51
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Lee SH, Lee B, Shim JH, Lee KW, Yun JW, Kim SY, Kim TY, Kim YH, Ko YH, Chung HC, Yu CS, Lee J, Rha SY, Kim TW, Jung KH, Im SA, Moon HG, Cho S, Kang JH, Kim J, Kim SK, Ryu HS, Ha SY, Kim JI, Chung YJ, Kim C, Kim HL, Park WY, Noh DY, Park K. Landscape of Actionable Genetic Alterations Profiled from 1,071 Tumor Samples in Korean Cancer Patients. Cancer Res Treat 2018; 51:211-222. [PMID: 29690749 PMCID: PMC6333975 DOI: 10.4143/crt.2018.132] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/19/2018] [Indexed: 12/15/2022] Open
Abstract
Purpose With the emergence of next-generation sequencing (NGS) technology, profiling a wide range of genomic alterations has become a possibility resulting in improved implementation of targeted cancer therapy. In Asian populations, the prevalence and spectrum of clinically actionable genetic alterations has not yet been determined because of a lack of studies examining high-throughput cancer genomic data. Materials and Methods To address this issue, 1,071 tumor samples were collected from five major cancer institutes in Korea and analyzed using targeted NGS at a centralized laboratory. Samples were either fresh frozen or formalin-fixed, paraffin embedded (FFPE) and the quality and yield of extracted genomic DNA was assessed. In order to estimate the effect of sample condition on the quality of sequencing results, tissue preparation method, specimen type (resected or biopsied) and tissue storage time were compared. Results We detected 7,360 non-synonymous point mutations, 1,164 small insertions and deletions, 3,173 copy number alterations, and 462 structural variants. Fifty-four percent of tumors had one or more clinically relevant genetic mutation. The distribution of actionable variants was variable among different genes. Fresh frozen tissues, surgically resected specimens, and recently obtained specimens generated superior sequencing results over FFPE tissues, biopsied specimens, and tissues with long storage duration. Conclusion In order to overcome, challenges involved in bringing NGS testing into routine clinical use, a centralized laboratory model was designed that could improve the NGS workflows, provide appropriate turnaround times and control costs with goal of enabling precision medicine.
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Affiliation(s)
- Se-Hoon Lee
- Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea
| | - Boram Lee
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea.,Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Joon Ho Shim
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea.,Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kwang Woo Lee
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Won Yun
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea.,Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sook-Young Kim
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae-You Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Yeul Hong Kim
- Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea
| | - Young Hyeh Ko
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyun Cheol Chung
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Chang Sik Yu
- Department of Colon & Rectal Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jeeyun Lee
- Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sun Young Rha
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Tae Won Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyung Hae Jung
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seock-Ah Im
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Hyeong-Gon Moon
- Department of Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sukki Cho
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Jin Hyoung Kang
- Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jihun Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang Kyum Kim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sang Yun Ha
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong Il Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Yeun-Jun Chung
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Cheolmin Kim
- Department of Medical Informatics, Pusan National University School of Medicine, Yangsan, Korea
| | - Hyung-Lae Kim
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, Korea
| | - Woong-Yang Park
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea.,Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Kor
| | - Dong-Young Noh
- Department of Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Keunchil Park
- Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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McCoach CE, Blakely CM, Banks KC, Levy B, Chue BM, Raymond VM, Le AT, Lee CE, Diaz J, Waqar SN, Purcell WT, Aisner DL, Davies KD, Lanman RB, Shaw AT, Doebele RC. Clinical Utility of Cell-Free DNA for the Detection of ALK Fusions and Genomic Mechanisms of ALK Inhibitor Resistance in Non-Small Cell Lung Cancer. Clin Cancer Res 2018; 24:2758-2770. [PMID: 29599410 DOI: 10.1158/1078-0432.ccr-17-2588] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/06/2018] [Accepted: 03/20/2018] [Indexed: 01/01/2023]
Abstract
Purpose: Patients with advanced non-small cell lung cancer (NSCLC) whose tumors harbor anaplastic lymphoma kinase (ALK) gene fusions benefit from treatment with ALK inhibitors (ALKi). Analysis of cell-free circulating tumor DNA (cfDNA) may provide a noninvasive way to identify ALK fusions and actionable resistance mechanisms without an invasive biopsy.Patients and Methods: The Guardant360 (G360; Guardant Health) deidentified database of NSCLC cases was queried to identify 88 consecutive patients with 96 plasma-detected ALK fusions. G360 is a clinical cfDNA next-generation sequencing (NGS) test that detects point mutations, select copy number gains, fusions, insertions, and deletions in plasma.Results: Identified fusion partners included EML4 (85.4%), STRN (6%), and KCNQ, KLC1, KIF5B, PPM1B, and TGF (totaling 8.3%). Forty-two ALK-positive patients had no history of targeted therapy (cohort 1), with tissue ALK molecular testing attempted in 21 (5 negative, 5 positive, and 11 tissue insufficient). Follow-up of 3 of the 5 tissue-negative patients showed responses to ALKi. Thirty-one patients were tested at known or presumed ALKi progression (cohort 2); 16 samples (53%) contained 1 to 3 ALK resistance mutations. In 13 patients, clinical status was unknown (cohort 3), and no resistance mutations or bypass pathways were identified. In 6 patients with known EGFR-activating mutations, an ALK fusion was identified on progression (cohort 4; 4 STRN, 1 EML4; one both STRN and EML4); five harbored EGFR T790M.Conclusions: In this cohort of cfDNA-detected ALK fusions, we demonstrate that comprehensive cfDNA NGS provides a noninvasive means of detecting targetable alterations and characterizing resistance mechanisms on progression. Clin Cancer Res; 24(12); 2758-70. ©2018 AACR.
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Affiliation(s)
- Caroline E McCoach
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Collin M Blakely
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | | | - Benjamin Levy
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Ben M Chue
- Lifespring Cancer Treatment Center, Seattle, Washington
| | | | - Anh T Le
- University of Colorado Cancer Center, Aurora, Colorado
| | | | - Joseph Diaz
- Guardant Health Inc., Redwood City, California
| | - Saiama N Waqar
- Washington University School of Medicine, St. Louis, Missouri
| | | | - Dara L Aisner
- University of Colorado Cancer Center, Aurora, Colorado
| | | | | | - Alice T Shaw
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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53
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Olmedillas‐López S, García‐Olmo DC, García‐Arranz M, Peiró‐Pastor R, Aguado B, García‐Olmo D. Liquid biopsy by NGS: differential presence of exons (DPE) in cell-free DNA reveals different patterns in metastatic and nonmetastatic colorectal cancer. Cancer Med 2018; 7:1706-1716. [PMID: 29573240 PMCID: PMC5943476 DOI: 10.1002/cam4.1399] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 01/15/2018] [Accepted: 01/26/2018] [Indexed: 12/22/2022] Open
Abstract
Next‐generation sequencing (NGS) has been proposed as a suitable tool for liquid biopsy in colorectal cancer (CRC), although most studies to date have focused almost exclusively on sequencing of panels of potential clinically actionable genes. We evaluated the clinical value of whole‐exome sequencing (WES) of cell‐free DNA (cfDNA) circulating in plasma, with the goal of identifying differential clinical profiles in patients with CRC. To this end, we applied an original concept, “differential presence of exons” (DPE). We determined differences in levels of 379 exons in plasma cfDNA and used DPE analysis to cluster and classify patients with disseminated and localized disease. The resultant bioinformatics analysis pipeline allowed us to design a predictive DPE algorithm in a small subset of patients that could not be initially classified based on the selection criteria. This DPE suggests that these nucleic acids could be actively released by both tumor and nontumor cells as a means of intercellular communication and might thus play a role in the process of malignant transformation. DPE is a new technique for the study of plasma cfDNA by WES that might have predictive and prognostic value in patients with CRC.
