comparison to other tumour pathology (p < 0.01). Nodal disease was associated with a lower RS (p = 0.012) on univariate analysis, with menopausal status (p = 0.43) not influencing the RS on univariate or multivariate analysis. CONCLUSIONS Genomic assays offer the potential for risk-stratified decision making regarding the use of chemotherapy. They can help reduce unnecessary chemotherapy treatment and identify a subgroup of patients with more adverse genomic tumour biology. A recent publication by Health Improvement Scotland (HIS) has updated guidance on use of the RS test for NHS Scotland. It suggests to limit its use to the intermediate risk PREDICT group. Our study shows the impact of the RS test in the low and high risk PREDICT groups. The implementation across Scotland has resulted in a notable shift in practice, leading to a significant reduction in chemotherapy administration in the setting of high risk PREDICT scores returning low risk RS. There has also been utility for the test in the low risk PREDICT group to detect a small subgroup with a high RS. We have found the PR score to have a strong independent association with high risk RS. This finding was not evaluated by the key RS test papers, and the potential prognostic information provided by the PR score as a surrogate biomarker is an outstanding question that requires more research to validate.
Collapse
Affiliation(s)
- A L Peters
- Beatson West of Scotland Cancer Centre, Gartnavel Hospital, NHS Greater Glasgow & Clyde, 1053 Great Western Rd, Glasgow G12 0YN, UK; Cancer Research UK (CRUK) Scotland Institute, Switchback Road, Bearsden, Glasgow G61 1BD, UK.
| | - P S Hall
- Edinburgh Cancer Research Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, UK
| | - L B Jordan
- Ninewells Hospital & Medical School, NHS Tayside, Department of Pathology, Dundee, DD1 9SY, UK
| | - F Y Soh
- Raigmore Hospital, NHS Highland, Department of Oncology, Inverness IV2 3UJ, UK
| | - L Hannington
- Beatson West of Scotland Cancer Centre, Gartnavel Hospital, NHS Greater Glasgow & Clyde, 1053 Great Western Rd, Glasgow G12 0YN, UK
| | - S Makaranka
- Aberdeen Royal Infirmary, NHS Grampian, Department of Breast Surgery, Aberdeen AB25 2ZN, UK
| | - G Urquhart
- Aberdeen Royal Infirmary, NHS Grampian, Department of Oncology, Aberdeen AB25 2ZN, UK
| | - M Vallet
- Edinburgh Cancer Research Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, UK
| | - D Cartwright
- Beatson West of Scotland Cancer Centre, Gartnavel Hospital, NHS Greater Glasgow & Clyde, 1053 Great Western Rd, Glasgow G12 0YN, UK; Cancer Research UK (CRUK) Scotland Institute, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - H Marashi
- Beatson West of Scotland Cancer Centre, Gartnavel Hospital, NHS Greater Glasgow & Clyde, 1053 Great Western Rd, Glasgow G12 0YN, UK
| | - B Elsberger
- Aberdeen Royal Infirmary, NHS Grampian, Department of Breast Surgery, Aberdeen AB25 2ZN, UK
| |
Collapse
|
2
|
Ardicli S, Aldevir O, Aksu E, Gumen A. The variation in the beta-casein genotypes and its effect on milk yield and genomic values in Holstein-Friesian cows. Anim Biotechnol 2023; 34:4116-4125. [PMID: 37830164 DOI: 10.1080/10495398.2023.2267614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
The A2 milk marker is gaining popularity worldwide; thus, many farms plan to convert their dairy cattle herds to the A2A2 genotype. Variation in beta-casein genotypes needs to be monitored in large dairy cattle populations. Therefore we aimed to evaluate the genotypic distributions, population genetics, and diversity parameters in Holstein-Friesian cows. A total of 1200 cattle were genotyped using the Affymetrix® Axiom® array system. We performed an association analysis regarding the CSN2 genotypes and phenotypic traits, including lactation and test-day milk yield. We next evaluated the effects of the genotypes considering the genetic merit of the animals. Animals were grouped based on their PTAs for milk production, fat, protein, and daughter pregnancy rate. Thus, we tested the genotype × genetic merit interaction for significance. The A2 allele frequency is remarkably high (0.68), and the heterozygous genotype is predominant (46.25%). The marker showed intermediate variability and diversity levels, indicating a considerable frequency of the A1A1 genotype (9.33%) remains in the population. ANOVA results showed no significant association between the CSN2 genotypes and milk yield traits. A similar finding is valid for the genotype × genetic merit regarding the genomic test results. The data presented here may be helpful for further investigations and applications on A2 milk production.
