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van Schaik LF, Engelhardt EG, Wilthagen EA, Steeghs N, Fernández Coves A, Joore MA, van Harten WH, Retèl VP. Factors for a broad technology assessment of comprehensive genomic profiling in advanced cancer, a systematic review. Crit Rev Oncol Hematol 2024; 202:104441. [PMID: 39002790 DOI: 10.1016/j.critrevonc.2024.104441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/12/2024] [Accepted: 07/06/2024] [Indexed: 07/15/2024] Open
Abstract
Comprehensive Genomic Profiling (CGP) allows for the identification of many targets. Reimbursement decision-making is, however, challenging because besides the health benefits of on-label treatments and costs, other factors related to diagnostic and treatment pathways may also play a role. The aim of this study was to identify which other factors are relevant for the technology assessment of CGP and to summarize the available evidence for these factors. After a scoping search and two expert sessions, five factors were identified: feasibility, test journey, wider implications of diagnostic results, organisation of laboratories, and "scientific spillover". Subsequently, a systematic search identified 83 studies collecting mainly evidence for the factors "test journey" and "wider implications of diagnostic results". Its nature was, however, of limited value for decision-making. We recommend the use of comparative strategies, uniformity in outcome definitions, and the inclusion of a comprehensive set of factors in future evidence generation.
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Affiliation(s)
- L F van Schaik
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, P.O. Box 90103, Amsterdam 1006 BE, the Netherlands; Erasmus School of Health Policy and Management, Erasmus University Rotterdam, Rotterdam, the Netherlands.
| | - E G Engelhardt
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, P.O. Box 90103, Amsterdam 1006 BE, the Netherlands.
| | - E A Wilthagen
- Scientific Information Service, Netherlands Cancer Institute, Antoni van Leeuwenhoek, Plesmanlaan 121, Amsterdam CX 1066, the Netherlands.
| | - N Steeghs
- Department of Medical Oncology, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam CX 1066, the Netherlands.
| | - A Fernández Coves
- Department of Clinical Epidemiology and Medical Technology Assessment (KEMTA), P. Debyelaan 25, Oxford Building, P.O. Box 5800a, Maastricht, Limburg, the Netherlands; Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, The Netherlands.
| | - M A Joore
- Department of Clinical Epidemiology and Medical Technology Assessment (KEMTA), P. Debyelaan 25, Oxford Building, P.O. Box 5800a, Maastricht, Limburg, the Netherlands; Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, The Netherlands.
| | - W H van Harten
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, P.O. Box 90103, Amsterdam 1006 BE, the Netherlands; Department of Health Technology and Services Research, University of Twente, Enschede, the Netherlands.
| | - V P Retèl
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, P.O. Box 90103, Amsterdam 1006 BE, the Netherlands; Erasmus School of Health Policy and Management, Erasmus University Rotterdam, Rotterdam, the Netherlands.
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2
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Nakata E, Kawai H, Fujiwara T, Kunisada T, Inoue H, Futagawa M, Katayama H, Itano T, Ozaki T. Clinicopathological and histological analysis of secondary malignant giant cell tumors of bone without radiotherapy. Oncol Lett 2022; 24:319. [PMID: 35949597 PMCID: PMC9353873 DOI: 10.3892/ol.2022.13439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 06/08/2022] [Indexed: 11/24/2022] Open
Abstract
Giant cell tumor of bone (GCTB) is an intermediate bone tumor that rarely undergoes malignant transformation. Secondary malignant GCTB (SMGCTB) is defined as a lesion in which high-grade sarcoma occurs at the site of previously treated GCTB. The present study retrospectively reviewed the medical records of patients with GCTB treated at Okayama University Hospital between April 1986 and April 2020. The clinicopathological and histological features of patients with SMGCTB without prior radiotherapy were investigated. A total of three patients (4%) with SMGCTB were detected, and the tumor sites were the distal ulna, distal femur and sacrum. Two of the patients had been treated with curettage and bone graft, and one had been treated with denosumab. In all cases, the lesions were made up of two components, the conventional GCTB component and the malignant component. The Ki67 labeling index was higher in the malignant components of SMGCTB and metastatic lesions compared with that in primary and recurrent conventional GCTB, or the conventional GCTB component of SMGCTB. Moreover, p53 expression was higher in these same components in patients who underwent curettage and bone grafting; however, there was no difference in the patient that received denosumab treatment. In this patient, clinical cancer genomic profiling revealed loss of CDKN2A, CDKN2B and MTAP expression. All three patients developed distant metastasis. The patients with SMGCTB in the ulna and femur died 13 and 54 months after detection of malignant transformation, respectively. The patient with SMGCTB in the sacrum received carbon-ion radiotherapy to the sacrum and pazopanib; the treatment was effective and the patient was alive at the last follow-up 3 years later. In conclusion, p53 may be associated with malignant transformation in GCTB. Future studies should investigate the association of between denosumab treatment and malignant transformation, as well as molecular targeted therapy to improve the clinical outcomes of SMGCTB.
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Affiliation(s)
- Eiji Nakata
- Department of Orthopedic Surgery, Okayama University Hospital, Okayama 700‑8558, Japan
| | - Hotaka Kawai
- Department of Oral Pathology and Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700‑8558, Japan
| | - Tomohiro Fujiwara
- Department of Orthopedic Surgery, Okayama University Hospital, Okayama 700‑8558, Japan
| | - Toshiyuki Kunisada
- Department of Orthopedic Surgery, Okayama University Hospital, Okayama 700‑8558, Japan
| | - Hirofumi Inoue
- Department of Pathology, Okayama University Hospital, Okayama 700‑8558, Japan
| | - Mashu Futagawa
- Department of Clinical Genomic Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700‑8558, Japan
| | - Haruyoshi Katayama
- Department of Orthopedic Surgery, Okayama University Hospital, Okayama 700‑8558, Japan
| | - Takuto Itano
- Department of Orthopedic Surgery, Okayama University Hospital, Okayama 700‑8558, Japan
| | - Toshifumi Ozaki
- Department of Orthopedic Surgery, Okayama University Hospital, Okayama 700‑8558, Japan
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3
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Quy PN, Fukuyama K, Kanai M, Kou T, Kondo T, Yoshioka M, Matsubara J, Sakuma T, Minamiguchi S, Matsumoto S, Muto M. Inter-assay variability of next-generation sequencing-based gene panels. BMC Med Genomics 2022; 15:86. [PMID: 35428255 PMCID: PMC9013031 DOI: 10.1186/s12920-022-01230-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 04/04/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Tumor heterogeneity has been known to cause inter-assay discordance among next-generation sequencing (NGS) results. However, whether preclinical factors such as sample type, sample quality and analytical features of gene panel can affect the concordance between two different assays remains largely unexplored. METHODS Replicate sets of DNA samples extracted from formalin-fixed paraffin-embedded tissues (FFPE) (n = 20) and fresh frozen (FF) tissues (n = 10) were herein analyzed using a tumor-only (TO) and paired tumor-normal (TN) gene panel in laboratories certified by the Clinical Laboratory Improvement Amendment. Reported variants from the TO and TN panels were then compared. Furthermore, additional FFPE samples were sequentially sliced from the same FFPE block and submitted to another TN panel assay. RESULTS Substantial discordance (71.8%) was observed between the results of the two panels despite using identical DNA samples, with the discordance rate being significantly higher for FFPE samples (p < 0.05). Among the 99 variants reported only in the TO panel, 32.3% were consistent with germline variants, which were excluded in the TN panel, while 30.3% had an allele frequency of less than 5%, some of which were highly likely to be artificial calls. The comparison of two independent TN panel assay results from the same FFPE block also showed substantial discordance rate (55.3%). CONCLUSIONS In the context of clinical settings, our comparative analysis revealed that inter-NGS assay discordance commonly occurred due to sample types and the different analytical features of each panel.