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Affiliation(s)
- Susana Olmedillas‐López
- New Therapies LaboratoryFoundation Health Research Institute‐Fundación Jiménez Díaz University Hospital (FIIS‐FJD)MadridSpain
| | - Dolores C. García‐Olmo
- Experimental Research UnitGeneral University Hospital of AlbaceteAlbaceteSpain
- Institut de Recerca Biomèdica de LleidaCentre de Recerca Experimental Biomèdica Aplicada (CREBA)LleidaSpain
| | - Mariano García‐Arranz
- New Therapies LaboratoryFoundation Health Research Institute‐Fundación Jiménez Díaz University Hospital (FIIS‐FJD)MadridSpain
- Department of SurgerySchool of MedicineUniversidad Autónoma de Madrid (UAM)MadridSpain
| | - Ramón Peiró‐Pastor
- Genomics and NGS ServiceCentro de Biología Molecular Severo Ochoa (CBMSO)CSIC‐UAMMadridSpain
| | - Begoña Aguado
- Genomics and NGS ServiceCentro de Biología Molecular Severo Ochoa (CBMSO)CSIC‐UAMMadridSpain
| | - Damián García‐Olmo
- New Therapies LaboratoryFoundation Health Research Institute‐Fundación Jiménez Díaz University Hospital (FIIS‐FJD)MadridSpain
- Department of SurgerySchool of MedicineUniversidad Autónoma de Madrid (UAM)MadridSpain
- Department of SurgeryFundación Jiménez Díaz University HospitalMadridSpain
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54
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Hahn AW, Gill DM, Maughan B, Agarwal A, Arjyal L, Gupta S, Streeter J, Bailey E, Pal SK, Agarwal N. Correlation of genomic alterations assessed by next-generation sequencing (NGS) of tumor tissue DNA and circulating tumor DNA (ctDNA) in metastatic renal cell carcinoma (mRCC): potential clinical implications. Oncotarget 2018; 8:33614-33620. [PMID: 28431395 PMCID: PMC5464894 DOI: 10.18632/oncotarget.16833] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/25/2017] [Indexed: 12/28/2022] Open
Abstract
Introduction Tumor tissue and circulating tumor DNA (ctDNA) next-generation sequencing (NGS) testing are frequently performed to detect genomic alterations (GAs) to help guide treatment in metastatic renal cell carcinoma (mRCC), especially after progression on standard systemic therapy. Our objective was to assess if GAs detected by ctDNA NGS are different from those detected by tumor tissue NGS, specifically in patients with mRCC, and if these platforms are interchangeable or complimentary. Results When controlling for genes tested by both platforms, the median mutation rate for ctDNA was similar to tissue (median 3.0 vs. 1.0, p = 0.14). However, the concordance rate between the two platforms was only 8.6%. When comparing GAs by molecular pathway, GAs in tumor tissue were more common for the DNA repair and epigenetic pathways. Materials and Methods Results of NGS testing from tumor tissue and ctDNA from 19 sequential mRCC patients were compared. GAs in each were statistically evaluated using the Wilcoxon signed-rank test. The Fischer's exact test was used to compare the incidence of mutations in selected molecular pathways. Conclusions When controlling for genes tested by both platforms, similar number of GAs were detected by both tissue and ctDNA based NGS. However, there was discordance in the type of GAs detected suggesting that ctDNA NGS may be more reflective of dynamic tumor genomic heterogeneity. Hence, these two platforms may be considered complementary to each other, rather than interchangeable, for assessment of tumor GAs to guide selection of targeted clinical trial therapies.
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Affiliation(s)
- Andrew W Hahn
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - David M Gill
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Benjamin Maughan
- Division of Medical Oncology, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Archana Agarwal
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Lubina Arjyal
- Division of Medical Oncology, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Sumati Gupta
- Division of Medical Oncology, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Jessica Streeter
- Department of Pharmacy, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Erin Bailey
- Department of Pharmacy, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Sumanta K Pal
- Department of Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Neeraj Agarwal
- Division of Medical Oncology, Huntsman Cancer Institute, Salt Lake City, UT, USA
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55
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Chae YK, Davis AA, Carneiro BA, Chandra S, Mohindra N, Kalyan A, Kaplan J, Matsangou M, Pai S, Costa R, Jovanovic B, Cristofanilli M, Platanias LC, Giles FJ. Concordance between genomic alterations assessed by next-generation sequencing in tumor tissue or circulating cell-free DNA. Oncotarget 2018; 7:65364-65373. [PMID: 27588476 PMCID: PMC5323161 DOI: 10.18632/oncotarget.11692] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/10/2016] [Indexed: 02/06/2023] Open
Abstract
Genomic analysis of tumor tissue is the standard technique for identifying DNA alterations in malignancies. Genomic analysis of circulating tumor cell-free DNA (cfDNA) represents a relatively non-invasive method of assessing genomic alterations using peripheral blood. We compared the concordance of genomic alterations between cfDNA and tissue biopsies in this retrospective study. Twenty-eight patients with advanced solid tumors with paired next-generation sequencing tissue and cfDNA biopsies were identified. Sixty-five genes were common to both assays. Concordance was defined as the presence or absence of the identical genomic alteration(s) in a single gene on both molecular platforms. Including all aberrations, the average number of alterations per patient for tissue and cfDNA analysis was 4.82 and 2.96, respectively. When eliminating alterations not detectable in the cfDNA assay, mean number of alterations for tissue and cfDNA was 3.21 and 2.96, respectively. Overall, concordance was 91.9–93.9%. However, the concordance rate decreased to 11.8–17.1% when considering only genes with reported genomic alterations in either assay. Over 50% of mutations detected in either technique were not detected using the other biopsy technique, indicating a potential complementary role of each assay. Across 5 genes (TP53, EGFR, KRAS, APC, CDKN2A), sensitivity and specificity were 59.1% and 94.8%, respectively. Potential explanations for the lack of concordance include differences in assay platform, spatial and temporal factors, tumor heterogeneity, interval treatment, subclones, and potential germline DNA contamination. These results highlight the importance of prospective studies to evaluate concordance of genomic findings between distinct platforms that ultimately may inform treatment decisions.
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Affiliation(s)
- Young Kwang Chae
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University, Chicago, IL, USA.,Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Andrew A Davis
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Benedito A Carneiro
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University, Chicago, IL, USA.,Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Sunandana Chandra
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University, Chicago, IL, USA.,Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Nisha Mohindra
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Aparna Kalyan
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University, Chicago, IL, USA.,Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Jason Kaplan
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University, Chicago, IL, USA.,Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Maria Matsangou
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University, Chicago, IL, USA.,Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Sachin Pai
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Ricardo Costa
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Borko Jovanovic
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Massimo Cristofanilli
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University, Chicago, IL, USA.,Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Leonidas C Platanias
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University, Chicago, IL, USA.,Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA.,Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| | - Francis J Giles
- Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University, Chicago, IL, USA.,Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
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Villaflor V, Won B, Nagy R, Banks K, Lanman RB, Talasaz A, Salgia R. Biopsy-free circulating tumor DNA assay identifies actionable mutations in lung cancer. Oncotarget 2018; 7:66880-66891. [PMID: 27602770 PMCID: PMC5341844 DOI: 10.18632/oncotarget.11801] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 08/13/2016] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION The potential of oncogene-driven targeted therapy is perhaps most fully realized in non-small cell lung cancer (NSCLC), given the number of genomic targets and approved matched therapies. However, invasive tissue biopsy at the time of each disease progression may not be possible and is associated with high morbidity and cost. Use of newly available "liquid biopsies" can circumvent these issues. RESULTS 83% of subjects had at least one genomic alteration identified in plasma. Most commonly mutated genes were TP53, KRAS and EGFR. Subjects with no detectable ctDNA were more likely to have small volume disease, lepidic growth pattern, mucinous tumors or isolated leptomeningeal disease. METHODS Subjects were individuals with NSCLC undergoing analysis of cell-free circulating tumor DNA using a validated, commercially-available next-generation sequencing assay at a single institution. Demographic, clinicopathologic information and results from tissue and plasma-based genomic testing were reviewed for each subject. CONCLUSIONS This is the first clinic-based series of NSCLC patients assessing outcomes of targeted therapies using a commercially available ctDNA assay. Over 80% of patients had detectable ctDNA, concordance between paired tissue and blood for truncal oncogenic drivers was high and patients with biomarkers identified in plasma had PFS in the expected range. These data suggest that biopsy-free ctDNA analysis is a viable first choice when the diagnostic tissue biopsy is insufficient for genotyping or at the time of progression when a repeated invasive tissue biopsy is not possible/preferred.
