Produção Nacional
Revisado por pares
Concordance Analysis of ALK Gene Fusion Detection Methods in Patients with Non–Small-Cell Lung Cancer from Chile, Brazil, and Peru
2021; Elsevier BV; Volume: 23; Issue: 9 Linguagem: Inglês
10.1016/j.jmoldx.2021.05.018
ISSN1943-7811
AutoresGonzalo Sepúlveda-Hermosilla, Matías Freire, Alejandro Blanco, Javier F. Cáceres, Rodrigo Lizana, Liliana Ramos, Rodrigo Assar, Diego Ampuero, Osvaldo Rudy Aren, Sara Chernilo, M. Loreto Spencer, Giuliano Bernal, Jacqueline Flores, Germán Rasse, Carolina Sánchez‐Rodríguez, Katherine Marcelain, Solange Rivas, Gabriela P. Branco, María Galli de Amorim, Diana Noronha Nunes, Emmanuel Dias‐Neto, H. Freitas, Cristina Fernández, Paola Pérez, Ricardo Armisén, Luiz H. Araujo, Luís A. Pires, Nils Gunnar Skare, Gustavo Girotto, Manuela Zereu, H. Freitas, Hakaru Tadokoro, Ana Caroline Zimmer Gelatti, Jose Fernando Moura, Clarissa Mathias, Pedro R. de Marchi, Fernando Silva, Mayler Olombrada Nunes de Santos, Marianna Deway Andrade Dracoulakis, Renata Pinho Costa, Luciana Castro, Paulo Guilherme de Oliveira Salles, Clodoaldo Zago Campos, M Livia, Sara Chernilo, Osvaldo Arén Frontera, Eduardo Yañez Ruiz, Mónica Ahumada Olea, Giuliano Bernal, M. Loreto Spencer, Alejandro Ortega Vasquez, Germán Rasse, Juan Bertoglio, Jose David Zorrilla Silvera, Hernan Moron Escobar, Luis Riva Gonzalez, Luis López, José Luis Fernando Hurtado De Mendoza Acurio, G Mendoza, Alfredo Aguilar, Gerardo Campos Siccha, Ricardo Sanchez Sevillano, Cristina Fernández, Sylvia Chandía, Pablo Araos, Ana Mejías, Francisca Angulo, Carolina Sánchez‐Rodríguez, Jessica Troncoso, D. Jara, Marcela Astete, María Jesús Galleguillos, Emmanuel Dias‐Neto, H. Freitas, María Galli de Amorim, Diana Noronha Nunes, Gabriela P. Branco, Marina Eloi, Melissa Pool Pizzi, Jordana Silva, Thais Fernanda Bartelli, Katherine Marcelain, Jessica Toro, Luciana Oliveira-Cruz, Daniela Diez, Solange Rivas,
Tópico(s)Genetic factors in colorectal cancer
ResumoAbout 4% to 7% of the non–small-cell lung cancer patients have anaplastic lymphoma kinase (ALK) rearrangements, and specific targeted therapies improve patients' outcomes significantly. ALK gene fusions are detected by immunohistochemistry or fluorescent in situ hybridization as gold standards in South America. Next-generation sequencing–based assays are a reliable alternative, able to perform simultaneous detection of multiple events from a single sample. We analyzed 4240 non–small-cell lung cancer samples collected in 37 hospitals from Chile, Brazil, and Peru, where ALK rearrangements were determined as part of their standard of care (SofC) using either immunohistochemistry or fluorescent in situ hybridization. A subset of 1450 samples was sequenced with the Oncomine Focus Assay (OFA), and the concordance with the SofC tests was measured. An orthogonal analysis was performed using a real-time quantitative PCR echinoderm microtubule-associated protein-like 4-ALK fusion detection kit. ALK fusion prevalence is similar for Chile (3.67%; N = 2142), Brazil (4.05%; N = 1013), and Peru (4.59%; N = 675). Although a comparison between OFA and SofC assays showed similar sensitivity, OFA had significantly higher specificity and higher positive predictive value, which opens new opportunities for a more specific determination of ALK gene rearrangements. About 4% to 7% of the non–small-cell lung cancer patients have anaplastic lymphoma kinase (ALK) rearrangements, and specific targeted therapies improve patients' outcomes significantly. ALK gene fusions are detected by immunohistochemistry or fluorescent in situ hybridization as gold standards in South America. Next-generation sequencing–based assays are a reliable alternative, able to perform simultaneous detection of multiple events from a single sample. We analyzed 4240 non–small-cell lung cancer