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Petiti J, Itri F, Signorino E, Frolli A, Fava C, Armenio M, Marini S, Giugliano E, Lo Iacono M, Saglio G, Cilloni D. Detection of SF3B1 p.Lys700Glu Mutation by PNA-PCR Clamping in Myelodysplastic Syndromes and Myeloproliferative Neoplasms. J Clin Med 2022; 11:jcm11051267. [PMID: 35268357 PMCID: PMC8911290 DOI: 10.3390/jcm11051267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/08/2022] [Accepted: 02/23/2022] [Indexed: 01/25/2023] Open
Abstract
Mutations in SF3B1 are found in 20% of myelodysplastic syndromes and 5–10% of myeloproliferative neoplasms, where they are considered important for diagnosis and therapy decisions. Sanger sequencing and NGS are the currently available methods to identify SF3B1 mutations, but both are time-consuming and expensive techniques that are not practicable in most small-/medium-sized laboratories. To identify the most frequent SF3B1 mutation, p.Lys700Glu, we developed a novel fast and cheap assay based on PNA-PCR clamping. After setting the optimal PCR conditions, the limit of detection of PNA-PCR clamping was evaluated, and the method allowed up to 0.1% of mutated SF3B1 to be identified. Successively, PNA-PCR clamping and Sanger sequencing were used to blind test 90 DNA from patients affected by myelodysplastic syndromes and myeloproliferative neoplasms for the SF3B1 p.Lys700Glu mutation. PNA-PCR clamping and Sanger sequencing congruently identified 75 negative and 13 positive patients. Two patients identified as positive by PNA-PCR clamping were missed by Sanger analysis. The discordant samples were analyzed by NGS, which confirmed the PNA-PCR clamping result, indicating that these samples contained the SF3B1 p.Lys700Glu mutation. This approach could easily increase the characterization of myelodysplastic syndromes and myeloproliferative neoplasms in small-/medium-sized laboratories, and guide patients towards more appropriate therapy.
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Affiliation(s)
- Jessica Petiti
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (F.I.); (E.S.); (A.F.); (C.F.); (G.S.); (D.C.)
- Correspondence: (J.P.); (M.L.I.); Tel.: +39-011-670-5480 (J.P.); +39-011-670-5489 (M.L.I.)
| | - Federico Itri
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (F.I.); (E.S.); (A.F.); (C.F.); (G.S.); (D.C.)
| | - Elisabetta Signorino
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (F.I.); (E.S.); (A.F.); (C.F.); (G.S.); (D.C.)
| | - Antonio Frolli
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (F.I.); (E.S.); (A.F.); (C.F.); (G.S.); (D.C.)
| | - Carmen Fava
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (F.I.); (E.S.); (A.F.); (C.F.); (G.S.); (D.C.)
| | - Marco Armenio
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy;
| | - Silvia Marini
- Division of Internal Medicine and Hematology, San Luigi Gonzaga Hospital, 10043 Orbassano, Italy; (S.M.); (E.G.)
| | - Emilia Giugliano
- Division of Internal Medicine and Hematology, San Luigi Gonzaga Hospital, 10043 Orbassano, Italy; (S.M.); (E.G.)
| | - Marco Lo Iacono
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (F.I.); (E.S.); (A.F.); (C.F.); (G.S.); (D.C.)
- Correspondence: (J.P.); (M.L.I.); Tel.: +39-011-670-5480 (J.P.); +39-011-670-5489 (M.L.I.)
| | - Giuseppe Saglio
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (F.I.); (E.S.); (A.F.); (C.F.); (G.S.); (D.C.)
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (F.I.); (E.S.); (A.F.); (C.F.); (G.S.); (D.C.)
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Tonello M, Baratti D, Sammartino P, Di Giorgio A, Robella M, Sassaroli C, Framarini M, Valle M, Macrì A, Graziosi L, Coccolini F, Lippolis PV, Roberta G, Deraco M, Biacchi D, Santullo F, Vaira M, Di Lauro K, D'Acapito F, Carboni F, Giuffrè G, Donini A, Fugazzola P, Faviana P, Lorena S, Scapinello A, Del Bianco P, Sommariva A. Microsatellite and RAS/RAF Mutational Status as Prognostic Factors in Colorectal Peritoneal Metastases Treated with Cytoreductive Surgery and Hyperthermic Intraperitoneal Chemotherapy (HIPEC). Ann Surg Oncol 2021; 29:3405-3417. [PMID: 34783946 DOI: 10.1245/s10434-021-11045-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/20/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Cytoreductive surgery (CRS) with hyperthermic intraperitoneal chemotherapy (HIPEC) leads to prolonged survival for selected patients with colorectal (CRC) peritoneal metastases (PM). This study aimed to analyze the prognostic role of micro-satellite (MS) status and RAS/RAF mutations for patients treated with CRS. METHODS Data were collected from 13 Italian centers with PM expertise within a collaborative group of the Italian Society of Surgical Oncology. Clinical and pathologic variables and KRAS/NRAS/BRAF mutational and MS status were correlated with overall survival (OS) and disease-free survival (DFS). RESULTS The study enrolled 437 patients treated with CRS-HIPEC. The median OS was 42.3 months [95% confidence interval (CI), 33.4-51.2 months], and the median DFS was 13.6 months (95% CI, 12.3-14.9 months). The local (peritoneal) DFS was 20.5 months (95% CI, 16.4-24.6 months). In addition to the known clinical factors, KRAS mutations (p = 0.005), BRAF mutations (p = 0.01), and MS status (p = 0.04) were related to survival. The KRAS- and BRAF-mutated patients had a shorter survival than the wild-type (WT) patients (5-year OS, 29.4% and 26.8% vs 51.5%, respectively). The patients with micro-satellite instability (MSI) had a longer survival than the patients with micro-satellite stability (MSS) (5-year OS, 58.3% vs 36.7%). The MSI/WT patients had the best prognosis. The MSS/WT and MSI/mutated patients had similar survivals, whereas the MSS/mutated patients showed the worst prognosis (5-year OS, 70.6%, 48.1%, 23.4%; p = 0.0001). In the multivariable analysis, OS was related to the Peritoneal Cancer Index [hazard ratio (HR), 1.05 per point], completeness of cytoreduction (CC) score (HR, 2.8), N status (HR, 1.6), signet-ring (HR, 2.4), MSI/WT (HR, 0.5), and MSS/WT-MSI/mutation (HR, 0.4). Similar results were obtained for DFS. CONCLUSION For patients affected by CRC-PM who are eligible for CRS, clinical and pathologic criteria need to be integrated with molecular features (KRAS/BRAF mutation). Micro-satellite status should be strongly considered because MSI confers a survival advantage over MSS, even for mutated patients.
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Affiliation(s)
- Marco Tonello
- Unit of Surgical Oncology of the Esophagus and Digestive Tract, Surgical Oncology Department, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Dario Baratti
- Peritoneal Surface Malignancy Unit, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Sammartino
- Cytoreductive Surgery and HIPEC Unit, Department of Surgery "Pietro Valdoni", Sapienza University of Rome, Rome, Italy
| | - Andrea Di Giorgio
- Surgical Unit of Peritoneum and Retroperitoneum, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Manuela Robella
- Surgical Oncology Unit, Candiolo Cancer Institute, Candiolo, Turin, Italy
| | - Cinzia Sassaroli
- Colorectal Surgical Oncology, Abdominal Oncology Department, Fondazione Giovanni Pascale" IRCCS, Naples, Italy
| | - Massimo Framarini
- General and Oncologic Surgery, Morgagni-Pierantoni Hospital, AUSL Romagna, Forlì, Italy
| | - Mario Valle
- Peritoneal Malignancies Unit, INT "Regina Elena", Rome, Italy
| | - Antonio Macrì
- Peritoneal Surface Malignancy and Soft Tissue Sarcoma Program, University of Messina, Messina, Italy
| | - Luigina Graziosi
- General and Emergency Surgery Department, Santa Maria della Misericordia Hospital, University of Perugia, Perugia, Italy
| | - Federico Coccolini
- General Emergency and Trauma Surgery, Bufalini Hospital, Cesena, Italy.,General Emergency and Trauma Surgery, Pisa University Hospital, Pisa, Italy
| | - Piero Vincenzo Lippolis
- General and Peritoneal Surgery, Department of Surgery, Hospital University Pisa (AOUP), Pisa, Italy
| | - Gelmini Roberta
- General and Oncological Surgery Unit, AOU of Modena University of Modena and Reggio Emilia, Modena, Italy
| | - Marcello Deraco
- Peritoneal Surface Malignancy Unit, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Daniele Biacchi
- Cytoreductive Surgery and HIPEC Unit, Department of Surgery "Pietro Valdoni", Sapienza University of Rome, Rome, Italy
| | - Francesco Santullo
- Surgical Unit of Peritoneum and Retroperitoneum, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Marco Vaira
- Surgical Oncology Unit, Candiolo Cancer Institute, Candiolo, Turin, Italy
| | - Katia Di Lauro
- Department of Advanced Biomedical Sciences, "Federico II" University, Naples, Italy
| | - Fabrizio D'Acapito
- General and Oncologic Surgery, Morgagni-Pierantoni Hospital, AUSL Romagna, Forlì, Italy
| | - Fabio Carboni
- Peritoneal Malignancies Unit, INT "Regina Elena", Rome, Italy
| | - Giuseppe Giuffrè
- Department of Human Pathology in Adult and Developmental Age 'Gaetano Barresi', Section of Pathology, University of Messina, Messina, Italy
| | - Annibale Donini
- General and Emergency Surgery Department, Santa Maria della Misericordia Hospital, University of Perugia, Perugia, Italy
| | - Paola Fugazzola
- General Emergency and Trauma Surgery, Bufalini Hospital, Cesena, Italy
| | - Pinuccia Faviana
- Pathological Anatomy III, Laboratory Medicine Department, Hospital University Pisa (AOUP), Pisa, Italy
| | - Sorrentino Lorena
- General and Oncological Surgery Unit, AOU of Modena University of Modena and Reggio Emilia, Modena, Italy
| | | | - Paola Del Bianco
- Clinical Research Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Antonio Sommariva
- Unit of Surgical Oncology of the Esophagus and Digestive Tract, Surgical Oncology Department, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy.
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Hua X, Kratz M, Malen RC, Dai JY, Lindström S, Zheng Y, Newcomb PA. Association between post-treatment circulating biomarkers of inflammation and survival among stage II-III colorectal cancer patients. Br J Cancer 2021; 125:806-815. [PMID: 34230610 DOI: 10.1038/s41416-021-01458-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/09/2021] [Accepted: 06/02/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Biomarker studies on colorectal cancer (CRC) prognosis are limited to pre-diagnostic or pre-operative measures. Post-treatment biomarkers are not well understood for their associations with CRC survival. METHODS We included 306 eligible incident stage II-III CRC cases from the population-based Seattle Colon Cancer Family Registry. Concentrations of C-reactive protein (CRP), interleukin-6 (IL-6), monocyte chemoattractant protein-1 (MCP-1), adiponectin, and leptin were measured using post-treatment plasma samples. Adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) for all-cause and CRC-specific mortality were calculated using Cox proportional hazard models. RESULTS Elevated levels of CRP, IL-6, MCP-1, and adiponectin were significantly associated with a higher risk of all-cause mortality within 10 years post blood draw with HRs (95% CI) of 1.32 (1.10-2.59), 2.72 (2.07-3.56), 1.97 (1.18-3.28) and 1.71 (1.14-2.58), respectively. IL-6 and adiponectin had a dose-response effect (Ptrend < 0.0001). For CRC-specific mortality, we observed positive associations for CRP (HR = 1.75, 95% CI: 1.2-2.56), IL-6 (HR = 5.02, 95% CI: 2.92-8.59), MCP-1 (HR = 3.78, 95% CI: 1.41-10.08), and adiponectin (HR = 3.16, 95% CI: 1.27-7.86), and inverse association for leptin (HR = 0.44, 95% CI: 0.29-0.68) within the first year of blood draw, whereas the association for IL-6 remained statistically significant over 10 years. CONCLUSION Our results support the role of chronic inflammation in CRC progression and suggested several post-treatment inflammatory biomarkers, particularly IL-6, are promising prognostic markers for stage II-III CRC patients.