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Affiliation(s)
- Victoria Villaflor
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Brian Won
- University of Chicago School of Medicine, MC 2115, Chicago, IL 60637, USA
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Rachiglio AM, Esposito Abate R, Sacco A, Pasquale R, Fenizia F, Lambiase M, Morabito A, Montanino A, Rocco G, Romano C, Nappi A, Iaffaioli RV, Tatangelo F, Botti G, Ciardiello F, Maiello MR, De Luca A, Normanno N. Limits and potential of targeted sequencing analysis of liquid biopsy in patients with lung and colon carcinoma. Oncotarget 2018; 7:66595-66605. [PMID: 27448974 PMCID: PMC5341823 DOI: 10.18632/oncotarget.10704] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 05/29/2016] [Indexed: 12/12/2022] Open
Abstract
The circulating free tumor DNA (ctDNA) represents an alternative, minimally invasive source of tumor DNA for molecular profiling. Targeted sequencing with next generation sequencing (NGS) can assess hundred mutations starting from a low DNA input. We performed NGS analysis of ctDNA from 44 patients with metastatic non-small-cell lung carcinoma (NSCLC) and 35 patients with metastatic colorectal carcinoma (CRC). NGS detected EGFR mutations in 17/22 plasma samples from EGFR-mutant NSCLC patients (sensitivity 77.3%). The concordance rate between tissue and plasma in NSCLC was much lower for other mutations such as KRAS that, based on the allelic frequency and the fraction of neoplastic cells, were likely to be sub-clonal. NGS also identified EGFR mutations in plasma samples from two patients with EGFR wild type tumor tissue. Both mutations were confirmed by droplet digital PCR (ddPCR) in both plasma and tissue samples. In CRC, the sensitivity of the NGS plasma analysis for RAS mutations was 100% (6/6) in patients that had not resection of the primary tumor before blood drawing, and 46.2% (6/13) in patients with primary tumor resected before enrollment. Our study showed that NGS is a suitable method for plasma testing. However, its clinical sensitivity is significantly affected by the presence of the primary tumor and by the heterogeneity of driver mutations.
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Affiliation(s)
- Anna Maria Rachiglio
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Riziero Esposito Abate
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Alessandra Sacco
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Raffaella Pasquale
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Francesca Fenizia
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Matilde Lambiase
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Alessandro Morabito
- Thoraco-Pulmonary, Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Agnese Montanino
- Thoraco-Pulmonary, Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Gaetano Rocco
- Thoracic Surgery, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Carmen Romano
- Gastro-Intestinal Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Anna Nappi
- Gastro-Intestinal Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Rosario Vincenzo Iaffaioli
- Gastro-Intestinal Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Fabiana Tatangelo
- Surgical Pathology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Gerardo Botti
- Surgical Pathology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Fortunato Ciardiello
- Department of Clinical and Experimental Medicine 'F. Magrassi' - Medical Oncology, Seconda Università degli Studi di Napoli, Napoli, Italy
| | - Monica R Maiello
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Nicola Normanno
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy.,Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
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Furuki H, Yamada T, Takahashi G, Iwai T, Koizumi M, Shinji S, Yokoyama Y, Takeda K, Taniai N, Uchida E. Evaluation of liquid biopsies for detection of emerging mutated genes in metastatic colorectal cancer. Eur J Surg Oncol 2018; 44:975-982. [PMID: 29452859 DOI: 10.1016/j.ejso.2018.01.224] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/19/2018] [Accepted: 01/24/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Detection of gene mutations is important for planning molecular targeted therapy. Although most gene mutations are concordant between primary colon cancers and their liver metastases, new mutations can emerge in metastases. The liquid biopsy is a newly developed, gene analytic method to detect mutations in metastatic tumors. In this prospective study, we evaluated the applicability of liquid biopsies in the detection of mutations in primary and metastatic tumors. METHODS We included 22 patients with liver metastases from colorectal cancer and extracted DNA from primary colorectal tumors, metastatic liver tumors, and peripheral blood (liquid biopsy). Next-generation sequencing (NGS) and digital PCR were performed to detect mutations in these three sample types. RESULTS We found a total of 36 different mutations in samples from primary tumors, liver metastases, and liquid biopsies using NGS. Twenty-eight of these mutations were found in all three types of samples, whereas liquid biopsy did not identify four mutations that had been found in both primary tumors and liver metastases, but did identify four mutations that were found in liver tumors but not in primary tumors. The sensitivity of liquid biopsies for detecting mutations in liver metastases was 64% (23/36) using NGS and 89% (32/36, P = 0.02) using dPCR. The specificities of NGS and dPCR were 100% (23/23) and 100% (32/32), respectively. CONCLUSIONS Emerging mutations, which are not found in primary tumors, can be detected in their metastases and liquid biopsies.
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Affiliation(s)
- Hiroyasu Furuki
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Takeshi Yamada
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan.
| | - Goro Takahashi
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Takuma Iwai
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Michihiro Koizumi
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Seiichi Shinji
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Yasuyuki Yokoyama
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Kohki Takeda
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Nobuhiko Taniai
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Eiji Uchida
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
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Moon DH, Lindsay DP, Hong S, Wang AZ. Clinical indications for, and the future of, circulating tumor cells. Adv Drug Deliv Rev 2018; 125:143-150. [PMID: 29626548 DOI: 10.1016/j.addr.2018.04.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 03/14/2018] [Accepted: 04/02/2018] [Indexed: 12/16/2022]
Abstract
Circulating tumor cells (CTCs) are cells that have detached from the primary tumor and entered circulation with potential to initiate a site of metastasis. Currently, CTC detection using CellSearch is cleared by the Food and Drug Administration for monitoring metastatic breast, prostate, and colorectal cancers as a prognostic biomarker for progression-free and overall survival. Accumulating evidence suggests CTCs have similar prognostic value in other metastatic and non-metastatic settings. Current research efforts are focused on extending the utility of CTCs beyond a prognostic biomarker to help guide clinical decision-making. These include using CTCs as a screening tool for diagnosis, liquid biopsy for molecular profiling, predictive biomarker to specific therapies, and monitoring tool to assess response and guide changes to treatment. CTCs have unique advantages vs circulating tumor DNA in this endeavor. Indications for CTCs in daily practice will expand as isolation techniques improve and clinical studies validating their utility continue to grow.
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Affiliation(s)
- Dominic H Moon
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, 101 Manning Drive, Chapel Hill, NC 27599, USA
| | - Daniel P Lindsay
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, 101 Manning Drive, Chapel Hill, NC 27599, USA
| | - Seungpyo Hong
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI 53705, USA; Yonsei Frontier Lab, Yonsei University, Seoul 03722, Republic of Korea
| | - Andrew Z Wang
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, 101 Manning Drive, Chapel Hill, NC 27599, USA.
