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Kalashnikova E, Aushev VN, Malashevich AK, Tin A, Krinshpun S, Salari R, Scalise CB, Ram R, Malhotra M, Ravi H, Sethi H, Sanchez S, Hagelstrom RT, Brevnov M, Rabinowitz M, Moshkevich S, Zimmermann BG, Liu MC, Aleshin A. Correlation between variant allele frequency and mean tumor molecules with tumor burden in patients with solid tumors. Mol Oncol 2023. [PMID: 38037739 DOI: 10.1002/1878-0261.13557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 12/21/2022] [Revised: 10/03/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023] Open
Abstract
Several studies have demonstrated the prognostic value of circulating tumor DNA (ctDNA); however, the correlation of mean tumor molecules (MTM)/ml of plasma and mean variant allele frequency (mVAF; %) with clinical parameters is yet to be understood. In this study, we analyzed ctDNA data in a pan-cancer cohort of 23 543 patients who had ctDNA testing performed using a personalized, tumor-informed assay (Signatera™, mPCR-NGS assay). For ctDNA-positive patients, the correlation between MTM/ml and mVAF was examined. Two subanalyses were performed: (a) to establish the association of ctDNA with tumor volume and (b) to assess the correlation between ctDNA dynamics and patient outcomes. On a global cohort, a positive correlation between MTM/ml and mVAF was observed. Among 18 426 patients with longitudinal ctDNA measurements, 13.3% had discordant trajectories between MTM/ml and mVAF at subsequent time points. In metastatic patients receiving immunotherapy (N = 51), changes in ctDNA levels expressed both in MTM/ml and mVAF showed a statistically significant association with progression-free survival; however, the correlation with MTM/ml was numerically stronger.
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2
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Halloran PF, Reeve J, Madill-Thomsen KS, Kaur N, Ahmed E, Cantos C, Al Haj Baddar N, Demko Z, Liang N, Swenerton RK, Zimmermann BG, Van Hummelen P, Prewett A, Rabinowitz M, Tabriziani H, Gauthier P, Billings P. Combining Donor-derived Cell-free DNA Fraction and Quantity to Detect Kidney Transplant Rejection Using Molecular Diagnoses and Histology as Confirmation. Transplantation 2022; 106:2435-2442. [PMID: 35765145 PMCID: PMC9698190 DOI: 10.1097/tp.0000000000004212] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/14/2022] [Accepted: 04/28/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Donor-derived cell-free DNA (dd-cfDNA) fraction and quantity have both been shown to be associated with allograft rejection. The present study compared the relative predictive power of each of these variables to the combination of the two, and developed an algorithm incorporating both variables to detect active rejection in renal allograft biopsies. METHODS The first 426 sequential indication biopsy samples collected from the Trifecta study ( ClinicalTrials.gov # NCT04239703) with microarray-derived gene expression and dd-cfDNA results were included. After exclusions to simulate intended clinical use, 367 samples were analyzed. Biopsies were assessed using the molecular microscope diagnostic system and histology (Banff 2019). Logistic regression analysis examined whether combining dd-cfDNA fraction and quantity adds predictive value to either alone. The first 149 sequential samples were used to develop a two-threshold algorithm and the next 218 to validate the algorithm. RESULTS In regression, the combination of dd-cfDNA fraction and quantity was found to be significantly more predictive than either variable alone ( P = 0.009 and P < 0.0001). In the test set, the area under the receiver operating characteristic curve of the two-variable system was 0.88, and performance of the two-threshold algorithm showed a sensitivity of 83.1% and specificity of 81.0% for molecular diagnoses and a sensitivity of 73.5% and specificity of 80.8% for histology diagnoses. CONCLUSIONS This prospective, biopsy-matched, multisite dd-cfDNA study in kidney transplant patients found that the combination of dd-cfDNA fraction and quantity was more powerful than either dd-cfDNA fraction or quantity alone and validated a novel two-threshold algorithm incorporating both variables.
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Affiliation(s)
- Philip F. Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, University of Alberta, Canada
| | - Jeff Reeve
- Alberta Transplant Applied Genomics Centre, Edmonton, University of Alberta, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - the Trifecta Investigators*
- Alberta Transplant Applied Genomics Centre, Edmonton, University of Alberta, Canada
- Natera Inc, San Carlos, CA
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3
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Ventura-Aguiar P, Ramirez-Bajo MJ, Rovira J, Bañón-Maneus E, Hierro N, Lazo M, Cuatrecasas M, Garcia-Criado M, Liang N, Swenerton RK, Cofan F, Cucchiari D, Esforzado N, Montagud-Marrahi E, Oppenheimer F, Piñeiro G, Revuelta I, Torregrosa V, Ahmed E, Soboleva K, Kaur N, Zimmermann BG, Al Haj Baddar N, Demko ZP, Escrig C, Tabriziani H, Gauthier P, Billings PR, Amor AJ, Ferrer J, Campistol JM, Diekmann F. Donor-derived Cell-free DNA Shows High Sensitivity for the Diagnosis of Pancreas Graft Rejection in Simultaneous Pancreas-kidney Transplantation. Transplantation 2022; 106:1690-1697. [PMID: 35289777 PMCID: PMC9311279 DOI: 10.1097/tp.0000000000004088] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/29/2021] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Pancreas graft status in simultaneous pancreas-kidney transplant (SPKTx) is currently assessed by nonspecific biochemical markers, typically amylase or lipase. Identifying a noninvasive biomarker with good sensitivity in detecting early pancreas graft rejection could improve SPKTx management. METHODS Here, we developed a pilot study to explore donor-derived cell-free DNA (dd-cfDNA) performance in predicting biopsy-proven acute rejection (P-BPAR) of the pancreas graft in a cohort of 36 SPKTx recipients with biopsy-matched plasma samples. dd-cfDNA was measured using the Prospera test (Natera, Inc.) and reported both as a fraction of the total cfDNA (fraction; %) and as concentration in the recipient's plasma (quantity; copies/mL). RESULTS In the absence of P-BPAR, dd-cfDNA was significantly higher in samples collected within the first 45 d after SPKTx compared with those measured afterward (median, 1.00% versus 0.30%; median, 128.2 versus 35.3 cp/mL, respectively with both; P = 0.001). In samples obtained beyond day 45, P-BPAR samples presented a significantly higher dd-cfDNA fraction (0.83 versus 0.30%; P = 0.006) and quantity (81.3 versus 35.3 cp/mL; P = 0.001) than stable samples. Incorporating dd-cfDNA quantity along with dd-cfDNA fraction outperformed dd-cfDNA fraction alone to detect active rejection. Notably, when using a quantity cutoff of 70 cp/mL, dd-cfDNA detected P-BPAR with a sensitivity of 85.7% and a specificity of 93.7%, which was more accurate than current biomarkers (area under curve of 0.89 for dd-cfDNA (cp/ml) compared with 0.74 of lipase and 0.46 for amylase). CONCLUSIONS dd-cfDNA measurement through a simple noninvasive blood test could be incorporated into clinical practice to help inform graft management in SPKTx patients.