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Affiliation(s)
- Xinwei Hua
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,University of Washington, Seattle, WA, USA.,Clinical and Translational Epidemiology Unit and Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mario Kratz
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,University of Washington, Seattle, WA, USA
| | - Rachel C Malen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James Y Dai
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,University of Washington, Seattle, WA, USA
| | - Sara Lindström
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,University of Washington, Seattle, WA, USA
| | - Yingye Zheng
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,University of Washington, Seattle, WA, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,University of Washington, Seattle, WA, USA.
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Yogo N, Hase T, Kasama T, Nishiyama K, Ozawa N, Hatta T, Shibata H, Sato M, Komeda K, Kawabe N, Matsuoka K, Chen-Yoshikawa TF, Kaji N, Tokeshi M, Baba Y, Hasegawa Y. Development of an immuno-wall device for the rapid and sensitive detection of EGFR mutations in tumor tissues resected from lung cancer patients. PLoS One 2020; 15:e0241422. [PMID: 33196648 PMCID: PMC7668601 DOI: 10.1371/journal.pone.0241422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
Detecting molecular targets in specimens from patients with lung cancer is essential for targeted therapy. Recently, we developed a highly sensitive, rapid-detection device (an immuno-wall device) that utilizes photoreactive polyvinyl alcohol immobilized with antibodies against a target protein via a streptavidin–biotin interaction. To evaluate its performance, we assayed epidermal growth factor receptor (EGFR) mutations, such as E746_A750 deletion in exon 19 or L858R substitution in exon 21, both of which are common in non-small cell lung cancer and important predictors of the treatment efficacy of EGFR tyrosine kinase inhibitors. The results showed that in 20-min assays, the devices detected as few as 1% (E746_A750 deletion) and 0.1% (L858R substitution) of mutant cells. Subsequent evaluation of detection of the mutations in surgically resected lung cancer specimens from patients with or without EGFR mutations and previously diagnosed using commercially available, clinically approved genotyping assays revealed diagnostic sensitivities of the immuno-wall device for E746_A750 deletion and L858R substitution of 85.7% and 87.5%, respectively, with specificities of 100% for both mutations. These results suggest that the immuno-wall device represents a good candidate next-generation diagnostic tool, especially for screening of EGFR mutations.
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Affiliation(s)
- Naoyuki Yogo
- Department of Respiratory Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
| | - Tetsunari Hase
- Department of Respiratory Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
- * E-mail:
| | - Toshihiro Kasama
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Keine Nishiyama
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Naoya Ozawa
- Department of Respiratory Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Takahiro Hatta
- Department of Respiratory Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Hirofumi Shibata
- Department of Respiratory Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Mitsuo Sato
- Department of Respiratory Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuki Komeda
- Department of Respiratory Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Nozomi Kawabe
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kohei Matsuoka
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Noritada Kaji
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan
| | - Manabu Tokeshi
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Japan
| | - Yoshinori Hasegawa
- Department of Respiratory Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan
- National Hospital Organization, Nagoya Medical Center, Nagoya, Japan
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Buscail L, Bournet B, Cordelier P. Role of oncogenic KRAS in the diagnosis, prognosis and treatment of pancreatic cancer. Nat Rev Gastroenterol Hepatol 2020; 17:153-168. [PMID: 32005945 DOI: 10.1038/s41575-019-0245-4] [Citation(s) in RCA: 373] [Impact Index Per Article: 93.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/21/2019] [Indexed: 02/08/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is predicted to be the second most common cause of death within the next 10 years. The prognosis for this disease is poor despite diagnostic progress and new chemotherapeutic regimens. The oncogenic KRAS mutation is the major event in pancreatic cancer; it confers permanent activation of the KRAS protein, which acts as a molecular switch to activate various intracellular signalling pathways and transcription factors inducing cell proliferation, migration, transformation and survival. Several laboratory methods have been developed to detect KRAS mutations in biological samples, including digital droplet PCR (which displays high sensitivity). Clinical studies have revealed that a KRAS mutation assay in fine-needle aspiration material combined with cytopathology increases the sensitivity, accuracy and negative predictive value of cytopathology for a positive diagnosis of pancreatic cancer. In addition, the presence of KRAS mutations in serum and plasma (liquid biopsies) correlates with a worse prognosis. The presence of mutated KRAS can also have therapeutic implications, whether at the gene level per se, during its post-translational maturation, interaction with nucleotides and after activation of the various oncogenic signals. Further pharmacokinetic and toxicological studies on new molecules are required, especially small synthetic molecules, before they can be used in the therapeutic arsenal for pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Louis Buscail
- Department of Gastroenterology, University of Toulouse III, Rangueil Hospital, Toulouse, France. .,INSERM UMR 1037, Toulouse Centre for Cancer Research, University of Toulouse III, Toulouse, France.
| | - Barbara Bournet
- Department of Gastroenterology, University of Toulouse III, Rangueil Hospital, Toulouse, France.,INSERM UMR 1037, Toulouse Centre for Cancer Research, University of Toulouse III, Toulouse, France
| | - Pierre Cordelier
- INSERM UMR 1037, Toulouse Centre for Cancer Research, University of Toulouse III, Toulouse, France
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Petiti J, Rosso V, Croce E, Franceschi V, Andreani G, Dragani M, De Gobbi M, Lunghi M, Saglio G, Fava C, Lo Iacono M, Cilloni D. Highly Sensitive Detection of IDH2 Mutations in Acute Myeloid Leukemia. J Clin Med 2020; 9:jcm9010271. [PMID: 31963812 PMCID: PMC7019902 DOI: 10.3390/jcm9010271] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 11/16/2022] Open
Abstract
Background: Acute myeloid leukemia is a heterogeneous hematological disease, characterized by karyotypic and molecular alterations. Mutations in IDH2 have a role in diagnosis and as a minimal residue disease marker. Often the variant allele frequency during follow up is less than 20%, which represents the limit of detection of Sanger sequencing. Therefore, the development of sensitive methodologies to identify IDH2 mutations might help to monitor patients’ response to therapy. We compared three different methods to identify and monitor IDH2 mutations in patients’ specimens. Methods: Performances of PNA-PCR clamping, droplet digital PCR and Sanger for IDH2 status identification were evaluated and compared in 96 DNA patients’ specimens. Results: In contrast with Sanger sequencing, our results highlighted the concordance between PNA clamping and digital PCR. Furthermore, PNA-PCR clamping was able to detect more mutated DNA with respect to Sanger sequencing that showed several false negatives independently from the allelic frequency. Conclusions: We found that PNA-PCR clamping and digital PCR identified IDH2 mutations in DNA samples with comparable results in a percentage significantly higher compared to Sanger sequencing. PNA-PCR clamping can be used even in laboratories not equipped for sophisticated analyses, decreasing cost and time for IDH2 characterization.
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Affiliation(s)
- Jessica Petiti
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
- Correspondence: (J.P.); (D.C.); Tel.: +39-011-9026800 (J.P.); +39-011-9026610 (D.C.); Fax: +39-11-9038636 (J.P. & D.C.)
| | - Valentina Rosso
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Eleonora Croce
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Vanessa Franceschi
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Giacomo Andreani
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Matteo Dragani
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Marco De Gobbi
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Monia Lunghi
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale, Corso Giuseppe Mazzini, 18, 28100 Novara, Italy;
| | - Giuseppe Saglio
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Carmen Fava
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Marco Lo Iacono
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
- Correspondence: (J.P.); (D.C.); Tel.: +39-011-9026800 (J.P.); +39-011-9026610 (D.C.); Fax: +39-11-9038636 (J.P. & D.C.)
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7
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Pang SW, Awi NJ, Armon S, Lim WWD, Low JSH, Peh KB, Peh SC, Teow SY. Current Update of Laboratory Molecular Diagnostics Advancement in Management of Colorectal Cancer (CRC). Diagnostics (Basel) 2019; 10:E9. [PMID: 31877940 PMCID: PMC7168209 DOI: 10.3390/diagnostics10010009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/11/2019] [Accepted: 11/23/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) continues to be one of the most common cancers globally. The incidence has increased in developing countries in the past few decades, this could be partly attributed to aging populations and unhealthy lifestyles. While the treatment of CRC has seen significant improvement since the advent of target-specific therapies and personalized medicine, CRC is oftentimes detected at late or advanced stages, thereby reducing the efficacy of treatment. Hence, screening for early detection is still the key to combat CRC and to increase overall survival (OS). Considering that the field of medical diagnostics is moving towards molecular diagnostics, CRC can now be effectively screened and diagnosed with high accuracy and sensitivity. Depending on the tumor genotype and genetic profile of the individual, personalized treatments including tyrosine kinase inhibitor therapy and immunotherapy can be administered. Notably, there can be no one single treatment that is effective for all CRC patients due to the variation in tumor genetics, which highlights the importance of molecular diagnostics. This review provides insights on therapeutic modalities, molecular biomarkers, advancement of diagnostic technologies, and current challenges in managing CRC.