Collapse
Affiliation(s)
- Sena Ardicli
- Department of Genetics, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Ozgur Aldevir
- Department of Obstetrics and Gynecology, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | | | - Ahmet Gumen
- Department of Obstetrics and Gynecology, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| |
Collapse
|
3
|
Licata L, Cosentini D, De Sanctis R, Iorfida M, Caremoli ER, Vingiani A, Simoncini EL, Pruneri G, Munzone E, Bianchini G, Zambelli A, Tondini C. Multigene signatures for early breast cancer in clinical practice: A report of the Lombardy genomic assays for breast cancer working group. Front Oncol 2023; 13:1081885. [PMID: 36950554 PMCID: PMC10025563 DOI: 10.3389/fonc.2023.1081885] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/15/2023] [Indexed: 03/08/2023] Open
Abstract
The increasing understanding of breast cancer biology has provided the basis for the development of multigene signatures aimed to improve the capability of clinicians to assess patients' prognostication and risk stratification. Incorporating these tools in clinical practice has profoundly impacted on the decision-making process for the adjuvant therapy of patients with ER+/HER2- early breast cancer and the results from prospective adjuvant trials have strengthened the clinical utility of multigene signatures in this setting. In July 2019, Lombardy was the first Region in Italy to reimburse genomic testing for patients with ER+/HER2- early breast cancer. Three years later, a group of investigators from six referral Cancer Centers in Lombardy convened to debate the use of multigene signatures in clinical practice and share their own experience with the tests after reimbursement. Here, we reviewed relevant data on the role of multigene signatures in tailoring adjuvant chemotherapy for patients with ER+/HER2- early breast cancer and discussed about the optimal use of these assays in current clinical practice. As the treatment landscape of early breast cancer evolves and novel questions about the possible additional applications of multigene assays arise, we also provide our viewpoint on the potential implementation of the assays in the evolving scenario ER+/HER2- early breast cancer treatment.
Collapse
Affiliation(s)
- Luca Licata
- Department of Medical Oncology, San Raffaele Hospital, Milan, Italy
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milan, Italy
- *Correspondence: Luca Licata,
| | - Deborah Cosentini
- Medical Oncology Unit, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Rita De Sanctis
- Medical Oncology and Hematology Unit, IRCCS - Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Monica Iorfida
- Division of Medical Senology, IEO, European Institute of Oncology, Milan, Italy
| | | | - Andrea Vingiani
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Faculty of Medicine and Surgery, University of Milan, Milan, Italy
| | | | - Giancarlo Pruneri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Faculty of Medicine and Surgery, University of Milan, Milan, Italy
| | - Elisabetta Munzone
- Division of Medical Senology, IEO, European Institute of Oncology, Milan, Italy
| | - Giampaolo Bianchini
- Department of Medical Oncology, San Raffaele Hospital, Milan, Italy
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milan, Italy
| | - Alberto Zambelli
- Medical Oncology and Hematology Unit, IRCCS - Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Carlo Tondini
- Oncology Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| |
Collapse
|
4
|
Pitini E, Migliara G, Baccolini V, Isonne C, Mazzalai E, Turatto F, Salerno C, Pagano F, Menzano MT, De Vito C, Marzuillo C, Villari P. Managing the introduction of genomic applications into the National Health Service: A special challenge for health technology assessment in Italy. Front Public Health 2022; 10:932093. [PMID: 36033790 PMCID: PMC9399489 DOI: 10.3389/fpubh.2022.932093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/04/2022] [Indexed: 01/25/2023] Open
Abstract
In recent years, the rapid proliferation of genomic tests for use in clinical practice has prompted healthcare systems to use a health technology assessment (HTA) approach to distinguish valuable from unwarranted applications. In this study, we narratively review the Italian HTA mechanisms for medical devices (MDs), both at the national and regional levels, and discuss the opportunity and benefits of extending them to genomic technologies, for which a dedicated assessment path was advocated by the National Plan for Public Health Genomics in 2017. We found that the National Health Technology Assessment Program for MDs, completed in 2019, had developed a structured pathway for the HTA of MDs; it established a hub-and-spoke structure, run by a governmental institution, and put in place transparent methodological procedures to cover all four HTA phases (i.e., proposal and prioritization, assessment, appraisal, and dissemination). However, several factors have hindered its adoption, and the regions are at different stages of its implementation. For these reasons, efforts should be made to ensure its effective deployment, both at national and regional levels. In addition, we argue that to harmonize the institutional roles and methodological procedures adopted, the time has come to concentrate resources on a single pathway for the assessment of all technologies that include both MDs and genomic applications.