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Affiliation(s)
- Pedro Ventura-Aguiar
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
| | - Maria Jose Ramirez-Bajo
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Jordi Rovira
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Elisenda Bañón-Maneus
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Natalia Hierro
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Marta Lazo
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Miriam Cuatrecasas
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
| | - M.A. Garcia-Criado
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
| | | | | | - Federic Cofan
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - David Cucchiari
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
| | - Nuria Esforzado
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
| | - Enrique Montagud-Marrahi
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
| | - Federic Oppenheimer
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Gaston Piñeiro
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
| | - Ignacio Revuelta
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Vicens Torregrosa
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
| | - Ebad Ahmed
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Karina Soboleva
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Navchetan Kaur
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Bernhard G. Zimmermann
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Nour Al Haj Baddar
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Zachary P. Demko
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Cesar Escrig
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Hossein Tabriziani
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Philippe Gauthier
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Paul R. Billings
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Antonio J. Amor
- Radiology Department, Center for Imaging Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Joana Ferrer
- Endocrinology Department, Hospital Clinic, Barcelona, Spain
| | - Josep M. Campistol
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Fritz Diekmann
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
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Loupakis F, Sharma S, Derouazi M, Murgioni S, Biason P, Rizzato MD, Rasola C, Renner D, Shchegrova S, Koyen Malashevich A, Malhotra M, Sethi H, Zimmermann BG, Aleshin A, Moshkevich S, Billings PR, Sedgwick JD, Schirripa M, Munari G, Cillo U, Pilati P, Dei Tos AP, Zagonel V, Lonardi S, Fassan M. Detection of Molecular Residual Disease Using Personalized Circulating Tumor DNA Assay in Patients With Colorectal Cancer Undergoing Resection of Metastases. JCO Precis Oncol 2021; 5:PO.21.00101. [PMID: 34327297 PMCID: PMC8315303 DOI: 10.1200/po.21.00101] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/16/2021] [Accepted: 06/16/2021] [Indexed: 02/07/2023] Open
Abstract
PURPOSE More than 50% of patients with stage IV colorectal cancer (metastatic colorectal cancer [mCRC]) relapse postresection. The efficacy of postoperative systemic treatment is limited in this setting. Thus, these patients would greatly benefit from the use of a reliable prognostic biomarker, such as circulating tumor DNA (ctDNA) to identify minimal or molecular residual disease (MRD). PATIENTS AND METHODS We analyzed a cohort of 112 patients with mCRC who had undergone metastatic resection with curative intent as part of the PREDATOR clinical trial. The study evaluated the prognostic value of ctDNA, correlating MRD status postsurgery with clinical outcomes by using a personalized and tumor-informed ctDNA assay (bespoke multiple PCR, next-generation sequencing assay). Postresection, systemic therapy was given to 39.2% of the patients at the discretion of the treating physician. RESULTS Postsurgical, MRD positivity was observed in 54.4% (61 of 112) of patients, of which 96.7% (59 of 61) progressed at the time of data cutoff (hazard ratio [HR]: 5.8; 95% CI, 3.5 to 9.7; P < .001). MRD-positive status was also associated with an inferior overall survival: HR: 16.0; 95% CI, 3.9 to 68.0; P < .001. At the time of analyses, 96% (49 of 51) of patients were alive in the MRD-negative arm compared with 52.4% (32 of 61) in the MRD-positive arm. Patients who did not receive systemic therapy and were MRD-negative in the combined ctDNA analysis at two time points had an overall survival of 100%. In the multivariate analysis, ctDNA-based MRD status was the most significant prognostic factor associated with disease-free survival (HR: 5.78; 95% CI, 3.34 to 10.0; P < .001). CONCLUSION This study confirms that in mCRC undergoing resection of metastases, postoperative MRD analysis is a strong prognostic biomarker. It holds promises for being implemented in clinical decision making, informing clinical trial design, and further translational research.
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Affiliation(s)
- Fotios Loupakis
- Oncology Unit 1, Department Oncology, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Veneto, Italy
| | | | - Madiha Derouazi
- Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT
- AMAL Therapeutics, Genève, Switzerland
| | - Sabina Murgioni
- Oncology Unit 1, Department Oncology, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Veneto, Italy
| | - Paola Biason
- Oncology Unit 1, Department Oncology, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Veneto, Italy
| | - Mario Domenico Rizzato
- Oncology Unit 1, Department Oncology, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Veneto, Italy
| | - Cosimo Rasola
- Oncology Unit 1, Department Oncology, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Veneto, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | | | | | | | | | | | | | | | | | | | - Jonathon D. Sedgwick
- Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT
| | - Marta Schirripa
- Oncology Unit 1, Department Oncology, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Veneto, Italy
| | - Giada Munari
- Oncology Unit 1, Department Oncology, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Veneto, Italy
| | - Umberto Cillo
- Hepatobiliary Surgery and Liver Transplant Unit, Department of Surgery, Oncology and Gastroenterology, University of Padua, Italy
| | - Pierluigi Pilati
- Unit of Surgical Oncology of the Digestive Tract, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy
| | - Angelo Paolo Dei Tos
- Unit of Surgical Pathology, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Vittorina Zagonel
- Oncology Unit 1, Department Oncology, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Veneto, Italy
| | - Sara Lonardi
- Oncology Unit 3, Department of Oncology, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Castelfranco Veneto, Veneto, Italy
- Early Phase Clinical Trial Unit, Department of Oncology, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Veneto, Italy
| | - Matteo Fassan
- Unit of Surgical Pathology, Department of Medicine (DIMED), University of Padua, Padua, Italy
- Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Veneto, Italy
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5
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Henriksen TV, Reinert T, Christensen E, Sethi H, Birkenkamp-Demtröder K, Gögenur M, Gögenur I, Zimmermann BG, Dyrskjøt L, Andersen CL. The effect of surgical trauma on circulating free DNA levels in cancer patients-implications for studies of circulating tumor DNA. Mol Oncol 2020; 14:1670-1679. [PMID: 32471011 PMCID: PMC7400779 DOI: 10.1002/1878-0261.12729] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [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: 01/16/2020] [Revised: 04/01/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
Detection of circulating tumor DNA (ctDNA) post‐treatment is an emerging marker of residual disease. ctDNA constitutes only a minor fraction of the cell‐free DNA (cfDNA) circulating in cancer patients, complicating ctDNA detection. This is exacerbated by trauma‐induced cfDNA. To guide optimal blood sample timing, we investigated the duration and magnitude of surgical trauma‐induced cfDNA in patients with colorectal or bladder cancer. DNA levels were quantified in paired plasma samples collected before and up to 6 weeks after surgery from 436 patients with colorectal cancer and 47 patients with muscle‐invasive bladder cancer. To assess whether trauma‐induced cfDNA fragments are longer than ordinary cfDNA fragments, the concentration of short (< 1 kb) and long (> 1 kb) fragments was determined for 91 patients. Previously reported ctDNA data from 91 patients with colorectal cancer and 47 patients with bladder cancer were used to assess how trauma‐induced DNA affects ctDNA detection. The total cfDNA level increased postoperatively—both in patients with colorectal cancer (mean threefold) and bladder cancer (mean eightfold). The DNA levels were significantly increased up to 4 weeks after surgery in both patient cohorts (P = 0.0005 and P ≤ 0.0001). The concentration of short, but not long, cfDNA fragments increased postoperatively. Of 25 patients with radiological relapse, eight were ctDNA‐positive and 17 were ctDNA‐negative in the period with trauma‐induced DNA. Analysis of longitudinal samples revealed that five of the negative patients became positive shortly after the release of trauma‐induced cfDNA had ceased. In conclusion, surgery was associated with elevated cfDNA levels, persisting up to 4 weeks, which may have masked ctDNA in relapse patients. Trauma‐induced cfDNA was of similar size to ordinary cfDNA. To mitigate the impact of trauma‐induced cfDNA on ctDNA detection, it is recommended that a second blood sample collected after week 4 is analyzed for patients initially ctDNA negative.