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Affiliation(s)
- Siew-Wai Pang
- Department of Medical Sciences, School of Healthcare and Medical Sciences, Sunway University, Jalan Universiti, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Noel Jacques Awi
- Department of Medical Sciences, School of Healthcare and Medical Sciences, Sunway University, Jalan Universiti, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Subasri Armon
- Pathology Department, Hospital Kuala Lumpur, Jalan Pahang, Kuala Lumpur 50588, Malaysia
| | - Wendy Wan-Dee Lim
- Sunway Medical Centre, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - John Seng-Hooi Low
- Sunway Medical Centre, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Kaik-Boo Peh
- Mahkota Medical Centre, Mahkota Melaka, Jalan Merdeka, Melaka 75000, Malaysia
| | - Suat-Cheng Peh
- Department of Medical Sciences, School of Healthcare and Medical Sciences, Sunway University, Jalan Universiti, Bandar Sunway, Subang Jaya 47500, Malaysia
- Sunway Medical Centre, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Sin-Yeang Teow
- Department of Medical Sciences, School of Healthcare and Medical Sciences, Sunway University, Jalan Universiti, Bandar Sunway, Subang Jaya 47500, Malaysia
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8
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Yarom N, Gresham G, Boame N, Jonker D. KRAS Status as a Predictor of Chemotherapy Activity in Patients With Metastatic Colorectal Cancer. Clin Colorectal Cancer 2019; 18:e309-e315. [PMID: 31547963 DOI: 10.1016/j.clcc.2019.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/14/2019] [Accepted: 05/08/2019] [Indexed: 01/09/2023]
Abstract
BACKGROUND KRAS mutations occur in 40% of colorectal cancers (CRCs), affecting the efficacy of agents targeting the epidermal growth factor receptor. However, the effect of KRAS mutation status on the activity of non-epidermal growth factor receptor-targeting chemotherapy has not been fully elucidated. The aim of the present study is to evaluate the effect of KRAS status on the activity of different chemotherapeutic regimens. PATIENTS AND METHODS A retrospective chart review of chemotherapy-treated patients with metastatic CRC with known KRAS status was undertaken. Chemotherapy effects were measured by progression-free survival, time to chemotherapy resistance, and overall survival. Analysis was performed for the different chemotherapy regimens, and according to the KRAS mutation status while adjusting for potential confounders. RESULTS KRAS mutations were detected in 43% of 223 patients with metastatic CRC who were treated at the Ottawa Hospital. The baseline distribution of KRAS wild-type (WT) and mutant status was similar. The median follow-up was 27.2 months. Regimens received included single agents or combinations of 2 or 3 chemotherapies. Among those treated with capecitabine-based regimens, survival was longer for patients with KRAS WT status (hazard ratio, 0.47; 95% confidence interval, 0.23-0.95; P < .0001) when compared with those with mutant status. The median overall survival was 46.7 versus 32.6 months for patients with KRAS WT versus mutant status, respectively. The time to chemotherapy resistance was also significantly longer for patients with WT status (hazard ratio, 0.49; 95% confidence interval, 0.25-0.97; P = .0398). A trend for progression-free survival did not reach statistical significance. CONCLUSION Patients with KRAS WT tumors may benefit more from capecitabine-based treatments than patients with mutant status. Further research is needed to explain this data.
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Affiliation(s)
- Nirit Yarom
- The Oncology Institute, Assaf Harofeh Medical Center affiliated with Tel Aviv University, Be'er Ya'akov, Israel.
| | - Gillian Gresham
- Johns Hopkins Bloomberg School of Public Health, Cedars-Sinai, Baltimore, MD
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9
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Buscail E, Maulat C, Muscari F, Chiche L, Cordelier P, Dabernat S, Alix-Panabières C, Buscail L. Liquid Biopsy Approach for Pancreatic Ductal Adenocarcinoma. Cancers (Basel) 2019; 11:cancers11060852. [PMID: 31248203 PMCID: PMC6627808 DOI: 10.3390/cancers11060852] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/01/2019] [Accepted: 06/14/2019] [Indexed: 01/10/2023] Open
Abstract
Pancreatic cancer is a public health problem because of its increasing incidence, the absence of early diagnostic tools, and its aggressiveness. Despite recent progress in chemotherapy, the 5-year survival rate remains below 5%. Liquid biopsies are of particular interest from a clinical point of view because they are non-invasive biomarkers released by primary tumours and metastases, remotely reflecting disease burden. Pilot studies have been conducted in pancreatic cancer patients evaluating the detection of circulating tumour cells, cell-free circulating tumour DNA, exosomes, and tumour-educated platelets. There is heterogeneity between the methods used to isolate circulating tumour elements as well as the targets used for their identification. Performances for the diagnosis of pancreatic cancer vary depending of the technique but also the stage of the disease: 30–50% of resectable tumours are positive and 50–100% are positive in locally advanced and/or metastatic cases. A significant prognostic value is demonstrated in 50–70% of clinical studies, irrespective of the type of liquid biopsy. Large prospective studies of homogeneous cohorts of patients are lacking. One way to improve diagnostic and prognostic performances would be to use a combined technological approach for the detection of circulating tumour cells, exosomes, and DNA.
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Affiliation(s)
- Etienne Buscail
- INSERM U1035, Bordeaux University, 33000 Bordeaux, France.
- Department of Digestive Surgery, Bordeaux University Hospital, 33600 Pessac, France.
| | - Charlotte Maulat
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, 31330 Toulouse, France.
- Department of Digestive Surgery, Toulouse University Hospital, 31059 Toulouse, France.
| | - Fabrice Muscari
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, 31330 Toulouse, France.
- Department of Digestive Surgery, Toulouse University Hospital, 31059 Toulouse, France.
| | - Laurence Chiche
- INSERM U1035, Bordeaux University, 33000 Bordeaux, France.
- Department of Digestive Surgery, Bordeaux University Hospital, 33600 Pessac, France.
| | - Pierre Cordelier
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, 31330 Toulouse, France.
| | | | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), Montpellier Hospital and University of Montpellier, 34295 Montpellier, France.
| | - Louis Buscail
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, 31330 Toulouse, France.
- Department of Gastroenterology and Pancreatology, Toulouse University Hospital, 31059 Toulouse, France.
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10
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Allaway RJ, Fischer DA, de Abreu FB, Gardner TB, Gordon SR, Barth RJ, Colacchio TA, Wood M, Kacsoh BZ, Bouley SJ, Cui J, Hamilton J, Choi JA, Lange JT, Peterson JD, Padmanabhan V, Tomlinson CR, Tsongalis GJ, Suriawinata AA, Greene CS, Sanchez Y, Smith KD. Genomic characterization of patient-derived xenograft models established from fine needle aspirate biopsies of a primary pancreatic ductal adenocarcinoma and from patient-matched metastatic sites. Oncotarget 2017; 7:17087-102. [PMID: 26934555 PMCID: PMC4941373 DOI: 10.18632/oncotarget.7718] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 01/13/2016] [Indexed: 12/12/2022] Open
Abstract
N-of-1 trials target actionable mutations, yet such approaches do not test genomically-informed therapies in patient tumor models prior to patient treatment. To address this, we developed patient-derived xenograft (PDX) models from fine needle aspiration (FNA) biopsies (FNA-PDX) obtained from primary pancreatic ductal adenocarcinoma (PDAC) at the time of diagnosis. Here, we characterize PDX models established from one primary and two metastatic sites of one patient. We identified an activating KRAS G12R mutation among other mutations in these models. In explant cells derived from these PDX tumor models with a KRAS G12R mutation, treatment with inhibitors of CDKs (including CDK9) reduced phosphorylation of a marker of CDK9 activity (phospho-RNAPII CTD Ser2/5) and reduced viability/growth of explant cells derived from PDAC PDX models. Similarly, a CDK inhibitor reduced phospho-RNAPII CTD Ser2/5, increased apoptosis, and inhibited tumor growth in FNA-PDX and patient-matched metastatic-PDX models. In summary, PDX models can be constructed from FNA biopsies of PDAC which in turn can enable genomic characterization and identification of potential therapies.
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Affiliation(s)
- Robert J Allaway
- Department of Pharmacology and Toxicology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Dawn A Fischer
- Department of Surgery, Division of Surgical Oncology, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Francine B de Abreu
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Timothy B Gardner
- Department of Medicine, Section of Gastroenterology and Hepatology, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Stuart R Gordon
- Department of Medicine, Section of Gastroenterology and Hepatology, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Richard J Barth
- Department of Surgery, Division of Surgical Oncology, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA.,Dartmouth-Hitchcock Norris Cotton Cancer Center, Lebanon, NH 03756, USA
| | - Thomas A Colacchio
- Department of Surgery, Division of Surgical Oncology, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA.,Dartmouth-Hitchcock Norris Cotton Cancer Center, Lebanon, NH 03756, USA
| | - Matthew Wood
- Department of Pharmacology and Toxicology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA.,Current location: Department of Pathology, University of California, San Francisco, CA 94143, USA
| | - Balint Z Kacsoh
- Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, NH 03756, USA
| | - Stephanie J Bouley
- Department of Pharmacology and Toxicology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Jingxuan Cui
- Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, NH 03756, USA
| | - Joanna Hamilton
- Department of Pharmacology and Toxicology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA.,Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Jungbin A Choi
- Department of Pharmacology and Toxicology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Joshua T Lange
- Department of Pharmacology and Toxicology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Jason D Peterson
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | | | - Craig R Tomlinson
- Department of Pharmacology and Toxicology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA.,Dartmouth-Hitchcock Norris Cotton Cancer Center, Lebanon, NH 03756, USA.,Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Gregory J Tsongalis
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA.,Dartmouth-Hitchcock Norris Cotton Cancer Center, Lebanon, NH 03756, USA
| | - Arief A Suriawinata
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Casey S Greene
- Dartmouth-Hitchcock Norris Cotton Cancer Center, Lebanon, NH 03756, USA.,Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, NH 03756, USA.,Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Yolanda Sanchez
- Department of Pharmacology and Toxicology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA.,Dartmouth-Hitchcock Norris Cotton Cancer Center, Lebanon, NH 03756, USA
| | - Kerrington D Smith
- Department of Surgery, Division of Surgical Oncology, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA.,Dartmouth-Hitchcock Norris Cotton Cancer Center, Lebanon, NH 03756, USA
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11
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Hua X, Phipps AI, Burnett-Hartman AN, Adams SV, Hardikar S, Cohen SA, Kocarnik JM, Ahnen DJ, Lindor NM, Baron JA, Newcomb PA. Timing of Aspirin and Other Nonsteroidal Anti-Inflammatory Drug Use Among Patients With Colorectal Cancer in Relation to Tumor Markers and Survival. J Clin Oncol 2017; 35:2806-2813. [PMID: 28617623 PMCID: PMC5562174 DOI: 10.1200/jco.2017.72.3569] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Purpose Regular use of aspirin is associated with improved survival for patients with colorectal cancer (CRC). However, the timing of and the subtype of CRC that would benefit the most from using aspirin and other nonsteroidal anti-inflammatory drugs (NSAIDs) in relation to survival is unclear. Patients and Methods In all, 2,419 patients age 18 to 74 years with incident invasive CRC who were diagnosed from 1997 to 2008 were identified from population-based cancer registries in the United States, Canada, and Australia. Detailed epidemiologic questionnaires were administered at study enrollment and at 5-year follow-up. Survival outcomes were completed through linkage to national death registries. BRAF- and KRAS-mutation status, microsatellite instability, and CpG island methylator phenotype were also evaluated. Cox proportional hazards regression was used to estimate hazard ratios (HRs) and 95% CIs for overall survival (OS) and CRC-specific survival. Results After a median of 10.8 years of follow-up since diagnosis, 381 deaths (100 as a result of CRC) were observed. Compared with nonusers, postdiagnostic aspirin-only users had more favorable OS (HR, 0.75; 95% CI, 0.59 to 0.95) and CRC-specific survival (HR, 0.44; 95% CI, 0.25 to 0.71), especially among those who initiated aspirin use (OS: HR, 0.64; 95% CI, 0.47 to 0.86; CRC-specific survival: HR, 0.40; 95% CI, 0.20 to 0.80). The association between any NSAID use after diagnosis and OS differed significantly by KRAS-mutation status ( Pinteraction = .01). Use of any NSAID after diagnosis was associated with improved OS only among participants with KRAS wild-type tumors (HR, 0.60; 95% CI, 0.46 to 0.80) but not among those with KRAS-mutant tumors (HR, 1.24; 95% CI, 0.78 to 1.96). Conclusion Among long-term CRC survivors, regular use of NSAIDs after CRC diagnosis was significantly associated with improved survival in individuals with KRAS wild-type tumors.