Collapse
Affiliation(s)
- Erica Pitini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy,*Correspondence: Erica Pitini
| | - Giuseppe Migliara
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Valentina Baccolini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Claudia Isonne
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Elena Mazzalai
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Federica Turatto
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Carla Salerno
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Federica Pagano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Maria Teresa Menzano
- Italian Ministry of Health, General Directorate for Health Prevention, Rome, Italy
| | - Corrado De Vito
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Carolina Marzuillo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Paolo Villari
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| |
Collapse
|
5
|
Pitini E, Baccolini V, Migliara G, Isonne C, Sindoni A, Mazzalai E, Turatto F, De Vito C, Marzuillo C, Villari P. Time to Align: A Call for Consensus on the Assessment of Genetic Testing. Front Public Health 2021; 9:807695. [PMID: 34938716 PMCID: PMC8685239 DOI: 10.3389/fpubh.2021.807695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
In this paper, we updated our 2018 systematic review aimed to identify and compare ad hoc designed frameworks for genetic testing evaluation. Overall, we identified 30 frameworks (29 in the first systematic review and one in the update): they were mainly based on the ACCE model, whereas a minority were adjustments of the more traditional Health Technology Assessment (HTA) approach. After discussing the strengths and weaknesses of the retrieved frameworks, this perspective calls for consensus on the assessment of genetic testing. In line with the recent European recommendations that encouraged the generation of comparable evidence across Member States, we believe that the time has come to align all the ideas that have emerged over the last few decades and find a sustainable and sharable tool for the evaluation of genetic and genomic applications. Therefore, we suggest stopping the evaluation of such technologies using ad hoc strategies-affected by validation, implementation, and adoption issues-and we propose to use a general HTA approach, particularly the European reference tool for the assessment of health technologies, the EUnetHTA HTA core model, that is built on solid theoretical and methodological principles and provides a comprehensive assessment of the technologies value.
Collapse
Affiliation(s)
- Erica Pitini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Valentina Baccolini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Giuseppe Migliara
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Claudia Isonne
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Alessandro Sindoni
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Elena Mazzalai
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Federica Turatto
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Corrado De Vito
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Carolina Marzuillo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Paolo Villari
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| |
Collapse
|
6
|
Moisseev A, Albert E, Lubarsky D, Schroeder D, Clark J. Transcriptomic and Genomic Testing to Guide Individualized Treatment in Chemoresistant Gastric Cancer Case. Biomedicines 2020; 8:biomedicines8030067. [PMID: 32210001 PMCID: PMC7148467 DOI: 10.3390/biomedicines8030067] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/20/2020] [Accepted: 03/20/2020] [Indexed: 12/20/2022] Open
Abstract
Gastric cancer is globally the fifth leading cause of cancer death. We present a case report describing the unique genomic characteristics of an Epstein–Barr virus-negative gastric cancer with esophageal invasion and regional lymph node metastasis. Genomic tests were performed first with the stomach biopsy using platforms FoundationOne, OncoDNA, and Oncopanel at Dana Farber Institute. Following neoadjuvant chemotherapy, residual tumor was resected and the stomach and esophageal residual tumor samples were compared with the initial biopsy by whole exome sequencing and molecular pathway analysis platform Oncobox. Copy number variation profiling perfectly matched the whole exome sequencing results. A moderate agreement was seen between the diagnostic platforms in finding mutations in the initial biopsy. Final data indicate somatic activating mutation Q546K in PIK3CA gene, somatic frameshifts in PIH1D1 and FBXW7 genes, stop-gain in TP53BP1, and a few somatic mutations of unknown significance. RNA sequencing analysis revealed upregulated expressions of MMP7, MMP9, BIRC5, and PD-L1 genes and strongly differential regulation of several molecular pathways linked with the mutations identified. According to test results, the patient received immunotherapy with anti-PD1 therapy and is now free of disease for 2 years. Our data suggest that matched tumor and normal tissue analyses have a considerable advantage over tumor biopsy-only genomic tests in stomach cancer.