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Affiliation(s)
- Tenna V Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Thomas Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Emil Christensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | | | | | - Mikail Gögenur
- Center for Surgical Sciences, Zealand University Hospital, Køge, Denmark
| | - Ismail Gögenur
- Center for Surgical Sciences, Zealand University Hospital, Køge, Denmark
| | | | | | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
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6
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Reinert T, Henriksen TV, Christensen E, Sharma S, Salari R, Sethi H, Knudsen M, Nordentoft I, Wu HT, Tin AS, Heilskov Rasmussen M, Vang S, Shchegrova S, Frydendahl Boll Johansen A, Srinivasan R, Assaf Z, Balcioglu M, Olson A, Dashner S, Hafez D, Navarro S, Goel S, Rabinowitz M, Billings P, Sigurjonsson S, Dyrskjøt L, Swenerton R, Aleshin A, Laurberg S, Husted Madsen A, Kannerup AS, Stribolt K, Palmelund Krag S, Iversen LH, Gotschalck Sunesen K, Lin CHJ, Zimmermann BG, Lindbjerg Andersen C. Analysis of Plasma Cell-Free DNA by Ultradeep Sequencing in Patients With Stages I to III Colorectal Cancer. JAMA Oncol 2019; 5:1124-1131. [PMID: 31070691 PMCID: PMC6512280 DOI: 10.1001/jamaoncol.2019.0528] [Citation(s) in RCA: 466] [Impact Index Per Article: 93.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Importance Novel sensitive methods for detection and monitoring of residual disease can improve postoperative risk stratification with implications for patient selection for adjuvant chemotherapy (ACT), ACT duration, intensity of radiologic surveillance, and, ultimately, outcome for patients with colorectal cancer (CRC). Objective To investigate the association of circulating tumor DNA (ctDNA) with recurrence using longitudinal data from ultradeep sequencing of plasma cell-free DNA in patients with CRC before and after surgery, during and after ACT, and during surveillance. Design, Setting, and Participants In this prospective, multicenter cohort study, ctDNA was quantified in the preoperative and postoperative settings of stages I to III CRC by personalized multiplex, polymerase chain reaction-based, next-generation sequencing. The study enrolled 130 patients at the surgical departments of Aarhus University Hospital, Randers Hospital, and Herning Hospital in Denmark from May 1, 2014, to January 31, 2017. Plasma samples (n = 829) were collected before surgery, postoperatively at day 30, and every third month for up to 3 years. Main Outcomes and Measures Outcomes were ctDNA measurement, clinical recurrence, and recurrence-free survival. Results A total of 130 patients with stages I to III CRC (mean [SD] age, 67.9 [10.1] years; 74 [56.9%] male) were enrolled in the study; 5 patients discontinued participation, leaving 125 patients for analysis. Preoperatively, ctDNA was detectable in 108 of 122 patients (88.5%). After definitive treatment, longitudinal ctDNA analysis identified 14 of 16 relapses (87.5%). At postoperative day 30, ctDNA-positive patients were 7 times more likely to relapse than ctDNA-negative patients (hazard ratio [HR], 7.2; 95% CI, 2.7-19.0; P < .001). Similarly, shortly after ACT ctDNA-positive patients were 17 times (HR, 17.5; 95% CI, 5.4-56.5; P < .001) more likely to relapse. All 7 patients who were ctDNA positive after ACT experienced relapse. Monitoring during and after ACT indicated that 3 of the 10 ctDNA-positive patients (30.0%) were cleared by ACT. During surveillance after definitive therapy, ctDNA-positive patients were more than 40 times more likely to experience disease recurrence than ctDNA-negative patients (HR, 43.5; 95% CI, 9.8-193.5 P < .001). In all multivariate analyses, ctDNA status was independently associated with relapse after adjusting for known clinicopathologic risk factors. Serial ctDNA analyses revealed disease recurrence up to 16.5 months ahead of standard-of-care radiologic imaging (mean, 8.7 months; range, 0.8-16.5 months). Actionable mutations were identified in 81.8% of the ctDNA-positive relapse samples. Conclusions and Relevance Circulating tumor DNA analysis can potentially change the postoperative management of CRC by enabling risk stratification, ACT monitoring, and early relapse detection.
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Affiliation(s)
- Thomas Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | - Emil Christensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | - Michael Knudsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Søren Laurberg
- Department of Surgery, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Katrine Stribolt
- Department of Pathology, Regional Hospital Randers, Randers, Denmark
| | | | - Lene H Iversen
- Department of Surgery, Aarhus University Hospital, Aarhus, Denmark
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7
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Coombes RC, Page K, Salari R, Hastings RK, Armstrong A, Ahmed S, Ali S, Cleator S, Kenny L, Stebbing J, Rutherford M, Sethi H, Boydell A, Swenerton R, Fernandez-Garcia D, Gleason KLT, Goddard K, Guttery DS, Assaf ZJ, Wu HT, Natarajan P, Moore DA, Primrose L, Dashner S, Tin AS, Balcioglu M, Srinivasan R, Shchegrova SV, Olson A, Hafez D, Billings P, Aleshin A, Rehman F, Toghill BJ, Hills A, Louie MC, Lin CHJ, Zimmermann BG, Shaw JA. Personalized Detection of Circulating Tumor DNA Antedates Breast Cancer Metastatic Recurrence. Clin Cancer Res 2019; 25:4255-4263. [PMID: 30992300 DOI: 10.1158/1078-0432.ccr-18-3663] [Citation(s) in RCA: 231] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/06/2019] [Accepted: 04/11/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Up to 30% of patients with breast cancer relapse after primary treatment. There are no sensitive and reliable tests to monitor these patients and detect distant metastases before overt recurrence. Here, we demonstrate the use of personalized circulating tumor DNA (ctDNA) profiling for detection of recurrence in breast cancer. EXPERIMENTAL DESIGN Forty-nine primary patients with breast cancer were recruited following surgery and adjuvant therapy. Plasma samples (n = 208) were collected every 6 months for up to 4 years. Personalized assays targeting 16 variants selected from primary tumor whole-exome data were tested in serial plasma for the presence of ctDNA by ultradeep sequencing (average >100,000X). RESULTS Plasma ctDNA was detected ahead of clinical or radiologic relapse in 16 of the 18 relapsed patients (sensitivity of 89%); metastatic relapse was predicted with a lead time of up to 2 years (median, 8.9 months; range, 0.5-24.0 months). None of the 31 nonrelapsing patients were ctDNA-positive at any time point across 156 plasma samples (specificity of 100%). Of the two relapsed patients who were not detected in the study, the first had only a local recurrence, whereas the second patient had bone recurrence and had completed chemotherapy just 13 days prior to blood sampling. CONCLUSIONS This study demonstrates that patient-specific ctDNA analysis can be a sensitive and specific approach for disease surveillance for patients with breast cancer. More importantly, earlier detection of up to 2 years provides a possible window for therapeutic intervention.