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Affiliation(s)
- Pham Nguyen Quy
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keita Fukuyama
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Real World Data Research and Development, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masashi Kanai
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
| | - Tadayuki Kou
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomohiro Kondo
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Yoshioka
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junichi Matsubara
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomohiro Sakuma
- Biomedical Department, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Sachiko Minamiguchi
- Department of Diagnostic Pathology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shigemi Matsumoto
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Real World Data Research and Development, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manabu Muto
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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4
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Aoyagi Y, Kano Y, Tohyama K, Matsudera S, Kumaki Y, Takahashi K, Mitsumura T, Harada Y, Sato A, Nakamura H, Sueoka E, Aragane N, Kimura K, Onishi I, Takemoto A, Akahoshi K, Ono H, Ishikawa T, Tokunaga M, Nakagawa T, Oshima N, Nakamura R, Takagi M, Asakage T, Uetake H, Tanabe M, Miyake S, Kinugasa Y, Ikeda S. Clinical utility of comprehensive genomic profiling in Japan: Result of PROFILE-F study. PLoS One 2022; 17:e0266112. [PMID: 35358259 PMCID: PMC8970371 DOI: 10.1371/journal.pone.0266112] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/14/2022] [Indexed: 11/18/2022] Open
Abstract
Introduction
Clinical sequencing has provided molecular and therapeutic insights into the field of clinical oncology. However, despite its significance, its clinical utility in Japanese patients remains unknown. Here, we examined the clinical utility of tissue-based clinical sequencing with FoundationOne® CDx and FoundationOne® Heme. Between August 2018 and August 2019, 130 Japanese pretreated patients with advanced solid tumors were tested with FoundationOne® CDx or FoundationOne® Heme.
Results
The median age of 130 patients was 60.5 years (range: 3 to 84 years), and among them, 64 were males and 66 were females. Major cancer types were gastrointestinal cancer (23 cases) and hepatic, biliary, and pancreatic cancer (21 cases). A molecular tumor board had been completed on all 130 cases by October 31, 2019. The median number of gene alterations detected by Foundation testing, excluding variants of unknown significance (VUS) was 4 (ranged 0 to 21) per case. Of the 130 cases, one or more alterations were found in 123 cases (94.6%), and in 114 cases (87.7%), actionable alterations with candidates for therapeutic agents were found. In 29 (22.3%) of them, treatment corresponding to the gene alteration was performed. Regarding secondary findings, 13 cases (10%) had an alteration suspected of a hereditary tumor. Of the 13 cases, only one case received a definite diagnosis of hereditary tumor.
Conclusions
Our study showed that clinical sequencing might be useful for detecting gene alterations in various cancer types and exploring treatment options. However, many issues still need to be improved.
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Affiliation(s)
- Yasuko Aoyagi
- Department of Precision Cancer Medicine, Center for Innovative Cancer Treatment, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University, Tokyo, Japan
- * E-mail: (YA); (SI)
| | - Yoshihito Kano
- Department of Precision Cancer Medicine, Center for Innovative Cancer Treatment, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Clinical Oncology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kohki Tohyama
- Department of Precision Cancer Medicine, Center for Innovative Cancer Treatment, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shotaro Matsudera
- Department of Precision Cancer Medicine, Center for Innovative Cancer Treatment, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Specialized Surgeries, Tokyo Medical and Dental University, Tokyo, Japan
- First Department of Surgery, Dokkyo Medical University, Tochigi, Japan
| | - Yuichi Kumaki
- Department of Specialized Surgeries, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kenta Takahashi
- Department of Obstetrics and Gynecology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiro Mitsumura
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yohei Harada
- Division of Hematology, Respiratory Medicine and Oncology, Faculty of Medicine, Saga University, Saga, Japan
| | - Akemi Sato
- Department of Transfusion Medicine, Saga University Hospital, Saga, Japan
| | - Hideaki Nakamura
- Department of Transfusion Medicine, Saga University Hospital, Saga, Japan
| | - Eisaburo Sueoka
- Department of Transfusion Medicine, Saga University Hospital, Saga, Japan
| | - Naoko Aragane
- Division of Hematology, Respiratory Medicine and Oncology, Faculty of Medicine, Saga University, Saga, Japan
| | - Koichiro Kimura
- Department of Radiology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Iichiro Onishi
- Department of Pathology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akira Takemoto
- Department of Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keiichi Akahoshi
- Department of Hepato-Biliary-Pancreatic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroaki Ono
- Department of Hepato-Biliary-Pancreatic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Toshiaki Ishikawa
- Department of Specialized Surgeries, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masanori Tokunaga
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tsuyoshi Nakagawa
- Department of Specialized Surgeries, Tokyo Medical and Dental University, Tokyo, Japan
| | - Noriko Oshima
- Department of Obstetrics and Gynecology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Reiko Nakamura
- Department of Obstetrics and Gynecology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masatoshi Takagi
- Department of Pediatrics, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiro Asakage
- Department of Head and Neck Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Uetake
- Department of Specialized Surgeries, Tokyo Medical and Dental University, Tokyo, Japan
| | - Minoru Tanabe
- Department of Hepato-Biliary-Pancreatic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoshi Miyake
- Department of Clinical Oncology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yusuke Kinugasa
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sadakatsu Ikeda
- Department of Precision Cancer Medicine, Center for Innovative Cancer Treatment, Tokyo Medical and Dental University, Tokyo, Japan
- * E-mail: (YA); (SI)
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5
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Zhao W, Zhang M, Wang G, Liu E, Jiang G, Zhang Y, Zhang D, Jian X, Zhao H, Zhang C, Li W. The GNAQ T96S mutation abrogates the ability of wild-type GNAQ to induce apoptosis by phosphorylating ANXA2 in natural killer/T cell lymphoma. Cancer Sci 2022; 113:2288-2296. [PMID: 35293080 PMCID: PMC9277252 DOI: 10.1111/cas.15333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 11/28/2022] Open
Abstract
Our previous study identified Annexin A2 (ANXA2) as a Gaq-interacting partner in natural killer/T cell lymphoma (NKTCL) cells transfected with the GNAQ T96S mutation vector by immunoprecipitation and mass spectrometry; however, the detailed molecular mechanisms by which GNAQ T96S might regulate ANXA2 remain to be defined in NKTCL. Herein, we found that the GNAQ T96S mutation significantly promotes the phosphorylation of ANXA2 at the Y24 site, whereas phosphorylation of ANXA2 abolishes the ability of wild-type GNAQ to trigger cell apoptosis. Further investigation revealed that a GNAQ T96S peptide inhibitor induced apoptosis by competing with ANXA2 binding to GNAQ T96S in NKTCL cells. In vivo animal experiments demonstrated that a GNAQ T96S peptide inhibitor suppresses the growth of NKTCL cells carrying the GNAQ T96S mutation. Our current data suggest a role for GNAQ T96S/Src/ANXA2 in mediating the apoptosis of NKTCL cells, and the GNAQ T96S peptide may be a promising agent for therapy in NKTCL patients.
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Affiliation(s)
- Wugan Zhao
- Department of Pathology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
| | - Min Zhang
- The School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, PR China
| | - Guannan Wang
- Department of Pathology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
| | - Enjie Liu
- Department of Pathology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
| | - Guozhong Jiang
- Department of Pathology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
| | - Yanping Zhang
- Department of Pathology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
| | - Dandan Zhang
- Department of Pathology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
| | - Xiangyu Jian
- Department of Pathology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
| | - Haiyu Zhao
- Department of Pathology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
| | - Chongli Zhang
- Department of Pathology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
| | - Wencai Li
- Department of Pathology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
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6
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Sicklick JK, Kato S, Okamura R, Patel H, Nikanjam M, Fanta PT, Hahn ME, De P, Williams C, Guido J, Solomon BM, McKay RR, Krie A, Boles SG, Ross JS, Lee JJ, Leyland-Jones B, Lippman SM, Kurzrock R. Molecular profiling of advanced malignancies guides first-line N-of-1 treatments in the I-PREDICT treatment-naïve study. Genome Med 2021; 13:155. [PMID: 34607609 PMCID: PMC8491393 DOI: 10.1186/s13073-021-00969-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 09/15/2021] [Indexed: 01/07/2023] Open
Abstract
Background Malignancies are molecularly complex and become more resistant with each line of therapy. We hypothesized that offering matched, individualized combination therapies to patients with treatment-naïve, advanced cancers would be feasible and efficacious. Patients with newly diagnosed unresectable/metastatic, poor-prognosis cancers were enrolled in a cross-institutional prospective study. Methods A total of 145 patients were included in the study. Genomic profiling (tissue and/or circulating tumor DNA) was performed in all patients, and PD-L1 immunohistochemistry, tumor mutational burden, and microsatellite status assessment were performed in a subset of patients. We evaluated safety and outcomes: disease-control rate (stable disease for ≥ 6 months or partial or complete response), progression-free survival (PFS), and overall survival (OS). Results Seventy-six of 145 patients (52%) were treated, most commonly for non-colorectal gastrointestinal cancers, carcinomas of unknown primary, and hepatobiliary malignancies (53% women; median age, 63 years). The median number of deleterious genomic alterations per patient was 5 (range, 0–15). Fifty-four treated patients (71%) received ≥ 1 molecularly matched therapy, demonstrating the feasibility of administering molecularly matched therapy. The Matching Score, which reflects the percentage of targeted alterations, correlated linearly with progression-free survival (R2 = 0.92; P = 0.01), and high (≥ 60%) Matching Score was an independent predictor of improved disease control rate [OR 3.31 (95% CI 1.01–10.83), P = 0.048], PFS [HR 0.55 (0.28–1.07), P = 0.08], and OS [HR 0.42 (0.21–0.85), P = 0.02]. Serious adverse event rates were similar in the unmatched and matched groups. Conclusions Personalized combination therapies targeting a majority of a patient’s molecular alterations have antitumor activity as first-line treatment. These findings underscore the feasibility and importance of using tailored N-of-1 combination therapies early in the course of lethal malignancies. Trial registration I-PREDICT (NCT02534675) was registered on August 25, 2015. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00969-w.
