1
|
Boscolo Bielo L, Trapani D, Repetto M, Crimini E, Valenza C, Belli C, Criscitiello C, Marra A, Subbiah V, Curigliano G. Variant allele frequency: a decision-making tool in precision oncology? Trends Cancer 2023; 9:1058-1068. [PMID: 37704501 DOI: 10.1016/j.trecan.2023.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/15/2023]
Abstract
Precision oncology requires additional predictive biomarkers for targeted therapy selection. Variant allele frequency (VAF), measuring the proportion of variant alleles within a genomic locus, provides insights into tumor clonality in somatic genomic testing, yielding a strong rationale for targeting dominant cancer cell populations. The prognostic and predictive roles of VAF have been evaluated across different studies. Yet, the absence of validated VAF thresholds and a lack of standardization between sequencing assays currently hampers its clinical utility. Therefore, analytical and clinical validation must be further examined. This Review summarizes the evidence regarding the use of VAF as a predictive biomarker and discusses challenges and opportunities for its clinical implementation as a decision-making tool for targeted therapy selection.
Collapse
Affiliation(s)
- Luca Boscolo Bielo
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Dario Trapani
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Matteo Repetto
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Early Drug Development service, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Edoardo Crimini
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Carmine Valenza
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Carmen Belli
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy
| | - Carmen Criscitiello
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Antonio Marra
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy
| | - Vivek Subbiah
- Drug Development Unit, Sarah Cannon Research Institute, Nashville, TN, USA
| | - Giuseppe Curigliano
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.
| |
Collapse
|
2
|
Mangum R, Reuther J, Baksi KS, Gandhi I, Zabriskie RC, Recinos A, Raesz-Martinez R, Lin FY, Potter SL, Sher AC, Kralik SF, Mohila CA, Chintagumpala MM, Muzny D, Hu J, Gibbs RA, Fisher KE, Bernini JC, Gill J, Griffin TC, Tomlinson GE, Vallance KL, Plon SE, Roy A, Parsons DW. Circulating tumor DNA sequencing of pediatric solid and brain tumor patients: An institutional feasibility study. Pediatr Hematol Oncol 2023; 40:719-738. [PMID: 37366551 PMCID: PMC10592361 DOI: 10.1080/08880018.2023.2228837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/15/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023]
Abstract
The potential of circulating tumor DNA (ctDNA) analysis to serve as a real-time "liquid biopsy" for children with central nervous system (CNS) and non-CNS solid tumors remains to be fully elucidated. We conducted a study to investigate the feasibility and potential clinical utility of ctDNA sequencing in pediatric patients enrolled on an institutional clinical genomics trial. A total of 240 patients had tumor DNA profiling performed during the study period. Plasma samples were collected at study enrollment from 217 patients and then longitudinally from a subset of patients. Successful cell-free DNA extraction and quantification occurred in 216 of 217 (99.5%) of these initial samples. Twenty-four patients were identified whose tumors harbored 30 unique variants that were potentially detectable on a commercially-available ctDNA panel. Twenty of these 30 mutations (67%) were successfully detected by next-generation sequencing in the ctDNA from at least one plasma sample. The rate of ctDNA mutation detection was higher in patients with non-CNS solid tumors (7/9, 78%) compared to those with CNS tumors (9/15, 60%). A higher ctDNA mutation detection rate was also observed in patients with metastatic disease (9/10, 90%) compared to non-metastatic disease (7/14, 50%), although tumor-specific variants were detected in a few patients in the absence of radiographic evidence of disease. This study illustrates the feasibility of incorporating longitudinal ctDNA analysis into the management of relapsed or refractory patients with childhood CNS or non-CNS solid tumors.
Collapse
Affiliation(s)
- Ross Mangum
- Center for Cancer and Blood Disorders, Phoenix Children’s Hospital, Phoenix, Arizona
| | - Jacquelyn Reuther
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
| | - Koel Sen Baksi
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Ilavarasi Gandhi
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
| | - Ryan C. Zabriskie
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Alva Recinos
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Robin Raesz-Martinez
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Frank Y. Lin
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Samara L. Potter
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio
- Department of Pediatrics, The Ohio State University, Columbus, Ohio
| | - Andrew C. Sher
- Department of Radiology, Texas Children’s Hospital, Houston, Texas
| | | | - Carrie A. Mohila
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - Murali M. Chintagumpala
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Jianhong Hu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Kevin E. Fisher
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - Juan Carlos Bernini
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Jonathan Gill
- Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy C. Griffin
- Department of Hematology Oncology, The Children’s Hospital of San Antonio, Baylor College of Medicine, San Antonio, Texas
| | - Gail E Tomlinson
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, Texas
| | - Kelly L. Vallance
- Hematology and Oncology, Cook Children’s Medical Center, Fort Worth, Texas
| | - Sharon E. Plon
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Angshumoy Roy
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - D. Williams Parsons
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
3
|
Grancher A, Beaussire L, Manfredi S, Le Malicot K, Dutherage M, Verdier V, Mulot C, Bouché O, Phelip JM, Levaché CB, Deguiral P, Coutant S, Sefrioui D, Emile JF, Laurent-Puig P, Bibeau F, Michel P, Sarafan-Vasseur N, Lepage C, Di Fiore F. Postoperative circulating tumor DNA detection is associated with the risk of recurrence in patients resected for a stage II colorectal cancer. Front Oncol 2022; 12:973167. [PMID: 36439476 PMCID: PMC9685416 DOI: 10.3389/fonc.2022.973167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/17/2022] [Indexed: 11/11/2022] Open
Abstract
Circulating tumor DNA (ctDNA) is reported to be promising in localized colorectal cancer (CRC). The present study aimed to retrospectively evaluate the impact of ctDNA in patients with a resected stage II CRC from the PROGIGE 13 trial with available paired tumor and blood samples. A group of recurrent patients were matched one-to-one with nonrecurrent patients according to sex, tumor location, treatment sequence, and blood collection timing. CtDNA was analyzed by digital PCR according to NGS of tumors. Disease-free survival (DFS) and overall survival (OS) were analyzed based on ctDNA, and the risks of recurrence and death were determined. A total of 134 patients were included, with 67 patients in each group. At least one alteration was identified in 115/134 tumors. Postoperative ctDNA was detected in 10/111 (9.0%) informative samples and was detected more frequently in the recurrent group (16.7% versus 1.8%; p = 0.02). The median DFS of ctDNA+ versus ctDNA- patients was 16.8 versus 54 months (p = 0.002), respectively, and the median OS was 51.3 versus 69.5 months (p = 0.03), respectively. CtDNA was associated with recurrence (ORa = 11.13, p = 0.03) and death (HRa = 3.15, p = 0.01). In conclusion, the presence of postoperative ctDNA is associated with both recurrence and survival in stage II CRC.
Collapse
Affiliation(s)
- Adrien Grancher
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
- *Correspondence: Adrien Grancher,
| | - Ludivine Beaussire
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, Rouen, France
| | - Sylvain Manfredi
- Burgundy Digestive Cancer Registry, INSERM, Lipides, Nutrition, Cancers (LNC)-UMR1231, University Bourgogne Franche-Comté, Dijon, France
| | - Karine Le Malicot
- Burgundy Digestive Cancer Registry, INSERM, Lipides, Nutrition, Cancers (LNC)-UMR1231, University Bourgogne Franche-Comté, Dijon, France
| | - Marie Dutherage
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
| | - Vincent Verdier
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
| | - Claire Mulot
- Paris University, Biology Resources Center EPIGENETEC, Paris, France
| | - Olivier Bouché
- Department of Digestive Oncology, University Hospital of Reims, Reims, France
| | - Jean-Marc Phelip
- Department of Gastroenterology and Digestive Oncology, University Hospital of Saint Etienne, Saint Etienne, France
| | - Charles-Briac Levaché
- Department of Radiotherapy and Medical Oncology, Polyclinique Francheville, Périgueux, France
| | - Philippe Deguiral
- Department of Gastroenterology, St Nazaire Hospital, Saint-Nazaire, France
| | - Sophie Coutant
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
| | - David Sefrioui
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
| | - Jean-François Emile
- Department of Pathology, Hôpital Ambroise-Paré, Boulogne-Billancourt, France
| | - Pierre Laurent-Puig
- Department of Biology, Georges Pompidou Hospital, Assistance Publique des Hôpitaux de Paris (APHP), Paris, France
| | - Frédéric Bibeau
- Department of Pathology, Caen University Hospital, Caen, France
| | - Pierre Michel
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
| | - Nasrin Sarafan-Vasseur
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
| | - Côme Lepage
- Burgundy Digestive Cancer Registry, INSERM, Lipides, Nutrition, Cancers (LNC)-UMR1231, University Bourgogne Franche-Comté, Dijon, France
| | - Frederic Di Fiore
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, Rouen, France
| |
Collapse
|
4
|
Ganesamoorthy D, Robertson AJ, Chen W, Hall MB, Cao MD, Ferguson K, Lakhani SR, Nones K, Simpson PT, Coin LJM. Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content. BMC Cancer 2022; 22:85. [PMID: 35057759 PMCID: PMC8772083 DOI: 10.1186/s12885-021-09160-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/27/2021] [Indexed: 12/03/2022] Open
Abstract
Background Circulating cell-free DNA (cfDNA) in the plasma of cancer patients contains cell-free tumour DNA (ctDNA) derived from tumour cells and it has been widely recognized as a non-invasive source of tumour DNA for diagnosis and prognosis of cancer. Molecular profiling of ctDNA is often performed using targeted sequencing or low-coverage whole genome sequencing (WGS) to identify tumour specific somatic mutations or somatic copy number aberrations (sCNAs). However, these approaches cannot efficiently detect all tumour-derived genomic changes in ctDNA. Methods We performed WGS analysis of cfDNA from 4 breast cancer patients and 2 patients with benign tumours. We sequenced matched germline DNA for all 6 patients and tumour samples from the breast cancer patients. All samples were sequenced on Illumina HiSeqXTen sequencing platform and achieved approximately 30x, 60x and 100x coverage on germline, tumour and plasma DNA samples, respectively. Results The mutational burden of the plasma samples (1.44 somatic mutations/Mb of genome) was higher than the matched tumour samples. However, 90% of high confidence somatic cfDNA variants were not detected in matched tumour samples and were found to comprise two background plasma mutational signatures. In contrast, cfDNA from the di-nucleosome fraction (300 bp–350 bp) had much higher proportion (30%) of variants shared with tumour. Despite high coverage sequencing we were unable to detect sCNAs in plasma samples. Conclusions Deep sequencing analysis of plasma samples revealed higher fraction of unique somatic mutations in plasma samples, which were not detected in matched tumour samples. Sequencing of di-nucleosome bound cfDNA fragments may increase recovery of tumour mutations from plasma. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-09160-1.
Collapse
|
5
|
Ye P, Cai P, Xie J, Zhang J. Reliability of BRAF mutation detection using plasma sample: A systematic review and meta-analysis. Medicine (Baltimore) 2021; 100:e28382. [PMID: 34941166 PMCID: PMC8701458 DOI: 10.1097/md.0000000000028382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/10/2021] [Accepted: 12/01/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Testing of B-Raf proto-oncogene (BRAF) mutation in tumor is necessary before targeted therapies are given. When tumor samples are not available, plasma samples are commonly used for the testing of BRAF mutation. The aim of this study was to investigate the diagnostic accuracy of BRAF mutation testing using plasma sample of cancer patients. METHODS Databases of Pubmed, Embase, and Cochrane Library were searched for eligible studies investigating BRAF mutation in paired tissue and plasma samples of cancer patients. A total of 798 publications were identified after database searching. After removing 229 duplicated publications, 569 studies were screened using the following exclusion criteria: (1) BRAF mutation not measured in plasma or in tumor sample; (2) lacking BRAF-wildtype or BRAF-mutated samples; (3) tissue and plasma samples not paired; (4) lacking tumor or plasma samples; (5) not plasma sample; (6) not cancer; (7) un-interpretable data. Accuracy data and relevant information were extracted from each eligible study by 2 independent researchers and analyzed using statistical software. RESULTS After pooling the accuracy data from 3943 patients of the 53 eligible studies, the pooled sensitivity, specificity, and diagnostic odds ratio of BRAF mutation testing using plasma sample were 69%, 98%, and 55.78, respectively. Area under curve of summary receiver operating characteristic curve was 0.9435. Subgroup analysis indicated that BRAF mutation testing using plasma had overall higher accuracy (diagnostic odds ratio of 89.17) in colorectal cancer, compared to melanoma and thyroid carcinoma. In addition, next-generation sequencing had an overall higher accuracy in detecting BRAF mutation using plasma sample (diagnostic odds ratio of 63.90), compared to digital polymerase chain reaction (PCR) and conventional PCR, while digital PCR showed the highest sensitivity (74%) among the 3 techniques. CONCLUSION BRAF testing using plasma sample showed an overall high accuracy compared to paired tumor tissue sample, which could be used for cancer genotyping when tissue sample is not available. Large prospective studies are needed to further investigate the accuracy of BRAF mutation testing in plasma sample.
Collapse
Affiliation(s)
- Peng Ye
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, P.R. China
| | - Peiling Cai
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, P.R. China
| | - Jing Xie
- Department of Pathology and Clinical Laboratory, Sichuan Provincial Fourth People's Hospital, Chengdu, P.R. China
| | - Jie Zhang
- Adverse Drug Reaction Monitoring Center, Chengdu, P.R. China
| |
Collapse
|
6
|
Palande V, Siegal T, Detroja R, Gorohovski A, Glass R, Flueh C, Kanner AA, Laviv Y, Har-Nof S, Levy-Barda A, Viviana Karpuj M, Kurtz M, Perez S, Raviv Shay D, Frenkel-Morgenstern M. Detection of gene mutations and gene-gene fusions in circulating cell-free DNA of glioblastoma patients: an avenue for clinically relevant diagnostic analysis. Mol Oncol 2021; 16:2098-2114. [PMID: 34875133 PMCID: PMC9120899 DOI: 10.1002/1878-0261.13157] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 09/04/2021] [Accepted: 12/06/2021] [Indexed: 11/20/2022] Open
Abstract
Glioblastoma (GBM) is the most common type of glioma and is uniformly fatal. Currently, tumour heterogeneity and mutation acquisition are major impedances for tailoring personalized therapy. We collected blood and tumour tissue samples from 25 GBM patients and 25 blood samples from healthy controls. Cell‐free DNA (cfDNA) was extracted from the plasma of GBM patients and from healthy controls. Tumour DNA was extracted from fresh tumour samples. Extracted DNA was sequenced using a whole‐genome sequencing procedure. We also collected 180 tumour DNA datasets from GBM patients publicly available at the TCGA/PANCANCER project. These data were analysed for mutations and gene–gene fusions that could be potential druggable targets. We found that plasma cfDNA concentrations in GBM patients were significantly elevated (22.6 ± 5 ng·mL−1), as compared to healthy controls (1.4 ± 0.4 ng·mL−1) of the same average age. We identified unique mutations in the cfDNA and tumour DNA of each GBM patient, including some of the most frequently mutated genes in GBM according to the COSMIC database (TP53, 18.75%; EGFR, 37.5%; NF1, 12.5%; LRP1B, 25%; IRS4, 25%). Using our gene–gene fusion database, ChiTaRS 5.0, we identified gene–gene fusions in cfDNA and tumour DNA, such as KDR–PDGFRA and NCDN–PDGFRA, which correspond to previously reported alterations of PDGFRA in GBM (44% of all samples). Interestingly, the PDGFRA protein fusions can be targeted by tyrosine kinase inhibitors such as imatinib, sunitinib, and sorafenib. Moreover, we identified BCR–ABL1 (in 8% of patients), COL1A1–PDGFB (8%), NIN–PDGFRB (8%), and FGFR1–BCR (4%) in cfDNA of patients, which can be targeted by analogues of imatinib. ROS1 fusions (CEP85L–ROS1 and GOPC–ROS1), identified in 8% of patient cfDNA, might be targeted by crizotinib, entrectinib, or larotrectinib. Thus, our study suggests that integrated analysis of cfDNA plasma concentration, gene mutations, and gene–gene fusions can serve as a diagnostic modality for distinguishing GBM patients who may benefit from targeted therapy. These results open new avenues for precision medicine in GBM, using noninvasive liquid biopsy diagnostics to assess personalized patient profiles. Moreover, repeated detection of druggable targets over the course of the disease may provide real‐time information on the evolving molecular landscape of the tumour.