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Affiliation(s)
| | - Karen Page
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | | | - Robert K Hastings
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | - Anne Armstrong
- The Christie Foundation NHS Trust, Manchester, United Kingdom
| | - Samreen Ahmed
- Leicester Royal Infirmary, UHL NHS Trust, Leicester, United Kingdom
| | - Simak Ali
- Imperial College London, London, United Kingdom
| | | | - Laura Kenny
- Imperial College London, London, United Kingdom
| | | | - Mark Rutherford
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | | | | | | | | | | | | | - David S Guttery
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | | | | | | | - David A Moore
- University College London, Bloomsbury, London, United Kingdom
| | - Lindsay Primrose
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | - Bradley J Toghill
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | | | | | | | | | - Jaqueline A Shaw
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
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8
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Coombes RC, Armstrong A, Ahmed S, Page K, Hastings RK, Salari R, Sethi H, Boydell AR, Shchegrova SV, Fernandez-Garcia D, Gleason KL, Goddard K, Guttery DS, Assaf ZJ, Balcioglu M, Moore DA, Primrose L, Navarro SL, Aleshin A, Rehman F, Toghill BJ, Louie MC, Zimmermann BG, Lin CHJ, Shaw JA. Abstract P4-01-02: Early detection of residual breast cancer through a robust, scalable and personalized analysis of circulating tumour DNA (ctDNA) antedates overt metastatic recurrence. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p4-01-02] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background:
Many breast cancer patients relapse after primary treatment but there are no reliable tests to detect distant metastases before they become overt. Here we show earlier identification of recurring patients through a scalable personalised ctDNA analysis. The method is applicable to all patients, and not limited to hot-spot mutations typically detected by gene panels.
Methods:
Forty-nine non-metastatic breast cancer patients were recruited following surgery and adjuvant therapy. Plasma samples (n=208) were serially collected semi-annually. Using the analytically validated SignateraTM workflow, we determined mutational signatures from primary tumour whole exome data and designed personalised assays targeting 16 variants with high sensitivity by ultra-deep sequencing (average >100,000X). The patient-specific assay was used to detect the presence of the mutational signature in the plasma.
Results:
In 16 of 18 (89%) clinically-relapsing patients, ctDNA was detected ahead of metastatic relapse being diagnosed by clinical examination, radiological and biochemical (CA15-3) measurements, and remained ctDNA-positive through follow-up. Of the 2 patients not detected by ctDNA, one had a small local recurrence only (now resected) and the other had three primary tumours. None of the 31 non-relapsing patients were ctDNA-positive at any time point (n=142). Metastatic relapse was predicted by Signatera with high accuracy and a lead time of up to 2 years (median=9.5 months).
Conclusions:
The use of a scalable patient-specific ctDNA-based validated workflow detects breast cancer recurrence ahead of clinical detection. Accurate and earlier prediction by ctDNA analysis could provide a means of monitoring breast cancer patients in need of second-line salvage adjuvant therapy in order to prevent overt life-threatening metastatic progression.
Citation Format: Coombes RC, Armstrong A, Ahmed S, Page K, Hastings RK, Salari R, Sethi H, Boydell A-R, Shchegrova SV, Fernandez-Garcia D, Gleason KL, Goddard K, Guttery DS, Assaf ZJ, Balcioglu M, Moore DA, Primrose L, Navarro SL, Aleshin A, Rehman F, Toghill BJ, Louie MC, Zimmermann BG, Lin C-HJ, Shaw JA. Early detection of residual breast cancer through a robust, scalable and personalized analysis of circulating tumour DNA (ctDNA) antedates overt metastatic recurrence [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-01-02.
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Affiliation(s)
- RC Coombes
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - A Armstrong
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - S Ahmed
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - K Page
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - RK Hastings
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - R Salari
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - H Sethi
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - A-R Boydell
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - SV Shchegrova
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - D Fernandez-Garcia
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - KL Gleason
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - K Goddard
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - DS Guttery
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - ZJ Assaf
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - M Balcioglu
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - DA Moore
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - L Primrose
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - SL Navarro
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - A Aleshin
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - F Rehman
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - BJ Toghill
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - MC Louie
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - BG Zimmermann
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - C-HJ Lin
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
| | - JA Shaw
- Imperial College London, London, United Kingdom; Leicester Infirmary, Leicester, United Kingdom; The Christie Foundation NHS Trust, Manchester, United Kingdom; Natera, San Carlos, CA; University of Leicester, Leicester, United Kingdom
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9
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Abbosh C, Birkbak NJ, Wilson GA, Jamal-Hanjani M, Constantin T, Salari R, Le Quesne J, Moore DA, Veeriah S, Rosenthal R, Marafioti T, Kirkizlar E, Watkins TBK, McGranahan N, Ward S, Martinson L, Riley J, Fraioli F, Al Bakir M, Grönroos E, Zambrana F, Endozo R, Bi WL, Fennessy FM, Sponer N, Johnson D, Laycock J, Shafi S, Czyzewska-Khan J, Rowan A, Chambers T, Matthews N, Turajlic S, Hiley C, Lee SM, Forster MD, Ahmad T, Falzon M, Borg E, Lawrence D, Hayward M, Kolvekar S, Panagiotopoulos N, Janes SM, Thakrar R, Ahmed A, Blackhall F, Summers Y, Hafez D, Naik A, Ganguly A, Kareht S, Shah R, Joseph L, Quinn AM, Crosbie PA, Naidu B, Middleton G, Langman G, Trotter S, Nicolson M, Remmen H, Kerr K, Chetty M, Gomersall L, Fennell DA, Nakas A, Rathinam S, Anand G, Khan S, Russell P, Ezhil V, Ismail B, Irvin-Sellers M, Prakash V, Lester JF, Kornaszewska M, Attanoos R, Adams H, Davies H, Oukrif D, Akarca AU, Hartley JA, Lowe HL, Lock S, Iles N, Bell H, Ngai Y, Elgar G, Szallasi Z, Schwarz RF, Herrero J, Stewart A, Quezada SA, Peggs KS, Van Loo P, Dive C, Lin CJ, Rabinowitz M, Aerts HJWL, Hackshaw A, Shaw JA, Zimmermann BG, Swanton C. Corrigendum: Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature 2018; 554:264. [PMID: 29258292 DOI: 10.1038/nature25161] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This corrects the article DOI: 10.1038/nature22364.