samples collected in 37 hospitals from Chile, Brazil, and Peru, where ALK rearrangements were determined as part of their standard of care (SofC) using either immunohistochemistry or fluorescent in situ hybridization. A subset of 1450 samples was sequenced with the Oncomine Focus Assay (OFA), and the concordance with the SofC tests was measured. An orthogonal analysis was performed using a real-time quantitative PCR echinoderm microtubule-associated protein-like 4-ALK fusion detection kit. ALK fusion prevalence is similar for Chile (3.67%; N = 2142), Brazil (4.05%; N = 1013), and Peru (4.59%; N = 675). Although a comparison between OFA and SofC assays showed similar sensitivity, OFA had significantly higher specificity and higher positive predictive value, which opens new opportunities for a more specific determination of ALK gene rearrangements. Precision medicine is revolutionizing the diagnosis and treatment of cancer patients. 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Updated molecular testing guideline for the selection of lung cancer patients for treatment with targeted tyrosine kinase inhibitors: guideline from the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology.J Mol Diagn. 2018; 20: 129-159Abstract Full Text Full Text PDF PubMed Scopus (177) Google Scholar a combined effort from the International Association for the Study of Lung Cancer, the College of American Pathologists, and the Association for Molecular Pathology, recommends as minimum testing for EGFR, ALK, and ROS1 in lung adenocarcinomas. ALK rearrangements are present in 4% to 7% of lung adenocarcinomas. Numerous ALK inhibitors are approved to treat such tumors in many countries, including Latin America. ALK inhibitors have shown superiority over chemotherapy in first- and second-line treatment,15Shaw A.T. Kim D.-W. Nakagawa K. Seto T. Crinó L. Ahn M.-J. De Pas T. Besse B. Solomon B.J. Blackhall F. Wu Y.-L. Thomas M. O'Byrne K.J. Moro-Sibilot D. Camidge D.R. Mok T. Hirsch V. Riley G.J. Iyer S. Tassell V. Polli A. Wilner K.D. Jänne P.A. Crizotinib versus chemotherapy in advanced ALK-positive lung cancer.N Engl J Med. 2013; 368: 2385-2394Crossref PubMed Scopus (2753) Google Scholar,16Solomon B.J. Mok T. Kim D.-W. Wu Y.-L. Nakagawa K. Mekhail T. Filip E. Cappuzzo F. Paolini P. Usari T. Iyer S. Reisman A. Wilner K.D. Tursi J. Blackhall F. PROFILE 1014 Investigators First-line crizotinib versus chemotherapy in ALK-positive lung cancer.N Engl J Med. 2014; 371: 2167-2177Crossref PubMed Scopus (2319) Google Scholar and second-generation ALK inhibitors increased progression-free survival compared with the first-generation inhibitors.17Mok T. Camidge D.R. Gadgeel S.M. Rosell R. Dziadziuszko R. Kim D.-W. Pérol M. Ou S.-H.I. Ahn J.S. Shaw A.T. Bordgona W. Smoljanović Hilton M. Ruf T. Noé J. Peters S. Updated overall survival and final progression-free survival data for patients with treatment-naive advanced ALK-positive non-small-cell lung cancer in the ALEX study.Ann Oncol. 2020; 31: 1056-1064Abstract Full Text Full Text PDF PubMed Scopus (161) Google Scholar In clinical practice, fluorescence in situ hybridization (FISH) or immunohistochemistry (IHC) tests are the standard methods for testing ALK in many countries. Although IHC is a reliable and fast method, using different tests for EGFR, ALK, and ROS1 sequentially or in parallel is time-consuming, requires more biological material from tumors, and can be more expensive than performing multiplexed testing. Nowadays, tissue collection for diagnosis has been extensively optimized, reducing the invasiveness of the procedures and the amount of resected tissues. Precision medicine approaches should include the analysis in samples that are routinely preserved formalin-fixed, paraffin-embedded (FFPE) tissue or a small needle using multiplexed assays, capable of detecting all sort of genomic alterations, such as single-nucleotide variations, insertions/deletions, gene fusions, and copy number alterations, among others.5Hovelson D.H. McDaniel A.S. Cani A.K. Johnson B. Rhodes K. Williams P.D. Bandla S. Bien G. Choppa P. Hyland D. Gottimukkala R. Liu G. Manivannan M. Schageman J. Ballesteros-Villagrana E. Grasso G.S. Quist M.J. Yadati V. Amin A. Siddiqui J. Betz B.L. Knudsen K.E. Cooney K.A. Feng F.Y. Roh M.H. Nelson P.S. Liu C.