Collapse
Affiliation(s)
- Vikrant Palande
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Tali Siegal
- Neuro-Oncology Center, Rabin Medical Center, Petach Tikva, Israel and Hebrew University, 4941492, Jerusalem, Israel
| | - Rajesh Detroja
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | | | - Rainer Glass
- Department of Neurosurgery, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Charlotte Flueh
- Department of Neurosurgery, University Hospital of Schleswig-Holstein, Campus Kiel, 24105, Kiel, Germany
| | - Andrew A Kanner
- Department of Neurosurgery, Rabin Medical Center, Petach Tikva, 4941492, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yoseph Laviv
- Department of Neurosurgery, Rabin Medical Center, Petach Tikva, 4941492, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sagi Har-Nof
- Department of Neurosurgery, Rabin Medical Center, Petach Tikva, 4941492, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adva Levy-Barda
- Department of Pathology, Rabin Medical Center, Petach Tikva, 4941492, Israel
| | | | - Marina Kurtz
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Shira Perez
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Dorith Raviv Shay
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Milana Frenkel-Morgenstern
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel.,The Dangoor Centre For Personalized Medicine, Bar-Ilan University, Ramat Gan, 5290002, Israel
| |
Collapse
|
7
|
Roosan MR, Mambetsariev I, Pharaon R, Fricke J, Husain H, Reckamp KL, Koczywas M, Massarelli E, Bild AH, Salgia R. Usefulness of Circulating Tumor DNA in Identifying Somatic Mutations and Tracking Tumor Evolution in Patients With Non-small Cell Lung Cancer. Chest 2021; 160:1095-1107. [PMID: 33878340 PMCID: PMC8449001 DOI: 10.1016/j.chest.2021.04.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/21/2021] [Accepted: 04/01/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The usefulness of circulating tumor DNA (ctDNA) in detecting mutations and monitoring treatment response has not been well studied beyond a few actionable biomarkers in non-small cell lung cancer (NSCLC). RESEARCH QUESTION How does the usefulness of ctDNA analysis compare with that of solid tumor biopsy analysis in patients with NSCLC? METHODS We retrospectively evaluated 370 adult patients with NSCLC treated at the City of Hope between November 2015 and August 2019 to assess the usefulness of ctDNA in mutation identification, survival, concordance with matched tissue samples in 32 genes, and tumor evolution. RESULTS A total of 1,688 somatic mutations were detected in 473 ctDNA samples from 370 patients with NSCLC. Of the 473 samples, 177 showed at least one actionable mutation with currently available Food and Drug Administration-approved NSCLC therapies. MET and CDK6 amplifications co-occurred with BRAF amplifications (false discovery rate [FDR], < 0.01), and gene-level mutations were mutually exclusive in KRAS and EGFR (FDR, 0.0009). Low cumulative percent ctDNA levels were associated with longer progression-free survival (hazard ratio [HR], 0.56; 95% CI, 0.37-0.85; P = .006). Overall survival was shorter in patients harboring BRAF mutations (HR, 2.35; 95% CI, 1.24-4.6; P = .009), PIK3CA mutations (HR, 2.77; 95% CI, 1.56-4.9; P < .001) and KRAS mutations (HR, 2.32; 95% CI, 1.30-4.1; P = .004). Gene-level concordance was 93.8%, whereas the positive concordance rate was 41.6%. More mutations in targetable genes were found in ctDNA than in tissue biopsy samples. Treatment response and tumor evolution over time were detected in repeated ctDNA samples. INTERPRETATION Although ctDNA analysis exhibited similar usefulness to tissue biopsy analysis, more mutations in targetable genes were missed in tissue biopsy analyses. Therefore, the evaluation of ctDNA in conjunction with tissue biopsy samples may help to detect additional targetable mutations to improve clinical outcomes in advanced NSCLC.
Collapse
Affiliation(s)
| | | | | | - Jeremy Fricke
- City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Hatim Husain
- UC San Diego Health Moores Cancer Center, La Jolla, CA
| | - Karen L Reckamp
- City of Hope Comprehensive Cancer Center, Duarte, CA; Division of Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | | | - Andrea H Bild
- Division of Molecular Pharmacology, Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA
| | - Ravi Salgia
- City of Hope Comprehensive Cancer Center, Duarte, CA.
| |
Collapse
|
8
|
Haupts A, Vogel A, Foersch S, Hartmann M, Maderer A, Wachter N, Huber T, Kneist W, Roth W, Lang H, Moehler M, Hartmann N. Comparative analysis of nuclear and mitochondrial DNA from tissue and liquid biopsies of colorectal cancer patients. Sci Rep 2021; 11:16745. [PMID: 34408162 PMCID: PMC8373949 DOI: 10.1038/s41598-021-95006-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/20/2021] [Indexed: 01/05/2023] Open
Abstract
The current standard for molecular profiling of colorectal cancer (CRC) is using resected or biopsied tissue specimens. However, they are limited regarding sampling frequency, representation of tumor heterogeneity, and sampling can expose patients to adverse side effects. The analysis of cell-free DNA (cfDNA) from blood plasma, which is part of a liquid biopsy, is minimally invasive and in principle enables detection of all tumor-specific mutations. Here, we analyzed cfDNA originating from nucleus and mitochondria and investigated their characteristics and mutation status in a cohort of 18 CRC patients and 10 healthy controls using targeted next-generation sequencing (NGS) and digital PCR. Longitudinal analyses of nuclear cfDNA level and size during chemotherapy revealed a decreasing cfDNA content and a shift from short to long fragments, indicating an appropriate therapy response, while shortened cfDNAs and increased cfDNA content corresponded with tumor recurrence. Comparative NGS analysis of nuclear tissue and plasma DNA demonstrated a good patient-level concordance and cfDNA revealed additional variants in three of the cases. Analysis of mitochondrial cfDNA surprisingly revealed a higher plasma copy number in healthy subjects than in CRC patients. These results highlight the potential clinical utility of liquid biopsies in routine diagnostics and surveillance of CRC patients as complementation to tissue biopsies or as an attractive alternative in cases where tissue biopsies are risky or the quantity/quality does not allow testing.
Collapse
Affiliation(s)
- Anna Haupts
- Institute of Pathology, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany.
| | - Anne Vogel
- Institute of Pathology, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Sebastian Foersch
- Institute of Pathology, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Monika Hartmann
- Department of Internal Medicine I, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Annett Maderer
- Department of Internal Medicine I, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Nicolas Wachter
- Department of General, Visceral and Transplantation Surgery, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Tobias Huber
- Department of General, Visceral and Transplantation Surgery, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Werner Kneist
- Department of General, Visceral and Transplantation Surgery, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany.,Department of General and Visceral Surgery, St. Georg Hospital Eisenach gGmbH, Mühlhäuser Straße 94, 99817, Eisenach, Germany
| | - Wilfried Roth
- Institute of Pathology, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Hauke Lang
- Department of General, Visceral and Transplantation Surgery, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Markus Moehler
- Department of Internal Medicine I, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Nils Hartmann
- Institute of Pathology, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany.
| |
Collapse
|
9
|
Priskin K, Pólya S, Pintér L, Jaksa G, Csányi B, Enyedi MZ, Sági-Zsigmond E, Sükösd F, Oláh-Németh O, Kelemen G, Nikolényi A, Uhercsák G, Sántha D, Dobi Á, Szilágyi É, Valicsek E, Tordai L, Tóth R, Kahán Z, Haracska L. BC-Monitor: Towards a Routinely Accessible Circulating Tumor DNA-Based Tool for Real-Time Monitoring Breast Cancer Progression and Treatment Effectiveness. Cancers (Basel) 2021; 13:3489. [PMID: 34298704 PMCID: PMC8305126 DOI: 10.3390/cancers13143489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
Circulating tumor DNA (ctDNA) is increasingly employed in the screening, follow-up, and monitoring of the continuously evolving tumor; however, most ctDNA assays validated for clinical use cannot maintain the right balance between sensitivity, coverage, sample requirements, time, and cost. Here, we report our BC-monitor, a simple, well-balanced ctDNA diagnostic approach using a gene panel significant in breast cancer and an optimized multiplex PCR-based NGS protocol capable of identifying allele variant frequencies below 1% in cell-free plasma DNA. We monitored a cohort of 45 breast cancer patients prospectively enrolled into our study receiving neoadjuvant chemotherapy or endocrine therapy or palliative therapy for metastatic diseases. Their tumor mutation status was examined in the archived tumor samples and plasma samples collected before and continuously during therapy. Traceable mutations of the used 38-plex NGS assay were found in approximately two-thirds of the patients. Importantly, we detected new pathogenic variants in follow-up plasma samples that were not detected in the primary tumor and baseline plasma samples. We proved that the BC-monitor can pre-indicate disease progression four-six months earlier than conventional methods. Our study highlights the need for well-designed ctDNA monitoring during treatment and follow-up, integrated into a real-time treatment assessment, which could provide information on the active tumor DNA released into the blood.
Collapse
Affiliation(s)
- Katalin Priskin
- Delta Bio 2000 Ltd., 6726 Szeged, Hungary; (K.P.); (L.P.); (G.J.); (M.Z.E.); (E.S.-Z.)
| | - Sára Pólya
- Visal Plus Ltd., 6726 Szeged, Hungary; (S.P.); (B.C.)
| | - Lajos Pintér
- Delta Bio 2000 Ltd., 6726 Szeged, Hungary; (K.P.); (L.P.); (G.J.); (M.Z.E.); (E.S.-Z.)
| | - Gábor Jaksa
- Delta Bio 2000 Ltd., 6726 Szeged, Hungary; (K.P.); (L.P.); (G.J.); (M.Z.E.); (E.S.-Z.)
| | | | - Márton Zsolt Enyedi
- Delta Bio 2000 Ltd., 6726 Szeged, Hungary; (K.P.); (L.P.); (G.J.); (M.Z.E.); (E.S.-Z.)
| | - Eszter Sági-Zsigmond
- Delta Bio 2000 Ltd., 6726 Szeged, Hungary; (K.P.); (L.P.); (G.J.); (M.Z.E.); (E.S.-Z.)
| | - Farkas Sükösd
- Department of Pathology, University of Szeged, 6701 Szeged, Hungary;
| | - Orsolya Oláh-Németh
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Gyöngyi Kelemen
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Alíz Nikolényi
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Gabriella Uhercsák
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Dóra Sántha
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Ágnes Dobi
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Éva Szilágyi
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Erzsébet Valicsek
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - László Tordai
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Rozália Tóth
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Zsuzsanna Kahán
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Lajos Haracska
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Biological Research Centre, Institute of Genetics, 6726 Szeged, Hungary
| |
Collapse
|
10
|
Liu Q, Zhou D, Han T, Lu X, Hou B, Li M, Yang G, Li Q, Pei Z, Hong Y, Zhang Y, Chen W, Zheng H, He J, Dai J. A Noninvasive Multianalytical Approach for Lung Cancer Diagnosis of Patients with Pulmonary Nodules. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100104. [PMID: 34258160 PMCID: PMC8261512 DOI: 10.1002/advs.202100104] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/25/2021] [Indexed: 06/13/2023]
Abstract
Addressing the high false-positive rate of conventional low-dose computed tomography (LDCT) for lung cancer diagnosis, the efficacy of incorporating blood-based noninvasive testing for assisting practicing clinician's decision making in diagnosis of pulmonary nodules (PNs) is investigated. In this prospective observative study, next generation sequencing- (NGS-) based cell-free DNA (cfDNA) mutation profiling, NGS-based cfDNA methylation profiling, and blood-based protein cancer biomarker testing are performed for patients with PNs, who are diagnosed as high-risk patients through LDCT and subsequently undergo surgical resections, with tissue sections pathologically examined and classified. Using pathological classification as the gold standard, statistical and machine learning methods are used to select molecular markers associated with tissue's malignant classification based on a 98-patient discovery cohort (28 benign and 70 malignant), and to construct an integrative multianalytical model for tissue malignancy prediction. Predictive models based on individual testing platforms have shown varying levels of performance, while their final integrative model produces an area under the receiver operating characteristic curve (AUC) of 0.85. The model's performance is further confirmed on a 29-patient independent validation cohort (14 benign and 15 malignant, with power > 0.90), reproducing AUC of 0.86, which translates to an overall sensitivity of 80% and specificity of 85.7%.
Collapse
Affiliation(s)
- Quan‐Xing Liu
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
| | - Dong Zhou
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
| | - Tian‐Cheng Han
- GeneCast Biotechnology Co., Ltd88 Danshan Road, Xidong Chuangrong Building, Suite C‐1310WuxiJiangsu214104China
| | - Xiao Lu
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
| | - Bing Hou
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
| | - Man‐Yuan Li
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
| | - Gui‐Xue Yang
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
| | - Qing‐Yuan Li
- GeneCast Biotechnology Co., Ltd88 Danshan Road, Xidong Chuangrong Building, Suite C‐1310WuxiJiangsu214104China
| | - Zhi‐Hua Pei
- GeneCast Biotechnology Co., Ltd88 Danshan Road, Xidong Chuangrong Building, Suite C‐1310WuxiJiangsu214104China
| | - Yuan‐Yuan Hong
- GeneCast Biotechnology Co., Ltd88 Danshan Road, Xidong Chuangrong Building, Suite C‐1310WuxiJiangsu214104China
| | - Ya‐Xi Zhang
- GeneCast Biotechnology Co., Ltd88 Danshan Road, Xidong Chuangrong Building, Suite C‐1310WuxiJiangsu214104China
| | - Wei‐Zhi Chen
- GeneCast Biotechnology Co., Ltd88 Danshan Road, Xidong Chuangrong Building, Suite C‐1310WuxiJiangsu214104China
| | - Hong Zheng
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
| | - Ji He
- GeneCast Biotechnology Co., Ltd88 Danshan Road, Xidong Chuangrong Building, Suite C‐1310WuxiJiangsu214104China
| | - Ji‐Gang Dai
- Department of Thoracic Surgery, Xinqiao HospitalThird Military Medical University (Army Medical University)Xinqiao Main StreetChongqing400037China
| |
Collapse
|
11
|
Petrillo A, Salati M, Trapani D, Ghidini M. Circulating Tumor DNA as a Biomarker for Outcomes Prediction in Colorectal Cancer Patients. Curr Drug Targets 2021; 22:1010-1020. [PMID: 33155906 DOI: 10.2174/1389450121999201103194248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/07/2020] [Accepted: 08/23/2020] [Indexed: 12/24/2022]
Abstract
Circulating tumour DNA (ctDNA) is a novel tool that has been investigated in several types of tumours, including colorectal cancer (CRC). In fact, the techniques based on liquid biopsies are proposed as appealing non-invasive alternatives to tissue biopsy, adding more insights into tumour molecular profile, heterogeneity and for cancer detection and monitoring. Additionally, some analysis showed that in CRC patients, ctDNA seems to act as a biomarker able to predict the outcome (prognostic role) and the response to treatments (predictive role). In particular, in the early stage CRC (stage I-III), it could represent a time marker of adjuvant therapy as well as a marker of minimal residual disease and recurrence risk in addition to the already recognized risk factors. In metastatic CRC, the analysis of molecular tumour profile by ctDNA has shown to have high concordance with the tissue biopsy at diagnosis. Additionally, some studies demonstrated that ctDNA level during the treatment was linked with the early response to treatment and prognosis. Finally, the quantitative analysis of ctDNA and copy number alterations may be useful in order to detect resistance to therapy at the time of progression of disease and to help in finding new therapeutic targets.