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10
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Abbosh C, Birkbak NJ, Wilson GA, Jamal-Hanjani M, Constantin T, Salari R, Le Quesne J, Moore DA, Veeriah S, Rosenthal R, Marafioti T, Kirkizlar E, Watkins TBK, McGranahan N, Ward S, Martinson L, Riley J, Fraioli F, Al Bakir M, Grönroos E, Zambrana F, Endozo R, Bi WL, Fennessy FM, Sponer N, Johnson D, Laycock J, Shafi S, Czyzewska-Khan J, Rowan A, Chambers T, Matthews N, Turajlic S, Hiley C, Lee SM, Forster MD, Ahmad T, Falzon M, Borg E, Lawrence D, Hayward M, Kolvekar S, Panagiotopoulos N, Janes SM, Thakrar R, Ahmed A, Blackhall F, Summers Y, Hafez D, Naik A, Ganguly A, Kareht S, Shah R, Joseph L, Marie Quinn A, Crosbie PA, Naidu B, Middleton G, Langman G, Trotter S, Nicolson M, Remmen H, Kerr K, Chetty M, Gomersall L, Fennell DA, Nakas A, Rathinam S, Anand G, Khan S, Russell P, Ezhil V, Ismail B, Irvin-Sellers M, Prakash V, Lester JF, Kornaszewska M, Attanoos R, Adams H, Davies H, Oukrif D, Akarca AU, Hartley JA, Lowe HL, Lock S, Iles N, Bell H, Ngai Y, Elgar G, Szallasi Z, Schwarz RF, Herrero J, Stewart A, Quezada SA, Peggs KS, Van Loo P, Dive C, Lin CJ, Rabinowitz M, Aerts HJWL, Hackshaw A, Shaw JA, Zimmermann BG, Swanton C. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature 2017; 545:446-451. [PMID: 28445469 PMCID: PMC5812436 DOI: 10.1038/nature22364] [Citation(s) in RCA: 1092] [Impact Index Per Article: 156.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/13/2017] [Indexed: 12/13/2022]
Abstract
The early detection of relapse following primary surgery for non-small-cell lung cancer and the characterization of emerging subclones, which seed metastatic sites, might offer new therapeutic approaches for limiting tumour recurrence. The ability to track the evolutionary dynamics of early-stage lung cancer non-invasively in circulating tumour DNA (ctDNA) has not yet been demonstrated. Here we use a tumour-specific phylogenetic approach to profile the ctDNA of the first 100 TRACERx (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy (Rx)) study participants, including one patient who was also recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and analyse the tumour-volume detection limit. Through blinded profiling of postoperative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients who are very likely to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastasis, providing a new approach for ctDNA-driven therapeutic studies.
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MESH Headings
- Biopsy/methods
- Carcinoma, Non-Small-Cell Lung/blood
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/surgery
- Cell Lineage/genetics
- Cell Tracking
- Clone Cells/metabolism
- Clone Cells/pathology
- DNA Mutational Analysis
- DNA, Neoplasm/blood
- DNA, Neoplasm/genetics
- Disease Progression
- Drug Resistance, Neoplasm/genetics
- Early Detection of Cancer/methods
- Evolution, Molecular
- Humans
- Limit of Detection
- Lung Neoplasms/blood
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Lung Neoplasms/surgery
- Multiplex Polymerase Chain Reaction
- Neoplasm Metastasis/diagnosis
- Neoplasm Metastasis/genetics
- Neoplasm Metastasis/pathology
- Neoplasm Recurrence, Local/diagnosis
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/pathology
- Postoperative Care/methods
- Reproducibility of Results
- Tumor Burden
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Affiliation(s)
- Christopher Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gareth A Wilson
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Tudor Constantin
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Raheleh Salari
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - John Le Quesne
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - David A Moore
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Teresa Marafioti
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Pathology, University College London Hospitals, 21 University Street, London WC1 6JJ, UK
| | - Eser Kirkizlar
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Thomas B K Watkins
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Luke Martinson
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Joan Riley
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Francesco Fraioli
- Department of Nuclear Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London, NW1 2BU, UK
| | - Maise Al Bakir
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Eva Grönroos
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Francisco Zambrana
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Raymondo Endozo
- Department of Nuclear Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London, NW1 2BU, UK
| | - Wenya Linda Bi
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fiona M Fennessy
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicole Sponer
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Diana Johnson
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Joanne Laycock
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Seema Shafi
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Justyna Czyzewska-Khan
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Andrew Rowan
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tim Chambers
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nik Matthews
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Tumour Profiling Unit Genomics Facility, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Samra Turajlic
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Crispin Hiley
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Siow Ming Lee
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Oncology, University College London Hospitals, 250 Euston Road, London NW1 2BU, UK
| | - Martin D Forster
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Oncology, University College London Hospitals, 250 Euston Road, London NW1 2BU, UK
| | - Tanya Ahmad
- Department of Oncology, University College London Hospitals, 250 Euston Road, London NW1 2BU, UK
| | - Mary Falzon
- Department of Pathology, University College London Hospitals, 21 University Street, London WC1 6JJ, UK
| | - Elaine Borg
- Department of Pathology, University College London Hospitals, 21 University Street, London WC1 6JJ, UK
| | - David Lawrence
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Martin Hayward
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Shyam Kolvekar
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Nikolaos Panagiotopoulos
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Sam M Janes
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Respiratory Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, Rayne Building, University College London, 5 University Street, London WC1E 6JF, UK
| | - Ricky Thakrar
- Department of Respiratory Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Asia Ahmed
- Department of Radiology, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Fiona Blackhall
- Institute of Cancer Studies, University of Manchester, Oxford Road, Manchester M13 9PL, UK
- The Christie Hospital, Manchester M20 4BX, UK
| | | | - Dina Hafez
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Ashwini Naik
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Apratim Ganguly
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Stephanie Kareht
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Rajesh Shah
- Department of Cardiothoracic Surgery, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Leena Joseph
- Department of Pathology, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Anne Marie Quinn
- Department of Pathology, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Phil A Crosbie
- North West Lung Centre, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Babu Naidu
- Department of Thoracic Surgery, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK. University College London Hospitals NHS Foundation Trust, London, UK
| | - Gary Middleton
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Gerald Langman
- Department of Cellular Pathology, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
| | - Simon Trotter
- Department of Cellular Pathology, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