-J. Beer D.G. Wngaaard P. Chinnaiyan A.M. Sadis S. Rhodes D.R. Tomlins S.A. Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors.Neoplasia. 2015; 17: 385-399Crossref PubMed Scopus (160) Google Scholar Next-generation sequencing (NGS) of solid tumor tissues fulfills this need and harbors the promise to be the gold standard in molecular diagnostics. Currently, in-house NGS testing services and off-the-shelf kits are obtaining regulatory approval on a gene-by-gene basis. Independent initiatives to assess the accuracy of molecular panels in real-world conditions can help to speed up the adoption of NGS in clinical practice. Herein, we present the results of the NIRVANA (Validation of Molecular Diagnostic Technologies for Lung Cancer Patients) project, an international, multicentric study aimed to validate molecular diagnostic technologies in >4000 lung cancer patients from Chile, Brazil, and Peru. We present the prevalence of ALK gene fusion events in these three countries, as well as the concordance between the results of standard-of-care (SofC) ALK tests and the NGS-based Oncomine Focus Assay (OFA). To our knowledge, this is the largest study to assess the prevalence of ALK fusion in South American countries so far. The NIRVANA protocol was registered with the identifier NCT03220230 (https://clinicaltrials.gov, last accessed May 27, 2021) and approved by local ethics committees for each recruiting hospital in Chile, Brazil, and Peru. In Brazil, the National Ethics Committee (Comissão Nacional de Ética em Pesquisa) also approved and provided oversight of the study. All patients provided informed consent for access to clinical, demographic, and pathology information as well as to available FFPE embedded tumor tissue. Strategies to protect their identity and privacy included anonymization procedures and a unique eight-digit identifier. Patients received no treatment as part of this study. Eligible patients were aged >18 years, with a histologically or cytologically proven diagnosis of NSCLC. Thirty-seven sites participated in this protocol: 9 in Chile, 19 in Brazil, and 9 in Peru. All data were electronically captured and subjected to a 100% on-site source data verification, following Good Clinical Practice guidelines. Prospective and retrospective samples were accepted, from either the primary tumor or metastatic sites, and most patients were treatment naïve at the time of tissue biopsy. FFPE sections (5 μm thick of at least 5% cellularity18Goswami R.S. Luthra R. Singh R.R. Patel K.P. Routbort M.J. Aldape K.D. Yao H. Dang H.D. Barkoh B.A. Manekia J. Medeiros L.J. Roy-Chowdhuri S. Stewart J. Broaddus R.R. Chen H. Identification of factors affecting the success of next-generation sequencing testing in solid tumors.Am J Clin Pathol. 2016; 145: 222-237Crossref PubMed Google Scholar,19Singh R.R. Patel K.Y. Routbort M.J. Reddy N.G. Barkoh B.A. Handal B. Kanagal-Shamanna R. Greaves W.O. Medeiros L.J. Aldape K.D. Luthra R. Clinical validation of a next-generation sequencing screen for mutational hotspots in 46 cancer-related genes.J Mol Diagn. 