Collapse
Affiliation(s)
| | - Massimiliano Salati
- Department of Oncology and Hematology, University Hospital of Modena, Modena, Italy
| | - Dario Trapani
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy
| | - Michele Ghidini
- Oncology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| |
Collapse
|
12
|
Ye P, Cai P, Xie J, Wei Y. The diagnostic accuracy of digital PCR, ARMS and NGS for detecting KRAS mutation in cell-free DNA of patients with colorectal cancer: A systematic review and meta-analysis. PLoS One 2021; 16:e0248775. [PMID: 33770081 PMCID: PMC7997033 DOI: 10.1371/journal.pone.0248775] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
Introduction Before anti-EGFR therapy is given to patients with colorectal cancer, it is required to determine KRAS mutation status in tumor. When tumor tissue is not available, cell-free DNA (liquid biopsy) is commonly used as an alternative. Due to the low abundance of tumor-derived DNA in cell-free DNA samples, methods with high sensitivity were preferred, including digital polymerase chain reaction, amplification refractory mutation system and next-generation sequencing. The aim of this systemic review and meta-analysis was to investigate the accuracy of those methods in detecting KRAS mutation in cell-free DNA sample from patients with colorectal cancer. Methods Literature search was performed in Pubmed, Embase, and Cochrane Library. After removing duplicates from the 170 publications found by literature search, eligible studies were identified using pre-defined criteria. Quality of the publications and relevant data were assessed and extracted thereafter. Meta-DiSc and STATA softwares were used to pool the accuracy parameters from the extracted data. Results A total of 33 eligible studies were identified for this systemic review and meta-analysis. After pooling, the overall sensitivity, specificity, and diagnostic odds ratio were 0.77 (95%CI: 0.74–0.79), 0.87 (95%CI: 0.85–0.89), and 23.96 (95%CI: 13.72–41.84), respectively. The overall positive and negative likelihood ratios were 5.55 (95%CI: 3.76–8.19) and 0.29 (95%CI: 0.21–0.38), respectively. Area under curve of the summarized ROC curve was 0.8992. Conclusion Digital polymerase chain reaction, amplification refractory mutation system, and next-generation sequencing had overall high accuracy in detecting KRAS mutation in cell-free DNA sample. Large prospective randomized clinical trials are needed to further convince the accuracy and usefulness of KRAS mutation detection using cfDNA/liquid biopsy samples in clinical practice. Trial registration PROSPERO CRD42020176682; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=176682.
Collapse
Affiliation(s)
- Peng Ye
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan Province, People’s Republic of China
- * E-mail: (PY); (YW)
| | - Peiling Cai
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan Province, People’s Republic of China
| | - Jing Xie
- Department of Pathology and Clinical Laboratory, Sichuan Provincial Fourth People’s Hospital, Chengdu, Sichuan Province, People’s Republic of China
| | - Yuanyuan Wei
- Department of Physiology, School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan Province, People’s Republic of China
- * E-mail: (PY); (YW)
| |
Collapse
|
13
|
Dasari A, Morris VK, Allegra CJ, Atreya C, Benson AB, Boland P, Chung K, Copur MS, Corcoran RB, Deming DA, Dwyer A, Diehn M, Eng C, George TJ, Gollub MJ, Goodwin RA, Hamilton SR, Hechtman JF, Hochster H, Hong TS, Innocenti F, Iqbal A, Jacobs SA, Kennecke HF, Lee JJ, Lieu CH, Lenz HJ, Lindwasser OW, Montagut C, Odisio B, Ou FS, Porter L, Raghav K, Schrag D, Scott AJ, Shi Q, Strickler JH, Venook A, Yaeger R, Yothers G, You YN, Zell JA, Kopetz S. ctDNA applications and integration in colorectal cancer: an NCI Colon and Rectal-Anal Task Forces whitepaper. Nat Rev Clin Oncol 2020; 17:757-770. [PMID: 32632268 PMCID: PMC7790747 DOI: 10.1038/s41571-020-0392-0] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
An increasing number of studies are describing potential uses of circulating tumour DNA (ctDNA) in the care of patients with colorectal cancer. Owing to this rapidly developing area of research, the Colon and Rectal-Anal Task Forces of the United States National Cancer Institute convened a panel of multidisciplinary experts to summarize current data on the utility of ctDNA in the management of colorectal cancer and to provide guidance in promoting the efficient development and integration of this technology into clinical care. The panel focused on four key areas in which ctDNA has the potential to change clinical practice, including the detection of minimal residual disease, the management of patients with rectal cancer, monitoring responses to therapy, and tracking clonal dynamics in response to targeted therapies and other systemic treatments. The panel also provides general guidelines with relevance for ctDNA-related research efforts, irrespective of indication.
Collapse
Affiliation(s)
- Arvind Dasari
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Van K Morris
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Chloe Atreya
- University of California at San Francisco Comprehensive Cancer Center, San Francisco, CA, USA
| | - Al B Benson
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - Patrick Boland
- Department of Medicine, Roswell Park Cancer Center, Buffalo, NY, USA
| | - Ki Chung
- Division of Hematology & Oncology, Medical University of South Carolina, Charleston, SC, USA
| | - Mehmet S Copur
- CHI Health St Francis Cancer Treatment Center, Grand Island, NE, USA
| | - Ryan B Corcoran
- Department of Medical Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Dustin A Deming
- Division of Hematology, Medical Oncology and Palliative Care, Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrea Dwyer
- University of Colorado Cancer Center, Aurora, CO, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Cathy Eng
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Thomas J George
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Marc J Gollub
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Stanley R Hamilton
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Howard Hochster
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Theodore S Hong
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MD, USA
| | - Federico Innocenti
- Center for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, NC, USA
| | - Atif Iqbal
- Section of Colorectal Surgery, Division of Surgery, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Samuel A Jacobs
- National Adjuvant Surgical and Bowel Project Foundation/NRG Oncology, Pittsburgh, PA, USA
| | - Hagen F Kennecke
- Department of Oncology, Virginia Mason Cancer Institute, Seattle, WA, USA
| | - James J Lee
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA, USA
| | - Christopher H Lieu
- Division of Medical Oncology, University of Colorado Cancer Center, Aurora, CO, USA
| | - Heinz-Josef Lenz
- Department of Preventive Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - O Wolf Lindwasser
- Coordinating Center for Clinical Trials, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clara Montagut
- Hospital del Mar-Institut Hospital del Mar d'Investigacions Mèdiques, Universitat Pompeu Fabra, Barcelona, Spain
| | - Bruno Odisio
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fang-Shu Ou
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Laura Porter
- Patient Advocate, NCI Colon Task Force, Boston, MA, USA
| | - Kanwal Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Deborah Schrag
- Division of Population Sciences, Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aaron J Scott
- Division of Hematology and Oncology, Banner University of Arizona Cancer Center, Tucson, AZ, USA
| | - Qian Shi
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - John H Strickler
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Alan Venook
- University of California at San Francisco Comprehensive Cancer Center, San Francisco, CA, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Greg Yothers
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Y Nancy You
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason A Zell
- Department of Epidemiology, Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, CA, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
14
|
Arshad J, Roberts A, Ahmed J, Cotta J, Pico BA, Kwon D, Trent JC. Utility of Circulating Tumor DNA in the Management of Patients With GI Stromal Tumor: Analysis of 243 Patients. JCO Precis Oncol 2020; 4:66-73. [DOI: 10.1200/po.19.00253] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
PURPOSE GI stromal tumor (GIST) is the most common sarcoma of the GI tract. Management of patients with GIST is determined by KIT, PDGFRA, or other genomic alterations. Tissue-based next-generation sequencing (NGS) analysis is the standard approach for diagnosis, prognosis, and treatment selection. However, circulating tumor DNA (ctDNA)–based NGS is a novel and noninvasive alternative. METHODS ctDNA sequencing results were evaluated in blood samples from 243 de-identified patients within the Guardant360 database. Under an approved institutional review board protocol, a retrospective analysis was performed on 45 single-institution patients. RESULTS Of 243 patients, 114 (47%) were women, and the median age was 59 years (range, 17-90 years). Patients with no alterations and variations of uncertain significance were excluded. Of the 162 patients with known pathogenic mutations, KIT was the most common (56%), followed by NF (7%), PDGFRA (6%), PI3KCA (6%), KRAS (5%), and others (6%). Most tumors harbored an actionable KIT or PDGFRA mutation. Our institutional cohort (n = 45) had 16 (35%) KIT exon 11 mutations, 3 (6%) KIT exon 9 mutations, and 1 (2%) PDGFRA mutation detected on ctDNA. Resistance mutations were observed in KIT exon 17 (8 patients), exon 13 (3 patients), and in both (3 patients). Our comparison of ctDNA with tissue NGS revealed a positive predictive value (PPV) of 100%. Failure of concordance was observed in patients with localized or low disease burden. From the time of ctDNA testing, the median overall survival was not reached, whereas the median progression-free survival was 7 months. CONCLUSION ctDNA provides a rapid, noninvasive analysis of current mutations with a high PPV for patients with metastatic GIST. ctDNA-based testing may help to define the optimal choice of therapy on the basis of resistance mutations and should be studied prospectively.
Collapse
Affiliation(s)
- Junaid Arshad
- University of Miami, Miller School of Medicine/Sylvester Comprehensive Cancer Center, Miami, FL
| | | | | | - Jared Cotta
- University of Miami, Miller School of Medicine/Sylvester Comprehensive Cancer Center, Miami, FL
| | - Brian A. Pico
- University of Miami, Miller School of Medicine/Sylvester Comprehensive Cancer Center, Miami, FL
| | - Deukoo Kwon
- University of Miami, Miller School of Medicine/Sylvester Comprehensive Cancer Center, Miami, FL
| | - Jonathan C. Trent
- University of Miami, Miller School of Medicine/Sylvester Comprehensive Cancer Center, Miami, FL
| |
Collapse
|
15
|
Pessoa LS, Heringer M, Ferrer VP. ctDNA as a cancer biomarker: A broad overview. Crit Rev Oncol Hematol 2020; 155:103109. [PMID: 33049662 DOI: 10.1016/j.critrevonc.2020.103109] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/17/2020] [Accepted: 09/07/2020] [Indexed: 02/07/2023] Open
Abstract
Circulating tumor DNA (ctDNA) in fluids has gained attention because ctDNA seems to identify tumor-specific abnormalities, which could be used for diagnosis, follow-up of treatment, and prognosis: the so-called liquid biopsy. Liquid biopsy is a minimally invasive approach and presents the sum of ctDNA from primary and secondary tumor sites. It has been possible not only to quantify the amount of ctDNA but also to identify (epi)genetic changes. Specific mutations in genes have been identified in the plasma of patients with several types of cancer, which highlights ctDNA as a possible cancer biomarker. However, achieving detectable concentrations of ctDNA in body fluids is not an easy task. ctDNA fragments present a short half-life, and there are no cut-off values to discriminate high and low ctDNA concentrations. Here, we discuss the use of ctDNA as a cancer biomarker, the main methodologies, the inherent difficulties, and the clinical predictive value of ctDNA.
Collapse
Affiliation(s)
- Luciana Santos Pessoa
- Brain's Biomedicine Laboratory, Paulo Niemeyer State Brain Institute, Rio de Janeiro, Rio de Janeiro, Brazil; Center for Experimental Surgery, Graduate Program in Surgical Sciences, Department of Surgery, Faculty of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Manoela Heringer
- Brain's Biomedicine Laboratory, Paulo Niemeyer State Brain Institute, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Valéria Pereira Ferrer
- Department of Cellular and Molecular Biology, Institute of Biology, Fluminense Federal University, Niteroi, Rio de Janeiro, Brazil.
| |
Collapse
|
16
|
Cario CL, Chen E, Leong L, Emami NC, Lopez K, Tenggara I, Simko JP, Friedlander TW, Li PS, Paris PL, Carroll PR, Witte JS. A machine learning approach to optimizing cell-free DNA sequencing panels: with an application to prostate cancer. BMC Cancer 2020; 20:820. [PMID: 32859160 PMCID: PMC7456018 DOI: 10.1186/s12885-020-07318-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/18/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cell-free DNA's (cfDNA) use as a biomarker in cancer is challenging due to genetic heterogeneity of malignancies and rarity of tumor-derived molecules. Here we describe and demonstrate a novel machine-learning guided panel design strategy for improving the detection of tumor variants in cfDNA. Using this approach, we first generated a model to classify and score candidate variants for inclusion on a prostate cancer targeted sequencing panel. We then used this panel to screen tumor variants from prostate cancer patients with localized disease in both in silico and hybrid capture settings. METHODS Whole Genome Sequence (WGS) data from 550 prostate tumors was analyzed to build a targeted sequencing panel of single point and small (< 200 bp) indel mutations, which was subsequently screened in silico against prostate tumor sequences from 5 patients to assess performance against commonly used alternative panel designs. The panel's ability to detect tumor-derived cfDNA variants was then assessed using prospectively collected cfDNA and tumor foci from a test set 18 prostate cancer patients with localized disease undergoing radical proctectomy. RESULTS The panel generated from this approach identified as top candidates mutations in known driver genes (e.g. HRAS) and prostate cancer related transcription factor binding sites (e.g. MYC, AR). It outperformed two commonly used designs in detecting somatic mutations found in the cfDNA of 5 prostate cancer patients when analyzed in an in silico setting. Additionally, hybrid capture and 2500X sequencing of cfDNA molecules using the panel resulted in detection of tumor variants in all 18 patients of a test set, where 15 of the 18 patients had detected variants found in multiple foci. CONCLUSION Machine learning-prioritized targeted sequencing panels may prove useful for broad and sensitive variant detection in the cfDNA of heterogeneous diseases. This strategy has implications for disease detection and monitoring when applied to the cfDNA isolated from prostate cancer patients.
Collapse
Affiliation(s)
- Clinton L Cario
- Program in Biological and Medical Informatics, University of California, San Francisco, California, 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, 94158, USA
| | - Emmalyn Chen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, 94158, USA
| | - Lancelote Leong
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, 94158, USA
| | - Nima C Emami
- Program in Biological and Medical Informatics, University of California, San Francisco, California, 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, 94158, USA
| | - Karen Lopez
- Department of Urology, University of California, San Francisco, California, 94158, USA
| | - Imelda Tenggara
- Department of Urology, University of California, San Francisco, California, 94158, USA
| | - Jeffry P Simko
- Department of Urology, University of California, San Francisco, California, 94158, USA
- Department of Anatomic Pathology, University of California, San Francisco, California, 94158, USA
| | - Terence W Friedlander
- Division of Hematology/Oncology, University of California, San Francisco, California, 94158, USA
| | - Patricia S Li
- Division of Hematology/Oncology, University of California, San Francisco, California, 94158, USA
| | - Pamela L Paris
- Department of Urology, University of California, San Francisco, California, 94158, USA
- Division of Hematology/Oncology, University of California, San Francisco, California, 94158, USA
| | - Peter R Carroll
- Department of Urology, University of California, San Francisco, California, 94158, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, 94158, USA.