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Cao B, Zhou X, Yang W, Ma J, Zhou W, Fan D, Hong L. The role of cell-free DNA in predicting colorectal cancer prognosis. Expert Rev Gastroenterol Hepatol 2018; 12:39-48. [PMID: 28838275 DOI: 10.1080/17474124.2017.1372191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Colorectal cancer is a cancer of the digestive system with poor prognosis. Cell-free DNA has received much attention with its unique predominance, especially in colorectal cancer. Areas covered: This study has summarized recent advancements and challenges regarding cell-free DNA in predicting CRC prognosis. Furthermore, the authors make predictions on the potential developments concerning cell-free DNA in future prognosis prediction techniques. Expert commentary: Cell-free DNA has the value of predicting CRC prognosis as an important biomarke. Further clinical trials should be performed to promote translating cell-free DNA into clinical applications.
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Affiliation(s)
- Bo Cao
- a The First Brigade of Student , Fourth Military Medical University , Xi'an , China
| | - Xin Zhou
- a The First Brigade of Student , Fourth Military Medical University , Xi'an , China
| | - Wanli Yang
- b State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases , Fourth Military Medical University , Xi'an , China
| | - Jiaojiao Ma
- b State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases , Fourth Military Medical University , Xi'an , China
| | - Wei Zhou
- b State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases , Fourth Military Medical University , Xi'an , China
| | - Daiming Fan
- b State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases , Fourth Military Medical University , Xi'an , China
| | - Liu Hong
- b State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases , Fourth Military Medical University , Xi'an , China
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Circulating Tumor DNA is Effective for Detection of KRAS Mutation in Colorectal Cancer: A Meta-Analysis. Int J Biol Markers 2017; 32:e421-e427. [PMID: 28885658 DOI: 10.5301/ijbm.5000295] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2017] [Indexed: 12/31/2022]
Abstract
Background Circulating tumor DNA (ctDNA) offers a novel and minimally invasive approach to the detection of the KRAS oncogene mutation in colorectal cancer. This study was conducted to compare the prognostic value of ctDNA with that of the current gold standard tumor tissue analysis. Methods A systematic literature review was conducted to identify relevant articles published from inception to December 27, 2016; the PubMed, Web of Science, Embase, Wanfang and China National Knowledge Infrastructure databases were searched. Pooled specificity, sensitivity, positive likelihood ratio, negative likelihood ratio and diagnostic odds ratio (DOR) estimates and areas under summary receiver operating characteristic (AUSROC) curves were calculated. We also performed subgroup and sensitivity analyses. Results Twenty-three studies with 1,715 colorectal cancer patients were included. The overall sensitivity and specificity were 0.75 (95% confidence interval [CI], 0.66-0.82) and 0.98 (CI, 0.95-0.99), respectively. The positive likelihood ratio was 31.8 (95% CI, 14.8-68.3), and the negative likelihood ratio was 0.26 (95% CI, 0.19-0.36). In addition, the AUSROC and DOR were 0.96 (95% CI, 0.93-0.97) and 123 (95% CI, 52-291), respectively. Substantial heterogeneity was observed across studies (I2 = 95%, 95% CI, 91-99). None of the subgroups investigated, including those defined by blood sample type, study region, TNM stage, detection site and detection method, could indicate the source of the observed heterogeneity. The results of the sensitivity analysis indicated that the results of our meta-analysis were stable. Conclusions Circulating tumor DNA may serve as a viable alternative to tissue analysis for the detection of KRAS mutations in colorectal cancer.
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Creemers SG, Korpershoek E, Atmodimedjo PN, Dinjens WNM, van Koetsveld PM, Feelders RA, Hofland LJ. Identification of Mutations in Cell-Free Circulating Tumor DNA in Adrenocortical Carcinoma: A Case Series. J Clin Endocrinol Metab 2017; 102:3611-3615. [PMID: 28973495 DOI: 10.1210/jc.2017-00174] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/27/2017] [Indexed: 02/13/2023]
Abstract
CONTEXT The disease course of adrenocortical carcinoma (ACC) patients is heterogeneous. A marker for prognosis and treatment response would facilitate choices for diagnosis and therapy. In other cancer types, circulating cell-free tumor DNA predicted tumor dynamics. CASE DESCRIPTIONS The present pilot study included six patients. Next-generation sequencing (NGS) showed mutations in three ACC cases. From these patients, blood was drawn before (1 to 2 weeks) and after surgery and cell-free circulating DNA (cfDNA) was isolated. Tumor-specific mutations were found in the cfDNA of one of the three patients, with metastasized ACC at diagnosis. NGS of the tumor showed an NRAS mutation (c.182A>G:p.Q61R) in 78%, a TP53 mutation (c.856G>A:p.E286K) in 60%, and a TERT gene mutation (1295250C>T) in 28% of the reads. The preoperative cfDNA showed the same mutations at a frequency of 64%, 32%, and 2%, respectively. The postoperative cfDNA showed the same mutations but at lower frequencies (52%, 16%, and 3%, respectively). The patient was postoperatively treated with mitotane and chemotherapy. No mutations were detected in the corresponding leukocyte DNA or in the cfDNA from the two other patients. CONCLUSIONS To the best of our knowledge, we report for the first time mutations occurring at high levels in cfDNA collected before and after surgery from one of three patients, after previous identification in the tumor. However, in the cfDNA from two patients with known mutations, we were unable to reliably detect mutations in the cfDNA. Our results indicate that mutation detection in cfDNA can vary among ACC patients, and other approaches might be required to detect the tumor response and monitor progressive disease.
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Affiliation(s)
- Sara G Creemers
- Division of Endocrinology, Department of Internal Medicine, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Esther Korpershoek
- Department of Pathology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Peter M van Koetsveld
- Division of Endocrinology, Department of Internal Medicine, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Richard A Feelders
- Division of Endocrinology, Department of Internal Medicine, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Leo J Hofland
- Division of Endocrinology, Department of Internal Medicine, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
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Schwaederlé MC, Patel SP, Husain H, Ikeda M, Lanman RB, Banks KC, Talasaz A, Bazhenova L, Kurzrock R. Utility of Genomic Assessment of Blood-Derived Circulating Tumor DNA (ctDNA) in Patients with Advanced Lung Adenocarcinoma. Clin Cancer Res 2017; 23:5101-5111. [PMID: 28539465 PMCID: PMC5581668 DOI: 10.1158/1078-0432.ccr-16-2497] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/07/2017] [Accepted: 05/18/2017] [Indexed: 12/11/2022]
Abstract
Purpose: Genomic alterations in blood-derived circulating tumor DNA (ctDNA) from patients with non-small cell lung adenocarcinoma (NSCLC) were ascertained and correlated with clinical characteristics and therapeutic outcomes.Experimental Design: Comprehensive plasma ctDNA testing was performed in 88 consecutive patients; 34 also had tissue next-generation sequencing; 29, other forms of genotyping; and 25 (28.4%) had no tissue molecular tests because of inadequate tissue or biopsy contraindications.Results: Seventy-two patients (82%) had ≥1 ctDNA alteration(s); among these, 75% carried alteration(s) potentially actionable by FDA-approved (61.1%) or experimental drug(s) in clinical trials (additional 13.9%). The most frequent alterations were in the TP53 (44.3% of patients), EGFR (27.3%), MET (14.8%), KRAS (13.6%), and ALK (6.8%) genes. The concordance rate for EGFR alterations was 80.8% (100% vs. 61.5%; ≤1 vs. >1 month between ctDNA and tissue tests; P = 0.04) for patients with any detectable ctDNA alterations. Twenty-five patients (28.4%) received therapy matching ≥1 ctDNA alteration(s); 72.3% (N = 16/22) of the evaluable matched patients achieved stable disease ≥6 months (SD) or partial response (PR). Five patients with ctDNA-detected EGFR T790M were subsequently treated with a third generation EGFR inhibitor; all five achieved SD ≥ 6 months/PR. Patients with ≥1 alteration with ≥5% variant allele fraction (vs. < 5%) had a significantly shorter median survival (P = 0.012).Conclusions: ctDNA analysis detected alterations in the majority of patients, with potentially targetable aberrations found at expected frequencies. Therapy matched to ctDNA alterations demonstrated appreciable therapeutic efficacy, suggesting clinical utility that warrants future prospective studies. Clin Cancer Res; 23(17); 5101-11. ©2017 AACR.