Collapse
Affiliation(s)
- Alexey Moisseev
- Institute for personalized medicine, I.M. Sechenov First Moscow State Medical University, 119048 Moscow, Russia;
- Correspondence: ; Tel.: +7(926)1443639
| | - Eugene Albert
- Institute for personalized medicine, I.M. Sechenov First Moscow State Medical University, 119048 Moscow, Russia;
| | | | - David Schroeder
- Wellesley Internal Medicine, 372 Washington St Ste 2, Wellesley Hills, MA 02481, USA;
| | - Jeffrey Clark
- Department of Hematology and Oncology, Massachusetts General Hospital, 55 Fruit Street Boston, MA 02114, USA;
| |
Collapse
|
7
|
Abstract
The net benefit from investing in any technology is a function of the cost of implementation and the expected return in revenue. The objective of the present study was to quantify, using deterministic equations, the net monetary benefit from investing in genotyping of commercial females. Three case studies were presented reflecting dairy cows, beef cows and ewes based on Irish population parameters; sensitivity analyses were also performed. Parameters considered in the sensitivity analyses included the accuracy of genomic evaluations, replacement rate, proportion of female selection candidates retained as replacements, the cost of genotyping, the sire parentage error rate and the age of the female when it first gave birth. Results were presented as an annualised monetary net benefit over the lifetime of an individual, after discounting for the timing of expressions. In the base scenarios, the net benefit was greatest for dairy, followed by beef and then sheep. The net benefit improved as the reliability of the genomic evaluations improved and, in fact, a negative net benefit of genotyping was less frequent when the reliability of the genomic evaluations was high. The impact of a 10% point increase in genomic reliability was, however, greatest in sheep, followed by beef and then dairy. The net benefit of genotyping female selection candidates reduced as replacement rate increased. As genotyping costs increased, the net benefit reduced irrespective of the percentage of selection candidates kept, the replacement rate or even the population considered. Nonetheless, the association between the genotyping cost and the net benefit of genotyping differed by the percentage of selection candidates kept. Across all replacement rates evaluated, retaining 25% of the selection candidates resulted in the greatest net benefit when genotyping cost was low but the lowest net benefit when genotyping cost was high. Genotyping breakeven cost was non-linearly associated with the percentage of selection candidates retained, reaching a maximum when 50% of selection candidates were retained, irrespective of replacement rate, genomic reliability or the population. The genotyping breakeven cost was also non-linearly associated with replacement rate. The approaches outlined within provide the back-end framework for a decision support tool to quantify the net benefit of genotyping, once parameterised by the relevant population metrics.
Collapse
Affiliation(s)
- J E Newton
- Teagasc Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - D P Berry
- Teagasc Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| |
Collapse
|
8
|
Beaubier N, Tell R, Huether R, Bontrager M, Bush S, Parsons J, Shah K, Baker T, Selkov G, Taxter T, Thomas A, Bettis S, Khan A, Lau D, Lee C, Barber M, Cieslik M, Frankenberger C, Franzen A, Weiner A, Palmer G, Lonigro R, Robinson D, Wu YM, Cao X, Lefkofsky E, Chinnaiyan A, White KP. Clinical validation of the Tempus xO assay. Oncotarget 2018; 9:25826-25832. [PMID: 29899824 PMCID: PMC5995233 DOI: 10.18632/oncotarget.25381] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 03/21/2018] [Indexed: 01/01/2023] Open
Abstract
We have developed a clinically validated NGS assay that includes tumor, germline and RNA sequencing. We apply this assay to clinical specimens and cell lines, and we demonstrate a clinical sensitivity of 98.4% and positive predictive value of 100% for the clinically actionable variants measured by the assay. We also demonstrate highly accurate copy number measurements and gene rearrangement identification.