- Department of Urology, University of California, San Francisco, California, 94158, USA.
| |
Collapse
|
17
|
Chang WJ, Sung JS, Lee SY, Kang EJ, Kwon NJ, Kim HM, Shin SW, Choi JY, Choi YJ, Kim JW, Park KH, Kim YH. The Clinical Significance of RAS, PIK3CA, and PTEN Mutations in Non-Small Cell Lung Cancer Using Cell-Free DNA. J Clin Med 2020; 9:jcm9082642. [PMID: 32823871 PMCID: PMC7465200 DOI: 10.3390/jcm9082642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 12/22/2022] Open
Abstract
Mutations in the EGFR gene downstream signaling pathways may cause receptor-independent pathway activation, making tumors unresponsive to EGFR inhibitors. However, the clinical significance of RAS, PIK3CA or PTEN mutations in NSCLC is unclear. In this study, patients who were initially diagnosed with NSCLC or experienced recurrence after surgical resection were enrolled, and blood samples was collected. Ultra-deep sequencing analysis of cfDNA using Ion AmpliSeq Cancer Hotspot Panel v2 with Proton platforms was conducted. RAS/PIK3CA/PTEN mutations were frequently detected in cfDNA in stage IV NSCLC (58.1%), and a high proportion of the patients (47.8%) with mutations had bone metastases at diagnosis. The frequency of RAS/PIK3CA/PTEN mutations in patients with activating EGFR mutation was 61.7%. The median PFS for EGFR-TKIs was 15.1 months in patients without RAS/PIK3CA/PTEN mutations, and 19.9 months in patients with mutations (p = 0.549). For patients with activating EGFR mutations, the overall survival was longer in patients without RAS/PIK3CA/PTEN mutations (53.8 months vs. 27.4 months). For the multivariate analysis, RAS/PIK3CA/PTEN mutations were independent predictors of poor prognosis in patients with activating EGFR mutations. In conclusion, RAS, PIK3CA and PTEN mutations do not hamper EGFR-TKI treatment outcome; however, they predict a poor OS when activating EGFR mutations coexist.
Collapse
Affiliation(s)
- Won Jin Chang
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul 02841, Korea; (W.J.C.); (S.W.S.); (J.Y.C.); (Y.J.C.); (J.W.K.); (K.H.P.)
| | - Jae Sook Sung
- Cancer Research Institute, Korea University, Seoul 02841, Korea;
| | - Sung Yong Lee
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Korea; (S.Y.L.); (E.J.K.)
| | - Eun Joo Kang
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Korea; (S.Y.L.); (E.J.K.)
| | - Nak-Jung Kwon
- Macrogen, 254, Beotkkot-ro, Geumcheon-gu, Seoul 08511, Korea; (N.-J.K.); (H.M.K.)
| | - Hae Mi Kim
- Macrogen, 254, Beotkkot-ro, Geumcheon-gu, Seoul 08511, Korea; (N.-J.K.); (H.M.K.)
| | - Sang Won Shin
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul 02841, Korea; (W.J.C.); (S.W.S.); (J.Y.C.); (Y.J.C.); (J.W.K.); (K.H.P.)
| | - Jung Yoon Choi
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul 02841, Korea; (W.J.C.); (S.W.S.); (J.Y.C.); (Y.J.C.); (J.W.K.); (K.H.P.)
| | - Yoon Ji Choi
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul 02841, Korea; (W.J.C.); (S.W.S.); (J.Y.C.); (Y.J.C.); (J.W.K.); (K.H.P.)
| | - Ju Won Kim
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul 02841, Korea; (W.J.C.); (S.W.S.); (J.Y.C.); (Y.J.C.); (J.W.K.); (K.H.P.)
| | - Kyong Hwa Park
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul 02841, Korea; (W.J.C.); (S.W.S.); (J.Y.C.); (Y.J.C.); (J.W.K.); (K.H.P.)
- Cancer Research Institute, Korea University, Seoul 02841, Korea;
| | - Yeul Hong Kim
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul 02841, Korea; (W.J.C.); (S.W.S.); (J.Y.C.); (Y.J.C.); (J.W.K.); (K.H.P.)
- Cancer Research Institute, Korea University, Seoul 02841, Korea;
- Correspondence: ; Tel.: +82-2-920-5569; Fax: +82-2-920-6622
| |
Collapse
|
18
|
He Z, Chen Z, Tan M, Elingarami S, Liu Y, Li T, Deng Y, He N, Li S, Fu J, Li W. A review on methods for diagnosis of breast cancer cells and tissues. Cell Prolif 2020; 53:e12822. [PMID: 32530560 PMCID: PMC7377933 DOI: 10.1111/cpr.12822] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/10/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023] Open
Abstract
Breast cancer has seriously been threatening physical and mental health of women in the world, and its morbidity and mortality also show clearly upward trend in China over time. Through inquiry, we find that survival rate of patients with early‐stage breast cancer is significantly higher than those with middle‐ and late‐stage breast cancer, hence, it is essential to conduct research to quickly diagnose breast cancer. Until now, many methods for diagnosing breast cancer have been developed, mainly based on imaging and molecular biotechnology examination. These methods have great contributions in screening and confirmation of breast cancer. In this review article, we introduce and elaborate the advances of these methods, and then conclude some gold standard diagnostic methods for certain breast cancer patients. We lastly discuss how to choose the most suitable diagnostic methods for breast cancer patients. In general, this article not only summarizes application and development of these diagnostic methods, but also provides the guidance for researchers who work on diagnosis of breast cancer.
Collapse
Affiliation(s)
- Ziyu He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China.,State Key Laboratory of Bioelectronics, School of Biological and Medical Engineering, Southeast University, Nanjing, China
| | - Miduo Tan
- Surgery Department of Galactophore, Central Hospital of Zhuzhou City, Zhuzhou, China
| | - Sauli Elingarami
- School of Life Sciences and Bioengineering (LiSBE), The Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | - Yuan Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China.,State Key Laboratory of Bioelectronics, School of Biological and Medical Engineering, Southeast University, Nanjing, China
| | - Taotao Li
- Hunan Provincial Key Lab of Dark Tea and Jin-hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China.,State Key Laboratory of Bioelectronics, School of Biological and Medical Engineering, Southeast University, Nanjing, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Juan Fu
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Wen Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| |
Collapse
|
19
|
Pairawan S, Hess KR, Janku F, Sanchez NS, Mills Shaw KR, Eng C, Damodaran S, Javle M, Kaseb AO, Hong DS, Subbiah V, Fu S, Fogelman DR, Raymond VM, Lanman RB, Meric-Bernstam F. Cell-free Circulating Tumor DNA Variant Allele Frequency Associates with Survival in Metastatic Cancer. Clin Cancer Res 2020; 26:1924-1931. [PMID: 31852833 PMCID: PMC7771658 DOI: 10.1158/1078-0432.ccr-19-0306] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 06/13/2019] [Accepted: 12/12/2019] [Indexed: 01/05/2023]
Abstract
PURPOSE Physicians are expected to assess prognosis both for patient counseling and for determining suitability for clinical trials. Increasingly, cell-free circulating tumor DNA (cfDNA) sequencing is being performed for clinical decision making. We sought to determine whether variant allele frequency (VAF) in cfDNA is associated with prognosis. EXPERIMENTAL DESIGN We performed a retrospective analysis of 298 patients with metastatic disease who underwent clinical comprehensive cfDNA analysis and assessed association between VAF and overall survival. RESULTS cfDNA mutations were detected in 240 patients (80.5%). Median overall survival (OS) was 11.5 months. cfDNA mutation detection and number of nonsynonymous mutations (NSM) significantly differed between tumor types, being lowest in appendiceal cancer and highest in colon cancer. Having more than one NSM detected was associated with significantly worse OS (HR = 2.3; P < 0.0001). VAF was classified by quartiles, Q1 lowest, Q4 highest VAF. Higher VAF levels were associated with a significantly worse overall survival (VAF Q3 HR 2.3, P = 0.0069; VAF Q4 HR = 3.8, P < 0.0001) on univariate analysis. On multivariate analysis, VAF Q4, male sex, albumin level <3.5 g/dL, number of nonvisceral metastatic sites >0 and number of prior therapies >4 were independent predictors of worse OS. CONCLUSIONS Higher levels of cfDNA VAF and a higher number of NSMs were associated with worse OS in patients with metastatic disease. Further study is needed to determine optimal VAF thresholds for clinical decision making and the utility of cfDNA VAF as a prognostic marker in different tumor types.
Collapse
Affiliation(s)
- Seyed Pairawan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kenneth R Hess
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Filip Janku
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nora S Sanchez
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kenna R Mills Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cathy Eng
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Senthilkumar Damodaran
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Milind Javle
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ahmed O Kaseb
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David S Hong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Siqing Fu
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David R Fogelman
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| |
Collapse
|
20
|
Maia MC, Salgia M, Pal SK. Harnessing cell-free DNA: plasma circulating tumour DNA for liquid biopsy in genitourinary cancers. Nat Rev Urol 2020; 17:271-291. [PMID: 32203306 DOI: 10.1038/s41585-020-0297-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2020] [Indexed: 12/11/2022]
Abstract
In the era of precision oncology, liquid biopsy techniques, especially the use of plasma circulating tumour DNA (ctDNA) analysis, represent a paradigm shift in the use of genomic biomarkers with considerable implications for clinical practice. Compared with tissue-based tumour DNA analysis, plasma ctDNA is more convenient to test, more readily accessible, faster to obtain and less invasive, minimizing procedure-related risks and offering the opportunity to perform serial monitoring. Additionally, genomic profiles of ctDNA have been shown to reflect tumour heterogeneity, which has important implications for the identification of resistant clones and selection of targeted therapy well before clinical and radiographic changes occur. Moreover, plasma ctDNA testing can also be applied to cancer screening, risk stratification and quantification of minimal residual disease. These features provide an unprecedented opportunity for early treatment of patients, improving the chances of treatment success.
Collapse
Affiliation(s)
- Manuel Caitano Maia
- Department of Medical Oncology, Centro de Oncologia do Paraná, Curitiba, PR, Brazil. .,Latin American Cooperative Oncology Group, Genitourinary Group, Porto Alegre, Brazil.
| | - Meghan Salgia
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Sumanta K Pal
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| |
Collapse
|
21
|
Porter A, Natsuhara M, Daniels GA, Patel SP, Sacco AG, Bykowski J, Banks KC, Cohen EEW. Next generation sequencing of cell free circulating tumor DNA in blood samples of recurrent and metastatic head and neck cancer patients. Transl Cancer Res 2020; 9:203-209. [PMID: 35117174 PMCID: PMC8798156 DOI: 10.21037/tcr.2019.12.70] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 11/04/2019] [Indexed: 11/06/2022]
Abstract
Background Effective targeted therapy is lacking in head and neck cancer (HNC). The use of next generation sequencing (NGS) has been suggested as a way to potentially expand therapeutic options and improve outcomes. This study was performed in order to further characterize blood sample cell-free circulating tumor DNA (ctDNA) in advanced HNC patients, to determine its ability to identify actionable mutations, and to elucidate its potential role in patient management. Methods Retrospective analysis of 60 patients with recurrent and metastatic (R/M) HNCs who underwent molecular profiling of blood samples utilizing Guardant360, a 70-gene ctDNA NGS platform. ctDNA sequencing data was compared to tumor NGS data, when available. Best response to therapy was assessed using RECIST measures. Results The most common tumor type was oropharyngeal squamous cell carcinoma (n=21). Other cancer types included salivary gland (n=8) and thyroid (n=4). The most common mutations identified by blood analysis were TP53 (68% of patients), PIK3CA (34% of patients), NOTCH1 (20% of patients), and ARID1A (15% of patients). These findings were consistent with results from tumor sequencing data (n=30) where TP53 (48%) and PIK3CA (24%) were also the most common. Seventy-three percent (n=22) of patients had alterations identified in blood that were not present in tumor specimens. In patients with squamous cell carcinoma, 66% had an off-label option identified and 90% had a trial option identified, while 50% of patients with salivary primaries had off-label option identified and 75% had trial options identified. All patients (n=3, 100%) with thyroid primaries had off-label and clinical trial options identified. Of patients with actionable mutations, 13% (n=8) received matched targeted therapy (MTT). Three patients had stable disease (37.5%), 3 had progressive disease (37.5%), and 2 (25%) were not evaluated at the time of follow up. Of those who did not receive targeted therapy (n=21), 11 patients had stable disease (52.4%), 9 had progressive disease (42.9%), and 1 had a complete response (4.8%). Conclusions Alterations identified by ctDNA may help inform management decisions in advanced HNC. The majority of patients had unique mutations identified on ctDNA. The role of NGS of ctDNA should be explored in future studies.
Collapse
Affiliation(s)
- Ashleigh Porter
- Division of Hematology/Oncology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Mandy Natsuhara
- Division of Hematology/Oncology, Moores Cancer Center, La Jolla, CA, USA
| | - Gregory A Daniels
- Division of Hematology/Oncology, Moores Cancer Center, La Jolla, CA, USA
| | | | | | - Julie Bykowski
- Division of Hematology/Oncology, Moores Cancer Center, La Jolla, CA, USA
| | - Kimberly C Banks
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, CA, USA
| | - Ezra E W Cohen
- Division of Hematology/Oncology, Moores Cancer Center, La Jolla, CA, USA
| |
Collapse
|
22
|
Jiang J, Adams HP, Yao L, Yaung S, Lal P, Balasubramanyam A, Fuhlbrück F, Tikoo N, Lovejoy AF, Froehler S, Fang LT, Achenbach HJ, Floegel R, Krügel R, Palma JF. Concordance of Genomic Alterations by Next-Generation Sequencing in Tumor Tissue versus Cell-Free DNA in Stage I-IV Non-Small Cell Lung Cancer. J Mol Diagn 2019; 22:228-235. [PMID: 31837429 DOI: 10.1016/j.jmoldx.2019.10.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 09/17/2019] [Accepted: 10/17/2019] [Indexed: 02/07/2023] Open
Abstract
Molecular biomarkers hold promise for personalization of cancer treatment. However, a typical tumor biopsy may be difficult to acquire and may not capture genetic variations within or across tumors. Given these limitations, tumor genotyping using next-generation sequencing of plasma-derived circulating tumor (ct)-DNA has the potential to transform non-small cell lung cancer (NSCLC) management. Importantly, mutations detected in biopsied tissue must also be detected in plasma-derived ctDNA at different disease stages. Using the AVENIO ctDNA Surveillance kit (research use only), mutations in ctDNA from NSCLC subjects were compared with those identified in matched tumor tissue samples, retrospectively. Plasma and tissue samples were collected from 141 treatment-naïve NSCLC subjects (stage I, n = 48; stage II, n = 37; stage III, n = 33; stage IV, n = 23). In plasma samples, the median numbers of variants per subject were 4, 6, 8, and 9 in those with stage I, II, III, and IV disease, respectively. The corresponding values in tissue samples were 5, 5, 6, and 4. The overall tissue-plasma concordance of stage II through IV was 62.2% by AVENIO software call. On multivariate analysis, concordance was positively and significantly associated with tumor size and cancer stage. Next-generation sequencing-based analyses with the AVENIO ctDNA Surveillance kit could be an alternative approach to detecting genetic variations in plasma-derived ctDNA isolated from NSCLC subjects.
Collapse
Affiliation(s)
- John Jiang
- Roche Sequencing Solutions, Pleasanton, California
| | | | - Lijing Yao
- Roche Sequencing Solutions, Pleasanton, California
| | | | - Preeti Lal
- Roche Sequencing Solutions, Pleasanton, California
| | | | | | - Nalin Tikoo
- Roche Molecular Systems, Pleasanton, California
| | | | | | - Li Tai Fang
- Roche Sequencing Solutions, Pleasanton, California
| | | | - Ralph Floegel
- Department of Thoracic Surgery, Lungenklinik Lostau, Lostau, Germany
| | - Rainer Krügel
- Department of Pneumology/Thoracic Surgery, Johanniter Krankenhaus im Fläming Treuenbrietzen, Treuenbrietzen, Germany
| | - John F Palma
- Roche Sequencing Solutions, Pleasanton, California.
| |
Collapse
|
23
|
Jahangiri L, Hurst T. Assessing the Concordance of Genomic Alterations between Circulating-Free DNA and Tumour Tissue in Cancer Patients. Cancers (Basel) 2019; 11:cancers11121938. [PMID: 31817150 PMCID: PMC6966532 DOI: 10.3390/cancers11121938] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/23/2022] Open
Abstract
Somatic alterations to the genomes of solid tumours, which in some cases represent actionable drivers, provide diagnostic and prognostic insight into these complex diseases. Spatial and longitudinal tracking of somatic genomic alterations (SGAs) in patient tumours has emerged as a new avenue of investigation, not only as a disease monitoring strategy, but also to improve our understanding of heterogeneity and clonal evolution from diagnosis through disease progression. Furthermore, analysis of circulating-free DNA (cfDNA) in the so-called "liquid biopsy" has emerged as a non-invasive method to identify genomic information to inform targeted therapy and may also capture the heterogeneity of the primary and metastatic tumours. Considering the potential of cfDNA analysis as a translational laboratory tool in clinical practice, establishing the extent to which cfDNA represents the SGAs of tumours, particularly actionable driver alterations, becomes a matter of importance, warranting standardisation of methods and practices. Here, we assess the utilisation of cfDNA for molecular profiling of SGAs in tumour tissue across a broad range of solid tumours. Moreover, we examine the underlying factors contributing to discordance of detected SGAs between cfDNA and tumour tissue.