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Affiliation(s)
- Jason K Sicklick
- Department of Surgery, Division of Surgical Oncology, UC San Diego School of Medicine, San Diego, CA, USA. .,Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.
| | - Shumei Kato
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Ryosuke Okamura
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Hitendra Patel
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Mina Nikanjam
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Paul T Fanta
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Michael E Hahn
- Department of Radiology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Pradip De
- Avera Cancer Institute, Sioux Falls, SD, USA
| | | | - Jessica Guido
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA
| | | | - Rana R McKay
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Amy Krie
- Avera Cancer Institute, Sioux Falls, SD, USA
| | - Sarah G Boles
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, MA, USA.,Departments of Pathology and Urology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - J Jack Lee
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Scott M Lippman
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA. .,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA.
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7
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Matsudera S, Kano Y, Aoyagi Y, Tohyama K, Takahashi K, Kumaki Y, Mitsumura T, Kimura K, Onishi I, Takemoto A, Ban D, Ono H, Kudo A, Oshima N, Ogino K, Watanabe S, Tani Y, Yamaguchi T, Nakajima M, Morita S, Yamaguchi S, Takagi M, Ishikawa T, Nakagawa T, Okamoto K, Uetake H, Tanabe M, Miyake S, Tsuchioka T, Kojima K, Ikeda S. A Pilot Study Analyzing the Clinical Utility of Comprehensive Genomic Profiling Using Plasma Cell-Free DNA for Solid Tumor Patients in Japan (PROFILE Study). Ann Surg Oncol 2021; 28:8497-8505. [PMID: 33778906 DOI: 10.1245/s10434-021-09856-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/29/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND The clinical utility of plasma cell-free DNA in precision cancer medicine has not been established. A pilot study was conducted to investigate the clinical utility of comprehensive genomic profiling by liquid biopsy in a Japanese population. METHODS In this PROFILE study, 102 patients with advanced solid tumors who showed progression with standard systemic therapy underwent liquid biopsy between August 2017 and February 2020. Liquid biopsy was performed using Guardant360. RESULTS Of the 102 patients, 56 were women, and the median age was 65 years. Regarding the types of cancer, 31 were hepatobiliary and pancreatic cancer, 17 were gastrointestinal cancer, and 13 were breast cancer. Frequently altered genes were TP53 (53.9%, 46/102), KRAS (25.5%, 26/102), PIK3CA (19.6%, 20/102), and EGFR (17.6%, 18/102). At least one genetic aberration was detected in 92 patients (90.2%). Actionable mutation was discovered in 88 patients (86.3%), and 67 patients (65.7%) were clinical trial candidates. Of the 102 patients, 22 (21.6%) were able to receive biomarker-matched therapy. Their best responses were as follows: 1 complete response, 3 partial responses, 7 stable diseases, and 11 progressive diseases. Additionally, the treated patients were divided on the basis of matching scores (≥ 50% vs. < 50%). The patients were divided into high and low groups. The high group had a higher disease control rate (DCR) of 75% compared with 20% in the low group (P = 0.010). CONCLUSIONS The results indicate that liquid biopsy is useful for identifying actionable mutations associated with the clinical response of selected patients.
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Affiliation(s)
- Shotaro Matsudera
- Department of Precision Cancer Medicine, Center for Innovative Cancer Treatment, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan. .,Department of Specialized Surgeries, Tokyo Medical and Dental University, Tokyo, Japan. .,Department of Surgical Oncology, Graduate School of Medicine, Dokkyo Medical University, Tochigi, Japan.
| | - Yoshihito Kano
- Department of Precision Cancer Medicine, Center for Innovative Cancer Treatment, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan
| | - Yasuko Aoyagi
- Department of Precision Cancer Medicine, Center for Innovative Cancer Treatment, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan
| | - Kohki Tohyama
- Department of Precision Cancer Medicine, Center for Innovative Cancer Treatment, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan
| | - Kenta Takahashi
- Department of Obstetrics and Gynecology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuichi Kumaki
- Department of Specialized Surgeries, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiro Mitsumura
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Koichiro Kimura
- Department of Radiology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Iichiro Onishi
- Department of Pathology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akira Takemoto
- Department of Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Daisuke Ban
- Department of Hepatobiliary-Pancreatic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroaki Ono
- Department of Hepatobiliary-Pancreatic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Atsushi Kudo
- Department of Hepatobiliary-Pancreatic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Noriko Oshima
- Department of Obstetrics and Gynecology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kei Ogino
- Department of Specialized Surgeries, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shun Watanabe
- Department of Surgical Oncology, Graduate School of Medicine, Dokkyo Medical University, Tochigi, Japan
| | - Yukiko Tani
- Department of Surgical Oncology, Graduate School of Medicine, Dokkyo Medical University, Tochigi, Japan
| | - Takeshi Yamaguchi
- Department of Surgical Oncology, Graduate School of Medicine, Dokkyo Medical University, Tochigi, Japan
| | - Masanobu Nakajima
- Department of Surgical Oncology, Graduate School of Medicine, Dokkyo Medical University, Tochigi, Japan
| | - Shinji Morita
- Department of Surgical Oncology, Graduate School of Medicine, Dokkyo Medical University, Tochigi, Japan
| | - Satoru Yamaguchi
- Department of Surgical Oncology, Graduate School of Medicine, Dokkyo Medical University, Tochigi, Japan
| | - Masatoshi Takagi
- Department of Pediatrics, Tokyo Medical and Dental University, Tokyo, Japan
| | - Toshiaki Ishikawa
- Department of Specialized Surgeries, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tsuyoshi Nakagawa
- Department of Specialized Surgeries, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kentaro Okamoto
- Department of Specialized Surgeries, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Uetake
- Department of Specialized Surgeries, Tokyo Medical and Dental University, Tokyo, Japan
| | - Minoru Tanabe
- Department of Hepatobiliary-Pancreatic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoshi Miyake
- Department of Precision Cancer Medicine, Center for Innovative Cancer Treatment, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan
| | - Takashi Tsuchioka
- Department of Surgical Oncology, Graduate School of Medicine, Dokkyo Medical University, Tochigi, Japan
| | - Kazuyuki Kojima
- Department of Surgical Oncology, Graduate School of Medicine, Dokkyo Medical University, Tochigi, Japan
| | - Sadakatsu Ikeda
- Department of Precision Cancer Medicine, Center for Innovative Cancer Treatment, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan. .,Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
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8
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A simple method to estimate the in-house limit of detection for genetic mutations with low allele frequencies in whole-exome sequencing analysis by next-generation sequencing. BMC Genom Data 2021; 22:8. [PMID: 33602132 PMCID: PMC7893872 DOI: 10.1186/s12863-020-00956-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 12/16/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) has profoundly changed the approach to genetic/genomic research. Particularly, the clinical utility of NGS in detecting mutations associated with disease risk has contributed to the development of effective therapeutic strategies. Recently, comprehensive analysis of somatic genetic mutations by NGS has also been used as a new approach for controlling the quality of cell substrates for manufacturing biopharmaceuticals. However, the quality evaluation of cell substrates by NGS largely depends on the limit of detection (LOD) for rare somatic mutations. The purpose of this study was to develop a simple method for evaluating the ability of whole-exome sequencing (WES) by NGS to detect mutations with low allele frequency. To estimate the LOD of WES for low-frequency somatic mutations, we repeatedly and independently performed WES of a reference genomic DNA using the same NGS platform and assay design. LOD was defined as the allele frequency with a relative standard deviation (RSD) value of 30% and was estimated by a moving average curve of the relation between RSD and allele frequency. RESULTS Allele frequencies of 20 mutations in the reference material that had been pre-validated by droplet digital PCR (ddPCR) were obtained from 5, 15, 30, or 40 G base pair (Gbp) sequencing data per run. There was a significant association between the allele frequencies measured by WES and those pre-validated by ddPCR, whose p-value decreased as the sequencing data size increased. By this method, the LOD of allele frequency in WES with the sequencing data of 15 Gbp or more was estimated to be between 5 and 10%. CONCLUSIONS For properly interpreting the WES data of somatic genetic mutations, it is necessary to have a cutoff threshold of low allele frequencies. The in-house LOD estimated by the simple method shown in this study provides a rationale for setting the cutoff.