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Affiliation(s)
- Maria C Schwaederlé
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California.
| | - Sandip P Patel
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California
| | - Hatim Husain
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California
| | - Megumi Ikeda
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California
| | - Richard B Lanman
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California
| | - Kimberly C Banks
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California
| | - AmirAli Talasaz
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California
| | - Lyudmila Bazhenova
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California
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Chiara M, Pavesi G. Evaluation of Quality Assessment Protocols for High Throughput Genome Resequencing Data. Front Genet 2017; 8:94. [PMID: 28736571 PMCID: PMC5500642 DOI: 10.3389/fgene.2017.00094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/21/2017] [Indexed: 12/14/2022] Open
Abstract
Large-scale initiatives aiming to recover the complete sequence of thousands of human genomes are currently being undertaken worldwide, concurring to the generation of a comprehensive catalog of human genetic variation. The ultimate and most ambitious goal of human population scale genomics is the characterization of the so-called human “variome,” through the identification of causal mutations or haplotypes. Several research institutions worldwide currently use genotyping assays based on Next-Generation Sequencing (NGS) for diagnostics and clinical screenings, and the widespread application of such technologies promises major revolutions in medical science. Bioinformatic analysis of human resequencing data is one of the main factors limiting the effectiveness and general applicability of NGS for clinical studies. The requirement for multiple tools, to be combined in dedicated protocols in order to accommodate different types of data (gene panels, exomes, or whole genomes) and the high variability of the data makes difficult the establishment of a ultimate strategy of general use. While there already exist several studies comparing sensitivity and accuracy of bioinformatic pipelines for the identification of single nucleotide variants from resequencing data, little is known about the impact of quality assessment and reads pre-processing strategies. In this work we discuss major strengths and limitations of the various genome resequencing protocols are currently used in molecular diagnostics and for the discovery of novel disease-causing mutations. By taking advantage of publicly available data we devise and suggest a series of best practices for the pre-processing of the data that consistently improve the outcome of genotyping with minimal impacts on computational costs.
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Affiliation(s)
- Matteo Chiara
- Dipartimento di Bioscienze, Università di MilanoMilan, Italy
| | - Giulio Pavesi
- Dipartimento di Bioscienze, Università di MilanoMilan, Italy
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Mehrotra M, Singh RR, Chen W, Huang RS, Almohammedsalim AA, Barkoh BA, Simien CM, Hernandez M, Behrens C, Patel KP, Routbort MJ, Broaddus RR, Medeiros LJ, Wistuba II, Kopetz S, Luthra R. Study of Preanalytic and Analytic Variables for Clinical Next-Generation Sequencing of Circulating Cell-Free Nucleic Acid. J Mol Diagn 2017; 19:514-524. [DOI: 10.1016/j.jmoldx.2017.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 02/10/2017] [Accepted: 03/06/2017] [Indexed: 12/19/2022] Open
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Kim ST, Banks KC, Lee SH, Kim K, Park JO, Park SH, Park YS, Lim HY, Kang WK, Lanman RB, Talasaz A, Park K, Lee J. Prospective Feasibility Study for Using Cell-Free Circulating Tumor DNA-Guided Therapy in Refractory Metastatic Solid Cancers: An Interim Analysis. JCO Precis Oncol 2017; 1:1600059. [PMID: 32913970 PMCID: PMC7446388 DOI: 10.1200/po.16.00059] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Purpose Retrospective studies have demonstrated that cell-free circulating tumor DNA (ctDNA) hotspot testing predicts matched therapy response to first- and second-line therapies in patients with advanced non–small-cell lung cancer (NSCLC). However, no prospective outcomes studies have evaluated ctDNA-guided matched therapy decision making on the basis of comprehensive plasma genomic testing including all four major classes of alterations. Here, we report the clinical utility of this approach in advanced solid tumor cancers. Patients and Methods We conducted a multiple parallel cohort, open-label, clinical trial using ctDNA-guided matched therapy when tissue was insufficient or unobtainable for next-generation sequencing. Plasma-based digital sequencing identified point mutations in 70 genes and indels, fusions, and copy number amplifications in selected genes. Patients with prespecified targetable alterations in metastatic NSCLC, gastric cancer (GC), and other cancers were matched to several independent targeted agent trials at a tertiary academic center. Results Somatic alterations were detected in 59 patients with GC (78%), and 25 patients (33%) had targetable alterations (ERBB2, n = 11; MET, n = 5; FGFR2, n = 3; PIK3CA, n = 6). In NSCLC, 62 patients (85%) had somatic alterations, and 34 (47%) had targetable alterations (EGFR, n = 29; ALK, n = 2; RET, n = 1; ERBB2, n = 2). After confirmation of ctDNA findings on tissue (to meet trial eligibility criteria), 10 patients with GC and 17 patients with NSCLC received molecularly matched therapy. Response rate and disease control rate were 67% and 100%, respectively, in GC and 87% and 100%, respectively, in NSCLC. Response was independent of targeted alteration variant allele fraction in NSCLC (P = .63). Conclusion To our knowledge, this is the first prospective feasibility study of comprehensive ctDNA-guided treatment in advanced GC and lung cancers. Response rates in this interim analysis are similar to those in tissue-based targeted therapy studies.
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Affiliation(s)
- Seung Tae Kim
- , , , , , , , , , and , Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; and , , and , Guardant Health, Redwood City, CA
| | - Kimberly C Banks
- , , , , , , , , , and , Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; and , , and , Guardant Health, Redwood City, CA
| | - Se-Hoon Lee
- , , , , , , , , , and , Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; and , , and , Guardant Health, Redwood City, CA
| | - Kyung Kim
- , , , , , , , , , and , Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; and , , and , Guardant Health, Redwood City, CA
| | - Joon Oh Park
- , , , , , , , , , and , Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; and , , and , Guardant Health, Redwood City, CA
| | - Se Hoon Park
- , , , , , , , , , and , Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; and , , and , Guardant Health, Redwood City, CA
| | - Young Suk Park
- , , , , , , , , , and , Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; and , , and , Guardant Health, Redwood City, CA
| | - Ho Yeong Lim
- , , , , , , , , , and , Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; and , , and , Guardant Health, Redwood City, CA
| | - Won Ki Kang
- , , , , , , , , , and , Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; and , , and , Guardant Health, Redwood City, CA
| | - Richard B Lanman
- , , , , , , , , , and , Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; and , , and , Guardant Health, Redwood City, CA
| | - AmirAli Talasaz
- , , , , , , , , , and , Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; and , , and , Guardant Health, Redwood City, CA
| | - Keunchil Park
- , , , , , , , , , and , Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; and , , and , Guardant Health, Redwood City, CA
| | - Jeeyun Lee
- , , , , , , , , , and , Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; and , , and , Guardant Health, Redwood City, CA
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Sacher AG, Komatsubara KM, Oxnard GR. Application of Plasma Genotyping Technologies in Non-Small Cell Lung Cancer: A Practical Review. J Thorac Oncol 2017; 12:1344-1356. [PMID: 28611011 DOI: 10.1016/j.jtho.2017.05.022] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 05/04/2017] [Accepted: 05/25/2017] [Indexed: 10/19/2022]
Abstract
The rational treatment of metastatic NSCLC hinges on the timely detection of potentially targetable genomic alterations to guide therapy. Recent advances in highly sensitive genotyping technologies have allowed for development of novel plasma genotyping assays that are capable of noninvasively detecting targetable alterations in plasma cell-free DNA without reliance on traditional tissue genotyping. The rapid development of plasma genotyping has led to an explosion in the number of assay platforms available from both commercial and laboratory sources. The sheer number of such platforms has led to confusion among oncologists as to both the test characteristics and limitations of individual plasma genotyping assays and the clinical context in which these tests may be utilized either alone or in combination with traditional tissue genotyping. Reliable data from prospective validation against a tissue genotyping reference standard are available for only a limited number of platforms. Careful retrospective validation of alternative platforms utilizing paired tissue and plasma specimens collected under the auspices of clinical trials represent an alternative but reliable validation strategy. A consistent trend among these well-validated plasma genotyping assays has been the observation of high specificity and positive predictive value and more limited sensitivity. At present, validated assays can be considered actionable in instances in which a targetable genomic alteration is detected or an alternative nontargetable driver mutation is detected and can be used to infer the absence of one of the former.