Collapse
Affiliation(s)
- Leila Jahangiri
- Department of Life Sciences, Birmingham City University, Birmingham B15 3TN, UK;
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Lab blocks level 3, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Correspondence:
| | - Tara Hurst
- Department of Life Sciences, Birmingham City University, Birmingham B15 3TN, UK;
| |
Collapse
|
24
|
Moreno F, Gayarre J, López-Tarruella S, del Monte-Millán M, Picornell AC, Álvarez E, García-Saenz JÁ, Jerez Y, Márquez-Rodas I, Echavarría I, Palomero M, Bueno C, Aragón Bodí AM, Muñoz MS, González del Val R, Bueno O, Cebollero-Presmanes M, Ocaña I, Arias A, Romero P, Massarrah T, Ramos-Medina R, Martín M. Concordance of Genomic Variants in Matched Primary Breast Cancer, Metastatic Tumor, and Circulating Tumor DNA: The MIRROR Study. JCO Precis Oncol 2019; 3:1-16. [DOI: 10.1200/po.18.00263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
PURPOSE Genetic heterogeneity between primary tumors and their metastatic lesions has been documented in several breast cancer studies. However, the selection of therapy for patients with metastatic breast cancer and the search for biomarkers for targeted therapy are often based on findings from the primary tumor, mainly because of the difficulty of distant metastasis core biopsies. New methods for monitoring genomic changes in metastatic breast cancer are needed (ie, circulating tumor DNA [ctDNA] genomic analysis). The objectives of this study were to assess the concordance of genomic variants between primary and metastatic tumor tissues and the sensitivity of plasma ctDNA analysis to identify variants detected in tumor biopsies. PATIENTS AND METHODS Next-generation sequencing technology was used to assess the genomic mutation profile of a panel of 54 cancer genes in matched samples of primary tumor, metastatic tumor, and plasma from 40 patients with metastatic breast cancer. RESULTS Using Ion Torrent technology (ThermoFisher Scientific, Waltham, MA), we identified 110 variants that were common to the primary and metastatic tumors. ctDNA analysis had a sensitivity of 0.972 in detecting variants present in both primary and metastatic tissues. In addition, we identified 13 variants in metastatic tissue and ctDNA not present in primary tumor. CONCLUSION We identified genomic variants present in metastatic biopsies and plasma ctDNA that were not present in the primary tumor. Deep sequencing of plasma ctDNA detected most DNA variants previously identified in matched primary and metastatic tissues. ctDNA might aid in therapy selection and in the search for biomarkers for drug development in metastatic breast cancer.
Collapse
Affiliation(s)
- Fernando Moreno
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | - Javier Gayarre
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | - Sara López-Tarruella
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Universidad Complutense, Madrid, Spain
| | | | | | - Enrique Álvarez
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | | | - Yolanda Jerez
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | | | | | | | | | | | | | | | - Oscar Bueno
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | | | | | - Ainhoa Arias
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | - Paula Romero
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | | | | | - Miguel Martín
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Universidad Complutense, Madrid, Spain
| |
Collapse
|
25
|
Kim ST, Banks KC, Pectasides E, Kim SY, Kim K, Lanman RB, Talasaz A, An J, Choi MG, Lee JH, Sohn TS, Bae JM, Kim S, Park SH, Park JO, Park YS, Lim HY, Kim NKD, Park W, Lee H, Bass AJ, Kim K, Kang WK, Lee J. Impact of genomic alterations on lapatinib treatment outcome and cell-free genomic landscape during HER2 therapy in HER2+ gastric cancer patients. Ann Oncol 2019; 29:1037-1048. [PMID: 29409051 PMCID: PMC5913644 DOI: 10.1093/annonc/mdy034] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background To identify predictive markers for responders in lapatinib-treated patients and to demonstrate molecular changes during lapatinib treatment via cell-free genomics. Patients and methods We prospectively evaluated the efficacy of combining lapatinib with capecitabine and oxaliplatin as first line neoadjuvant therapy in patients with previously untreated, HER2-overexpressing advanced gastric cancer. A parallel biomarker study was conducted by simultaneously performing immunohistochemistry and next-generation sequencing (NGS) with tumor and blood samples. Results Complete response was confirmed in 7/32 patients (21.8%), 2 of whom received radical surgery with pathologic-confirmed complete response. Fifteen partial responses (46.8%) were observed, resulting in a 68.6% overall response rate. NGS of the 16 tumor specimens demonstrated that the most common co-occurring copy number alteration was CCNE1 amplification, which was present in 40% of HER2+ tumors. The relationship between CCNE1 amplification and lack of response to HER2-targeted therapy trended toward statistical significance (66.7% of non-responders versus 22.2% of responders harbored CCNE1 amplification; P = 0.08). Patients with high level ERBB2 amplification by NGS were more likely to respond to therapy, compared with patients with low level ERBB2 amplification (P = 0.02). Analysis of cfDNA showed that detectable ERBB2 copy number amplification in plasma was predictive to the response (100%, response rate) and changes in plasma-detected genomic alterations were associated with lapatinib sensitivity and/or resistance. The follow-up cfDNA genomics at disease progression demonstrated that there are emergences of other genomic aberrations such as MYC, EGFR, FGFR2 and MET amplifications. Conclusions The present study showed that HER2+ GC patients respond differently according to concomitant genomic aberrations beyond ERBB2, high ERBB2 amplification by NGS or cfDNA can be a positive predictor for patient selection, and tumor genomic alterations change significantly during targeted agent therapy.
Collapse
Affiliation(s)
- S T Kim
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - K C Banks
- Department of Medical Affair, Guardant Health, Dana-Farber Cancer Institute, Boston, USA
| | - E Pectasides
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - S Y Kim
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - K Kim
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - R B Lanman
- Department of Medical Affair, Guardant Health, Dana-Farber Cancer Institute, Boston, USA
| | - A Talasaz
- Department of Medical Affair, Guardant Health, Dana-Farber Cancer Institute, Boston, USA
| | - J An
- Sungkyunkwan University School of Medicine, Seoul, Korea; Department of Surgery, Samsung Medical Center, Seoul, Korea
| | - M G Choi
- Sungkyunkwan University School of Medicine, Seoul, Korea; Department of Surgery, Samsung Medical Center, Seoul, Korea
| | - J H Lee
- Sungkyunkwan University School of Medicine, Seoul, Korea; Department of Surgery, Samsung Medical Center, Seoul, Korea
| | - T S Sohn
- Sungkyunkwan University School of Medicine, Seoul, Korea; Department of Surgery, Samsung Medical Center, Seoul, Korea
| | - J M Bae
- Sungkyunkwan University School of Medicine, Seoul, Korea; Department of Surgery, Samsung Medical Center, Seoul, Korea
| | - S Kim
- Sungkyunkwan University School of Medicine, Seoul, Korea; Department of Surgery, Samsung Medical Center, Seoul, Korea
| | - S H Park
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - J O Park
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Y S Park
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - H Y Lim
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - N K D Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - W Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - H Lee
- Sungkyunkwan University School of Medicine, Seoul, Korea; Division of Gastroenterolog, Department of Medicine, Samsung Medical Center, Seoul, Korea
| | - A J Bass
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - K Kim
- Pathology and Translational Genomics, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - W K Kang
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - J Lee
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea.
| |
Collapse
|
26
|
Reece M, Saluja H, Hollington P, Karapetis CS, Vatandoust S, Young GP, Symonds EL. The Use of Circulating Tumor DNA to Monitor and Predict Response to Treatment in Colorectal Cancer. Front Genet 2019; 10:1118. [PMID: 31824558 PMCID: PMC6881479 DOI: 10.3389/fgene.2019.01118] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/16/2019] [Indexed: 12/20/2022] Open
Abstract
Background: Colorectal cancer is one of the most common cancers worldwide and has a high mortality rate following disease recurrence. Treatment efficacy is maximized by providing tailored cancer treatment, ideally involving surgical resection and personalized neoadjuvant and adjuvant therapies, including chemotherapy, radiotherapy and increasingly, targeted therapy. Early detection of recurrence or disease progression results in more treatable disease and is essential to improving survival outcomes. Recent advances in the understanding of tumor genetics have resulted in the discovery of circulating tumor DNA (ctDNA). A growing body of evidence supports the use of these sensitive biomarkers in detecting residual disease and diagnosing recurrence as well as enabling targeted and tumor-specific adjuvant therapies. Methods: A literature search in Pubmed was performed to identify all original articles preceding April 2019 that utilize ctDNA for the purpose of monitoring response to colorectal cancer treatment. Results: Ninety-two clinical studies were included. These studies demonstrate that ctDNA is a reliable measure of tumor burden. Studies show the utility of ctDNA in assessing the adequacy of surgical tumor clearance and changes in ctDNA levels reflect response to systemic treatments. ctDNA can be used in the selection of targeted treatments. The reappearance or increase in ctDNA, as well as the emergence of new mutations, correlates with disease recurrence, progression, and resistance to therapy, with ctDNA measurement allowing more sensitive monitoring than currently used clinical tools. Conclusions: ctDNA shows enormous promise as a sensitive biomarker for monitoring response to many treatment modalities and for targeting therapy. Thus, it is emerging as a new way for guiding treatment decisions-initiating, altering, and ceasing treatments, or prompting investigation into the potential for residual disease. However, many potentially useful ctDNA markers are available and more work is needed to determine which are best suited for specific purposes and for improving specific outcomes.
Collapse
Affiliation(s)
- Mifanwy Reece
- Colorectal Surgery, Division of Surgery & Perioperative Medicine, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Hariti Saluja
- Department of Medicine, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Paul Hollington
- Colorectal Surgery, Division of Surgery & Perioperative Medicine, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Christos S Karapetis
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,Department of Medical Oncology, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Sina Vatandoust
- Department of Medical Oncology, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Graeme P Young
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Erin L Symonds
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,Bowel Health Service, Flinders Medical Centre, Bedford Park, SA, Australia
| |
Collapse
|
27
|
Kastrisiou M, Zarkavelis G, Pentheroudakis G, Magklara A. Clinical Application of Next-Generation Sequencing as A Liquid Biopsy Technique in Advanced Colorectal Cancer: A Trick or A Treat? Cancers (Basel) 2019; 11:E1573. [PMID: 31623125 PMCID: PMC6826585 DOI: 10.3390/cancers11101573] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/01/2019] [Accepted: 10/13/2019] [Indexed: 12/24/2022] Open
Abstract
Owing to its advantages over prior relevant technologies, massive parallel or next-generation sequencing (NGS) is rapidly evolving, with growing applications in a wide range of human diseases. The burst in actionable molecular alterations in many cancer types advocates for the practicality of using NGS in the clinical setting, as it permits the parallel characterization of multiple genes in a cost- and time-effective way, starting from low-input DNA. In advanced clinical practice, the oncological management of colorectal cancer requires prior knowledge of KRAS, NRAS, and BRAF status, for the design of appropriate therapeutic strategies, with more gene mutations still surfacing as potential biomarkers. Tumor heterogeneity, as well as the need for serial gene profiling due to tumor evolution and the emergence of novel genetic alterations, have promoted the use of liquid biopsies-especially in the form of circulating tumor DNA (ctDNA)-as a promising alternative to tissue molecular analysis. This review discusses recent studies that have used plasma NGS in advanced colorectal cancer and summarizes the clinical applications, as well as the technical challenges involved in adopting this technique in a clinically beneficial oncological practice.
Collapse
Affiliation(s)
- Myrto Kastrisiou
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece.
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - George Zarkavelis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - George Pentheroudakis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - Angeliki Magklara
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece.
- Department of Biomedical Research, Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology-Hellas, 45110 Ioannina, Greece.
| |
Collapse
|
28
|
Wood DE, White JR, Georgiadis A, Van Emburgh B, Parpart-Li S, Mitchell J, Anagnostou V, Niknafs N, Karchin R, Papp E, McCord C, LoVerso P, Riley D, Diaz LA, Jones S, Sausen M, Velculescu VE, Angiuoli SV. A machine learning approach for somatic mutation discovery. Sci Transl Med 2019; 10:10/457/eaar7939. [PMID: 30185652 DOI: 10.1126/scitranslmed.aar7939] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 05/26/2018] [Accepted: 08/16/2018] [Indexed: 12/19/2022]
Abstract
Variability in the accuracy of somatic mutation detection may affect the discovery of alterations and the therapeutic management of cancer patients. To address this issue, we developed a somatic mutation discovery approach based on machine learning that outperformed existing methods in identifying experimentally validated tumor alterations (sensitivity of 97% versus 90 to 99%; positive predictive value of 98% versus 34 to 92%). Analysis of paired tumor-normal exome data from 1368 TCGA (The Cancer Genome Atlas) samples using this method revealed concordance for 74% of mutation calls but also identified likely false-positive and false-negative changes in TCGA data, including in clinically actionable genes. Determination of high-quality somatic mutation calls improved tumor mutation load-based predictions of clinical outcome for melanoma and lung cancer patients previously treated with immune checkpoint inhibitors. Integration of high-quality machine learning mutation detection in clinical next-generation sequencing (NGS) analyses increased the accuracy of test results compared to other clinical sequencing analyses. These analyses provide an approach for improved identification of tumor-specific mutations and have important implications for research and clinical management of cancer patients.
Collapse
Affiliation(s)
| | - James R White
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | | | | | | | | | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Noushin Niknafs
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Rachel Karchin
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Eniko Papp
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | | | - Peter LoVerso
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - David Riley
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Luis A Diaz
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Siân Jones
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Mark Sausen
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Victor E Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | | |
Collapse
|
29
|
Kaseb AO, Sánchez NS, Sen S, Kelley RK, Tan B, Bocobo AG, Lim KH, Abdel-Wahab R, Uemura M, Pestana RC, Qiao W, Xiao L, Morris J, Amin HM, Hassan MM, Rashid A, Banks KC, Lanman RB, Talasaz A, Mills-Shaw KR, George B, Haque A, Raghav KPS, Wolff RA, Yao JC, Meric-Bernstam F, Ikeda S, Kurzrock R. Molecular Profiling of Hepatocellular Carcinoma Using Circulating Cell-Free DNA. Clin Cancer Res 2019; 25:6107-6118. [PMID: 31363003 PMCID: PMC9292132 DOI: 10.1158/1078-0432.ccr-18-3341] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/15/2019] [Accepted: 07/25/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Molecular profiling has been used to select patients for targeted therapy and determine prognosis. Noninvasive strategies are critical to hepatocellular carcinoma (HCC) given the challenge of obtaining liver tissue biopsies. EXPERIMENTAL DESIGN We analyzed blood samples from 206 patients with HCC using comprehensive genomic testing (Guardant Health) of circulating tumor DNA (ctDNA). RESULTS A total of 153/206 (74.3%) were men; median age, 62 years (range, 18-91 years). A total of 181/206 patients had ≥1 alteration. The total number of alterations was 680 (nonunique); median number of alterations/patient was three (range, 1-13); median mutant allele frequency (% cfDNA), 0.49% (range, 0.06%-55.03%). TP53 was the common altered gene [>120 alterations (non-unique)] followed by EGFR, MET, ARID1A, MYC, NF1, BRAF, and ERBB2 [20-38 alterations (nonunique)/gene]. Of the patients with alterations, 56.9% (103/181) had ≥1 actionable alterations, most commonly in MYC, EGFR, ERBB2, BRAF, CCNE1, MET, PIK3CA, ARID1A, CDK6, and KRAS. In these genes, amplifications occurred more frequently than mutations. Hepatitis B (HBV)-positive patients were more likely to have ERBB2 alterations, 35.7% (5/14) versus 8.8% HBV-negative (P = 0.04). CONCLUSIONS This study represents the first large-scale analysis of blood-derived ctDNA in HCC in United States. The genomic distinction based on HCC risk factors and the high percentage of potentially actionable genomic alterations suggests potential clinical utility for this technology.