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Affiliation(s)
- Xinwei Hua
- Xinwei Hua, Amanda I. Phipps, Andrea N. Burnett-Hartman, Scott V. Adams, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, Fred Hutchinson Cancer Research Center; Xinwei Hua, Amanda I. Phipps, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, University of Washington, Seattle, WA; Andrea N. Burnett-Hartman, Kaiser Permanente Colorado Institute for Health Research; Dennis J. Ahnen, University of Colorado School of Medicine, and Gastroenterology of the Rockies, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; and John A. Baron, University of North Carolina, Chapel Hill, NC
| | - Amanda I. Phipps
- Xinwei Hua, Amanda I. Phipps, Andrea N. Burnett-Hartman, Scott V. Adams, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, Fred Hutchinson Cancer Research Center; Xinwei Hua, Amanda I. Phipps, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, University of Washington, Seattle, WA; Andrea N. Burnett-Hartman, Kaiser Permanente Colorado Institute for Health Research; Dennis J. Ahnen, University of Colorado School of Medicine, and Gastroenterology of the Rockies, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; and John A. Baron, University of North Carolina, Chapel Hill, NC
| | - Andrea N. Burnett-Hartman
- Xinwei Hua, Amanda I. Phipps, Andrea N. Burnett-Hartman, Scott V. Adams, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, Fred Hutchinson Cancer Research Center; Xinwei Hua, Amanda I. Phipps, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, University of Washington, Seattle, WA; Andrea N. Burnett-Hartman, Kaiser Permanente Colorado Institute for Health Research; Dennis J. Ahnen, University of Colorado School of Medicine, and Gastroenterology of the Rockies, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; and John A. Baron, University of North Carolina, Chapel Hill, NC
| | - Scott V. Adams
- Xinwei Hua, Amanda I. Phipps, Andrea N. Burnett-Hartman, Scott V. Adams, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, Fred Hutchinson Cancer Research Center; Xinwei Hua, Amanda I. Phipps, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, University of Washington, Seattle, WA; Andrea N. Burnett-Hartman, Kaiser Permanente Colorado Institute for Health Research; Dennis J. Ahnen, University of Colorado School of Medicine, and Gastroenterology of the Rockies, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; and John A. Baron, University of North Carolina, Chapel Hill, NC
| | - Sheetal Hardikar
- Xinwei Hua, Amanda I. Phipps, Andrea N. Burnett-Hartman, Scott V. Adams, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, Fred Hutchinson Cancer Research Center; Xinwei Hua, Amanda I. Phipps, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, University of Washington, Seattle, WA; Andrea N. Burnett-Hartman, Kaiser Permanente Colorado Institute for Health Research; Dennis J. Ahnen, University of Colorado School of Medicine, and Gastroenterology of the Rockies, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; and John A. Baron, University of North Carolina, Chapel Hill, NC
| | - Stacey A. Cohen
- Xinwei Hua, Amanda I. Phipps, Andrea N. Burnett-Hartman, Scott V. Adams, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, Fred Hutchinson Cancer Research Center; Xinwei Hua, Amanda I. Phipps, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, University of Washington, Seattle, WA; Andrea N. Burnett-Hartman, Kaiser Permanente Colorado Institute for Health Research; Dennis J. Ahnen, University of Colorado School of Medicine, and Gastroenterology of the Rockies, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; and John A. Baron, University of North Carolina, Chapel Hill, NC
| | - Jonathan M. Kocarnik
- Xinwei Hua, Amanda I. Phipps, Andrea N. Burnett-Hartman, Scott V. Adams, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, Fred Hutchinson Cancer Research Center; Xinwei Hua, Amanda I. Phipps, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, University of Washington, Seattle, WA; Andrea N. Burnett-Hartman, Kaiser Permanente Colorado Institute for Health Research; Dennis J. Ahnen, University of Colorado School of Medicine, and Gastroenterology of the Rockies, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; and John A. Baron, University of North Carolina, Chapel Hill, NC
| | - Dennis J. Ahnen
- Xinwei Hua, Amanda I. Phipps, Andrea N. Burnett-Hartman, Scott V. Adams, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, Fred Hutchinson Cancer Research Center; Xinwei Hua, Amanda I. Phipps, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, University of Washington, Seattle, WA; Andrea N. Burnett-Hartman, Kaiser Permanente Colorado Institute for Health Research; Dennis J. Ahnen, University of Colorado School of Medicine, and Gastroenterology of the Rockies, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; and John A. Baron, University of North Carolina, Chapel Hill, NC
| | - Noralane M. Lindor
- Xinwei Hua, Amanda I. Phipps, Andrea N. Burnett-Hartman, Scott V. Adams, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, Fred Hutchinson Cancer Research Center; Xinwei Hua, Amanda I. Phipps, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, University of Washington, Seattle, WA; Andrea N. Burnett-Hartman, Kaiser Permanente Colorado Institute for Health Research; Dennis J. Ahnen, University of Colorado School of Medicine, and Gastroenterology of the Rockies, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; and John A. Baron, University of North Carolina, Chapel Hill, NC
| | - John A. Baron
- Xinwei Hua, Amanda I. Phipps, Andrea N. Burnett-Hartman, Scott V. Adams, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, Fred Hutchinson Cancer Research Center; Xinwei Hua, Amanda I. Phipps, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, University of Washington, Seattle, WA; Andrea N. Burnett-Hartman, Kaiser Permanente Colorado Institute for Health Research; Dennis J. Ahnen, University of Colorado School of Medicine, and Gastroenterology of the Rockies, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; and John A. Baron, University of North Carolina, Chapel Hill, NC
| | - Polly A. Newcomb
- Xinwei Hua, Amanda I. Phipps, Andrea N. Burnett-Hartman, Scott V. Adams, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, Fred Hutchinson Cancer Research Center; Xinwei Hua, Amanda I. Phipps, Sheetal Hardikar, Stacey A. Cohen, Jonathan M. Kocarnik, and Polly A. Newcomb, University of Washington, Seattle, WA; Andrea N. Burnett-Hartman, Kaiser Permanente Colorado Institute for Health Research; Dennis J. Ahnen, University of Colorado School of Medicine, and Gastroenterology of the Rockies, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; and John A. Baron, University of North Carolina, Chapel Hill, NC
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12
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Molecular Diagnostics for Precision Medicine in Colorectal Cancer: Current Status and Future Perspective. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9850690. [PMID: 27699178 PMCID: PMC5028795 DOI: 10.1155/2016/9850690] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/10/2016] [Indexed: 02/08/2023]
Abstract
Precision medicine, a concept that has recently emerged and has been widely discussed, emphasizes tailoring medical care to individuals largely based on information acquired from molecular diagnostic testing. As a vital aspect of precision cancer medicine, targeted therapy has been proven to be efficacious and less toxic for cancer treatment. Colorectal cancer (CRC) is one of the most common cancers and among the leading causes for cancer related deaths in the United States and worldwide. By far, CRC has been one of the most successful examples in the field of precision cancer medicine, applying molecular tests to guide targeted therapy. In this review, we summarize the current guidelines for anti-EGFR therapy, revisit the roles of pathologists in an era of precision cancer medicine, demonstrate the transition from traditional “one test-one drug” assays to multiplex assays, especially by using next-generation sequencing platforms in the clinical diagnostic laboratories, and discuss the future perspectives of tumor heterogeneity associated with anti-EGFR resistance and immune checkpoint blockage therapy in CRC.
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13
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Hardikar S, Newcomb PA, Campbell PT, Win AK, Lindor NM, Buchanan DD, Makar KW, Jenkins MA, Potter JD, Phipps AI. Prediagnostic Physical Activity and Colorectal Cancer Survival: Overall and Stratified by Tumor Characteristics. Cancer Epidemiol Biomarkers Prev 2015; 24:1130-7. [PMID: 25976417 DOI: 10.1158/1055-9965.epi-15-0039] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/06/2015] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Physical activity is associated with a lower incidence of colorectal cancer; however, the relationship of physical activity with colorectal cancer survival is not yet clear. We evaluated the association between prediagnostic physical activity and colorectal cancer survival, overall and accounting for tumor markers associated with colorectal cancer survival: BRAF and KRAS mutation status and microsatellite instability (MSI) status. METHODS Participants were 20- to 74-year-old colorectal cancer patients diagnosed between 1998 and 2007 from the population-based Seattle Colon Cancer Family Registry (S-CCFR). Self-reported physical activity in the years preceding colorectal cancer diagnosis was summarized as average metabolic equivalent task hours per week (MET-h/wk; n = 1,309). Somatic BRAF and KRAS mutations and MSI status were evaluated on a subset of patients (n = 1043). Cox regression was used to estimate HRs and 95% confidence intervals (CI) for overall and disease-specific survival after adjusting for relevant confounders. Stratified analyses were conducted across categories of BRAF, KRAS, and MSI, as well as tumor stage and site. RESULTS Higher prediagnostic recreational physical activity was associated with significantly more favorable overall survival (HR for highest vs. lowest category, 0.70; 95% CI, 0.52-0.96); associations were similar for colorectal cancer-specific survival. Results consistently indicated a favorable association with physical activity across strata defined by tumor characteristics. CONCLUSION Individuals who were physically active before colorectal cancer diagnosis experienced better survival than those who were inactive or minimally active. IMPACT Our results support existing physical activity recommendations for colorectal cancer patients and suggest that the beneficial effect of activity is not specific to a particular molecular phenotype of colorectal cancer.
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Affiliation(s)
- Sheetal Hardikar
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Epidemiology, University of Washington, Seattle, Washington.
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Epidemiology, University of Washington, Seattle, Washington
| | - Peter T Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia
| | - Aung Ko Win
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, Arizona
| | - Daniel D Buchanan
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia. Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Karen W Makar
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mark A Jenkins
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Epidemiology, University of Washington, Seattle, Washington. Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Epidemiology, University of Washington, Seattle, Washington
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Dudley J, Tseng LH, Rooper L, Harris M, Haley L, Chen G, Gocke CD, Eshleman JR, Lin MT. Challenges posed to pathologists in the detection of KRAS mutations in colorectal cancers. Arch Pathol Lab Med 2015; 139:211-8. [PMID: 25611103 DOI: 10.5858/arpa.2013-0649-oa] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Detection of KRAS mutation is mandatory to predict response to anti-epidermal growth factor receptor monoclonal antibodies in patients with metastatic colorectal cancers. OBJECTIVE To demonstrate challenges posed to pathologists in the clinical detection of KRAS mutations in colorectal cancers. DESIGN In this retrospective analysis for quality assessment of the pyrosequencing assay, we survey the characteristics of 463 formalin-fixed, paraffin-embedded neoplastic tissues submitted for KRAS mutation detection during a 26-month period. RESULTS The KRAS mutation was detected in 39.2% of tumors. This included 2 tumors with complex pyrograms (GGT>GAG at codon 12 and GGC>GTT at codon 13, as resolved by a Pyromaker software program) and 3 tumors with an indeterminate percentage of mutant alleles (defined as 4% to 5% and confirmed by a next-generation sequencing platform). Among the 25 specimens (5.5%) with fewer than 20% tumor cells, 22 were resected after chemotherapy/radiation. Significant depletion of tumor cells was observed in rectal cancers resected after neoadjuvant therapy (31.0%) versus those without previous treatment (0%) (P = .01). We also explore other specimens with low tumor cellularity and potential causes of discrepancy between the estimated tumor cell percentage and detected mutant allele frequency, such as intratumor heterogeneity of KRAS mutation. CONCLUSIONS Neoadjuvant therapy may deplete tumor cells and confound the molecular diagnosis of KRAS mutations. Accurate detection of specimens with poor tumor cellularity requires the appropriate selection of neoplastic tissues, evaluation of tumor cellularity, use of assays with high sensitivity, and prospective quality assessment.