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9
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Jardim DL, Millis SZ, Ross JS, Woo MS, Ali SM, Kurzrock R. Cyclin Pathway Genomic Alterations Across 190,247 Solid Tumors: Leveraging Large-Scale Data to Inform Therapeutic Directions. Oncologist 2021; 26:e78-e89. [PMID: 32885893 PMCID: PMC7794175 DOI: 10.1634/theoncologist.2020-0509] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/14/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND We describe the landscape of cyclin and interactive gene pathway alterations in 190,247 solid tumors. METHODS Using comprehensive genomic profiling (315 genes, >500× coverage), samples were analyzed for alterations in activating/sensitizing cyclin genes (CDK4 amplification, CDK6 amplification, CCND1, CCND2, CCND3, CDKN2B [loss], CDKN2A [loss], SMARCB1), hormone genes (estrogen receptor 1 [ESR1], androgen receptor [AR]), and co-alterations in genes leading to cyclin inhibitor therapeutic resistance (RB1 and CCNE1). RESULTS Alterations in at least one cyclin activating/sensitizing gene occurred in 24% of malignancies. Tumors that frequently harbored at least one cyclin alteration were brain gliomas (47.1%), esophageal (40.3%) and bladder cancer (37.9%), and mesotheliomas (37.9%). The most frequent alterations included CDKN2A (13.9%) and CDKN2B loss (12.5%). Examples of unique patterns of alterations included CCND1 amplification in breast cancer (17.3%); CDK4 alterations in sarcomas (12%); CCND2 in testicular cancer (23.4%), and SMARCB1 mutations in kidney cancer (3% overall, 90% in malignant rhabdoid tumors). Alterations in resistance genes RB1 and CCNE1 affected 7.2% and 3.6% of samples. Co-occurrence analysis demonstrated a lower likelihood of concomitant versus isolated alterations in cyclin activating/sensitizing and resistance genes (odds ratio [OR], 0.35; p < .001), except in colorectal, cervical, and small intestine cancers. AR and cyclin activating/sensitizing alterations in prostate cancer co-occurred more frequently (vs. AR alterations and wild-type cyclin activating/sensitizing alterations) (OR, 1.79; p < .001) as did ESR1 and cyclin activating/sensitizing alterations in breast (OR, 1.62; p < .001) and cervical cancer (OR, 4.08; p = .04) (vs. ESR1 and cyclin wild-type activating/sensitizing alterations). CONCLUSION Cyclin pathway alterations vary according to tumor type/histology, informing opportunities for targeted therapy, including for rare cancers. IMPLICATIONS FOR PRACTICE Cyclin pathway genomic abnormalities are frequent in human solid tumors, with substantial variation according to tumor site and histology. Opportunities for targeted therapy emerge with comprehensive profiling of this pathway.
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Affiliation(s)
- Denis L. Jardim
- Department of Clinical Oncology, Hospital Sirio LibanesSão PauloBrazil
| | | | | | | | | | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, University of CaliforniaSan DiegoCaliforniaUSA
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10
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Horgan D, Ciliberto G, Conte P, Baldwin D, Seijo L, Montuenga LM, Paz-Ares L, Garassino M, Penault-Llorca F, Galli F, Ray-Coquard I, Querleu D, Capoluongo E, Banerjee S, Riegman P, Kerr K, Horbach B, Büttner R, Van Poppel H, Bjartell A, Codacci-Pisanelli G, Westphalen B, Calvo F, Koeva-Balabanova J, Hall S, Paradiso A, Kalra D, Cobbaert C, Varea Menendez R, Maravic Z, Fotaki V, Bennouna J, Cauchin E, Malats N, Gutiérrez-Ibarluzea I, Gannon B, Mastris K, Bernini C, Gallagher W, Buglioni S, Kent A, Munzone E, Belina I, Van Meerbeeck J, Duffy M, Sarnowska E, Jagielska B, Mee S, Curigliano G. Bringing Greater Accuracy to Europe's Healthcare Systems: The Unexploited Potential of Biomarker Testing in Oncology. Biomed Hub 2020; 5:182-223. [PMID: 33564664 DOI: 10.1159/000511209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 08/31/2020] [Indexed: 12/11/2022] Open
Abstract
Rapid and continuing advances in biomarker testing are not being matched by take-up in health systems, and this is hampering both patient care and innovation. It also risks costing health systems the opportunity to make their services more efficient and, over time, more economical. This paper sets out the potential of biomarker testing, the unfolding precision and range of possible diagnosis and prediction, and the many obstacles to adoption. It offers case studies of biomarker testing in breast, ovarian, prostate, lung, thyroid and colon cancers, and derives specific lessons as to the potential and actual use of each of them. It also draws lessons about how to improve access and alignment, and to remedy the data deficiencies that impede development. And it suggests solutions to outstanding issues - notably including funding and the tangled web of obtaining reimbursement or equivalent coverage that Europe's fragmented health system implies. It urges a European evolution towards an initial minimum testing scenario, which would guarantee universal access to a suite of biomarker tests for the currently most common conditions, and, further into the future, to an optimum testing scenario in which a much wider range of biomarker tests would be introduced and become part of a more sophisticated health system articulated around personalised medicine. For exploiting genomics to the full, it argues the need for a new policy framework for Europe. Biomarker testing is not an issue that can be treated in isolation, since the purpose of testing is to improve health. Its use is therefore always closely linked to specific health challenges and needs to be viewed in the broader policy context in the EU and more widely. The paper is the result of extensive engagement with experts and decision makers to develop the framework, and consequently represents a wide consensus of views on how healthcare systems should respond from push and pull factors at local, national and cross-border and EU level. It contains strong views and clear recommendations springing from the convictions of patients, clinicians, academics, medicines authorities, HTA bodies, payers, the diagnostic, pharmaceutical and ICT industries, and national policy makers.