| | - Marianne Nicolson
- Department of Medical Oncology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - Hardy Remmen
- Department of Cardiothoracic Surgery, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZD, UK
| | - Keith Kerr
- Department of Pathology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZD, UK
| | - Mahendran Chetty
- Department of Respiratory Medicine, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - Lesley Gomersall
- Department of Radiology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - Dean A Fennell
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Apostolos Nakas
- Department of Thoracic Surgery, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Sridhar Rathinam
- Department of Thoracic Surgery, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Girija Anand
- Department of Radiotherapy, North Middlesex University Hospital, London N18 1QX, UK
| | - Sajid Khan
- Department of Respiratory Medicine, Royal Free Hospital, Pond Street, London NW3 2QG, UK
- Department of Respiratory Medicine, Barnet and Chase Farm Hospitals, Wellhouse Lane, Barnet EN5 3DJ, UK
| | - Peter Russell
- Department of Respiratory Medicine, The Princess Alexandra Hospital, Hamstel Road, Harlow CM20 1QX, UK
| | - Veni Ezhil
- Department of Clinical Oncology, St.Luke's Cancer Centre, Royal Surrey County Hospital, Guildford GU2 7XX, UK
| | - Babikir Ismail
- Department of Pathology, Ashford and St. Peter's Hospital, Guildford Road, Chertsey, Surrey KT16 0PZ, UK
| | - Melanie Irvin-Sellers
- Department of Respiratory Medicine, Ashford and St. Peter's Hospital, Guildford Road, Chertsey, Surrey KT16 0PZ, UK
| | - Vineet Prakash
- Department of Radiology, Ashford and St. Peter's Hospital, Guildford Road, Chertsey, Surrey KT16 0PZ, UK
| | - Jason F Lester
- Department of Clinical Oncology, Velindre Hospital, Cardiff CF14 2TL, UK
| | | | - Richard Attanoos
- Department of Cellular Pathology, University Hospital of Wales and Cardiff University, Heath Park, Cardiff, UK
| | - Haydn Adams
- Department of Radiology, University Hospital Llandough, Cardiff CF64 2XX, UK
| | - Helen Davies
- Department of Respiratory Medicine, University Hospital Llandough, Cardiff CF64 2XX, UK
| | - Dahmane Oukrif
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Ayse U Akarca
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - John A Hartley
- University College London Experimental Cancer Medicine Centre GCLP Facility, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Helen L Lowe
- University College London Experimental Cancer Medicine Centre GCLP Facility, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Sara Lock
- Department of Respiratory Medicine, The Whittington Hospital NHS Trust, London, N19 5NF, UK
| | - Natasha Iles
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Harriet Bell
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Yenting Ngai
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Greg Elgar
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Zoltan Szallasi
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- MTA-SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, 1091 Budapest, Hungary
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Aengus Stewart
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Karl S Peggs
- Cancer Immunology Unit, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Research Department of Haematology, University College Cancer Institute, London WC1E 6DD, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Human Genetics, University of Leuven, B-3000 Leuven, Belgium
| | - Caroline Dive
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - C Jimmy Lin
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | | | - Hugo J W L Aerts
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215-5450, USA
| | - Allan Hackshaw
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Jacqui A Shaw
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | | | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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11
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Pelham RJ, Zimmermann BG, Kirkizlar E, Swenerton RK, Hoang B, Sakarya O, Babiarz JE, Wayham N, Constantin T, Sigurjonsson S, Rabinowitz M, Hill M. Abstract P4-02-03: Detection of single nucleotide variations and copy number variations in breast cancer tissue and ctDNA samples using single-nucleotide polymorphism-targeted massively multiplexed PCR. Cancer Res 2015. [DOI: 10.1158/1538-7445.sabcs14-p4-02-03] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genomic instability, the hallmark of cancer, presents with a variety of mutation types, most commonly single nucleotide variations (SNVs) and copy number variations (CNVs), which traditionally have required different methods for identification. It has proven challenging to simultaneously achieve sufficient breadth to detect CNVs and depth to detect SNVs on samples of limited input amount. The objective of this study was to validate a new methodology for detection of SNVs and CNVs in a single assay. We used a massively multiplex PCR/NGS approach combining an SNV panel covering 585 point mutation hotspots in breast cancer (Cosmic) and a CNV panel targeting 28,000 SNPs designed to detect copy number at chromosomes 1, 2, 13, 18, 21, and X, and focal regions 4p16, 5p15, 7q11, 15q, 17p, 22q11, and 22q13. We applied these panels to breast cancer cell lines and fresh frozen (FF) breast tumor samples; the presence of CNVs in circulating cell-free tumor DNA (ctDNA) in the plasma of breast cancer patients was also investigated.
The CNV assay methodology was validated using genomic DNA isolated from 96 human samples with known karyotype; sensitivity to single region deletions or duplications was 100% (71/71) and specificity was 100% for normal regions in the same samples. Single-molecule sensitivity for the detection of CNVs was established by analyzing isolated single cells. Performance of the mutation assay was demonstrated with the analysis of 5 matched tumor and normal cell lines, with 24 out of 27 SNVs known to be present in these cell lines detected. The 3 undetected SNVs were determined to be a result of assay design failure. Also, multiple somatic CNVs (median: 13) were detected in all 5 tumor cell lines. Analysis of the normal cell lines found no cancer related SNVs or CNVs.
In 32 FF tumor samples, 78.1% (25/32) had SNVs detected; of samples with SNVs, 88% (22/25) had SNVs in TP53 or PIK3CA. Of the same 32 FF breast tumor samples, 96.9% (31/32) showed full or partial CNVs in at least 1 and up to 15 regions; of the 31 samples with detected CNVs, 93.5% had a CNV of either 1q or 17p, two of the three most prevalent breast cancer CNVs (the 16q region was not represented in this panel). Overall, a combination of SNV and CNV testing allowed identification of genetic changes in 100% of the breast tumor samples, a significant improvement in diagnostic yield than using SNV detection alone.
Of the 12 breast cancer patients with matched tumor tissue and plasma samples, 83.3% (10/12) had CNVs detected in tissue. The CNVs present in each primary tumor sample were identified in corresponding plasma ctDNA samples (1 stage IIa, 7 stage IIb, and 2 stage III). The ctDNA fractions in these samples ranged from 0.58 to 4.33%; detection required as few as 86 heterozygous SNPs per CNV.
Analysis of ctDNA for cancer-associated mutations may allow earlier, safer and more accurate profiling and monitoring of breast cancer. Thus, this targeted PCR approach offers the promise of an assay able to detect both cancer-associated SNVs and CNVs in the same sample with good sensitivity and specificity, and improved detection rates compared to assays that only detect SNVs.
Citation Format: Robert J Pelham, Bernhard G Zimmermann, Eser Kirkizlar, Ryan K Swenerton, Bin Hoang, Onur Sakarya, Joshua E Babiarz, Nicholas Wayham, Tudor Constantin, Styrmir Sigurjonsson, Matthew Rabinowitz, Matthew Hill. Detection of single nucleotide variations and copy number variations in breast cancer tissue and ctDNA samples using single-nucleotide polymorphism-targeted massively multiplexed PCR [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-02-03.