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Affiliation(s)
- Jonathan Dudley
- From the Departments of Pathology (Drs Dudley, Tseng, Rooper, Chen, Gocke, Eshleman and Lin, Mr Harris, and Ms Haley) and Oncology (Drs Gocke and Eshleman), Johns Hopkins University School of Medicine, Baltimore, Maryland; the Department of Pathology, Massachusetts General Hospital, Boston (Dr Dudley); and the Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan (Dr Tseng)
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Kothari N, Schell MJ, Teer JK, Yeatman T, Shibata D, Kim R. Comparison of KRAS mutation analysis of colorectal cancer samples by standard testing and next-generation sequencing. J Clin Pathol 2014; 67:764-7. [PMID: 25004944 DOI: 10.1136/jclinpath-2014-202405] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AIMS Based on KRAS testing, the subset of patients with metastatic colorectal cancer (CRC) that could benefit from anti-EGFR therapy can be better delineated. Though KRAS testing has become significantly more prevalent over the last few years, methods for testing remain heterogeneous and discordance has been reported between methods. METHODS In this study, we examined a CRC patient population and compared KRAS testing done in Clinical Laboratory Improvement Amendments (CLIA) approved laboratories as part of standard clinical care and by next-generation sequencing (NGS) using the Illumina platform. Discordances were further evaluated with manual review of the NGS testing. RESULTS Out of 468 CRC patient samples, 77 had KRAS testing done by both CLIA assay and NGS. There were concordant results between testing methodologies in 74 out of 77 patients, or 96% (95% CI 89% to 99%). There were three patient samples that showed discordant results between the two methods of testing. Upon further investigation of the NGS results for the three discordant cases, one sample showed a low level of the mutation seen in the standard testing, one sample showed low tumour fraction and a third did not show any evidence of the mutation that was found with the standard assay. Five patients had KRAS mutations not typically tested with standard testing. CONCLUSIONS Overall there was a high concordance rate between NGS and standard testing for KRAS. However, NGS revealed mutations that are not tested for with standard KRAS assays that might have clinical impact with regards to the role for anti-EGFR therapy.
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Abstract
Activating mutation of KRAS plays a significant role in the pathogenesis of common human malignancies and molecular testing of KRAS mutation has emerged as an essential biomarker in the current practice of clinical oncology. The presence of KRAS mutation is generally associated with clinical aggressiveness of the cancer and reduced survival of the patient. Therapeutically, KRAS mutation testing has maximum utility in stratifying metastatic colorectal carcinoma and lung cancer patients for treatment with targeted therapy. Diagnostically, KRAS mutation testing is useful in the workup of pancreaticobiliary and thyroid cancers, particularly using cytological specimens. In the era of precision medicine, the role of KRAS mutation testing is poised to expand, likely in a setting of combinatorial therapeutic strategy and requiring additional mutation testing of its upstream and/or downstream effectors.
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Affiliation(s)
- Sudhir Perincheri
- Department of Pathology, Yale University School of Medicine, 310 Cedar Street, New Haven, CT 06520-8023, USA
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Ming Z, Jiang D, Hu Q, Li X, Huang J, Xu Y, Liu Y, Xu C, Hua X, Hou Y. Diagnostic application of PIK3CA mutation analysis in Chinese esophageal cancer patients. Diagn Pathol 2014; 9:153. [PMID: 25106743 PMCID: PMC4149237 DOI: 10.1186/s13000-014-0153-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 07/29/2014] [Indexed: 02/06/2023] Open
Abstract
Background The PIK3CA gene mutation was found to associate with prognosis and might affect molecular targeted therapy in esophageal carcinoma (EC). The aim of this study is to compare different methods for analyzing the PIK3CA gene mutation in EC. Methods Genomic DNA was extracted from 106 surgically resected EC patient tissues. The PIK3CA mutation status (exons 9 and 20) were screened by mutant-enrich liquid chip (ME-Liquidchip), Sanger sequencing, and pyrosequencing. And all samples with mutations were independently reassessed using amplification refractory mutation system (ARMS) methods again. Results PIK3CA mutation rates were identified as 11.3% (12/106) by ME-Liquidchip. 10 mutations occurred in exon 9 and 2 in exon 20, including G1624A:E542K (n = 4), G1633A:E545K (n = 6) and A3140G:H1047R (n = 2). The results were further verified by ARMS methods. Among these 12 cases characterized for PIK3CA mutation, however, only 7 and 6 cases were identified by Sanger sequencing (6.6%,7/106) and pyrosequencing (5.7%,6/106), respectively. Conclusion Sanger sequencing and pyrosequencing are less sensitive and are not efficiently applicable to the detection of PIK3CA mutation in EC samples. Choosing between ME-Liquidchip and ARMS will depend on laboratory facilities and expertise. Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/13000_2014_153
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xiuguo Hua
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Portier BP, Kanagal-Shamanna R, Luthra R, Singh R, Routbort MJ, Handal B, Reddy N, Barkoh BA, Zuo Z, Medeiros LJ, Aldape K, Patel KP. Quantitative assessment of mutant allele burden in solid tumors by semiconductor-based next-generation sequencing. Am J Clin Pathol 2014; 141:559-72. [PMID: 24619758 DOI: 10.1309/ajcp1jugqmw7zntl] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
OBJECTIVES Identification of tumor-specific somatic mutations has had a significant impact on both disease diagnosis and therapy selection. The ability of next-generation sequencing (NGS) to provide a quantitative assessment of mutant allele burden, in numerous target genes in a single assay, provides a significant advantage over conventional qualitative genotyping platforms. METHODS We assessed the quantitative capability of NGS and a primer extension-based matrix-assisted laser desorption ionization-time-of-flight (PE-MALDI) assay and directly correlated NGS mutant allele burden determination to morphologic assessment of tumor percentage in H&E-stained slides. RESULTS Our results show a 100% concordance between NGS and PE-MALDI in mutant allele detection and a significant correlation between NGS and PE-MALDI for determining mutant allele burden when mutant allele burden is 10% or more. CONCLUSIONS NGS-based mutation screening provides a quantitative assessment comparable to that of PE-MALDI. In addition, NGS also allows for a high degree of multiplexing and uses nanogram quantities of DNA, thereby preserving precious material for future analysis. Furthermore, this study provides evidence that H&E-based morphologic assessment of tumor burden does not correlate to actual tumor mutant allele burden frequency.
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Affiliation(s)
- Bryce P Portier
- Dept of Hematopathology, MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 149, Houston, TX 77030; e-mail:
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Balschun K, Wenke AK, Röcken C, Haag J. Detection of KRAS and BRAF mutations in advanced colorectal cancer by allele-specific single-base primer extension. Expert Rev Mol Diagn 2014; 11:799-802. [DOI: 10.1586/erm.11.75] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Katharina Balschun
- Institute of Pathology, Christian-Albrechts-University, Arnold-Heller-Str. 3, D-24105 Kiel, Germany
| | - Ann-Kathrin Wenke
- Institute of Pathology, Christian-Albrechts-University, Arnold-Heller-Str. 3, D-24105 Kiel, Germany
| | - Christoph Röcken
- Institute of Pathology, Christian-Albrechts-University, Arnold-Heller-Str. 3, D-24105 Kiel, Germany
| | - Jochen Haag
- Institute of Pathology, Christian-Albrechts-University, Arnold-Heller-Str. 3, D-24105 Kiel, Germany
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Molinari F, Frattini M. KRASmutational test for metastatic colorectal cancer patients: not just a technical problem. Expert Rev Mol Diagn 2014; 12:123-6. [DOI: 10.1586/erm.11.94] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Phipps AI, Makar KW, Newcomb PA. Descriptive profile of PIK3CA-mutated colorectal cancer in postmenopausal women. Int J Colorectal Dis 2013; 28:1637-42. [PMID: 23728594 PMCID: PMC3830592 DOI: 10.1007/s00384-013-1715-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/08/2013] [Indexed: 02/04/2023]
Abstract
PURPOSE Approximately 10-30 % of colorectal cancers exhibit somatic mutations in the phosphoinositide-3-kinase, catalytic, alpha polypeptide gene (PIK3CA). We evaluated the relationship between PIK3CA mutation status and demographic factors, lifestyle factors, and other tumor characteristics and the relationship between PIK3CA mutation status and colorectal cancer survival. METHODS The population-based study included postmenopausal women with invasive colorectal cancer diagnosed between 1998 and 2002 in Western Washington State. Participants were interviewed, and tumor specimens were tested for PIK3CA mutations in exons 9 and 20 hotspots, KRAS exon 2 mutations, BRAF p.V600E mutation, and microsatellite instability. We used Cox regression to evaluate the association between PIK3CA mutation status and disease-specific and overall survival. Stratified analyses were conducted by KRAS mutation status. RESULTS PIK3CA mutations were evident in approximately 13 % of cases (N = 35). Women with PIK3CA-mutated colorectal cancer were significantly more likely than those with PIK3CA wild-type disease to be non-white, to have proximal colon cancer, and to have KRAS-mutated tumors (p < 0.05). In Cox proportional hazards regression analyses, overall survival was poorer, although not statistically significantly so, for women with PIK3CA-mutated versus wild-type colorectal cancer (hazard ratio = 1.74, 95 % confidence interval 0.86-3.50). This association between PIK3CA mutation status and survival was evident only when analyses were restricted to cases without somatic KRAS mutations (hazard ratio = 2.94, 95 % confidence interval 1.12-7.73). CONCLUSIONS PIK3CA-mutated colorectal cancer appears to have a distinct epidemiologic profile that is of clinical significance. Women with PIK3CA-mutated colorectal cancer experience a poorer prognosis than those with PIK3CA wild-type disease.
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Affiliation(s)
- Amanda I. Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., M4-C308, Seattle, WA 98109, USA
| | - Karen W. Makar
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., M4-B402, Seattle, WA 98109, USA
| | - Polly A. Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., M4-B402, Seattle, WA 98109, USA
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Kitano S, Myers J, Nakamura J, Yamane A, Yamashita M, Nakayama M, Tsukahara Y, Ushida H, Liu W, Ratain MJ, Amano M. A novel fully automated molecular diagnostic system (AMDS) for colorectal cancer mutation detection. PLoS One 2013; 8:e62989. [PMID: 23671647 PMCID: PMC3650034 DOI: 10.1371/journal.pone.0062989] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 03/27/2013] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND KRAS, BRAF and PIK3CA mutations are frequently observed in colorectal cancer (CRC). In particular, KRAS mutations are strong predictors for clinical outcomes of EGFR-targeted treatments such as cetuximab and panitumumab in metastatic colorectal cancer (mCRC). For mutation analysis, the current methods are time-consuming, and not readily available to all oncologists and pathologists. We have developed a novel, simple, sensitive and fully automated molecular diagnostic system (AMDS) for point of care testing (POCT). Here we report the results of a comparison study between AMDS and direct sequencing (DS) in the detection of KRAS, BRAF and PI3KCA somatic mutations. METHODOLOGY/PRINCIPAL FINDING DNA was extracted from a slice of either frozen (n = 89) or formalin-fixed and paraffin-embedded (FFPE) CRC tissue (n = 70), and then used for mutation analysis by AMDS and DS. All mutations (n = 41 among frozen and 27 among FFPE samples) detected by DS were also successfully (100%) detected by the AMDS. However, 8 frozen and 6 FFPE samples detected as wild-type in the DS analysis were shown as mutants in the AMDS analysis. By cloning-sequencing assays, these discordant samples were confirmed as true mutants. One sample had simultaneous "hot spot" mutations of KRAS and PIK3CA, and cloning assay comfirmed that E542K and E545K were not on the same allele. Genotyping call rates for DS were 100.0% (89/89) and 74.3% (52/70) in frozen and FFPE samples, respectively, for the first attempt; whereas that of AMDS was 100.0% for both sample sets. For automated DNA extraction and mutation detection by AMDS, frozen tissues (n = 41) were successfully detected all mutations within 70 minutes. CONCLUSIONS/SIGNIFICANCE AMDS has superior sensitivity and accuracy over DS, and is much easier to execute than conventional labor intensive manual mutation analysis. AMDS has great potential for POCT equipment for mutation analysis.