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Affiliation(s)
- Adrian G Sacher
- Columbia University/New York-Presbyterian Hospital, New York, New York.
| | | | - Geoffrey R Oxnard
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Brigham and Women's Hospital, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts
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Wang X, Gao Y, Wang B, Zhang Z, Liang C, Feng H, Guo Y, Da J, Mo M, Zhang M, Ding F, Chen Z, Li H, Liu D. Analytic and Clinical Validation of an Ultrasensitive, Quantitative Polymerase Chain Reaction Assay for EGFR Mutation Analysis With Circulating Tumor DNA. Arch Pathol Lab Med 2017; 141:978-984. [PMID: 28537806 DOI: 10.5858/arpa.2016-0083-oa] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - The mutation analysis of epidermal growth factor receptor (EGFR) has become a common test to guide therapeutic decision making for lung cancer. Molecular testing with circulating tumor DNA in plasma allows diagnosis of mutations when tumor tissue is not available as well as monitoring treatment response with repeat biopsies. OBJECTIVES - To develop a timely and cost-effective assay that can accurately detect EGFR mutations in circulating tumor DNA and to evaluate the analytic and clinical performance of the assay. DESIGN - Analytic assessment was conducted with a set of reference materials carrying classic EGFR mutations. A recently developed Poisson distribution-based approach was employed to understand the assay sensitivity. Clinical evaluation was performed with 224 pairs of plasma and matched tissues from patients with stage I to IV disease. EGFR mutation rates of 390 consecutive plasma samples processed in the central service laboratory were compared with previously reported prevalence in an Asian population. RESULTS - Our results suggested that limit of detection for the EGFR quantitative polymerase chain reaction assay was 10 mutation copies, and the lowest detectable copy numbers could be extended to a single-digit level. The clinical sensitivity was 53.3% for all stages combined and 81.4% for late stages, with a high specificity of 100%. Clinical observations showed an overall positive finding rate of 32.5% and 41.4% for stage IV disease, which is consistent with previously reported EGFR mutation prevalence in an Asian population. CONCLUSIONS - Our results supported the clinical utility of the ultrasensitive, quantitative polymerase chain reaction assay for EGFR mutation analysis with circulating tumor DNA.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Deruo Liu
- From the Departments of Thoracic Surgery (Drs Wang, Zhang, and Liu; Messrs Liang and Feng; and Ms Guo) and Pathology (Mss Wang and Da), China-Japan Friendship Hospital, Beijing, China; the National Institute of Metrology, Beijing (Mr Gao); Beijing ACCB Biotech Ltd, Beijing (Drs Mo, Ding, Chen, and Li and Mr Zhang); and the Department of Biotechnology and Pharmaceutical Research, Yangze Delta Institute of Tsinghua University, Zhejiang, China (Dr Ding). Dr Wang and Mr Gao contributed equally to this article
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Janku F, Zhang S, Waters J, Liu L, Huang HJ, Subbiah V, Hong DS, Karp DD, Fu S, Cai X, Ramzanali NM, Madwani K, Cabrilo G, Andrews DL, Zhao Y, Javle M, Kopetz ES, Luthra R, Kim HJ, Gnerre S, Satya RV, Chuang HY, Kruglyak KM, Toung J, Zhao C, Shen R, Heymach JV, Meric-Bernstam F, Mills GB, Fan JB, Salathia NS. Development and Validation of an Ultradeep Next-Generation Sequencing Assay for Testing of Plasma Cell-Free DNA from Patients with Advanced Cancer. Clin Cancer Res 2017; 23:5648-5656. [PMID: 28536309 DOI: 10.1158/1078-0432.ccr-17-0291] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/22/2017] [Accepted: 05/18/2017] [Indexed: 01/04/2023]
Abstract
Purpose: Tumor-derived cell-free DNA (cfDNA) in plasma can be used for molecular testing and provide an attractive alternative to tumor tissue. Commonly used PCR-based technologies can test for limited number of alterations at the time. Therefore, novel ultrasensitive technologies capable of testing for a broad spectrum of molecular alterations are needed to further personalized cancer therapy.Experimental Design: We developed a highly sensitive ultradeep next-generation sequencing (NGS) assay using reagents from TruSeqNano library preparation and NexteraRapid Capture target enrichment kits to generate plasma cfDNA sequencing libraries for mutational analysis in 61 cancer-related genes using common bioinformatics tools. The results were retrospectively compared with molecular testing of archival primary or metastatic tumor tissue obtained at different points of clinical care.Results: In a study of 55 patients with advanced cancer, the ultradeep NGS assay detected 82% (complete detection) to 87% (complete and partial detection) of the aberrations identified in discordantly collected corresponding archival tumor tissue. Patients with a low variant allele frequency (VAF) of mutant cfDNA survived longer than those with a high VAF did (P = 0.018). In patients undergoing systemic therapy, radiological response was positively associated with changes in cfDNA VAF (P = 0.02), and compared with unchanged/increased mutant cfDNA VAF, decreased cfDNA VAF was associated with longer time to treatment failure (TTF; P = 0.03).Conclusions: Ultradeep NGS assay has good sensitivity compared with conventional clinical mutation testing of archival specimens. A high VAF in mutant cfDNA corresponded with shorter survival. Changes in VAF of mutated cfDNA were associated with TTF. Clin Cancer Res; 23(18); 5648-56. ©2017 AACR.