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Affiliation(s)
- Denis Horgan
- European Alliance for Personalised Medicine, Brussels, Belgium
| | | | | | - David Baldwin
- University of Nottingham, Nottingham, United Kingdom
| | - Luis Seijo
- Clinica Universidad de Navarra, CIBERES, Madrid, Spain
| | - Luis M Montuenga
- Center for Applied Medical Research (CIMA), University of Navarra and CIBERONC and IdisNa, Pamplona, Spain
| | - Luis Paz-Ares
- Hospital Doce de Octubre and CIBERONC, Madrid, Spain
| | | | | | | | | | | | | | - Susana Banerjee
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | - Keith Kerr
- Aberdeen University, Aberdeen, United Kingdom
| | | | | | | | | | | | - Benedikt Westphalen
- Grosshadern University Hospital, Ludwig-Maximilians University, Munich, Germany
| | | | | | | | | | - Dipak Kalra
- The European Institute for Innovation through Health Data (i∼HD), Gent, Belgium
| | - Christa Cobbaert
- European Federation of Clinical Chemistry and Laboratory Diagnostics, Milan, Italy
| | | | | | | | | | | | - Nuria Malats
- Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain
| | - Iñaki Gutiérrez-Ibarluzea
- EuroScan International Network, Cologne, Germany.,BIOEF, Basque Foundation for Health Innovation and Research, Barakaldo, Spain
| | | | | | - Chiara Bernini
- European Alliance for Personalised Medicine, Brussels, Belgium
| | | | | | - Alastair Kent
- Independent Patient Advocate, London, United Kingdom
| | | | - Ivica Belina
- Coalition of Healthcare Association, Zagreb, Croatia
| | - Jan Van Meerbeeck
- Antwerp University and Antwerp University Hospital, Antwerp, Belgium
| | | | | | - Beata Jagielska
- Maria Skłodowska-Curie Institute of Oncology, Warsaw, Poland
| | - Sarah Mee
- AstraZeneca, Cambridge, United Kingdom
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11
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Melas M, Subbiah S, Saadat S, Rajurkar S, McDonnell KJ. The Community Oncology and Academic Medical Center Alliance in the Age of Precision Medicine: Cancer Genetics and Genomics Considerations. J Clin Med 2020; 9:E2125. [PMID: 32640668 PMCID: PMC7408957 DOI: 10.3390/jcm9072125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 06/28/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022] Open
Abstract
Recent public policy, governmental regulatory and economic trends have motivated the establishment and deepening of community health and academic medical center alliances. Accordingly, community oncology practices now deliver a significant portion of their oncology care in association with academic cancer centers. In the age of precision medicine, this alliance has acquired critical importance; novel advances in nucleic acid sequencing, the generation and analysis of immense data sets, the changing clinical landscape of hereditary cancer predisposition and ongoing discovery of novel, targeted therapies challenge community-based oncologists to deliver molecularly-informed health care. The active engagement of community oncology practices with academic partners helps with meeting these challenges; community/academic alliances result in improved cancer patient care and provider efficacy. Here, we review the community oncology and academic medical center alliance. We examine how practitioners may leverage academic center precision medicine-based cancer genetics and genomics programs to advance their patients' needs. We highlight a number of project initiatives at the City of Hope Comprehensive Cancer Center that seek to optimize community oncology and academic cancer center precision medicine interactions.
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Affiliation(s)
- Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA;
| | - Shanmuga Subbiah
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Glendora, CA 91741, USA;
| | - Siamak Saadat
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Colton, CA 92324, USA;
| | - Swapnil Rajurkar
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Upland, CA 91786, USA;
| | - Kevin J. McDonnell
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA 91010, USA
- Center for Precision Medicine, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
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12
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Westphalen BC, Bokemeyer C, Büttner R, Fröhling S, Gaidzik VI, Glimm H, Hacker UT, Heinemann V, Illert AL, Keilholz U, Kindler T, Kirschner M, Schilling B, Siveke JT, Schroeder T, Tischler V, Wagner S, Weichert W, Zips D, Loges S. Conceptual framework for precision cancer medicine in Germany: Consensus statement of the Deutsche Krebshilfe working group 'Molecular Diagnostics and Therapy'. Eur J Cancer 2020; 135:1-7. [PMID: 32521293 DOI: 10.1016/j.ejca.2020.04.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 04/23/2020] [Indexed: 02/03/2023]
Abstract
Precision cancer medicine (PCM) holds great promises to offer more effective therapies to patients based on molecular profiling of their individual tumours. Although the PCM approach seems intuitive, multiple conceptional and structural challenges interfere with the broad implementation of PCM into clinical practice. Accordingly, concerted national and international efforts are needed to guide the further development and broad adoption of PCM in Germany. With support of the 'German Cancer Aid' (Deutsche Krebshilfe [DKH]) a task force 'Molecular Diagnostics and Therapy' was implemented. In two workshops supported by the DKH, delegates from the fourteen comprehensive cancer centresidentified key topics essential to implement quality-guided, harmonized and adaptable PCM. Based on an online questionnaire and using a modified Delphi approach, nine statements were drafted and evaluated within the group. These statements could serve as a basis to define a collaborative strategy for PCM in the future with the aim to sustain and further improve its quality.
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Affiliation(s)
- Benedikt C Westphalen
- Department of Internal Medicine III, University Hospital, LMU Munich and Comprehensive Cancer Center, Munich, Germany.
| | - Carsten Bokemeyer
- University Comprehensive Cancer Center Hamburg, Department of Oncology, Hematology with Section Bone Marrow Transplantation and Pneumology, University Medical Center Hamburg-Eppendorf, Germany
| | - Reinhard Büttner
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany; Network Genomic Medicine, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany
| | - Stefan Fröhling
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Verena I Gaidzik
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), Dresden, Germany; Center for Personalized Oncology, National Center for Tumour Diseases (NCT) Dresden and University Hospital Carl Gustav Carus Dresden at TU Dresden, Dresden, Germany; Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Dresden, Germany
| | - Ulrich T Hacker
- 1st Medical Department, University Cancer Center Leipzig (UCCL), University Leipzig Medical Center, Leipzig, Germany
| | - Volker Heinemann
- Department of Internal Medicine III, University Hospital, LMU Munich and Comprehensive Cancer Center, Munich, Germany
| | - Anna L Illert
- Department of Internal Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany; Comprehensive Cancer Center Freiburg, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; German Cancer Consortium (DKTK) and German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Thomas Kindler
- University Cancer Center Mainz, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Germany
| | - Bastian Schilling
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080, Würzburg, Germany; Department of Dermatology, University Hospital Würzburg, 97080, Würzburg, Germany
| | - Jens T Siveke
- Institute of Developmental Cancer Therapeutics, West German Cancer Center, University Medicine Essen, Essen, Germany; Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen), German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Thomas Schroeder
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty Heinrich-Heine University, Duesseldorf, Germany
| | - Verena Tischler
- Department of Pathology, University Hospital Bonn, Bonn, Germany
| | - Sebastian Wagner
- University Cancer Center Frankfurt (UCT), Department of Medicine, Hematology/Oncology, University Hospital, Goethe University, Frankfurt, Germany
| | - Wilko Weichert
- Institute of Pathology, Technische Universität München, 81675, Munich, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Daniel Zips
- Comprehensive Cancer Center Tübingen-Stuttgart, Germany
| | - Sonja Loges
- University Comprehensive Cancer Center Hamburg, Department of Oncology, Hematology with Section Bone Marrow Transplantation and Pneumology, University Medical Center Hamburg-Eppendorf, Germany.
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13
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Adashek JJ, Kato S, Parulkar R, Szeto CW, Sanborn JZ, Vaske CJ, Benz SC, Reddy SK, Kurzrock R. Transcriptomic silencing as a potential mechanism of treatment resistance. JCI Insight 2020; 5:134824. [PMID: 32493840 DOI: 10.1172/jci.insight.134824] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/29/2020] [Indexed: 12/14/2022] Open
Abstract
Next-generation sequencing (NGS) has not revealed all the mechanisms underlying resistance to genomically matched drugs. Here, we performed in 1417 tumors whole-exome tumor (somatic)/normal (germline) NGS and whole-transcriptome sequencing, the latter focusing on a clinically oriented 50-gene panel in order to examine transcriptomic silencing of putative driver alterations. In this large-scale study, approximately 13% of the somatic single nucleotide variants (SNVs) were unexpectedly not expressed as RNA; 23% of patients had ≥1 nonexpressed SNV. SNV-bearing genes consistently transcribed were TP53, PIK3CA, and KRAS; those with lower transcription rates were ALK, CSF1R, ERBB4, FLT3, GNAS, HNF1A, KDR, PDGFRA, RET, and SMO. We also determined the frequency of tumor mutations being germline, rather than somatic, in these and an additional 462 tumors with tumor/normal exomes; 33.8% of germline SNVs within the gene panel were rare (not found after filtering through variant information domains) and at risk of being falsely reported as somatic. Both the frequency of silenced variant transcription and the risk of falsely identifying germline mutations as somatic/tumor related are important phenomena. Therefore, transcriptomics is a critical adjunct to genomics when interrogating patient tumors for actionable alterations, because, without expression of the target aberrations, there will likely be therapeutic resistance.