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Affiliation(s)
- Shiro Kitano
- Technical Research Institute, Toppan Printing Co., Ltd., Chiba, Japan.
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KRAS-mutation status in relation to colorectal cancer survival: the joint impact of correlated tumour markers. Br J Cancer 2013; 108:1757-64. [PMID: 23511557 PMCID: PMC3668469 DOI: 10.1038/bjc.2013.118] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background: Mutations in the Kirsten Ras (KRAS) oncogene are common in colorectal cancer (CRC). The role of KRAS-mutation status as a prognostic factor, however, is unclear. We evaluated the relationship between KRAS-mutation status and CRC survival, considering heterogeneity in this association by tumour and patient characteristics. Methods: The population-based study included individuals diagnosed with CRC between 1998–2007 in Western Washington State. Tumour specimens were tested for KRAS exon 2 mutations, the BRAF p.V600E mutation, and microsatellite instability (MSI). We used Cox regression to estimate hazard ratios (HR) and 95% confidence intervals (CI) for the association between KRAS-mutation status and disease-specific and overall survival. Stratified analyses were conducted by age, sex, tumour site, stage, and MSI. We conducted additional analyses combining KRAS-mutation, BRAF-mutation, and MSI status. Results: Among 1989 cases, 31% had KRAS-mutated CRC. Kirsten Ras (KRAS)-mutated CRC was associated with poorer disease-specific survival (HR=1.37, 95% CI: 1.13–1.66). This association was not evident in cases who presented with distant-stage CRC. Cases with KRAS-wild-type/BRAF-wild-type/MSI-high CRC had the most favourable prognosis; those with CRC exhibiting a KRAS- or BRAF-mutation and no MSI had the poorest prognosis. Patterns were similar for overall survival. Conclusion: Kirsten Ras (KRAS)-mutated CRC was associated with statistically significantly poorer survival after diagnosis than KRAS-wild-type CRC.
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Recommendations from the EGAPP Working Group: can testing of tumor tissue for mutations in EGFR pathway downstream effector genes in patients with metastatic colorectal cancer improve health outcomes by guiding decisions regarding anti-EGFR therapy? Genet Med 2013; 15:517-27. [PMID: 23429431 DOI: 10.1038/gim.2012.184] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 12/21/2012] [Indexed: 12/31/2022] Open
Abstract
SUMMARY OF RECOMMENDATIONS The Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group (EWG) found that, for patients with metastatic colorectal cancer (mCRC) who are being considered for treatment with cetuximab or panitumumab, there is convincing evidence to recommend clinical use of KRAS mutation analysis to determine which patients are KRAS mutation positive and therefore unlikely to benefit from these agents before initiation of therapy. The level of certainty of the evidence was deemed high, and the magnitude of net health benefit from avoiding potentially ineffective and harmful treatment, along with promoting more immediate access to what could be the next most effective treatment, is at least moderate.The EWG found insufficient evidence to recommend for or against BRAF V600E testing for the same clinical scenario. The level of certainty for BRAF V600E testing to guide antiepidermal growth factor receptor (EGFR) therapy was deemed low. The EWG encourages further studies of the potential value of testing in patients with mCRC who were found to have tumors that are wild type (mutation negative) for KRAS to predict responsiveness to therapy.The EWG found insufficient evidence to recommend for or against testing for mutations in NRAS, or PIK3CA, and/or loss of expression of PTEN or AKT proteins. The level of certainty for this evidence was low. In the absence of supporting evidence, and with consideration of other contextual issues, the EWG discourages the use of these tests in guiding decisions on initiating anti-EGFR therapy with cetuximab or panitumumab unless further evidence supports improved clinical outcomes. RATIONALE It has been suggested that patients with mCRC whose tumors harbor certain mutations affecting EGFR pathway signaling are typically unresponsive to therapy with anti-EGFR antibodies (cetuximab and panitumumab). The EWG identified recent evidence reviews that have addressed this topic, and this recommendation statement is based on results of these reviews. In developing these recommendations the EWG considered evidence in the areas described below. ANALYTIC VALIDITY Although no research syntheses that have formally evaluated analytic validity of these tests were found, the EWG was able to draw the following conclusions from assessments included in the evidence reviews under consideration. There is adequate evidence that KRAS mutation analysis reliably and accurately detects common mutations (codons 12 and 13), whereas evidence was inadequate for less frequent KRAS mutations (e.g., codon 61). There is also adequate evidence that testing for BRAF V600E accurately and reliably detects the mutation. For common mutations in NRAS, PIK3CA, and expression of PTEN AKT, there is adequate evidence of accurate and reliable detection. However, much less data exist in support. Furthermore, in the specific context of mCRC, no evidence was found on the analytic validity of immunohistochemistry (IHC) assays for PTEN or AKT expression. CLINICAL VALIDITY For KRAS mutation analysis, the EWG found convincing evidence for association with treatment response to anti-EGFR therapy, independent of prognostic association. For BRAF V600E mutation testing, the EWG found insufficient evidence for association with treatment response to anti-EGFR therapy independent of prognostic association. The EWG found insufficient evidence for association of results of testing for mutations in NRAS or PIK3CA, and loss of expression of PTEN or ATK proteins, with treatment response to anti-EGFR therapy. CLINICAL UTILITY For KRAS mutation analysis, the EWG found adequate evidence that improved health outcomes are achieved by avoiding ineffective chemotherapy and potential side effects and expediting access to the next most effective treatment. Inadequate evidence was found regarding association of BRAF V600E mutation testing or loss of PTEN expression with improved health outcomes among patients with mCRC undergoing anti-EGFR therapy as compared with patients with tumors bearing wild-type BRAF sequence and PTEN expression levels, respectively. No evidence was found to support improved health outcomes associated with testing results for NRAS or PIK3CA variants, or AKT protein expression levels in this clinical scenario. CONTEXTUAL ISSUES CRC is an important and highly prevalent health problem. Improvements in mCRC outcomes associated with pharmacogenetic testing could have important clinical, and potentially public health, impacts. Adverse events related to cancer chemotherapy can be common and severe. Therefore, successfully optimizing treatment to maximize efficacy and minimize side effects is important for reducing mCRC-related morbidity and mortality.
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Peeters M, Oliner KS, Parker A, Siena S, Van Cutsem E, Huang J, Humblet Y, Van Laethem JL, André T, Wiezorek J, Reese D, Patterson SD. Massively parallel tumor multigene sequencing to evaluate response to panitumumab in a randomized phase III study of metastatic colorectal cancer. Clin Cancer Res 2013; 19:1902-12. [PMID: 23325582 DOI: 10.1158/1078-0432.ccr-12-1913] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To investigate whether EGF receptor (EGFR) pathway mutations predicted response to monotherapy with panitumumab, an anti-EGFR monoclonal antibody, in a randomized phase III study of metastatic colorectal cancer. EXPERIMENTAL DESIGN Using massively parallel multigene sequencing, we analyzed 320 samples for 9 genes, with multigene sequence data from 288 (90%) samples. RESULTS Mutation rates were: KRAS (45%), NRAS (5%), BRAF (7%), PIK3CA (9%), PTEN (6%), TP53 (60%), EGFR (1%), AKT1 (<1%), and CTNNB1 (2%). In the randomized study and open-label extension, 22 of 138 (16%) wild-type KRAS (codons 12/13/61) patients versus 0 of 103 mutant KRAS (codons 12/13) patients had objective responses. Of 6 mutant KRAS (codon 61) patients, 1 with a Q61H mutation achieved partial response during the extension. Among wild-type KRAS (codons 12/13/61) patients, 0 of 9 patients with NRAS mutations, 0 of 13 with BRAF mutations, 2 of 10 with PIK3CA mutations, 1 of 9 with PTEN mutations, and 1 of 2 with CTNNB1 mutations responded to panitumumab. No patients responded to best supportive care alone. Panitumumab treatment was associated with longer progression-free survival (PFS) among wild-type KRAS (codons 12/13/61) patients [HR, 0.39; 95% confidence interval (CI), 0.28-0.56]. Among wild-type KRAS patients, a treatment effect for PFS favoring panitumumab occurred in patients with wild-type NRAS (HR, 0.39; 95% CI, 0.27-0.56) and wild-type BRAF (HR, 0.37; 95% CI, 0.24-0.55) but not mutant NRAS (HR, 1.94; 95% CI, 0.44-8.44). CONCLUSIONS These results show the feasibility and potential clinical use of next-generation sequencing for evaluating predictive biomarkers.
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Affiliation(s)
- Marc Peeters
- Department of Oncology, Antwerp University Hospital, Edegem, Belgium.
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Improving the limit of detection for Sanger sequencing: a comparison of methodologies for KRAS variant detection. Biotechniques 2013; 53:182-188. [PMID: 22963480 DOI: 10.2144/000113913] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 07/27/2012] [Indexed: 11/23/2022] Open
Abstract
Fluorescent dye terminator Sanger sequencing (FTSS), with detection by automated capillary electrophoresis (CE), has long been regarded as the gold standard for variant detection. However, software analysis and base-calling algorithms used to detect mutations were largely optimized for resequencing applications in which different alleles were expected as heterozygous mixtures of 50%. Increasingly, the requirements for variant detection are an analytic sensitivity for minor alleles of <20%, in particular, when assessing the mutational status of heterogeneous tumor samples. Here, we describe a simple modification to the FTSS workflow that improves the limit of detection of cell-line gDNA mixtures from 50%-20% to 5% for G>A transitions and from 50%-5% to 5% for G>C and G>T transversions. In addition, we use two different sample types to compare the limit of detection of sequence variants in codons 12 and 13 of the KRAS gene between Sanger sequencing and other methodologies including shifted termination assay (STA) detection, single-base extension (SBE), pyrosequencing (PS), high- resolution melt (HRM), and real-time PCR (qPCR).