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Affiliation(s)
- Filip Janku
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | | | | | - Li Liu
- Illumina, Inc., San Diego, California
| | - Helen J Huang
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David S Hong
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel D Karp
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Siqing Fu
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xuyu Cai
- Illumina, Inc., San Diego, California
| | - Nishma M Ramzanali
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kiran Madwani
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Goran Cabrilo
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Debra L Andrews
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yue Zhao
- Illumina, Inc., San Diego, California
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - E Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Molecular Diagnostic Laboratory, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | | | | | | | - Chen Zhao
- Illumina, Inc., San Diego, California
| | | | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Maxwell KN, Soucier-Ernst D, Tahirovic E, Troxel AB, Clark C, Feldman M, Colameco C, Kakrecha B, Langer M, Lieberman D, Morrissette JJD, Paul MR, Pan TC, Yee S, Shih N, Carpenter E, Chodosh LA, DeMichele A. Comparative clinical utility of tumor genomic testing and cell-free DNA in metastatic breast cancer. Breast Cancer Res Treat 2017. [PMID: 28500398 DOI: 10.1007/s10549‐017‐4257‐x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
PURPOSE Breast cancer metastases differ biologically from primary disease; therefore, metastatic biopsies may assist in treatment decision making. Commercial genomic testing of both tumor and circulating tumor DNA have become available clinically, but utility of these tests in breast cancer management remains unclear. METHODS Patients undergoing a clinically indicated metastatic tumor biopsy were consented to the ongoing METAMORPH registry. Tumor and blood were collected at the time of disease progression before subsequent therapy, and patients were followed for response on subsequent treatment. Tumor testing (n = 53) and concurrent cell-free DNA (n = 32) in a subset of patients was performed using CLIA-approved assays. RESULTS The proportion of patients with a genomic alteration was lower in tumor than in blood (69 vs. 91%; p = 0.06). After restricting analysis to alterations covered on both platforms, 83% of tumor alterations were detected in blood, while 90% of blood alterations were detected in tumor. Mutational load specific for the panel genes was calculated for both tumor and blood. Time to progression on subsequent treatment was significantly shorter for patients whose tumors had high panel-specific mutational load (HR 0.31, 95% CI 0.12-0.78) or a TP53 mutation (HR 0.35, 95% CI 0.20-0.79), after adjusting for stage at presentation, hormone receptor status, prior treatment type, and number of lines of metastatic treatment. CONCLUSIONS Treating oncologists must distinguish platform differences from true biological heterogeneity when comparing tumor and cfDNA genomic testing results. Tumor and concurrent cfDNA contribute unique genomic information in metastatic breast cancer patients, providing potentially useful biomarkers for aggressive metastatic disease.
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Affiliation(s)
- Kara N Maxwell
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Danielle Soucier-Ernst
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Emin Tahirovic
- Department of Biostatistics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Andrea B Troxel
- Department of Population Health, NYU School of Medicine, New York, NY, USA
| | - Candace Clark
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Feldman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher Colameco
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Bijal Kakrecha
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Melissa Langer
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - David Lieberman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer J D Morrissette
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Matt R Paul
- Department of Cancer Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Tien-Chi Pan
- Department of Cancer Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Stephanie Yee
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Natalie Shih
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Erica Carpenter
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Lewis A Chodosh
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Department of Cancer Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, Division of Endocrinology, Diabetes and Metabolism at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Angela DeMichele
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Department of Biostatistics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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71
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Comparative clinical utility of tumor genomic testing and cell-free DNA in metastatic breast cancer. Breast Cancer Res Treat 2017; 164:627-638. [PMID: 28500398 DOI: 10.1007/s10549-017-4257-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 04/17/2017] [Indexed: 01/24/2023]
Abstract
PURPOSE Breast cancer metastases differ biologically from primary disease; therefore, metastatic biopsies may assist in treatment decision making. Commercial genomic testing of both tumor and circulating tumor DNA have become available clinically, but utility of these tests in breast cancer management remains unclear. METHODS Patients undergoing a clinically indicated metastatic tumor biopsy were consented to the ongoing METAMORPH registry. Tumor and blood were collected at the time of disease progression before subsequent therapy, and patients were followed for response on subsequent treatment. Tumor testing (n = 53) and concurrent cell-free DNA (n = 32) in a subset of patients was performed using CLIA-approved assays. RESULTS The proportion of patients with a genomic alteration was lower in tumor than in blood (69 vs. 91%; p = 0.06). After restricting analysis to alterations covered on both platforms, 83% of tumor alterations were detected in blood, while 90% of blood alterations were detected in tumor. Mutational load specific for the panel genes was calculated for both tumor and blood. Time to progression on subsequent treatment was significantly shorter for patients whose tumors had high panel-specific mutational load (HR 0.31, 95% CI 0.12-0.78) or a TP53 mutation (HR 0.35, 95% CI 0.20-0.79), after adjusting for stage at presentation, hormone receptor status, prior treatment type, and number of lines of metastatic treatment. CONCLUSIONS Treating oncologists must distinguish platform differences from true biological heterogeneity when comparing tumor and cfDNA genomic testing results. Tumor and concurrent cfDNA contribute unique genomic information in metastatic breast cancer patients, providing potentially useful biomarkers for aggressive metastatic disease.
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72
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Yang M, Topaloglu U, Petty WJ, Pagni M, Foley KL, Grant SC, Robinson M, Bitting RL, Thomas A, Alistar AT, Desnoyers RJ, Goodman M, Albright C, Porosnicu M, Vatca M, Qasem SA, DeYoung B, Kytola V, Nykter M, Chen K, Levine EA, Staren ED, D'Agostino RB, Petro RM, Blackstock W, Powell BL, Abraham E, Pasche B, Zhang W. Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages. J Hematol Oncol 2017; 10:100. [PMID: 28472989 PMCID: PMC5418716 DOI: 10.1186/s13045-017-0468-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 04/20/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Solid tumors residing in tissues and organs leave footprints in circulation through circulating tumor cells (CTCs) and circulating tumor DNAs (ctDNA). Characterization of the ctDNA portraits and comparison with tumor DNA mutational portraits may reveal clinically actionable information on solid tumors that is traditionally achieved through more invasive approaches. METHODS We isolated ctDNAs from plasma of patients of 103 lung cancer and 74 other solid tumors of different tissue origins. Deep sequencing using the Guardant360 test was performed to identify mutations in 73 clinically actionable genes, and the results were associated with clinical characteristics of the patient. The mutation profiles of 37 lung cancer cases with paired ctDNA and tumor genomic DNA sequencing were used to evaluate clonal representation of tumor in circulation. Five lung cancer cases with longitudinal ctDNA sampling were monitored for cancer progression or response to treatments. RESULTS Mutations in TP53, EGFR, and KRAS genes are most prevalent in our cohort. Mutation rates of ctDNA are similar in early (I and II) and late stage (III and IV) cancers. Mutation in DNA repair genes BRCA1, BRCA2, and ATM are found in 18.1% (32/177) of cases. Patients with higher mutation rates had significantly higher mortality rates. Lung cancer of never smokers exhibited significantly higher ctDNA mutation rates as well as higher EGFR and ERBB2 mutations than ever smokers. Comparative analysis of ctDNA and tumor DNA mutation data from the same patients showed that key driver mutations could be detected in plasma even when they were present at a minor clonal population in the tumor. Mutations of key genes found in the tumor tissue could remain in circulation even after frontline radiotherapy and chemotherapy suggesting these mutations represented resistance mechanisms. Longitudinal sampling of five lung cancer cases showed distinct changes in ctDNA mutation portraits that are consistent with cancer progression or response to EGFR drug treatment. CONCLUSIONS This study demonstrates that ctDNA mutation rates in the key tumor-associated genes are clinical parameters relevant to smoking status and mortality. Mutations in ctDNA may serve as an early detection tool for cancer. This study quantitatively confirms the hypothesis that ctDNAs in circulation is the result of dissemination of aggressive tumor clones and survival of resistant clones. This study supports the use of ctDNA profiling as a less-invasive approach to monitor cancer progression and selection of appropriate drugs during cancer evolution.