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Affiliation(s)
- Jacob J Adashek
- Department of Internal Medicine, University of South Florida, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Shumei Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California, San Diego, Moores Cancer Center, La Jolla, California, USA
| | | | | | | | | | | | | | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California, San Diego, Moores Cancer Center, La Jolla, California, USA
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14
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Precision oncology: the intention-to-treat analysis fallacy. Eur J Cancer 2020; 133:25-28. [PMID: 32422506 DOI: 10.1016/j.ejca.2020.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 12/29/2022]
Abstract
It has recently been suggested that precision oncology studies should be reanalysed using the intention-to-treat (ITT) methodology developed for randomized controlled clinical trials. This reanalysis dramatically decreases response rates in precision medicine studies. We contend that the ITT analysis of precision oncology trials is invalid. The ITT methodology was developed three decades ago to mitigate the problems of randomized trials, which try to ensure that both arms have an unselected patient population free from confounders. In contrast, precision oncology trials specifically select patients for confounders (that is biomarkers) that predict response. To demonstrate the issues inherent in an ITT reanalysis for precision cancer medicine studies, we take as an example the drug larotrectinib (TRK inhibitor) approved because of remarkable responses in malignancies harbouring NTRK fusions. Based on large-scale studies, NTRK fusions are found in ~0.31% of tumours. In a non-randomized pivotal study of larotrectinib, 75% of the 55 treated patients responded. Based upon the prevalence of NTRK fusions, ~18,000 patients would need to be screened to enrol the 55 treated patients. Utilizing the ITT methodology, the revised response rate to larotrectinib would be 0.23%. This is, of course, a dramatic underestimation of the efficacy of this now Food and Drug Administration (FDA)-approved drug. Similar issues can be shown for virtually any biomarker-based precision clinical trial. Therefore, retrofitting the ITT analysis developed for unselected patient populations in randomized trials yields misleading conclusions in precision medicine studies.
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15
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Rodon J, Soria JC, Berger R, Miller WH, Rubin E, Kugel A, Tsimberidou A, Saintigny P, Ackerstein A, Braña I, Loriot Y, Afshar M, Miller V, Wunder F, Bresson C, Martini JF, Raynaud J, Mendelsohn J, Batist G, Onn A, Tabernero J, Schilsky RL, Lazar V, Lee JJ, Kurzrock R. Genomic and transcriptomic profiling expands precision cancer medicine: the WINTHER trial. Nat Med 2019; 25:751-758. [PMID: 31011205 DOI: 10.1038/s41591-019-0424-4] [Citation(s) in RCA: 312] [Impact Index Per Article: 62.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/14/2019] [Indexed: 12/21/2022]
Abstract
Precision medicine focuses on DNA abnormalities, but not all tumors have tractable genomic alterations. The WINTHER trial ( NCT01856296 ) navigated patients to therapy on the basis of fresh biopsy-derived DNA sequencing (arm A; 236 gene panel) or RNA expression (arm B; comparing tumor to normal). The clinical management committee (investigators from five countries) recommended therapies, prioritizing genomic matches; physicians determined the therapy given. Matching scores were calculated post-hoc for each patient, according to drugs received: for DNA, the number of alterations matched divided by the total alteration number; for RNA, expression-matched drug ranks. Overall, 303 patients consented; 107 (35%; 69 in arm A and 38 in arm B) were evaluable for therapy. The median number of previous therapies was three. The most common diagnoses were colon, head and neck, and lung cancers. Among the 107 patients, the rate of stable disease ≥6 months and partial or complete response was 26.2% (arm A: 23.2%; arm B: 31.6% (P = 0.37)). The patient proportion with WINTHER versus previous therapy progression-free survival ratio of >1.5 was 22.4%, which did not meet the pre-specified primary end point. Fewer previous therapies, better performance status and higher matching score correlated with longer progression-free survival (all P < 0.05, multivariate). Our study shows that genomic and transcriptomic profiling are both useful for improving therapy recommendations and patient outcome, and expands personalized cancer treatment.
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Affiliation(s)
- Jordi Rodon
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Wilson H Miller
- Segal Cancer Centre, Jewish General Hospital, QCROC-Quebec Cancer Consortium and Rossy Cancer Network, McGill University, Montreal, Québec, Canada
| | - Eitan Rubin
- Ben-Gurion University of the Negev, Beersheva, Israel
| | | | - Apostolia Tsimberidou
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Irene Braña
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | | | | | - Fanny Wunder
- Worldwide Innovative Network (WIN) Association-WIN Consortium, Villejuif, France
| | - Catherine Bresson
- Worldwide Innovative Network (WIN) Association-WIN Consortium, Villejuif, France
| | | | | | - John Mendelsohn
- Worldwide Innovative Network (WIN) Association-WIN Consortium, Villejuif, France.,Sheikh Khalifa Bin Zayad Al Nahyan Institute for Personalized Cancer Therapy (IPCT), The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gerald Batist
- Segal Cancer Centre, Jewish General Hospital, QCROC-Quebec Cancer Consortium and Rossy Cancer Network, McGill University, Montreal, Québec, Canada
| | - Amir Onn
- Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Josep Tabernero
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Richard L Schilsky
- Worldwide Innovative Network (WIN) Association-WIN Consortium, Villejuif, France.,American Society of Clinical Oncology (ASCO), Alexandria, VA, USA
| | - Vladimir Lazar
- Worldwide Innovative Network (WIN) Association-WIN Consortium, Villejuif, France
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Razelle Kurzrock
- Worldwide Innovative Network (WIN) Association-WIN Consortium, Villejuif, France. .,University of California San Diego, Moores Cancer Center, San Diego, CA, USA.
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16
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Gornick MC, Ryan KA, Scherer AM, Roberts JS, De Vries RG, Uhlmann WR. Interpretations of the Term "Actionable" when Discussing Genetic Test Results: What you Mean Is Not What I Heard. J Genet Couns 2019; 28:334-342. [PMID: 30964581 PMCID: PMC10558004 DOI: 10.1007/s10897-018-0289-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 08/02/2018] [Indexed: 12/11/2022]
Abstract
In genomic medicine, the familiarity and inexactness of the term "actionable" can lead to multiple interpretations and mistaken beliefs about realistic treatment options. As part of a larger study focusing on public attitudes toward policies for the return of secondary genomic results, we looked at how members of the lay public interpret the term "medically actionable" in the context of genetic testing. We also surveyed a convenience sample of oncologists as part of a separate study and asked them to define the term "medically actionable." After being provided with a definition of the term, 21 out of 60 (35%) layperson respondents wrote an additional action not specified in the provided definition (12 mentioned "cure" and 9 mentioned environment or behavioral change) and 17 (28%) indicated "something can be done" with no action specified. In contrast, 52 surveyed oncologists did not mention environment, behavioral change, or cure. Based on our findings, we propose that rather than using the term "actionable" alone, providers should also say "what they mean" to reduce miscommunication and confusion that could negatively impact medical decision-making. Lastly, to guide clinicians during patient- provider discussion about genetic test results, we provide examples of phrasing to facilitate clearer communication and understanding of the term "actionable."
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Affiliation(s)
- Michele C. Gornick
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor, MI
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI
| | - Kerry A. Ryan
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor, MI
| | - Aaron M. Scherer
- University of Iowa Carver College of Medicine, Department of Internal Medicine, Iowa City, IA
| | - J. Scott Roberts
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor, MI
- Department of Health Behavior & Health Education, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Raymond G. De Vries
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor, MI
- Department of Learning Health Sciences, University of Michigan Medical School, Ann Arbor, MI
| | - Wendy R. Uhlmann
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor, MI
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI
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17
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Huang M, Hunter T, Slomovitz B, Schlumbrecht M. Impact of molecular testing in clinical practice in gynecologic cancers. Cancer Med 2019; 8:2013-2019. [PMID: 30848097 PMCID: PMC6536929 DOI: 10.1002/cam4.2064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/18/2018] [Accepted: 02/12/2019] [Indexed: 01/06/2023] Open
Abstract
Background With the growing understanding of the molecular and genetic profiles of cancers, targeted treatments are increasingly utilized in personalized cancer care. The objective of this study was to determine how these advances have translated into practice by examining how often molecular profiling of gynecological tumors led to treatment changes. Methods We identified women with gynecological cancers at our institution who had molecular tumor testing performed from November 2014 to June 2017. Clinicopathologic data were extracted from medical records. We determined (a) if molecular profiling identified actionable targets for which therapy is available, and (b) whether the patient's treatment course changed as a result of molecular profiling. Chi‐square, Wilcoxon rank‐sum, and Fisher's exact tests were used with a P < 0.05 considered statistically significant. Results We identified 152 patients with gynecologic cancers who underwent molecular profiling. Of the 152 patients, 116 (76.3%) had actionable mutations identified, with 41 (35.3%) patients having a treatment change. Stratified by cancer type, molecular profiling most frequently identified an actionable target in patients with endometrial cancer (73.6%). Changes in treatment occurred most frequently in patients with endometrial cancer, 22 (56.4%), and ovarian cancers, 16 (39%), as compared to patients with cervical and vulvar cancer (P = 0.02). Of those patients who received a change in treatment, 39 patients (95.1%) received an FDA‐approved therapeutic agent, while two patients (4.8%) were enrolled in a clinical trial. Conclusion Molecular profiling in gynecologic cancers often identified at least one actionable mutation; however, only in a minority of these cases was the course of treatment changed. Further studies are needed to elucidate optimal timing for testing to best utilize actionable information.