Collapse
Affiliation(s)
| | - Robert Tell
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | | | | | | | | | - Kaanan Shah
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Tim Baker
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Gene Selkov
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Tim Taxter
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | | | - Sam Bettis
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Aly Khan
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Denise Lau
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | | | | | - Marcin Cieslik
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Amy Franzen
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Ali Weiner
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Gary Palmer
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Robert Lonigro
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Dan Robinson
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yi-Mi Wu
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xuhong Cao
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Arul Chinnaiyan
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | | |
Collapse
|
9
|
Kim ST, Lee WS, Lanman RB, Mortimer S, Zill OA, Kim KM, Jang KT, Kim SH, Park SH, Park JO, Park YS, Lim HY, Eltoukhy H, Kang WK, Lee WY, Kim HC, Park K, Lee J, Talasaz A. Prospective blinded study of somatic mutation detection in cell-free DNA utilizing a targeted 54-gene next generation sequencing panel in metastatic solid tumor patients. Oncotarget 2015; 6:40360-9. [PMID: 26452027 DOI: 10.18632/oncotarget.5465] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/24/2015] [Indexed: 12/20/2022] Open
Abstract
Sequencing of the mutant allele fraction of circulating cell-free DNA (cfDNA) derived from tumors is increasingly utilized to detect actionable genomic alterations in cancer. We conducted a prospective blinded study of a comprehensive cfDNA sequencing panel with 54 cancer genes. To evaluate the concordance between cfDNA and tumor DNA (tDNA), sequencing results were compared between cfDNA from plasma and genomic tumor DNA (tDNA). Utilizing next generation digital sequencing technology (DST), we profiled approximately 78,000 bases encoding 512 complete exons in the targeted genes in cfDNA from plasma. Seventy-five patients were prospectively enrolled between February 2013 and March 2014, including 61 metastatic cancer patients and 14 clinical stage II CRC patients with matched plasma and tissue samples. Using the 54-gene panel, we detected at least one somatic mutation in 44 of 61 tDNA (72.1%) and 29 of 44 (65.9%) cfDNA. The overall concordance rate of cfDNA to tDNA was 85.9%, when all detected mutations were considered. We collected serial cfDNAs during cetuximab-based treatment in 2 metastatic KRAS wild-type CRC patients, one with acquired resistance and one with primary resistance. We demonstrate newly emerged KRAS mutation in cfDNA 1.5 months before radiologic progression. Another patient had a newly emerged PIK3CA H1047R mutation on cfDNA analysis at progression during cetuximab/irinotecan chemotherapy with gradual increase in allele frequency from 0.8 to 2.1%. This blinded, prospective study of a cfDNA sequencing showed high concordance to tDNA suggesting that the DST approach may be used as a non-invasive biopsy-free alternative to conventional sequencing using tumor biopsy.
Collapse
|
10
|
Abstract
INTRODUCTION The adoption of precision medicine (PM) has been limited in practice to date, and yet its promise has attracted research investments. Developing foundational economic approaches for directing proper use of PM and stimulating growth in this area from multiple perspectives is thus quite timely. METHODS Building on our previously developed expected value of individualized care (EVIC) framework, we conceptualize new decision-relevant metrics to better understand and forecast the expected value of PM. Several aspects of behavior at the patient, physician, and payer levels are considered that can inform the rate and manner in which PM innovations diffuse throughout the relevant population. We illustrate this framework and the methods using a retrospective evaluation of the use of OncotypeDx genomic test among breast cancer patients. RESULTS The enriched metrics can help inform many facets of PM decision making, such as evaluating alternative reimbursement levels for PM tests, implementation and education programs for physicians and patients, and decisions around research investments by manufacturers and public entities. We replicated prior published results on evaluation of OncotypeDx among breast cancer patients but also illustrated that those results are based on assumptions that are often not met in practice. Instead, we show how incorporating more practical aspects of behavior around PM could lead to drastically different estimates of value. CONCLUSION We believe that the framework and the methods presented can provide decision makers with more decision-relevant tools to explore the value of PM. There is a growing recognition that data on adoption is important to decision makers. More research is needed to develop prediction models for potential diffusion of PM technologies.
Collapse
Affiliation(s)
- Anirban Basu
- Pharmaceutical Outcomes Research and Policy Program, Department of Pharmacy, University of Washington, Seattle
- Departments of Health Services and Economics, University of Washington, Seattle
| | - Josh J. Carlson
- Pharmaceutical Outcomes Research and Policy Program, Department of Pharmacy, University of Washington, Seattle
| | - David L. Veenstra
- Pharmaceutical Outcomes Research and Policy Program, Department of Pharmacy, University of Washington, Seattle
| |
Collapse
|