Collapse
Affiliation(s)
- Ahmed O Kaseb
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Nora S Sánchez
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shiraj Sen
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robin K Kelley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Benjamin Tan
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Andrea G Bocobo
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Kian H Lim
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Reham Abdel-Wahab
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Arizona Clinical Oncology Department, Assiut University Hospital, Assiut, Egypt
| | - Marc Uemura
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Wei Qiao
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lianchun Xiao
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey Morris
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hesham M Amin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Manal M Hassan
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Asif Rashid
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | - Kenna R Mills-Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bhawana George
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Abedul Haque
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kanwal P S Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert A Wolff
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - James C Yao
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Funda Meric-Bernstam
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sadakatsu Ikeda
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, University of California San Diego, Moores Cancer Center, La Jolla, California.
| |
Collapse
|
30
|
Rolfo C, Raez L, Cristofanilli M. Regarding the Congruence Between 2 Circulating Tumor DNA Sequencing Assays. JAMA Oncol 2019; 4:1430. [PMID: 30027222 DOI: 10.1001/jamaoncol.2018.2320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Christian Rolfo
- University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore.,International Society of Liquid Biopsy, Granada, Spain
| | - Luis Raez
- International Society of Liquid Biopsy, Granada, Spain.,Memorial Cancer Institute, Pembroke Pines, Florida
| | - Massimo Cristofanilli
- International Society of Liquid Biopsy, Granada, Spain.,Robert H. Lurie Cancer Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| |
Collapse
|
31
|
Sánchez NS, Kahle MP, Bailey AM, Wathoo C, Balaji K, Demirhan ME, Yang D, Javle M, Kaseb A, Eng C, Subbiah V, Janku F, Raymond VM, Lanman RB, Mills Shaw KR, Meric-Bernstam F. Identification of Actionable Genomic Alterations Using Circulating Cell-Free DNA. JCO Precis Oncol 2019; 3:PO.19.00017. [PMID: 32923868 PMCID: PMC7448805 DOI: 10.1200/po.19.00017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2019] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Cell-free DNA (cfDNA) next-generation sequencing is a noninvasive approach for genomic testing. We report the frequency of identifying alterations and their clinical actionability in patients with advanced/metastatic cancer. PATIENTS AND METHODS Prospectively consented patients had cfDNA testing performed. Alterations were assessed for therapeutic implications. RESULTS We enrolled 575 patients with 37 tumor types. Of these patients, 438 (76.2%) had at least one alteration detected, and 205 (35.7%) had one or more alterations of high potential for clinical action. In diseases with 10 or more patients enrolled, 50% or more had at least one alteration deemed of high potential for clinical action. Trials were identified in 80% of patients (286 of 357) with any alteration and in 92% of patients (188 of 205) with one or more alterations of high potential for clinical action of whom 57.6% (118 of 205) had 6 or more months of follow-up available. Of these patients, 10% (12 of 118) had received genomically matched therapy through enrollment in clinical trials (n = 8), off-label drug use (n = 3), or standard of care (n = 1). Although 88.6% of all patients had a performance status of 0 or 1 upon enrollment, the primary reason for not acting on alterations was poor performance status at next treatment change (28.1%; 27 of 96). CONCLUSION cfDNA testing represents a readily accessible method for genomic testing and allows for detection of genomic alterations in most patients with advanced disease. Utility may be higher in patients interested in investigational therapeutics with adequate performance status. Additional study is needed to determine whether utility is enhanced by testing earlier in the treatment course.
Collapse
Affiliation(s)
- Nora S. Sánchez
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Chetna Wathoo
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kavitha Balaji
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Dong Yang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Milind Javle
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ahmed Kaseb
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Cathy Eng
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vivek Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Filip Janku
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | |
Collapse
|
32
|
Galvano A, Taverna S, Badalamenti G, Incorvaia L, Castiglia M, Barraco N, Passiglia F, Fulfaro F, Beretta G, Duro G, Vincenzi B, Tagliaferri P, Bazan V, Russo A. Detection of RAS mutations in circulating tumor DNA: a new weapon in an old war against colorectal cancer. A systematic review of literature and meta-analysis. Ther Adv Med Oncol 2019; 11:1758835919874653. [PMID: 31534493 PMCID: PMC6737868 DOI: 10.1177/1758835919874653] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 08/12/2019] [Indexed: 12/20/2022] Open
Abstract
Background: Tissue evaluation for RAS (KRAS or NRAS) gene status in metastatic colorectal cancer (mCRC) patients represent the standard of care to establish the optimal therapeutic strategy. Unfortunately, tissue biopsy is hampered by several critical limitations due to its invasiveness, difficulty to access to disease site, patient’s compliance and, more recently, neoplastic tissue spatial and temporal heterogeneity. Methods: The authors performed a systematic literature review to identify available trials with paired matched tissue and ctDNA RAS gene status evaluation. The authors searched EMBASE, MEDLINE, Cochrane, www.ClinicalTrials.gov, and abstracts from international meetings. In total, 19 trials comparing standard tissue RAS mutational status matched paired ctDNA evaluated through polymerase chain reaction (PCR), next generation sequencing (NGS) or beads, emulsions, amplification and magnetics (BEAMing) were identified. Results: The pooled sensitivity and specificity of ctDNA were 0.83 (95% CI: 0.80–0.85) and 0.91 (95% CI: 0.89–0.93) respectively. The pooled positive predictive value (PPV) and negative predictive value (NPV) of the ctDNA were 0.87 (95% CI: 0.81–0.92) and 0.87 (95% CI: 0.82–0.92), respectively. Positive likelihood ratio (PLR) was 8.20 (95% CI: 5.16–13.02) and the negative likelihood ratio (NLR) was 0.22 (95% CI: 0.16–0.30). The pooled diagnostic odds ratio (DOR) was 50.86 (95% CI: 26.15–98.76), and the area under the curve (AUC) of the summary receiver operational characteristics (sROC) curve was 0.94. Conclusion: The authors’ meta-analysis produced a complete and updated overview of ctDNA diagnostic accuracy to test RAS mutation in mCRC. Results provide a strong rationale to include the RAS ctDNA test into randomized clinical trials to validate it prospectively.
Collapse
Affiliation(s)
- Antonio Galvano
- Medical Oncology, Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Simona Taverna
- Medical Oncology, Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Giuseppe Badalamenti
- Medical Oncology, Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Lorena Incorvaia
- Medical Oncology, Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Marta Castiglia
- Medical Oncology, Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Nadia Barraco
- Medical Oncology, Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Francesco Passiglia
- Medical Oncology, Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Fabio Fulfaro
- Medical Oncology, Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | | | - Giovanni Duro
- Institute of Biomedicine and Molecular Immunology 'A. Monroy', National Research Council, Palermo, Italy
| | - Bruno Vincenzi
- Medical Oncology Department, Campus Bio-Medico University of Rome, Rome, Italy
| | - Pierosandro Tagliaferri
- Medical Oncology Unit, AUO 'Materdomini and Department of Experimental and Clinical Medicine', Magna Grecia University, Catanzaro, Italy
| | - Viviana Bazan
- Department of Experimental Biomedicine and Clinical Neurosciences, School of Medicine, University of Palermo, Palermo, Italy
| | - Antonio Russo
- Medical Oncology Director, Department of Oncology, A.O.U.P. P. Giaccone University Hospital, 2013 ESMO Designated Centers of Integrated Oncology and Palliative Care, Via del Vespro 129, Palermo, 90127, Italy
| |
Collapse
|
33
|
Choi IS, Kato S, Fanta PT, Leichman L, Okamura R, Raymond VM, Lanman RB, Lippman SM, Kurzrock R. Genomic Profiling of Blood-Derived Circulating Tumor DNA from Patients with Colorectal Cancer: Implications for Response and Resistance to Targeted Therapeutics. Mol Cancer Ther 2019; 18:1852-1862. [PMID: 31320401 DOI: 10.1158/1535-7163.mct-18-0965] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 12/03/2018] [Accepted: 07/12/2019] [Indexed: 11/16/2022]
Abstract
Molecular profiling of circulating tumor DNA (ctDNA) is a promising noninvasive tool. Here, next-generation sequencing (NGS) of blood-derived ctDNA was performed in patients with advanced colorectal cancer. We investigated ctDNA-derived genomic alterations, including potential actionability, concordance with tissue NGS, and serial dynamics in 78 patients with colorectal cancer using a clinical-grade NGS assay that detects single nucleotide variants (54-73 genes) and selected copy-number variants, fusions, and indels. Overall, 63 patients [80.8% (63/78)] harbored ctDNA alterations; 59 [75.6% (59/78)], ≥1 characterized alteration (variants of unknown significance excluded). All 59 patients had actionable alterations potentially targetable with FDA-approved drugs [on-label and/or off-label (N = 54) or with experimental drugs in clinical trials (additional five patients); University of California San Diego Molecular Tumor Board assessment]: 45, by OncoKB (http://oncokb.org/#/). The tissue and blood concordance rates for common specific alterations ranged from 62.3% to 86.9% (median = 5 months between tests). In serial samples from patients on anti-EGFR therapy, multiple emerging alterations in genes known to be involved in therapeutic resistance, including KRAS, NRAS, BRAF, EGFR, ERBB2, and MET were detected. In conclusion, over 80% of patients with stage IV colorectal cancer had detectable ctDNA, and the majority had potentially actionable alterations. Concordance between tissue and blood was between 62% and 87%, despite a median of 5 months between tests. Resistance alterations emerged on anti-EGFR therapy. Therefore, biopsy-free, noninvasive ctDNA analysis provides data relevant to the clinical setting. Importantly, sequential ctDNA analysis detects patterns of emerging resistance allowing for precision planning of future therapy.
Collapse
Affiliation(s)
- In Sil Choi
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California.,Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, South Korea
| | - Shumei Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California.
| | - Paul T Fanta
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California
| | - Lawrence Leichman
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California
| | - Ryosuke Okamura
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California
| | - Victoria M Raymond
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California
| | - Richard B Lanman
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California
| | - Scott M Lippman
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California
| |
Collapse
|
34
|
Bach S, Sluiter NR, Beagan JJ, Mekke JM, Ket JCF, van Grieken NCT, Steenbergen RDM, Ylstra B, Kazemier G, Tuynman JB. Circulating Tumor DNA Analysis: Clinical Implications for Colorectal Cancer Patients. A Systematic Review. JNCI Cancer Spectr 2019; 3:pkz042. [PMID: 32328554 PMCID: PMC7050033 DOI: 10.1093/jncics/pkz042] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/21/2019] [Accepted: 06/05/2019] [Indexed: 02/06/2023] Open
Abstract
Background Liquid biopsies could improve diagnosis, prognostication, and monitoring of colorectal cancer (CRC). Mutation, chromosomal copy number alteration, and methylation analysis in circulating tumor DNA (ctDNA) from plasma or serum has gained great interest. However, the literature is inconsistent on preferred candidate markers, hampering a clear direction for further studies and clinical translation. This review assessed the potential of ctDNA analysis for clinical utility. Methods A systematic review according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines was conducted up to December 3, 2018, followed by methodological quality assessment. Primary endpoints were accuracy for detection, prognostication, and monitoring. Results Eighty-four studies were included. For CRC detection, sensitivity was 75% using ctDNA mutation analysis and up to 96% using copy number analysis. Septin 9 (SEPT9) hypermethylation analysis showed sensitivities of 100% and specificities of 97%. Regarding prognostication, ctDNA KRAS mutations were associated with oncological outcome and could predict response to anti-epidermal growth factor receptor therapy. For monitoring, sequential ctDNA KRAS mutation analysis showed promise for detection of relapses or therapy resistance. Conclusions This comprehensive overview of ctDNA candidate markers demonstrates SEPT9 methylation analysis to be promising for CRC detection, and KRAS mutation analysis could assist in prognostication and monitoring. Prospective evaluation of marker panels in clinical decision making should bring ctDNA analysis into practice.
Collapse
Affiliation(s)
- Sander Bach
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Nina R Sluiter
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Jamie J Beagan
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Joost M Mekke
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Johannes C F Ket
- Medical Information Specialist/Literature Researcher Medical Library, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Nicole C T van Grieken
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Renske D M Steenbergen
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Geert Kazemier
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Jurriaan B Tuynman
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| |
Collapse
|
35
|
Iqbal M, Roberts A, Starr J, Mody K, Kasi PM. Feasibility and clinical value of circulating tumor DNA testing in patients with gastric adenocarcinomas. J Gastrointest Oncol 2019; 10:400-406. [PMID: 31183188 DOI: 10.21037/jgo.2019.01.14] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Gastric cancer is one of the leading causes of cancer worldwide, and this trend appears to be rising. Most patients are diagnosed at an advanced stage and thus prognosis is poor. Liquid biopsy, or circulating tumor DNA (ctDNA) testing, is emerging as a promising prognostic and/or predictive biomarker for patients with various types of malignancies. Its value and utility for patients with gastrointestinal malignancies, particularly gastric cancer is still being explored. There is ongoing research in other tumor types to suggest that ctDNA testing can be potentially used to identify tumor specific genomic alterations, predict tumor mutation burden, as well as help assess clinical response. We report on the feasibility and clinical value of ctDNA testing in patients with gastric cancers in a real time clinical context by reporting data on cohort of patients with gastric cancers (including those with gastroesophageal junction adenocarcinomas) treated at our institution.
Collapse
Affiliation(s)
- Madiha Iqbal
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Jason Starr
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, USA
| | - Kabir Mody
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, USA
| | | |
Collapse
|
36
|
Liquid biopsy for predictive mutational profiling of solid cancer: The pathologist’s perspective. J Biotechnol 2019; 297:66-70. [DOI: 10.1016/j.jbiotec.2019.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 02/07/2023]
|
37
|
Formisano L, Lu Y, Servetto A, Hanker AB, Jansen VM, Bauer JA, Sudhan DR, Guerrero-Zotano AL, Croessmann S, Guo Y, Ericsson PG, Lee KM, Nixon MJ, Schwarz LJ, Sanders ME, Dugger TC, Cruz MR, Behdad A, Cristofanilli M, Bardia A, O'Shaughnessy J, Nagy RJ, Lanman RB, Solovieff N, He W, Miller M, Su F, Shyr Y, Mayer IA, Balko JM, Arteaga CL. Aberrant FGFR signaling mediates resistance to CDK4/6 inhibitors in ER+ breast cancer. Nat Commun 2019; 10:1373. [PMID: 30914635 PMCID: PMC6435685 DOI: 10.1038/s41467-019-09068-2] [Citation(s) in RCA: 230] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 02/14/2019] [Indexed: 12/30/2022] Open
Abstract
Using an ORF kinome screen in MCF-7 cells treated with the CDK4/6 inhibitor ribociclib plus fulvestrant, we identified FGFR1 as a mechanism of drug resistance. FGFR1-amplified/ER+ breast cancer cells and MCF-7 cells transduced with FGFR1 were resistant to fulvestrant ± ribociclib or palbociclib. This resistance was abrogated by treatment with the FGFR tyrosine kinase inhibitor (TKI) lucitanib. Addition of the FGFR TKI erdafitinib to palbociclib/fulvestrant induced complete responses of FGFR1-amplified/ER+ patient-derived-xenografts. Next generation sequencing of circulating tumor DNA (ctDNA) in 34 patients after progression on CDK4/6 inhibitors identified FGFR1/2 amplification or activating mutations in 14/34 (41%) post-progression specimens. Finally, ctDNA from patients enrolled in MONALEESA-2, the registration trial of ribociclib, showed that patients with FGFR1 amplification exhibited a shorter progression-free survival compared to patients with wild type FGFR1. Thus, we propose breast cancers with FGFR pathway alterations should be considered for trials using combinations of ER, CDK4/6 and FGFR antagonists. Era+ breast cancer patients often develop resistance to endocrine therapy. Here, the authors show that FGFR1 amplification is a resistance mechanism to CDK4/6 inhibitor and endocrine therapy and that combined treatment with FGFR, CDK4/6, and anti-estrogens is a potential therapeutic strategy in Era+ breast cancer tumors.