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Affiliation(s)
- Marilyn Huang
- Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Tegan Hunter
- University of Miami Miller School of Medicine, Miami, Florida
| | - Brian Slomovitz
- Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Matthew Schlumbrecht
- Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
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18
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Okamura R, Boichard A, Kato S, Sicklick JK, Bazhenova L, Kurzrock R. Analysis of NTRK Alterations in Pan-Cancer Adult and Pediatric Malignancies: Implications for NTRK-Targeted Therapeutics. JCO Precis Oncol 2018; 2018. [PMID: 30637364 DOI: 10.1200/po.18.00183] [Citation(s) in RCA: 177] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Purpose Fusions that involve neurotrophic-tropomyosin receptor kinase (NTRK) genes are known drivers of oncogenesis. Therapies that target these ultra-rare, constitutionally active NTRK fusions have been remarkably effective. Herein, we analyze the prevalence of the full array of NTRK alterations-fusions, mutations, copy number alterations, and increased transcript expression-in diverse adult and pediatric tumor types to understand the landscape of NTRK aberrations in cancer. Methods We assessed 13,467 samples available from The Cancer Genome Atlas (adult tumors) and the St Jude PeCan database (pediatric tumors) for the prevalence of NTRK fusions, as well as associated genomic and transcriptomic co-aberrations in different tumor types. Results NTRK fusions were observed in 0.31% of adult tumors and in 0.34% of pediatric tumors. The most common gene partners were NTRK3 (0.16% of adult tumors) followed by NTRK1 (0.14% of pediatric tumors). NTRK fusions were found more commonly in pediatric melanoma (11.1% of samples), pediatric glioma (3.97%), and adult thyroid cancers (2.34%). Additional genomic and transcriptomic NTRK alterations- mutation, amplification, and mRNA overexpression-occurred in 14.2% of samples, whereas the frequency of alterations that implicated NTRK ligands and the NTRK co-receptor (p75NTR) ranged from 3.8% to 5.4%. Among 31 adult samples carrying NTRK fusions, co-alterations occurred often and usually involved the downstream phosphoinositide-3-kinase signaling pathway, cell-cycle machinery, other tyrosine-kinase receptors, and mitogen-activated protein kinase signals. Conclusion Whereas NTRK fusions are exceedingly rare, other NTRK abnormalities affect 14% of patients with cancer. Affecting these alterations has not yet been achievable in cancer. Genomic co-alterations occur frequently with NTRK fusions, but it is not known if co-targeting them can attenuate primary or secondary resistance to NTRK inhibitors.
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Affiliation(s)
- Ryosuke Okamura
- University of California, San Diego, Moores Cancer Center, La Jolla, CA
| | - Amélie Boichard
- University of California, San Diego, Moores Cancer Center, La Jolla, CA
| | - Shumei Kato
- University of California, San Diego, Moores Cancer Center, La Jolla, CA
| | - Jason K Sicklick
- University of California, San Diego, Moores Cancer Center, La Jolla, CA
| | | | - Razelle Kurzrock
- University of California, San Diego, Moores Cancer Center, La Jolla, CA
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19
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Galanina N, Kurzrock R. Successful implementation of genomically based treatment of chemotherapy refractory peripheral T-cell lymphoma (PTCL). Cancer Biol Ther 2018; 20:247-251. [PMID: 30307363 DOI: 10.1080/15384047.2018.1523857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
BACKGROUND The treatment of peripheral T-cell lymphoma (PTCL) after failure of standard therapy represents a significant clinical challenge as the best approach has not been defined. The outcomes of patients with peripheral T-cell lymphoma (PTCL) after relapse, in the absence of hematopoietic stem-cell transplantation, are poor with median overall survival is less than six months. Thus, relapsed/refractory PTCL presents an area of unmet medical need. CASE PRESENTATION Herein, we report an 84-year old woman with stage IV PTCL with extensive involvement of the bowel and abdominal pain. She was treated with cyclophosphamide, doxorubicin, vincristine and prednisone (CHOP) chemotherapy which was complicated by prolonged pancytopenia, without response. Disease progression was manifested by small bowel obstruction, for which she received palliative radiation therapy, further complicated by cardiac arrhythmia and sepsis. In the meantime, clinical-grade next generation sequencing of a lymph node (406 gene panel) showed six genomic alterations: NRAS Q61R, PTEN Q17*, CREBBP R768*, EP300 R1529*, SETD2 loss exons 19-21, along with an intermediate tumor mutational burden. Tissue PD-L1 staining was low positive by immunohistochemistry. The patient was discussed in Molecular Tumor Board with consensus opinion favoring a combination of the MEK inhibitor trametinib (for the NRAS alteration) and the checkpoint inhibitor nivolumab for the elevated mutational burden and PD-L1 positivity. Her abdominal pain resolved and she achieved a complete remission ongoing at 5+ months. Side effects at five months included only low-grade rash and peripheral edema. CONCLUSIONS Our observations suggest that matching patients with hematologic malignancies with customized combinations based on genomic sequencing warrants further study as a way to achieve and/or deepen responses, including in patients who are elderly and/or have refractory disease and significant disease-related complications.
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Affiliation(s)
- Natalie Galanina
- a Department of Medicine , Division of Hematology/Oncology , San Diego , CA , USA.,b Center for Personalized Cancer Therapy , University of California San Diego, Moores Cancer Center , San Diego , CA , USA
| | - Razelle Kurzrock
- a Department of Medicine , Division of Hematology/Oncology , San Diego , CA , USA.,b Center for Personalized Cancer Therapy , University of California San Diego, Moores Cancer Center , San Diego , CA , USA
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20
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Liu D, Zhang X, Zhou H, Lin X, Shi D, Shen S, Tian Y, Du B, Zhang H, Wang H, Wang Y, Zhang C. Multiplex Cell-Free DNA Reference Materials for Quality Control of Next-Generation Sequencing-Based In Vitro Diagnostic Tests of Colorectal Cancer Tolerance. J Cancer 2018; 9:3812-3823. [PMID: 30405853 PMCID: PMC6216012 DOI: 10.7150/jca.26816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/07/2018] [Indexed: 12/19/2022] Open
Abstract
Background: Liquid biopsies based on next-generation sequencing (NGS) assays are confronted with more opportunities and challenges. Widespread clinical implementation of NGS-based cancer in vitro diagnostic tests (IVDs) highlighted the urgency to establish reference materials (RMs) which could provide full control of the process from nucleic acid extraction to test report generation. Quality control based on cell-free DNA (cfDNA) RMs is especially important for liquid biopsies. Methods: Here, we used genomic DNA from thirteen cell lines to establish four negative cfDNA RMs (N1-N4) and four multiplex cfDNA RMs (L1-L4) at serial allelic frequencies ranging from approximately 2% to 0.1%. All the cfDNA RMs were quantified and validated via both droplet digital polymerase chain reaction (ddPCR) and NGS. These RMs were distributed to eight domestic manufacturers to collaboratively evaluate the performance of several domestic NGS-based cancer IVDs covering four major NGS platforms (NextSeq, HiSeq, Ion Proton, and BGISEQ). Results: Each multiplex RM has eleven colorectal cancer-related mutations, including six KRAS mutations (G12S, G12C, G12D, G12A, G12V, and G13D), three NRAS mutations (G12D, Q61R, and Q61K), one PIK3CA mutation (H1047R), and one BRAF mutation (V600E). Each mutation in the cfDNA RMs was quantified and validated via both ddPCR and NGS, showing the good relevance of mutant allelic frequency. These RMs were distributed to eight domestic manufacturers for collaborative evaluation. All eight manufacturers provided similar results by domestic NGS-based cancer IVDs, except for manufacturer #5. The coefficient of variation (CV) was increased with decreasing mutant allelic frequency, and poor repetition occurred when the allelic frequency was lower than 0.5%. Conclusions: These results indicated that these cfDNA RMs would be pivotal for NGS-based cancer IVDs, especially for liquid biopsies of colorectal cancer-related mutations and would guide the further development of RMs covering more onco-related mutations.