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KRAS mutation analysis on low percentage of colon cancer cells: the importance of quality assurance. Virchows Arch 2012; 462:39-46. [PMID: 23242173 DOI: 10.1007/s00428-012-1356-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 10/30/2012] [Accepted: 11/30/2012] [Indexed: 01/12/2023]
Abstract
KRAS mutation testing is mandatory for patients with metastatic colorectal cancer who are eligible for treatment with an epidermal growth factor receptor targeting agent, since tumors with a mutation are not sensitive to the drug. Several methods for mutation testing are in use and the need for external quality assurance has been demonstrated. An often little addressed but important issue in external quality assurance schemes is a low percentage of tumor cells in the test samples, where the analytical sensitivity of most tests becomes critical. Using artificial samples based on a mixture of cell lines with known mutation status of the KRAS gene, we assessed the reliability of a series of commonly used methods (Sanger sequencing, high resolution melting, pyrosequencing, and amplification refractory mutation system-polymerase chain reaction) on samples with 0, 2.5, 5, 10, and 15 % mutated cells. Nine laboratories throughout Europe participated and submitted a total of ten data sets. The limit of detection of each method differed, ranging from >15-5 % tumor cells. All methods showed a decreasing correct mutation call rate proportionally with decreasing percentage of tumor cells. Our findings indicate that laboratories and clinicians need to be aware of the decrease in correct mutation call rate proportionally with decreasing percentage of tumor cells and that external quality assurance schemes need to address the issue of low tumor cell percentage in the test samples.
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Goto K, Satouchi M, Ishii G, Nishio K, Hagiwara K, Mitsudomi T, Whiteley J, Donald E, McCormack R, Todo T. An evaluation study of EGFR mutation tests utilized for non-small-cell lung cancer in the diagnostic setting. Ann Oncol 2012; 23:2914-2919. [PMID: 22776705 DOI: 10.1093/annonc/mds121] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Epidermal growth factor receptor (EGFR) mutation is predictive for the efficacy of EGFR tyrosine kinase inhibitors in advanced non-small-cell lung cancer (NSCLC) treatment. We evaluated the performance, sensitivity, and concordance between five EGFR tests. MATERIALS AND METHODS DNA admixtures (n = 34; 1%-50% mutant plasmid DNA) and samples from NSCLC patients [116 formalin-fixed paraffin-embedded (FFPE) tissue, 29 matched bronchofiberscopic brushing (BB) cytology, and 20 additional pleural effusion (PE) cytology samples] were analyzed. EGFR mutation tests were PCR-Invader, peptide nucleic acid-locked nucleic acid PCR clamp, direct sequencing, Cycleave, and Scorpion Amplification Refractory Mutation System (ARMS). Analysis success, mutation status, and concordance rates were assessed. RESULTS All tests except direct sequencing detected four mutation types at ≥1% mutant DNA. Analysis success rates were 91.4%-100% (FFPE) and 100% (BB and PE cytology), respectively. Inter-assay concordance rates of successfully analyzed samples were 94.3%-100% (FFPE; kappa coefficients: 0.88-1.00), 93.1%-100% (BB cytology; 0.86-1.00), and 85.0%-100% (PE cytology; 0.70-1.00), and 93.1%-96.6% (0.86-0.93) between BB cytology and matched FFPE. CONCLUSIONS All EGFR assays carried out comparably in the analysis of FFPE and cytology samples. Cytology-derived DNA is a viable alternative to FFPE samples for analyzing EGFR mutations.
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Affiliation(s)
- K Goto
- Division of Thoracic Oncology, National Cancer Center Hospital East, Chiba.
| | - M Satouchi
- Department of Thoracic Oncology, Hyogo Cancer Center, Hyogo
| | - G Ishii
- Pathology Division, Innovative Medical Research Center, National Cancer Center Hospital East, Chiba
| | - K Nishio
- Department of Genome Biology, Kinki University School of Medicine, Osaka
| | - K Hagiwara
- Department of Respiratory Medicine, Saitama Medical University, Saitama
| | - T Mitsudomi
- Department of Thoracic Surgery, Aichi Cancer Center Hospital, Aichi, Japan
| | - J Whiteley
- Department of Personalised Healthcare and Biomarkers, AstraZeneca Pharmaceuticals, Macclesfield, UK
| | - E Donald
- Department of Personalised Healthcare and Biomarkers, AstraZeneca Pharmaceuticals, Macclesfield, UK
| | - R McCormack
- Department of Personalised Healthcare and Biomarkers, AstraZeneca Pharmaceuticals, Macclesfield, UK
| | - T Todo
- Department of Research and Development, AstraZeneca KK, Osaka, Japan
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Tan C, Du X. KRAS mutation testing in metastatic colorectal cancer. World J Gastroenterol 2012; 18:5171-80. [PMID: 23066310 PMCID: PMC3468848 DOI: 10.3748/wjg.v18.i37.5171] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 06/06/2012] [Accepted: 08/04/2012] [Indexed: 02/06/2023] Open
Abstract
The KRAS oncogene is mutated in approximately 35%-45% of colorectal cancers, and KRAS mutational status testing has been highlighted in recent years. The most frequent mutations in this gene, point substitutions in codons 12 and 13, were validated as negative predictors of response to anti-epidermal growth factor receptor antibodies. Therefore, determining the KRAS mutational status of tumor samples has become an essential tool for managing patients with colorectal cancers. Currently, a variety of detection methods have been established to analyze the mutation status in the key regions of the KRAS gene; however, several challenges remain related to standardized and uniform testing, including the selection of tumor samples, tumor sample processing and optimal testing methods. Moreover, new testing strategies, in combination with the mutation analysis of BRAF, PIK3CA and loss of PTEN proposed by many researchers and pathologists, should be promoted. In addition, we recommend that microsatellite instability, a prognostic factor, be added to the abovementioned concomitant analysis. This review provides an overview of KRAS biology and the recent advances in KRAS mutation testing. This review also addresses other aspects of status testing for determining the appropriate treatment and offers insight into the potential drawbacks of mutational testing.
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Ross JS. Clinical Implementation of KRAS Testing in Metastatic Colorectal Carcinoma: The Pathologist's Perspective. Arch Pathol Lab Med 2012; 136:1298-307. [DOI: 10.5858/arpa.2011-0478-ra] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—Mutation status of the KRAS gene identifies a distinct disease subtype of metastatic colorectal carcinoma that does not respond to antibody therapeutics targeting the epidermal growth factor receptor. This is currently the only validated marker in metastatic colorectal carcinoma with a clear implication in treatment selection. KRAS testing is widely accepted in clinical practice to guide metastatic colorectal carcinoma therapeutic decisions, and there are many commercially available platforms to perform the test.
Objective.—To evaluate the critical role of pathologists in the full implementation of KRAS testing by optimizing tumor tissue collection and fixation procedures and by choosing testing technologies and reliable Clinical Laboratory Improvement Amendments of 1988–certified laboratories to perform the tests.
Data Sources.—Prospective clinical trials, retrospective studies, and quality assessment and survey reports were identified in the following databases: PubMed, American Society of Clinical Oncology Proceedings (American Society of Clinical Oncology Annual Meeting and Gastrointestinal Cancer Symposium) and European Society for Medical Oncology Proceedings (Annals of Oncology European Society for Medical Oncology Congress and Annals of Oncology World Congress on Gastrointestinal Cancers).
Conclusions.—More bona fide standards are needed to address the variety of available test methods, which have different performance characteristics including speed, sensitivity to detect rare mutations, and technical requirements. Refined standards addressing timing of KRAS testing, laboratory performance and accuracy, quality assurance and control, proper tissue collection, and appropriate result reporting would also be greatly beneficial. Pathologists should be aware that the amount of information they need to manage will increase, because future trends and technological advances will enhance the predictive power of diagnostic tests or the scope of the biomarker panels tested routinely across tumor types.
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Affiliation(s)
- Jeffrey S. Ross
- From the Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York
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Bando I, Cillero L, Sanz-Ortega J, Llovet P, Pescador P, Ferrer M, de la Hoya M, Sastre J, García EDR, Caldés T. Study of KRAS new predictive marker in a clinical laboratory. Clin Transl Oncol 2012; 14:937-42. [PMID: 22865324 DOI: 10.1007/s12094-012-0886-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 02/19/2012] [Indexed: 12/31/2022]
Abstract
BACKGROUND The presence of somatic mutations in the KRAS gene has been identified as a reliable strong negative predictor for the response to targeting the epidermal growth factor receptor (EGFR), in patients with metastatic colorectal cancer and the use of anti-EGFR monoclonal antibodies such as Cetuximab and Panitumumab is now restricted to patients with no detectable KRAS mutations. Between 30 and 40 % of colorectal cancers contain a mutated KRAS oncogene. The aim of this study was to evaluate concordance between three methods to analyze KRAS mutational status in regard to clinical testing. METHODS We analyzed KRAS mutations in codons 12 and 13 of exon 2 in one hundred formalin-fixed paraffin-embedded (FFPE) colorectal cancer samples by three different methods: Direct Sequencing and two commercial kits on allele-specific oligonucleotide hybridization (KRAS StripAssay, Vienna Lab.) and Amplification Refractory Mutation System/Scorpions (ARMS/S; TheraScreen KRAS Mutation kit DxS) based on q-PCR. RESULTS We have found similar frequencies of KRAS mutations by TheraScreen and Strip-Assay (44 and 48 %), with a κ value of 0.90, indicating almost perfect agreement between methods. The frequency by direct sequencing was much lower (26 %) and the κ values were 0.67 (compared to TheraScreen) and 0.57 (compared to Strip-Assay) indicating low sensitivity. CONCLUSIONS On analyzing KRAS mutation in FFPE tumor samples, direct sequencing sensitivity is too low to be used in a clinical setting. Choosing between ARMS/S; TheraScreen KRAS Mutation kit DxS and KRAS StripAssay, Vienna Lab, will depend on laboratory facilities and expertise.
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Affiliation(s)
- Inmaculada Bando
- Laboratorio de Oncología Molecular, Planta Baja Sur, Hospital Clínico San Carlos, C/Martín Lagos s/n, Madrid, Spain
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Prognostic and predictive biomarkers for epidermal growth factor receptor-targeted therapy in colorectal cancer: beyond KRAS mutations. Crit Rev Oncol Hematol 2012; 85:45-81. [PMID: 22647972 DOI: 10.1016/j.critrevonc.2012.05.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 04/10/2012] [Accepted: 05/04/2012] [Indexed: 12/27/2022] Open
Abstract
The advent of the epidermal growth factor receptor (EGFR)-targeted monoclonal antibodies (mAbs), cetuximab and panitumumab has expanded the range of treatment options for metastatic colorectal cancer (CRC). Despite these agents have paved the way to individualized therapy, our understanding why some patients respond to treatment whereas others do not remain poor. The realization that detection of positive EGFR expression by IHC does not reliably predict clinical outcome of EGFR-targeted treatment has led to an intense search for alternative predictive biomarkers. Data derived from multiple phase III trials have indicated that KRAS mutations can be considered a highly specific negative biomarker of benefit to anti-EGFR mAbs. Oncologists are now facing emerging issues in the treatment of metastatic CRC, including the identification of additional genetic determinants of primary resistance to EGFR-targeted therapy for further improving selection of patients, the explanation of rare cases of patients carrying KRAS-mutated tumours who have been reported to respond to cetuximab and panitumumab and the discovery of mechanisms of secondary resistance to EGFR-targeted therapy. Current data suggest that, together with KRAS mutations, the evaluation of EGFR gene copy number (GCN), BRAF, NRAS, PIK3CA mutations or loss of PTEN expression could also be useful for selecting patients with reduced chance to benefit from anti-EGFR mAbs. This review aims to provide an updated of the most recent data on predictive and prognostic biomarkers within the EGFR pathway, the challenges this emerging field presents and the future role of these molecular markers in CRC treatment.