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Affiliation(s)
- Meng Yang
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Umit Topaloglu
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - W Jeffrey Petty
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Matthew Pagni
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Kristie L Foley
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Social Sciences and Health Policy, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Stefan C Grant
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Mac Robinson
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Rhonda L Bitting
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Alexandra Thomas
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Angela T Alistar
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Rodwige J Desnoyers
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Michael Goodman
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Carol Albright
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Mercedes Porosnicu
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Mihaela Vatca
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Shadi A Qasem
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Laboratory Medicine and Pathology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Barry DeYoung
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Laboratory Medicine and Pathology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Ville Kytola
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Institute for Biosciences and Medical Technology, University of Tampere, 33520, Tampere, Finland.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Matti Nykter
- Institute for Biosciences and Medical Technology, University of Tampere, 33520, Tampere, Finland
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China
| | - Edward A Levine
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of General Surgery-Section of Surgical Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Edgar D Staren
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of General Surgery-Section of Surgical Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Ralph B D'Agostino
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Robin M Petro
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - William Blackstock
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Radiation Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Bayard L Powell
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Edward Abraham
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Boris Pasche
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA. .,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA. .,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA. .,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
| | - Wei Zhang
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd., Winston-Salem, NC, 27157, USA. .,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA. .,Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA. .,Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA. .,Cancer Genomics and Precision Medicine, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, 27157, USA.
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Chae YK, Davis AA, Jain S, Santa-Maria C, Flaum L, Beaubier N, Platanias LC, Gradishar W, Giles FJ, Cristofanilli M. Concordance of Genomic Alterations by Next-Generation Sequencing in Tumor Tissue versus Circulating Tumor DNA in Breast Cancer. Mol Cancer Ther 2017; 16:1412-1420. [DOI: 10.1158/1535-7163.mct-17-0061] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/24/2017] [Accepted: 04/14/2017] [Indexed: 11/16/2022]
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74
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Goyal L, Saha SK, Liu LY, Siravegna G, Leshchiner I, Ahronian LG, Lennerz JK, Vu P, Deshpande V, Kambadakone A, Mussolin B, Reyes S, Henderson L, Sun JE, Van Seventer EE, Gurski JM, Baltschukat S, Schacher-Engstler B, Barys L, Stamm C, Furet P, Ryan DP, Stone JR, Iafrate AJ, Getz G, Porta DG, Tiedt R, Bardelli A, Juric D, Corcoran RB, Bardeesy N, Zhu AX. Polyclonal Secondary FGFR2 Mutations Drive Acquired Resistance to FGFR Inhibition in Patients with FGFR2 Fusion-Positive Cholangiocarcinoma. Cancer Discov 2017; 7:252-263. [PMID: 28034880 PMCID: PMC5433349 DOI: 10.1158/2159-8290.cd-16-1000] [Citation(s) in RCA: 355] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/21/2016] [Accepted: 12/27/2016] [Indexed: 12/16/2022]
Abstract
Genetic alterations in the fibroblast growth factor receptor (FGFR) pathway are promising therapeutic targets in many cancers, including intrahepatic cholangiocarcinoma (ICC). The FGFR inhibitor BGJ398 displayed encouraging efficacy in patients with FGFR2 fusion-positive ICC in a phase II trial, but the durability of response was limited in some patients. Here, we report the molecular basis for acquired resistance to BGJ398 in three patients via integrative genomic characterization of cell-free circulating tumor DNA (cfDNA), primary tumors, and metastases. Serial analysis of cfDNA demonstrated multiple recurrent point mutations in the FGFR2 kinase domain at progression. Accordingly, biopsy of post-progression lesions and rapid autopsy revealed marked inter- and intralesional heterogeneity, with different FGFR2 mutations in individual resistant clones. Molecular modeling and in vitro studies indicated that each mutation led to BGJ398 resistance and was surmountable by structurally distinct FGFR inhibitors. Thus, polyclonal secondary FGFR2 mutations represent an important clinical resistance mechanism that may guide the development of future therapeutic strategies.Significance: We report the first genetic mechanisms of clinical acquired resistance to FGFR inhibition in patients with FGFR2 fusion-positive ICC. Our findings can inform future strategies for detecting resistance mechanisms and inducing more durable remissions in ICC and in the wide variety of cancers where the FGFR pathway is being explored as a therapeutic target. Cancer Discov; 7(3); 252-63. ©2016 AACR.See related commentary by Smyth et al., p. 248This article is highlighted in the In This Issue feature, p. 235.
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MESH Headings
- Adult
- Antineoplastic Agents/therapeutic use
- Bile Duct Neoplasms/drug therapy
- Bile Duct Neoplasms/genetics
- Bile Duct Neoplasms/pathology
- Cell Cycle Proteins
- Cholangiocarcinoma/drug therapy
- Cholangiocarcinoma/genetics
- Cholangiocarcinoma/pathology
- Circulating Tumor DNA/genetics
- Drug Resistance, Neoplasm/genetics
- Female
- Gene Fusion
- Humans
- Male
- Membrane Transport Proteins
- Middle Aged
- Mutation
- Phenylurea Compounds/therapeutic use
- Pyrimidines/therapeutic use
- Receptor, Fibroblast Growth Factor, Type 2/antagonists & inhibitors
- Receptor, Fibroblast Growth Factor, Type 2/chemistry
- Receptor, Fibroblast Growth Factor, Type 2/genetics
- Receptor, Fibroblast Growth Factor, Type 3/chemistry
- Receptor, Fibroblast Growth Factor, Type 3/metabolism
- Transcription Factor TFIIIA/genetics
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Affiliation(s)
- Lipika Goyal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Supriya K Saha
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Leah Y Liu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Giulia Siravegna
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Torino, Italy
- Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute of Molecular Oncology (IFOM), Milano, Italy
| | - Ignaty Leshchiner
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Leanne G Ahronian
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Phuong Vu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Avinash Kambadakone
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Stephanie Reyes
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Laura Henderson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jiaoyuan Elisabeth Sun
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Emily E Van Seventer
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Joseph M Gurski
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Sabrina Baltschukat
- Novartis Institutes for BioMedical Research, Oncology Translational Research, Basel, Switzerland
| | | | - Louise Barys
- Novartis Institutes for BioMedical Research, Oncology Translational Research, Basel, Switzerland
| | - Christelle Stamm
- Novartis Institutes for BioMedical Research, Oncology Translational Research, Basel, Switzerland
| | - Pascal Furet
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, Basel, Switzerland
| | - David P Ryan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - James R Stone
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Gad Getz
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Diana Graus Porta
- Novartis Institutes for BioMedical Research, Oncology Translational Research, Basel, Switzerland
| | - Ralph Tiedt
- Novartis Institutes for BioMedical Research, Oncology Translational Research, Basel, Switzerland
| | - Alberto Bardelli
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Torino, Italy
| | - Dejan Juric
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
| | - Nabeel Bardeesy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
| | - Andrew X Zhu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
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Perakis S, Auer M, Belic J, Heitzer E. Advances in Circulating Tumor DNA Analysis. Adv Clin Chem 2017; 80:73-153. [PMID: 28431643 DOI: 10.1016/bs.acc.2016.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The analysis of cell-free circulating tumor DNA (ctDNA) is a very promising tool and might revolutionize cancer care with respect to early detection, identification of minimal residual disease, assessment of treatment response, and monitoring tumor evolution. ctDNA analysis, often referred to as "liquid biopsy" offers what tissue biopsies cannot-a continuous monitoring of tumor-specific changes during the entire course of the disease. Owing to technological improvements, efforts for the establishment of preanalytical and analytical benchmark, and the inclusion of ctDNA analyses in clinical trial, an actual clinical implementation has come within easy reach. In this chapter, recent advances of the analysis of ctDNA are summarized starting from the discovery of cell-free DNA, to methodological approaches and the clinical applicability.
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Affiliation(s)
- Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Martina Auer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria.
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Schwaederle M, Husain H, Fanta PT, Piccioni DE, Kesari S, Schwab RB, Patel SP, Harismendy O, Ikeda M, Parker BA, Kurzrock R. Use of Liquid Biopsies in Clinical Oncology: Pilot Experience in 168 Patients. Clin Cancer Res 2016; 22:5497-5505. [DOI: 10.1158/1078-0432.ccr-16-0318] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/29/2016] [Accepted: 05/02/2016] [Indexed: 11/16/2022]
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