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Affiliation(s)
- Donglai Liu
- Division II of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Xinyuan Zhang
- GeneCast Precision Medicine Technology Institute, Beijing, China
| | - Haiwei Zhou
- Division II of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Xiaojing Lin
- GeneCast Precision Medicine Technology Institute, Beijing, China
| | - Dawei Shi
- Division II of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Shu Shen
- Division II of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Yabin Tian
- Division II of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Bo Du
- GeneCast Precision Medicine Technology Institute, Beijing, China
| | - Henghui Zhang
- GeneCast Precision Medicine Technology Institute, Beijing, China
| | - Haibo Wang
- GeneCast Precision Medicine Technology Institute, Beijing, China
| | - Youchun Wang
- Division II of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Chuntao Zhang
- Division II of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
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21
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Parish AJ, Nguyen V, Goodman AM, Murugesan K, Frampton GM, Kurzrock R. GNAS, GNAQ, and GNA11 alterations in patients with diverse cancers. Cancer 2018; 124:4080-4089. [PMID: 30204251 DOI: 10.1002/cncr.31724] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 06/23/2018] [Accepted: 06/26/2018] [Indexed: 01/04/2023]
Abstract
BACKGROUND Advances in deep sequencing technology have uncovered a widespread, protumorigenic role of guanine nucleotide-binding (G protein) α (GNA) subunits, particularly GNA subunits Gs (GNAS), Gq (GNAQ), and G11 (GNA11) (GNA*), in a diverse collection of malignancies. The objectives of the current study were: 1) to determine GNA* aberration status in a cohort of 1348 patients with cancer and 2) to examine tumor mutational burden, overall survival rates, and treatment outcomes in patients with GNA*-positive tumors versus those with tumors that had wild-type GNA*. METHODS For each patient, clinical and genomic data were collected from medical records. Next-generation sequencing was performed for each patient (range, 182-236 genes). RESULTS Aberrations of GNA* genes were identified in a subset of patients who had 8 of the 12 cancer types examined, and a significant association was observed for appendiceal cancer and ocular melanoma (P < .0001 for both; multivariate analysis). Overall, 4.1% of the cancer population was affected. GNA* abnormalities were associated with higher numbers of co-alterations in univariate (but not multivariate) analysis and were most commonly accompanied by Aurora kinase A (AURKA), Cbl proto-oncogene (CBL), and LYN proto-oncogene (LYN) co-alterations (all P < .0001; multivariate analysis). GNA* alterations were correlated with a trend toward lower median overall survival (P = .085). The median tumor mutational burden was 4 mutations per megabase in both GNA*-altered and GNA* wild-type tumors. For this limited sample of GNA*-positive patients, longer survival was not correlated with any specific treatment regimens. CONCLUSIONS In the current sample, the genes GNAS, GNAQ, and GNA11 were widely altered across cancer types, and these alterations often were accompanied by specific genomic abnormalities in AURKA, CBL, and LYN. Therefore, targeting GNA* alterations may require drugs that address the GNA* signal and important co-alterations. Cancer 2018;00:000-000. © 2018 American Cancer Society.
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Affiliation(s)
- Austin J Parish
- Center for Personalized Cancer Therapy, University of California San Diego Moores Cancer Center, Louisiana Jolla, California
| | - Vi Nguyen
- Center for Personalized Cancer Therapy, University of California San Diego Moores Cancer Center, Louisiana Jolla, California
| | - Aaron M Goodman
- Center for Personalized Cancer Therapy, University of California San Diego Moores Cancer Center, Louisiana Jolla, California.,Division of Blood and Marrow Transplantation, Department of Medicine, University of California San Diego, Moores Cancer Center, Louisiana Jolla, California.,Division of Hematology/Oncology, Department of Medicine, University of California San Diego, Moores Cancer Center, Louisiana Jolla, California
| | | | | | - Razelle Kurzrock
- Center for Personalized Cancer Therapy, University of California San Diego Moores Cancer Center, Louisiana Jolla, California.,Division of Hematology/Oncology, Department of Medicine, University of California San Diego, Moores Cancer Center, Louisiana Jolla, California
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22
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Liu D, Zhou H, Shi D, Shen S, Tian Y, Wang L, Lou J, Cong R, Lu J, Zhang H, Zhao M, Zhu S, Cao Z, Jin R, Wang Y, Zhang X, Yang G, Wang Y, Zhang C. Quality Control of Next-generation Sequencing-based In vitro Diagnostic Test for Onco-relevant Mutations Using Multiplex Reference Materials in Plasma. J Cancer 2018; 9:1680-1688. [PMID: 29760807 PMCID: PMC5950598 DOI: 10.7150/jca.24126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/04/2018] [Indexed: 12/19/2022] Open
Abstract
Background: Widespread clinical implementation of next-generation sequencing (NGS)-based cancer in vitro diagnostic tests (IVDs) highlighted the urgency to establish reference materials which could provide full control of the process from nucleic acid extraction to test report generation. The formalin-fixed, paraffin-embedded (FFPE) tissue and blood plasma containing circulating tumor deoxyribonucleic acid (ctDNA) were mostly used for clinically detecting onco-relevant mutations. Methods: We respectively developed multiplex FFPE and plasma reference materials covering three clinically onco-relevant mutations within the epidermal growth factor receptor (EGFR) gene at serial allelic frequencies. All reference materials were quantified and validated via droplet digital polymerase chain reaction (ddPCR), and then were distributed to eight domestic manufacturers for the collaborative evaluation of the performance of several domestic NGS-based cancer IVDs covering four major NGS platforms (NextSeq, HiSeq, Ion Proton and BGISEQ). Results: All expected mutations except one at extremely low allelic frequencies were detected, despite some differences in coefficient of variation (CV) which increased with the decrease of allelic frequency (CVs ranging from 18% to 106%). It was worth noting that the CV value seemed to correlate with a particular mutation as well. The repeatability of determination of different mutations was L858R>T790M>19del. Conclusions: The results indicated our reference materials would be pivotal for quality control of NGS-based cancer IVDs and would guide the further development of reference materials covering more onco-relevant mutations.
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Affiliation(s)
- Donglai Liu
- Division II of In vitro Diagnostics for Infectious Diseases, Institute for In vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Haiwei Zhou
- Division II of In vitro Diagnostics for Infectious Diseases, Institute for In vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Dawei Shi
- Division II of In vitro Diagnostics for Infectious Diseases, Institute for In vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Shu Shen
- Division II of In vitro Diagnostics for Infectious Diseases, Institute for In vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Yabin Tian
- Division II of In vitro Diagnostics for Infectious Diseases, Institute for In vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Lin Wang
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Jiatao Lou
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Rong Cong
- GenoSaber Biotech Co. Ltd., Shanghai, China
| | - Juan Lu
- GenoSaber Biotech Co. Ltd., Shanghai, China
| | - Henghui Zhang
- Genecast Precision Medicine Technology Institute, Beijing, China
| | | | | | - Zhisheng Cao
- Novogene Bioinformatics Technology Co., Ltd., Beijing, China
| | - Ruilin Jin
- Annoroad Gene Technology Co., Ltd., Beijing, China
| | - Yin Wang
- Berry Genomics Co., Ltd., Beijing, China
| | | | | | - Youchun Wang
- Division II of In vitro Diagnostics for Infectious Diseases, Institute for In vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Chuntao Zhang
- Division II of In vitro Diagnostics for Infectious Diseases, Institute for In vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
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