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Reliability of KRAS mutation testing in metastatic colorectal cancer patients across five laboratories. BMC Res Notes 2012; 5:196. [PMID: 22534075 PMCID: PMC3441241 DOI: 10.1186/1756-0500-5-196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 04/25/2012] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Mutations in the KRAS gene are associated with poor response to epidermal growth factor receptor inhibitors used in the treatment of metastatic colorectal cancer. Factors influencing KRAS test results in tumor specimens include: tumor heterogeneity, sample handling, slide preparation, techniques for tumor enrichment, DNA preparation, assay design and sensitivity. We evaluated comparability and consistency of KRAS test results among five laboratories currently being used to determine KRAS mutation status of metastatic colorectal cancer specimens in a large, multi-center observational study. FINDINGS Twenty formalin-fixed paraffin-embedded human colorectal cancer samples from colon resections previously tested for KRAS mutations were selected based on mutation status (6 wild type, 8 codon 12 mutations, and 6 codon 13 mutations). We found good agreement across laboratories despite differences in mutation detection methods. Eighteen of twenty samples (90%) were concordant across all five labs. Discordant results are likely not due to laboratory error, but instead to tumor heterogeneity, contamination of the tumor sample with normal tissue, or analytic factors affecting assay sensitivity. CONCLUSIONS Our results indicate commercial and academic laboratories provide reliable results for the common KRAS gene mutations at codons 12 and 13 when an adequate percentage of tumor cells is present in the sample.
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Yang QH, Schmidt J, Soucy G, Odze R, Dejesa-Jamanila L, Arnold K, Kuslich C, Lash R. KRAS mutational status of endoscopic biopsies matches resection specimens. J Clin Pathol 2012; 65:604-7. [DOI: 10.1136/jclinpath-2012-200746] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
AimsThis study was performed to determine systematically whether KRAS mutational analysis in biopsy tissue is a reliable indicator of KRAS status in subsequent corresponding resection specimens.Methods30 colorectal cancer (CRC) patients with biopsy and corresponding subsequent surgical resection specimens were studied. KRAS mutational analysis was performed on each biopsy sample as well as two separate samples from each resection specimen by PCR and Sanger sequencing.ResultsOverall, KRAS mutations were identified in 12/30 (40%) of the tumours. There was 100% correlation between biopsy and resection specimens regarding the presence or absence of KRAS mutations. In fact, the same point mutation was identified in both biopsy and corresponding resection specimens in 12/12 (100%) cases. In addition, in two cases, there were two different point mutations detected within the same biopsy specimen.ConclusionThis study shows perfect correlation between KRAS mutation status in biopsy and resection specimens from an individual patient, and suggests that biopsy material is adequate for KRAS mutational analysis in CRC patients.
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Pharmacogenetic screening for drug therapy: From single gene markers to decision making in the next generation sequencing era. Pathology 2012; 44:166-80. [DOI: 10.1097/pat.0b013e32834f4d69] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Abstract
The determination of KRAS mutational status from tumor samples has become an important tool for patient management in colorectal and non-small-cell lung cancers. Mutations in critical areas of the gene, such as codons 12 and 13, are a negative predictor of response to anti-EGF receptor antibodies in colorectal cancer, and similarly are indicators of resistance to small-molecule tyrosine kinase inhibitors in non-small-cell lung cancer patients. A variety of laboratory methods have been developed to assess mutation status in key regions of the KRAS gene. Many of these methods, including allele-specific PCR, real-time PCR methods with melt-curve analysis, and nucleic acid sequencing techniques, provide the appropriate analytical performance to address tissue heterogeneity in tumor samples. The pathologist plays a key role in this process because assessment of morphological features of the tumor is important prior to molecular analysis. This article provides a summary of the performance characteristics of various molecular testing methods and addresses other key aspects of testing necessary to provide relevant information to help determine appropriate therapy choices.
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Affiliation(s)
- Steven M Anderson
- Laboratory Corporation of America®, 1904 Alexander Drive, Research Triangle Park, NC 27709, USA.
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Pinto P, Rocha P, Veiga I, Guedes J, Pinheiro M, Peixoto A, Pinto C, Fragoso M, Sanches E, Araújo A, Alves F, Coutinho C, Lopes P, Henrique R, Teixeira MR. Comparison of methodologies for KRAS mutation detection in metastatic colorectal cancer. Cancer Genet 2011; 204:439-46. [DOI: 10.1016/j.cancergen.2011.07.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 07/05/2011] [Accepted: 07/07/2011] [Indexed: 11/28/2022]
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Baas JM, Krens LL, Guchelaar HJ, Morreau H, Gelderblom H. Concordance of predictive markers for EGFR inhibitors in primary tumors and metastases in colorectal cancer: a review. Oncologist 2011; 16:1239-49. [PMID: 21742964 DOI: 10.1634/theoncologist.2011-0024] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Currently, only Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) mutational status is used as a decisional marker for epidermal growth factor receptor (EGFR) inhibitor therapy in colorectal cancer (CRC) patients. Concordance of KRAS status between primary tumors and metastases has always been considered to be close to perfect; however, cases of discordance have been reported. The actual rate of concordance of KRAS status remains unclear, as is the same for v-raf murine sarcoma viral oncogene homolog B1 (BRAF), phosphatidylinositol 3-kinase CA subunit (PIK3CA), and loss of phosphatase and tensin homologue deleted on chromosome ten (PTEN). Therefore, it is unknown whether it is necessary to perform mutational analysis on metastases instead of on (or in addition to) primary tumors. DESIGN A systematic literature search was conducted to collect all studies testing concordance of KRAS in CRC, and also of BRAF, PIK3CA, and loss of PTEN. RESULTS Twenty-one studies have reported concordance of KRAS, with an overall concordance rate of 93% (range, 76%-100%). Overall concordance rates of studies testing concordance of BRAF status and loss of PTEN were 98% and 68%, respectively. Three studies reported concordance of PIK3CA status (range, 89%-94%). CONCLUSION Though discordance of KRAS status does occur, it is uncommon. When considering the downsides of testing metastatic tissue in all patients along with the low incidence of discordance, we conclude that that testing the primary tumor (or whatever tissue available) is sufficient for clinical decision making on EGFR inhibitor therapy.
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Affiliation(s)
- Jara M Baas
- Department of Clinical Oncology, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
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Herreros-Villanueva M, Aggarwal G. KRAS assay selection: sensitivity and accuracy in clinical application. Mol Biol Rep 2011; 39:2467-70. [DOI: 10.1007/s11033-011-0997-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Accepted: 06/01/2011] [Indexed: 12/30/2022]
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40
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Molinari F, Felicioni L, Buscarino M, De Dosso S, Buttitta F, Malatesta S, Movilia A, Luoni M, Boldorini R, Alabiso O, Girlando S, Soini B, Spitale A, Di Nicolantonio F, Saletti P, Crippa S, Mazzucchelli L, Marchetti A, Bardelli A, Frattini M. Increased detection sensitivity for KRAS mutations enhances the prediction of anti-EGFR monoclonal antibody resistance in metastatic colorectal cancer. Clin Cancer Res 2011; 17:4901-14. [PMID: 21632860 DOI: 10.1158/1078-0432.ccr-10-3137] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE KRAS mutations represent the main cause of resistance to anti-epidermal growth factor receptor (EGFR) monoclonal antibodies (MoAbs) in metastatic colorectal cancer (mCRC). We evaluated whether highly sensitive methods for KRAS investigation improve the accuracy of predictions of anti-EGFR MoAbs efficacy. EXPERIMENTAL DESIGN We retrospectively evaluated objective tumor responses in mCRC patients treated with cetuximab or panitumumab. KRAS codons 12 and 13 were examined by direct sequencing, MALDI-TOF MS, mutant-enriched PCR, and engineered mutant-enriched PCR, which have a sensitivity of 20%, 10%, 0.1%, and 0.1%, respectively. In addition, we analyzed KRAS codon 61, BRAF, and PIK3CA by direct sequencing and PTEN expression by immunohistochemistry. RESULTS In total, 111 patients were considered. Direct sequencing revealed mutations in codons 12 and 13 of KRAS in 43/111 patients (39%) and BRAF mutations in 9/111 (8%), with almost all of these occurring in nonresponder patients. Using highly sensitive methods, we identified up to 13 additional KRAS mutations compared with direct sequencing, all occurring in nonresponders. By analyzing PIK3CA and PTEN, we found that of these 13 patients, 7 did not show any additional alteration in the PI3K pathway. CONCLUSIONS The application of highly sensitive methods for the detection of KRAS mutations significantly improves the identification of mCRC patients resistant to anti-EGFR MoAbs.
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Burns DK, Hughes AR, Power A, Wang SJ, Patterson SD. Designing pharmacogenomic studies to be fit for purpose. Pharmacogenomics 2010; 11:1657-67. [DOI: 10.2217/pgs.10.140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The 2010 US FDA–Drug Industry Association (DIA) Pharmacogenomics Workshop, the fifth in a series of meetings that begun in 2002, brought together multidisciplinary experts from regulatory authorities, medical research, healthcare and drug development. This article summarizes the ‘Designing Pharmacogenomic Studies to be Fit for Purpose’ track in which considerations regarding the use of retrospective and prospective studies were examined in relation to their ability to influence treatment decisions and labeling for drugs. The aim of the session, using real-world examples (KRAS/panitumumab and HLA-B*5701/abacavir), was to identify good scientific principles that would guide the design of studies to identify subgroups of responders during development programs (including marketed drugs), which could subsequently be used to guide treatment decisions.
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Affiliation(s)
- Daniel K Burns
- Deane Drug Discovery Institute, Duke University, R David Thomas Executive Training Center, 1 Science Drive, Box 90344, Durham, NC 27708, USA
| | - Arlene R Hughes
- Genetics GlaxoSmithKline, 5 Moore Drive, PO Box 13398, Research Triangle Park, NC 27709, USA
| | - Aidan Power
- Molecular Medicine, Pfizer PharmaTherapeutics Research, Eastern Point Road, Groton, CT 06340, USA
| | - Sue-Jane Wang
- Office of Biostatistics, Office of Translational Sciences, Center for Drug Evaluation & Research, US FDAMailstop W021, Room 3562, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
- Johns Hopkins University, MD, USA
| | - Scott D Patterson
- Medical Sciences, Amgen, Inc., 1 Amgen Center Drive, MS 38-3-A, Thousand Oaks, CA 91320, USA
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Wang G, Kelley RK. KRAS mutational analysis for colorectal cancer. Application: pharmacogenomic. PLOS CURRENTS 2010; 2:k/-/-/27yi6810q97hp/1. [PMID: 20877448 PMCID: PMC2940138 DOI: 10.1371/currents.rrn1175] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Accepted: 09/01/2010] [Indexed: 01/29/2023]
Abstract
KRAS mutational analysis is a genetic test used in clinical practice for determining the status of the KRAS gene (wild type or mutant) in tumors from patients with metastatic colorectal cancer (CRC). Persons whose tumors are wild type may respond to therapies cetuximab (Erbitux) or panitumumab (Vectibix).
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Affiliation(s)
- Grace Wang
- Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California, San Francisco, USA
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