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Zimmermann BG, Kirkizlar E, Hill M, Constantin T, Sigurjonsson S, Hoanga B, Chopra N, Rabinowitz M. Non-invasive Cell-free Tumor DNA-based Detection of Breast Cancer-related Copy Number Variations. Cancer Genet 2014. [DOI: 10.1016/j.cancergen.2014.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Babiarz JE, Zimmermann BG, Constantin T, Swenerton R, Kirkizlar E, Wayham N, Rabinowitz M, Hill M. Detection of Copy Number Variations in Breast Cancer Samples Using Single-nucleotide Polymorphism-targeted Massively Multiplexed PCR. Cancer Genet 2014. [DOI: 10.1016/j.cancergen.2014.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Barrett AN, Zimmermann BG, Wang D, Holloway A, Chitty LS. Implementing prenatal diagnosis based on cell-free fetal DNA: accurate identification of factors affecting fetal DNA yield. PLoS One 2011; 6:e25202. [PMID: 21998643 PMCID: PMC3187716 DOI: 10.1371/journal.pone.0025202] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 08/30/2011] [Indexed: 11/18/2022] Open
Abstract
Objective Cell-free fetal DNA is a source of fetal genetic material that can be used for non-invasive prenatal diagnosis. Usually constituting less than 10% of the total cell free DNA in maternal plasma, the majority is maternal in origin. Optimizing conditions for maximizing yield of cell-free fetal DNA will be crucial for effective implementation of testing. We explore factors influencing yield of fetal DNA from maternal blood samples, including assessment of collection tubes containing cell-stabilizing agents, storage temperature, interval to sample processing and DNA extraction method used. Methods Microfluidic digital PCR was performed to precisely quantify male (fetal) DNA, total DNA and long DNA fragments (indicative of maternal cellular DNA). Real-time qPCR was used to assay for the presence of male SRY signal in samples. Results Total cell-free DNA quantity increased significantly with time in samples stored in K3EDTA tubes, but only minimally in cell stabilizing tubes. This increase was solely due to the presence of additional long fragment DNA, with no change in quantity of fetal or short DNA, resulting in a significant decrease in proportion of cell-free fetal DNA over time. Storage at 4°C did not prevent these changes. Conclusion When samples can be processed within eight hours of blood draw, K3EDTA tubes can be used. Prolonged transfer times in K3EDTA tubes should be avoided as the proportion of fetal DNA present decreases significantly; in these situations the use of cell stabilising tubes is preferable. The DNA extraction kit used may influence success rate of diagnostic tests.
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Affiliation(s)
- Angela N. Barrett
- NE Thames Regional Molecular Genetics Laboratories, Great Ormond Street Hospital for Children, London, United Kingdom
- University College London Institute of Child Health, London, United Kingdom
| | | | - Darrell Wang
- University College London Institute of Child Health, London, United Kingdom
| | - Andrew Holloway
- University College Hospital NHS Foundation Trust, London, United Kingdom
| | - Lyn S. Chitty
- University College London Institute of Child Health, London, United Kingdom
- University College Hospital NHS Foundation Trust, London, United Kingdom
- * E-mail:
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Abstract
Prenatal diagnosis of fetal aneuploidies and chromosomal anomalies is likely to undergo a profound change in the near future. On the one hand this is mediated by new technical developments, such as chromosomal microarrays, which allow a much more precise delineation of minute sub-microscopic chromosomal aberrancies than the classical G-band karyotype. This will be of particular interest when investigating pregnancies at risk of unexplained development delay, intellectual disability or certain forms of autism. On the other hand, great strides have been made in the non-invasive determination of fetal genetic traits, largely through the analysis of cell-free fetal nucleic acids. It is hoped that, with the assistance of cutting-edge tools such as digital PCR or next generation sequencing, the long elusive goal of non-invasive prenatal diagnosis for fetal aneuploidies can finally be attained.
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Affiliation(s)
- Sinuhe Hahn
- Department of Biomedicine, University Women's Hospital, University Clinics Basel, Hebelstrasse 20, CH-4031, Switzerland.
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Sikora A, Zimmermann BG, Rusterholz C, Birri D, Kolla V, Lapaire O, Hoesli I, Kiefer V, Jackson L, Hahn S. Detection of Increased Amounts of Cell-Free Fetal DNA with Short PCR Amplicons. Clin Chem 2010; 56:136-8. [DOI: 10.1373/clinchem.2009.132951] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Aim: A digital PCR approach has recently been suggested to detect greater amounts of cell-free fetal DNA in maternal plasma than conventional real-time quantitative PCR (qPCR). Because the digital qPCR approach uses shorter PCR amplicons than the real-time qPCR assay, we investigated whether a real-time qPCR assay appropriately modified for such short amplicons would improve the detection of cell-free fetal DNA.
Method: We developed a novel universal-template (UT) real-time qPCR assay that was specific for the DYS14 sequence on Y chromosome and had a short amplicon size of 50 bp. We examined this “short” assay with 50 maternal plasma samples and compared the results with those for a conventional real-time qPCR assay of the same locus but with a longer amplicon (84 bp).
Results: Qualitatively, both assays detected male cell-free fetal DNA with the same specificity and detection capability. Quantitatively, however, the new UT real-time qPCR assay for shorter amplicons detected, on average, almost 1.6-fold more cell-free fetal DNA than the conventional real-time qPCR assay with longer amplicons.
Conclusions: The use of short PCR amplicons improves the detection of cell-free fetal DNA. This feature may prove useful in attempts to detect cell-free fetal DNA under conditions in which the amount of template is low, such as in samples obtained early in pregnancy.
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Affiliation(s)
- Aleksandra Sikora
- University Women’s Hospital, Department of Biomedicine, Basel, Switzerland
| | | | - Corinne Rusterholz
- University Women’s Hospital, Department of Biomedicine, Basel, Switzerland
| | - Daniella Birri
- University Women’s Hospital, Department of Biomedicine, Basel, Switzerland
| | - Varaprasad Kolla
- University Women’s Hospital, Department of Biomedicine, Basel, Switzerland
| | - Olav Lapaire
- University Women’s Hospital, Department of Biomedicine, Basel, Switzerland
| | - Irene Hoesli
- University Women’s Hospital, Department of Biomedicine, Basel, Switzerland
| | - Vivian Kiefer
- University Women’s Hospital, Department of Biomedicine, Basel, Switzerland
| | - Laird Jackson
- Division of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA
| | - Sinuhe Hahn
- University Women’s Hospital, Department of Biomedicine, Basel, Switzerland
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Zimmermann BG, Grill S, Holzgreve W, Zhong XY, Jackson LG, Hahn S. Digital PCR: a powerful new tool for noninvasive prenatal diagnosis? Prenat Diagn 2009; 28:1087-93. [PMID: 19003785 DOI: 10.1002/pd.2150] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent reports have indicated that digital PCR may be useful for the noninvasive detection of fetal aneuploidies by the analysis of cell-free DNA and RNA in maternal plasma or serum. In this review we provide an insight into the underlying technology and its previous application in the determination of the allelic frequencies of oncogenic alterations in cancer specimens. We also provide an indication of how this new technology may prove useful for the detection of fetal aneuploidies and single gene Mendelian disorders.