Collapse
Affiliation(s)
- Luigi Formisano
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Yao Lu
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | | | - Ariella B Hanker
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA.,UTSW Simmons Cancer Center, Dallas, TX, 75230, USA.,Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Valerie M Jansen
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Joshua A Bauer
- Departments of Biochemistry, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Dhivya R Sudhan
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA.,UTSW Simmons Cancer Center, Dallas, TX, 75230, USA
| | - Angel L Guerrero-Zotano
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Sarah Croessmann
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Yan Guo
- Vanderbilt Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, 37232-6307, TN, USA
| | - Paula Gonzalez Ericsson
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Kyung-Min Lee
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Mellissa J Nixon
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Luis J Schwarz
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Melinda E Sanders
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA.,Departments of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Teresa C Dugger
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | | | - Amir Behdad
- Robert H Lurie Comprehensive Cancer Center, Chicago, 60611, IL, USA
| | | | - Aditya Bardia
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, 02114, MA, USA
| | - Joyce O'Shaughnessy
- Baylor University Medical Center, Texas Oncology, , US Oncology, Dallas, 75246, TX, USA
| | | | | | - Nadia Solovieff
- Novartis Institutes for Biomedical Research, Cambridge, 02139, MA, USA
| | - Wei He
- Novartis Institutes for Biomedical Research, Cambridge, 02139, MA, USA
| | - Michelle Miller
- Novartis Pharmaceuticals Corporation, East Hanover, 07936, NJ, USA
| | - Fei Su
- Novartis Pharmaceuticals Corporation, East Hanover, 07936, NJ, USA
| | - Yu Shyr
- Vanderbilt Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, 37232-6307, TN, USA
| | - Ingrid A Mayer
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA.,Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Justin M Balko
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Carlos L Arteaga
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA. .,UTSW Simmons Cancer Center, Dallas, TX, 75230, USA. .,Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA.
| |
Collapse
|
38
|
Chae YK, Davis AA, Agte S, Pan A, Simon NI, Iams WT, Cruz MR, Tamragouri K, Rhee K, Mohindra N, Villaflor V, Park W, Lopes G, Giles FJ. Clinical Implications of Circulating Tumor DNA Tumor Mutational Burden (ctDNA TMB) in Non-Small Cell Lung Cancer. Oncologist 2019; 24:820-828. [PMID: 30867242 DOI: 10.1634/theoncologist.2018-0433] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 02/06/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Tissue tumor mutational burden (TMB) has emerged as a potential biomarker predicting response to anti-programmed cell death-1 protein receptor (PD-1)/programmed cell death-1 protein ligand (PD-L1) therapy, but few studies have explored using circulating tumor DNA (ctDNA) TMB in non-small cell lung cancer (NSCLC). MATERIALS AND METHODS A total of 136 patients with NSCLC with ctDNA testing were retrospectively evaluated from a single institution, along with a validation cohort from a second institution. ctDNA TMB was derived using the number of detected mutations over the DNA sequencing length. RESULTS Higher ctDNA TMB was significantly correlated with smoking history (p < .05, chi-squared test). Among patients treated with immune checkpoint inhibitors (n = 20), higher ctDNA TMB was significantly correlated with shorter progressive free survival (PFS) and overall survival (OS; 45 vs. 355 days; hazard ratio [HR], 5.6; 95% confidence interval [CI], 1.3-24.6; p < .01, and OS 106 days vs. not reached; HR, 6.0; 95% CI, 1.3-27.1; p < .01, respectively). In a small independent validation cohort (n = 12), there was a nonsignificant numerical difference for higher ctDNA TMB predicting shorter OS but not PFS. ctDNA TMB was not correlated with RECIST tumor burden estimation in the subset of patients treated with immune checkpoint blockade. CONCLUSION The findings indicate that higher ctDNA TMB, at the current commercial sequencing length, reflects worse clinical outcomes. IMPLICATIONS FOR PRACTICE Biomarkers to identify patients who will respond to immune checkpoint blockade are critical. Tissue tumor mutational burden (TMB) has emerged as a viable biomarker to predict response to anti-PD-1/PD-L1 therapy, but few studies have explored the meaning and potential clinical significance of noninvasive, blood-based TMB. Here, we investigated circulating tumor DNA (ctDNA) TMB and present data demonstrating that current ctDNA TMB may reflect tumor burden and that ctDNA panels with a greater number of mutations may be necessary to more accurately reflect tissue TMB.
Collapse
MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antineoplastic Agents, Immunological/pharmacology
- Antineoplastic Agents, Immunological/therapeutic use
- B7-H1 Antigen/antagonists & inhibitors
- B7-H1 Antigen/immunology
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/mortality
- Circulating Tumor DNA/blood
- Circulating Tumor DNA/genetics
- Drug Resistance, Neoplasm/genetics
- Female
- Follow-Up Studies
- Humans
- Kaplan-Meier Estimate
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/immunology
- Lung Neoplasms/mortality
- Male
- Middle Aged
- Mutation Rate
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- Programmed Cell Death 1 Receptor/immunology
- Progression-Free Survival
- Response Evaluation Criteria in Solid Tumors
- Retrospective Studies
- Tumor Burden
Collapse
Affiliation(s)
- Young Kwang Chae
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois, USA
| | - Andrew A Davis
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois, USA
| | - Sarita Agte
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois, USA
| | - Alan Pan
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Nicholas I Simon
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Wade T Iams
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois, USA
| | - Marcelo R Cruz
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Keerthi Tamragouri
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kyunghoon Rhee
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Nisha Mohindra
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois, USA
| | - Victoria Villaflor
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois, USA
| | - Wungki Park
- Division of Hematology and Medical Oncology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Gilberto Lopes
- Division of Hematology and Medical Oncology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Francis J Giles
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois, USA
| |
Collapse
|
39
|
Circulating tumor DNA applications in monitoring the treatment of metastatic colorectal cancer patients. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2019. [PMCID: PMC7009314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Colorectal cancer is the third most common cancer worldwide. New cancer treatment strategies such as monoclonal antibodies against growth factor and angiogenesis receptors have improved the overall survival (OS) and progression-free survival (PFS) in metastatic colorectal cancer (mCRC) patients. However, acquired resistance could happen after these therapies. Circulating tumor DNA (ctDNA) is the DNA fraction derived from tumor cells which could be applied as a non-invasive method for detecting tumor mutations before, during, and after therapies. Here, we reviewed most of the studies examining ctDNA as treatment monitoring in mCRC patients who receive different target therapies. Also, we compared ctDNA with other existing cancer-treatment monitoring methods.
Collapse
|
40
|
Osumi H, Shinozaki E, Takeda Y, Wakatsuki T, Ichimura T, Saiura A, Yamaguchi K, Takahashi S, Noda T, Zembutsu H. Clinical relevance of circulating tumor DNA assessed through deep sequencing in patients with metastatic colorectal cancer. Cancer Med 2018; 8:408-417. [PMID: 30575318 PMCID: PMC6346227 DOI: 10.1002/cam4.1913] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 12/16/2022] Open
Abstract
Because circulating tumor DNA (ctDNA) studies focusing on only one or a few genes to monitor the disease progress or treatment response are unlikely to find its clinical significance, the development of cell‐free DNA (cfDNA) panel covering hundreds of mutation hot spots is important for the establishment of clinically practical ctDNA detection system. We enrolled 101 patients with metastatic colorectal cancer (mCRC) who received chemotherapy. Amplicon‐based genomic profiling of 14 genes, which are commonly mutated in CRC, in plasma by next‐generation sequencing (NGS) was carried out to evaluate the feasibility of this assay and was compared with their clinical parameters and RAS status in matched tissue samples. Somatic mutations of the 14 genes in plasma cfDNA were detected in 88 patients (87.1%) with mCRC. Mutations in TP53, KRAS, and APC genes were detected in 70 (69.3%), 39 (38.6%), and 24 (23.7%) patients, respectively. Mutant allele frequencies in plasma were significantly associated with metastasis (liver, P = 0.00004, lymph node, P = 0.008, number of metastatic organs, P = 0.0006), tumor markers (CEA, P = 0.000007, CA19‐9, P = 0.006, LDH, P = 0.00001), and tumor diameter (maximum, P = 0.00002, sum of diameter, P = 0.00009). The overall concordance rate of RAS status between ctDNA and matched tissue was 77.2% (78/101). Our data confirmed that mutant allele in cfDNA can be sensitively detected by amplicon‐based NGS system. These results suggest that ctDNA could be a novel diagnostic biomarker to monitor changes in mutational status and tumor burden in patients with mCRC.
Collapse
Affiliation(s)
- Hiroki Osumi
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Eiji Shinozaki
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yoshinori Takeda
- Department of Hepato-Biliary-Pancreatic Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takeru Wakatsuki
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takashi Ichimura
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Akio Saiura
- Department of Hepato-Biliary-Pancreatic Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kensei Yamaguchi
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Shunji Takahashi
- Department of Medical Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tetsuo Noda
- Cancer Precision Medicine Center, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hitoshi Zembutsu
- Cancer Precision Medicine Center, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| |
Collapse
|
41
|
Mansukhani S, Barber LJ, Kleftogiannis D, Moorcraft SY, Davidson M, Woolston A, Proszek PZ, Griffiths B, Fenwick K, Herman B, Matthews N, O'Leary B, Hulkki S, Gonzalez De Castro D, Patel A, Wotherspoon A, Okachi A, Rana I, Begum R, Davies MN, Powles T, von Loga K, Hubank M, Turner N, Watkins D, Chau I, Cunningham D, Lise S, Starling N, Gerlinger M. Ultra-Sensitive Mutation Detection and Genome-Wide DNA Copy Number Reconstruction by Error-Corrected Circulating Tumor DNA Sequencing. Clin Chem 2018; 64:1626-1635. [PMID: 30150316 PMCID: PMC6214522 DOI: 10.1373/clinchem.2018.289629] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/17/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Circulating free DNA sequencing (cfDNA-Seq) can portray cancer genome landscapes, but highly sensitive and specific technologies are necessary to accurately detect mutations with often low variant frequencies. METHODS We developed a customizable hybrid-capture cfDNA-Seq technology using off-the-shelf molecular barcodes and a novel duplex DNA molecule identification tool for enhanced error correction. RESULTS Modeling based on cfDNA yields from 58 patients showed that this technology, requiring 25 ng of cfDNA, could be applied to >95% of patients with metastatic colorectal cancer (mCRC). cfDNA-Seq of a 32-gene, 163.3-kbp target region detected 100% of single-nucleotide variants, with 0.15% variant frequency in spike-in experiments. Molecular barcode error correction reduced false-positive mutation calls by 97.5%. In 28 consecutively analyzed patients with mCRC, 80 out of 91 mutations previously detected by tumor tissue sequencing were called in the cfDNA. Call rates were similar for point mutations and indels. cfDNA-Seq identified typical mCRC driver mutations in patients in whom biopsy sequencing had failed or did not include key mCRC driver genes. Mutations only called in cfDNA but undetectable in matched biopsies included a subclonal resistance driver mutation to anti-EGFR antibodies in KRAS, parallel evolution of multiple PIK3CA mutations in 2 cases, and TP53 mutations originating from clonal hematopoiesis. Furthermore, cfDNA-Seq off-target read analysis allowed simultaneous genome-wide copy number profile reconstruction in 20 of 28 cases. Copy number profiles were validated by low-coverage whole-genome sequencing. CONCLUSIONS This error-corrected, ultradeep cfDNA-Seq technology with a customizable target region and publicly available bioinformatics tools enables broad insights into cancer genomes and evolution. CLINICALTRIALSGOV IDENTIFIER NCT02112357.
Collapse
Affiliation(s)
- Sonia Mansukhani
- Centre for Evolution and Cancer, Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Louise J Barber
- Centre for Evolution and Cancer, Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Dimitrios Kleftogiannis
- Centre for Evolution and Cancer, Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Sing Yu Moorcraft
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Michael Davidson
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Andrew Woolston
- Centre for Evolution and Cancer, Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | | | - Beatrice Griffiths
- Centre for Evolution and Cancer, Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Kerry Fenwick
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Bram Herman
- Diagnostics and Genomics Group, Agilent Technologies Inc., Santa Clara, CA
| | - Nik Matthews
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Ben O'Leary
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK
| | - Sanna Hulkki
- Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | | | - Anisha Patel
- Department for Radiology, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Andrew Wotherspoon
- Department of Histopathology, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Aleruchi Okachi
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Isma Rana
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Ruwaida Begum
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Matthew N Davies
- Centre for Evolution and Cancer, Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Thomas Powles
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Katharina von Loga
- Centre for Evolution and Cancer, Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Michael Hubank
- Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Nick Turner
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK
- Breast Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - David Watkins
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Ian Chau
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - David Cunningham
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Stefano Lise
- Centre for Evolution and Cancer, Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Naureen Starling
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Marco Gerlinger
- Centre for Evolution and Cancer, Division of Molecular Pathology, The Institute of Cancer Research, London, UK;
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| |
Collapse
|
42
|
Sacher AG. Fundamental Concepts in the Application of Plasma Genotyping (Liquid Biopsy) to EGFR Mutation Detection in Non–Small-Cell Lung Cancer. JCO Precis Oncol 2018; 2:1-12. [DOI: 10.1200/po.17.00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plasma genotyping has rapidly evolved from an investigational technology into a standard-of-care tool used to direct therapy in metastatic non–small-cell lung cancer (NSCLC). Multiple testing platforms exist for plasma genotyping, each with unique test characteristics and scientific validation. The optimal use and interpretation of plasma genotyping requires understanding of cell-free DNA biology, the assay characteristics of the available testing technologies, and the application of testing in each clinical scenario. Current recommendations for plasma genotyping in metastatic NSCLC are limited to patients with newly diagnosed disease and those with acquired resistance to targeted therapy, in particular, epidermal growth factor receptor (EGFR) kinase inhibitors. In newly diagnosed metastatic NSCLC, under certain circumstances, plasma genotyping is useful for the detection of targetable genomic alterations or nontargetable driver alterations (eg, KRAS) that are mutually exclusive with targetable alterations. In patients with acquired resistance to therapy, such as EGFR T790M-mediated acquired resistance to EGFR kinase inhibitors, plasma genotyping may detect resistance mutations missed by standard tissue genotyping because of tumor heterogeneity. In both scenarios, the high specificity and positive predictive value of validated plasma genotyping assays allow for the reliable selection of therapy on the basis of a positive plasma genotyping result. However, the modest sensitivity of these assays requires that negative results be confirmed by tissue genotyping with repeat biopsy, if necessary. There is considerable potential for plasma genotyping in the detection of early-stage disease, for patients at risk for disease recurrence, and as an integrated biomarker of therapeutic response in clinical trials of novel therapies.