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Wei F, Wang J, Liao W, Zimmermann BG, Wong DT, Ho CM. Electrochemical detection of low-copy number salivary RNA based on specific signal amplification with a hairpin probe. Nucleic Acids Res 2008; 36:e65. [PMID: 18487624 PMCID: PMC2441804 DOI: 10.1093/nar/gkn299] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [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] [Indexed: 11/15/2022] Open
Abstract
We developed a technique for electrochemical detection of salivary mRNA employing a hairpin probe (HP). Steric hindrance (SH) suppresses unspecific signal and generates a signal-on amplification process for target detection. The stem-loop configuration brings the reporter end of the probe into close proximity with the surface and makes it unavailable for binding with the mediator. Target binding opens the hairpin structure of the probe, and the mediator can then bind to the accessible reporter. Horseradish peroxidase is utilized to generate electrochemical signal. This signal-on process is characterized by a low basal signal, a strong positive readout and a large dynamic range. The SH is controlled via hairpin design and electrical field. By applying electric field control to HPs, the limit of detection of RNA is about 0.4 fM, which is 10 000-fold more sensitive than conventional linear probes. Endogenous Interleukin-8 mRNA is detected with the HP, and good correlation with the quantitative PCR technique is obtained. The resultant process allows a simple setup and by reducing the number of steps it is suited for the point-of-care detection of specific nucleic acid sequences from complex body fluids such as saliva.
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Affiliation(s)
- Fang Wei
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA, USA
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Hu Z, Zimmermann BG, Zhou H, Wang J, Henson BS, Yu W, Elashoff D, Krupp G, Wong DT. Exon-level expression profiling: a comprehensive transcriptome analysis of oral fluids. Clin Chem 2008; 54:824-32. [PMID: 18356245 DOI: 10.1373/clinchem.2007.096164] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND The application of global gene expression profiling to saliva samples is hampered by the presence of partially fragmented and degraded RNAs that are difficult to amplify and detect with the prevailing technologies. Moreover, the often limited volume of saliva samples is a challenge to quantitative PCR (qPCR) validation of multiple candidates. The aim of this study was to provide proof-of-concept data on the combination of a universal mRNA-amplification method with exon arrays for candidate selection and a multiplex preamplification method for easy validation. METHODS We used a universal mRNA-specific linear-amplification strategy in combination with Affymetrix Exon Arrays to amplify salivary RNA from 18 healthy individuals on the nanogram scale. Multiple selected candidates were preamplified in one multiplex reverse transcription PCR reaction, cleaned up enzymatically, and validated by qPCR. RESULTS We defined a salivary exon core transcriptome (SECT) containing 851 transcripts of genes that have highly similar expression profiles in healthy individuals. A subset of the SECT transcripts was verified by qPCR analysis. Informatics analysis of the SECT revealed several functional clusters and sequence motifs. Sex-specific salivary exon biomarkers were identified and validated in tests with samples from healthy individuals. CONCLUSIONS It is feasible to use samples containing fragmented RNAs to conduct high-resolution expression profiling with coverage of the entire transcriptome and to validate multiple targets from limited amounts of sample.
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Affiliation(s)
- Zhanzhi Hu
- Dental Research Institute, 73-017 Center for Health Sciences, University of California, Los Angeles, CA 90095-1668, USA
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Abstract
Head and neck squamous cell carcinoma (HNSCC) affects almost 1 million people worldwide per year. Despite therapeutic advances the overall survival rate remains low because diagnosis often occurs only at advanced stages with poor prognosis. Like in most cancers, the implementation of an early detection scheme would have a positive impact on this disease. Similarly, as oral cancer has a very high recurrence rate, the early identification of recurrence or second primary tumors is an important challenge. HNSCC detection is currently based on expert clinical examination of the upper aerodigestive tract and histologic analysis of suspicious areas, but it may be undetectable in hidden sites, and unfortunately visual screening for oral lesions is an often neglected part of dental healthcare. Our group is actively pursuing the assembly of a toolbox for the molecular analysis of oral fluid. Here we present our current status utilizing the salivary transcriptome for oral cancer diagnostics.
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Affiliation(s)
- Bernhard G Zimmermann
- UCLA Dental Research Institute, 73-017 Center for Health Sciences, 10833 Le Conte Avenue, Los Angeles, CA 90095-1668, USA
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Huang DJ, Zimmermann BG, Holzgreve W, Hahn S. Improvement of methods for the isolation of cell-free fetal DNA from maternal plasma: comparison of a manual and an automated method. Ann N Y Acad Sci 2007; 1075:308-12. [PMID: 17108225 DOI: 10.1196/annals.1368.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [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: 11/12/2022]
Abstract
The low amount of cell-free fetal DNA present in the maternal circulation poses significant challenges to its use in future diagnostic applications, and ways of increasing the yield of this potential marker extracted from maternal plasma are constantly being explored. In this study, we compared two methods of DNA extraction, a manual and an automated method. Our analysis revealed that although the manual method yielded overall more total cell-free DNA, the automated system yielded higher quantities of cell-free DNA of fetal origin. Furthermore, the DNA isolated using the automated system appeared to be of greater purity than that isolated by the manual method, with fewer inhibitors to downstream real-time PCR reactions.
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Affiliation(s)
- Dorothy J Huang
- University Women's Hospital/Department of Research, Spitalstrasse 21, CH 4031 Basel, Switzerland
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23
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Abstract
DNA of fetal origin is present in the plasma of pregnant women. The quantitative measurement of circulatory fetal DNA (cfDNA) by real-time quantitative PCR (qPCR) has been applied to investigate a possible correlation between increased levels and pregnancy-related disorders. However, as the levels of cfDNA are close to the detection limit (LOD) of the method used, the measurements may not be reliable. This is also problematic for the evaluation of preanalytical steps, such as DNA extraction and cfDNA enrichment by size separation. We optimized a protocol for the qPCR analysis of the multi-copy sequence DYS14 on the Y chromosome. This was compared with an established assay for the single-copy SRY gene. Probit regression analysis showed that the limit of detection (LOD) of the DYS14 assay, (0.4 genome equivalents (GE)) and limit of quantification (LOQ) were 10-fold lower in comparison to SRY (4 GE). The levels of cfDNA obtained from the first trimester of pregnancy could be quantified with high precision by the DYS14 assay (CV below 25%) as opposed to the SRY measurements (26-140%). Additionally, fetal sex was correctly determined in all instances. The low copy numbers of fetal DNA in plasma of women in the first trimester of pregnancy can be measured reliably, targeting the DYS14 that is present in multiple copies per Y chromosome.
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Affiliation(s)
- Bernhard G Zimmermann
- Laboratory for Prenatal Medicine, Department of Research/University Women's Hospital, University of Basel, Switzerland.
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Huang DJ, Zimmermann BG, Holzgreve W, Hahn S. Use of an Automated Method Improves the Yield and Quality of Cell-Free Fetal DNA Extracted from Maternal Plasma. Clin Chem 2005; 51:2419-20. [PMID: 16306116 DOI: 10.1373/clinchem.2005.056010] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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