Collapse
Affiliation(s)
- Adrian G. Sacher
- Adrian G. Sacher, Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario
| |
Collapse
|
43
|
Dudnik E, Twito T, Faull I, Dvir A, Soussan-Gutman L, Purim O, Lanman RB. Circulating Cell-Free Tumor DNA in the Management of Double Primary Tumors. JCO Precis Oncol 2018; 2:1-6. [DOI: 10.1200/po.17.00238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Elizabeth Dudnik
- Elizabeth Dudnik and Ofer Purim, Davidoff Cancer Center, Rabin Medical Center, Petach Tikva; Tal Twito, Addie Dvir, and Lior Soussan-Gutman, TEVA Pharmaceuticals Industries, Shoam, Israel; and Iris Faull and Richard B. Lanman, Guardant Health, Redwood City, CA
| | - Tal Twito
- Elizabeth Dudnik and Ofer Purim, Davidoff Cancer Center, Rabin Medical Center, Petach Tikva; Tal Twito, Addie Dvir, and Lior Soussan-Gutman, TEVA Pharmaceuticals Industries, Shoam, Israel; and Iris Faull and Richard B. Lanman, Guardant Health, Redwood City, CA
| | - Iris Faull
- Elizabeth Dudnik and Ofer Purim, Davidoff Cancer Center, Rabin Medical Center, Petach Tikva; Tal Twito, Addie Dvir, and Lior Soussan-Gutman, TEVA Pharmaceuticals Industries, Shoam, Israel; and Iris Faull and Richard B. Lanman, Guardant Health, Redwood City, CA
| | - Addie Dvir
- Elizabeth Dudnik and Ofer Purim, Davidoff Cancer Center, Rabin Medical Center, Petach Tikva; Tal Twito, Addie Dvir, and Lior Soussan-Gutman, TEVA Pharmaceuticals Industries, Shoam, Israel; and Iris Faull and Richard B. Lanman, Guardant Health, Redwood City, CA
| | - Lior Soussan-Gutman
- Elizabeth Dudnik and Ofer Purim, Davidoff Cancer Center, Rabin Medical Center, Petach Tikva; Tal Twito, Addie Dvir, and Lior Soussan-Gutman, TEVA Pharmaceuticals Industries, Shoam, Israel; and Iris Faull and Richard B. Lanman, Guardant Health, Redwood City, CA
| | - Ofer Purim
- Elizabeth Dudnik and Ofer Purim, Davidoff Cancer Center, Rabin Medical Center, Petach Tikva; Tal Twito, Addie Dvir, and Lior Soussan-Gutman, TEVA Pharmaceuticals Industries, Shoam, Israel; and Iris Faull and Richard B. Lanman, Guardant Health, Redwood City, CA
| | - Richard B. Lanman
- Elizabeth Dudnik and Ofer Purim, Davidoff Cancer Center, Rabin Medical Center, Petach Tikva; Tal Twito, Addie Dvir, and Lior Soussan-Gutman, TEVA Pharmaceuticals Industries, Shoam, Israel; and Iris Faull and Richard B. Lanman, Guardant Health, Redwood City, CA
| |
Collapse
|
44
|
Bogenberger JM, DeLeon TT, Arora M, Ahn DH, Borad MJ. Emerging role of precision medicine in biliary tract cancers. NPJ Precis Oncol 2018; 2:21. [PMID: 30302397 PMCID: PMC6170410 DOI: 10.1038/s41698-018-0064-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 08/13/2018] [Accepted: 08/15/2018] [Indexed: 12/14/2022] Open
Abstract
Biliary tracts cancers (BTCs) are a diverse group of aggressive malignancies with an overall poor prognosis. Genomic characterization has uncovered many putative clinically actionable aberrations that can also facilitate the prognostication of patients. As such, comprehensive genomic profiling is playing a growing role in the clinical management of BTCs. Currently however, there is only one precision medicine approved by the US Food and Drug Administration (FDA) for the treatment of BTCs. Herein, we highlight the prevalence and prognostic, diagnostic, and predictive significance of recurrent mutations and other genomic aberrations with current clinical implications or emerging relevance to clinical practice. Some ongoing clinical trials, as well as future areas of exploration for precision oncology in BTCs are highlighted.
Collapse
Affiliation(s)
- James M. Bogenberger
- Division of Hematology/Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ USA
| | - Thomas T. DeLeon
- Division of Hematology/Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ USA
| | - Mansi Arora
- Division of Hematology/Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ USA
| | - Daniel H. Ahn
- Division of Hematology/Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ USA
| | - Mitesh J. Borad
- Division of Hematology/Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ USA
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN USA
- Mayo Clinic Cancer Center, Mayo Clinic, Phoenix, AZ USA
| |
Collapse
|
45
|
Clinical Application of Genomic Profiling With Circulating Tumor DNA for Management of Advanced Non–Small-cell Lung Cancer in Asia. Clin Lung Cancer 2018; 19:e601-e608. [DOI: 10.1016/j.cllc.2018.04.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/07/2018] [Accepted: 04/24/2018] [Indexed: 11/21/2022]
|
46
|
The Clinical Impact of Comprehensive Genomic Testing of Circulating Cell-Free DNA in Advanced Lung Cancer. J Thorac Oncol 2018; 13:1705-1716. [PMID: 30121392 DOI: 10.1016/j.jtho.2018.07.101] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/10/2018] [Accepted: 07/24/2018] [Indexed: 01/22/2023]
Abstract
INTRODUCTION Next-generation sequencing (NGS) of cell-free circulating tumor DNA (cfDNA) enables noninvasive genomic analysis of NSCLC patients. Although plasma-detected genomic alterations (GAs) have been shown to predict targeted therapy response, evidence of durability of response is lacking or limited to small cohorts as is the impact of cfDNA NGS results on clinical decisions. METHODS This retrospective study of stage IIIB/IV NSCLC patients between the years 2014 and 2017 in Israel used cfDNA NGS (Guardant360; Guardant Health, Inc., Redwood City, California) to identify targetable GAs. RESULTS We consecutively tested 116 NSCLC patients, 41.4% before first-line therapy (group A), 34.5% upon progression on chemotherapy or immunotherapy (group B1), and 24.1% upon progression on EGFR tyrosine kinase inhibitors (group B2). Targetable GAs were found in 31% of group A (15 of 48 patients), 32.5% in group B1 (13 of 40 patients) and 71% in group B2 (20 of 28 patients). Treatment decision was changed to targeted therapy in 23% (11 of 48 patients), 25% (10 of 40 patients) and 32% (9 of 28 patients), respectively (total cohort 26%; 30/116). Objective response rate (Response Evaluation Criteria in Solid Tumors) was 43% (12 of 28 patients) including one complete response, partial response in 39% (11 of 28 patients), stable disease in 32% (9 of 28 patients), and progressive disease in 25% (7 of 28 patients). Disease control rate was 75% for 5 months median treatment duration. CONCLUSIONS Comprehensive cfDNA testing impacted clinical decisions in one-quarter to one-third of initial and subsequent lines of treatment in advanced NSCLC patients. This retrospective study extends previous reports by showing that responses based on cfDNA are durable and change treatment decisions at initial presentation and at progression.
Collapse
|
47
|
Odegaard JI, Vincent JJ, Mortimer S, Vowles JV, Ulrich BC, Banks KC, Fairclough SR, Zill OA, Sikora M, Mokhtari R, Abdueva D, Nagy RJ, Lee CE, Kiedrowski LA, Paweletz CP, Eltoukhy H, Lanman RB, Chudova DI, Talasaz A. Validation of a Plasma-Based Comprehensive Cancer Genotyping Assay Utilizing Orthogonal Tissue- and Plasma-Based Methodologies. Clin Cancer Res 2018; 24:3539-3549. [PMID: 29691297 DOI: 10.1158/1078-0432.ccr-17-3831] [Citation(s) in RCA: 276] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 03/15/2018] [Accepted: 04/20/2018] [Indexed: 11/16/2022]
Abstract
Purpose: To analytically and clinically validate a circulating cell-free tumor DNA sequencing test for comprehensive tumor genotyping and demonstrate its clinical feasibility.Experimental Design: Analytic validation was conducted according to established principles and guidelines. Blood-to-blood clinical validation comprised blinded external comparison with clinical droplet digital PCR across 222 consecutive biomarker-positive clinical samples. Blood-to-tissue clinical validation comprised comparison of digital sequencing calls to those documented in the medical record of 543 consecutive lung cancer patients. Clinical experience was reported from 10,593 consecutive clinical samples.Results: Digital sequencing technology enabled variant detection down to 0.02% to 0.04% allelic fraction/2.12 copies with ≤0.3%/2.24-2.76 copies 95% limits of detection while maintaining high specificity [prevalence-adjusted positive predictive values (PPV) >98%]. Clinical validation using orthogonal plasma- and tissue-based clinical genotyping across >750 patients demonstrated high accuracy and specificity [positive percent agreement (PPAs) and negative percent agreement (NPAs) >99% and PPVs 92%-100%]. Clinical use in 10,593 advanced adult solid tumor patients demonstrated high feasibility (>99.6% technical success rate) and clinical sensitivity (85.9%), with high potential actionability (16.7% with FDA-approved on-label treatment options; 72.0% with treatment or trial recommendations), particularly in non-small cell lung cancer, where 34.5% of patient samples comprised a directly targetable standard-of-care biomarker.Conclusions: High concordance with orthogonal clinical plasma- and tissue-based genotyping methods supports the clinical accuracy of digital sequencing across all four types of targetable genomic alterations. Digital sequencing's clinical applicability is further supported by high rates of technical success and biomarker target discovery. Clin Cancer Res; 24(15); 3539-49. ©2018 AACR.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Oliver A Zill
- Guardant Health, Redwood City, California.,Genentech, South San Francisco, California
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Ou SHI, Nagasaka M, Zhu VW. Liquid Biopsy to Identify Actionable Genomic Alterations. Am Soc Clin Oncol Educ Book 2018; 38:978-997. [PMID: 30231331 PMCID: PMC6865813 DOI: 10.1200/edbk_199765] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Liquid biopsy has been used extensively in solid malignancies to detect actionable driver mutations, to monitor treatment response, to detect recurrence, to identify resistance mechanisms, and to prognosticate outcome. Although many liquid biopsy sequencing platforms are being used, only five test kits have received government approval. We review representative literature on these government-approved liquid biopsy kits, which are primarily used to detect EGFR mutation in lung cancer and RAS ( KRAS, NRAS, BRAF) mutations in colorectal carcinoma. Another emerging use of single-gene liquid biopsy is to detect PIK3CA mutations and to understand resistance to hormonal blockade in breast and prostate cancers. The two most commonly used next-generation sequencing (NGS) liquid biopsy tests (Guardant 360, Guardant Health; FoundationACT, Foundation Medicine Inc.) are discussed. The ability and the applicability of NGS platform to detect tumor mutation burden are also addressed. Finally, the use of circulating tumor DNA (ctDNA) to detect minimal residual disease may be the most important use of ctDNA in the setting of tumor heterogeneity. The ability to identify "shedders" and "nonshedders" of ctDNA may provide important insight into the clinicopathologic characteristics of the tumor and portend important prognostic significance regarding survival.
Collapse
Affiliation(s)
- Sai-Hong Ignatius Ou
- From Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Orange, CA; Karmanos Cancer Center, Wayne State University, Detroit, MI; Hematology/Oncology Section, Veterans Affairs Long Beach Healthcare System, Long Beach, CA
| | - Misako Nagasaka
- From Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Orange, CA; Karmanos Cancer Center, Wayne State University, Detroit, MI; Hematology/Oncology Section, Veterans Affairs Long Beach Healthcare System, Long Beach, CA
| | - Viola W Zhu
- From Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Orange, CA; Karmanos Cancer Center, Wayne State University, Detroit, MI; Hematology/Oncology Section, Veterans Affairs Long Beach Healthcare System, Long Beach, CA
| |
Collapse
|
49
|
Zill OA, Banks KC, Fairclough SR, Mortimer SA, Vowles JV, Mokhtari R, Gandara DR, Mack PC, Odegaard JI, Nagy RJ, Baca AM, Eltoukhy H, Chudova DI, Lanman RB, Talasaz A. The Landscape of Actionable Genomic Alterations in Cell-Free Circulating Tumor DNA from 21,807 Advanced Cancer Patients. Clin Cancer Res 2018; 24:3528-3538. [DOI: 10.1158/1078-0432.ccr-17-3837] [Citation(s) in RCA: 211] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/19/2018] [Accepted: 05/11/2018] [Indexed: 11/16/2022]
|
50
|
Phallen J, Sausen M, Adleff V, Leal A, Hruban C, White J, Anagnostou V, Fiksel J, Cristiano S, Papp E, Speir S, Reinert T, Orntoft MBW, Woodward BD, Murphy D, Parpart-Li S, Riley D, Nesselbush M, Sengamalay N, Georgiadis A, Li QK, Madsen MR, Mortensen FV, Huiskens J, Punt C, van Grieken N, Fijneman R, Meijer G, Husain H, Scharpf RB, Diaz LA, Jones S, Angiuoli S, Ørntoft T, Nielsen HJ, Andersen CL, Velculescu VE. Direct detection of early-stage cancers using circulating tumor DNA. Sci Transl Med 2018; 9:9/403/eaan2415. [PMID: 28814544 DOI: 10.1126/scitranslmed.aan2415] [Citation(s) in RCA: 703] [Impact Index Per Article: 117.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/13/2017] [Accepted: 07/22/2017] [Indexed: 12/12/2022]
Abstract
Early detection and intervention are likely to be the most effective means for reducing morbidity and mortality of human cancer. However, development of methods for noninvasive detection of early-stage tumors has remained a challenge. We have developed an approach called targeted error correction sequencing (TEC-Seq) that allows ultrasensitive direct evaluation of sequence changes in circulating cell-free DNA using massively parallel sequencing. We have used this approach to examine 58 cancer-related genes encompassing 81 kb. Analysis of plasma from 44 healthy individuals identified genomic changes related to clonal hematopoiesis in 16% of asymptomatic individuals but no alterations in driver genes related to solid cancers. Evaluation of 200 patients with colorectal, breast, lung, or ovarian cancer detected somatic mutations in the plasma of 71, 59, 59, and 68%, respectively, of patients with stage I or II disease. Analyses of mutations in the circulation revealed high concordance with alterations in the tumors of these patients. In patients with resectable colorectal cancers, higher amounts of preoperative circulating tumor DNA were associated with disease recurrence and decreased overall survival. These analyses provide a broadly applicable approach for noninvasive detection of early-stage tumors that may be useful for screening and management of patients with cancer.
Collapse
Affiliation(s)
- Jillian Phallen
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Mark Sausen
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Vilmos Adleff
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Alessandro Leal
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Carolyn Hruban
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - James White
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jacob Fiksel
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Stephen Cristiano
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Eniko Papp
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Savannah Speir
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Thomas Reinert
- Department of Molecular Medicine, Aarhus University Hospital, DK-8200 Aarhus, Denmark
| | | | - Brian D Woodward
- Division of Hematology and Oncology, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Derek Murphy
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | | | - David Riley
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | | | | | | | - Qing Kay Li
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | - Frank Viborg Mortensen
- Department of Surgical Gastroenterology, Aarhus University Hospital, DK-8000 Aarhus, Denmark
| | - Joost Huiskens
- Department of Surgery, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Department of Medical Oncology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Cornelis Punt
- Department of Medical Oncology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Nicole van Grieken
- Department of Pathology, VU University Medical Center, Amsterdam 1081 HV, Netherlands
| | - Remond Fijneman
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 1066 CX, Netherlands
| | - Gerrit Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 1066 CX, Netherlands
| | - Hatim Husain
- Division of Hematology and Oncology, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert B Scharpf
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Luis A Diaz
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Siân Jones
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Sam Angiuoli
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Torben Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, DK-8200 Aarhus, Denmark
| | - Hans Jørgen Nielsen
- Department of Surgical Gastroenterology 360, Hvidovre Hospital, Hvidovre, Denmark
| | | | - Victor E Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| |
Collapse
|