2013; 15: 607-622Abstract Full Text Full Text PDF PubMed Scopus (261) Google Scholar) were obtained for hematoxylin and eosin staining and pathology verification (one slide), ALK IHC (two slides, one for the test and one for a negative control), and DNA and RNA purification (two to eight slides, see below) at each hospital pathology service, following a validated tissue sectioning protocol compatible with downstream assays. Supplemental Figure S1 provides a general layout of the study processes. ALK IHC tests were performed using the Ventana anti-ALK (D5F3) rabbit monoclonal primary antibody (CE-IVD, Roche, Santiago, Chile) in combination with the OptiView DAB IHC Detection kit and OptiView Amplification Kit in a fully automated immunohistochemistry assay on the Ventana BenchMark XT and Ventana BenchMark GX slide stainer (Roche). ALK FISH was performed according to Abbott Vysis recommendation (Abbott Laboratories, Chicago, IL). Ventana and Vysis Break Part tests were aggregated as SofC ALK tests. The results of the SofC ALK tests were reported to attending physicians. DNA and RNA extraction from FFPE samples and sequencing were performed in five central laboratories that were trained in the procedures for sample handling, nucleic acid extraction, and sequencing to harmonize the technical procedures and ensure the quality and integrity of the data, supported also by regular proficiency tests with certified controls (HD736, HD783, and HD784, Horizon Discovery, Cambridge, UK). The OFA (Thermo Fisher Scientific, Carlsbad, CA) is a panel of 52 target genes designed for the analysis of DNA and RNA/cDNA derived from FFPE tissue. DNA and RNA was isolated and quantified using the RecoverAll and Qubit dsDNA/RNA HS kits (Thermo Fisher Scientific). DNA and RNA libraries were prepared according to the OFA library guideline and were sequenced in the Ion Personal Genome Machine System (Thermo Fisher Scientific). As a quality metrics threshold, 200,000 reads were aimed for DNA (80% on target) and 5000 reads for RNA, requiring the presence of at least three of five control amplicons. ALK fusions were identified with the breakpoint assay method from the OFA panel, when a minimum of 20 reads at the breakpoint region was observed. All analyses have followed OFA's Analysis Workflow version 2.1, operating in the Torrent Browser and Ion Reporter server (Thermo Fisher Scientific). Considering an ALK prevalence of 3% to 5% in reference populations, a sample size was estimated to reach levels of sensitivity and specificity with an error interval (95% CI) of ≤0.05 points.20Lu M.-J. Zhong W.-H. Liu Y.-X. Miao H.-Z. Li Y.-C. Ji M.-H. Sample size for assessing agreement between two methods of measurement by Bland-Altman method.Int J Biostat. 2016; 12Crossref PubMed Scopus (108) Google Scholar,21Travis W.D. The 2015 WHO classification of lung tumors.Pathologe. 2014; 35 Suppl 2: 188Crossref PubMed Scopus (88) Google Scholar It was assumed that both SofC ALK and OFA were binary tests that yield either a positive or a negative result (excluding other results from the analyses). Therefore, it was estimated that 120 SofC ALK-positive cases were needed. The efficiency of the tests against the gold standards was measured with indexes like sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy. The general agreement of the pair was determined with McNemar χ2 and Cohen κ methods.22Travis W.D. Brambilla E. Nicholson A.G. Yatabe Y. Austin J.H.M. Beasley M.B. Chirieac L.R. Dacic S. Duhig E. Fliedler D.B. Geisinger K. Hirsch F.R. Ishikawa Y. Kerr K.M. Nogiuchi M. Pelosi G. Powell C.A. Tsao M.S. Wistuba I. WHO Panel The 2015 World Health Organization classification of lung tumors: impact of genetic, clinical and radiologic advances since the 2004 classification.J Thorac Oncol. 2015; 10: 1243-1260Abstract Full Text Full Text PDF PubMed Scopus (2326) Google Scholar To estimate the analytical performance for the detection of ALK fusions by SofC and OFA, an echinoderm microtubule-associated protein-like 4 (ELM4)-ALK Fusion gene detection kit was used as a real-time quantitative PCR (qPCR)–based validated benchmark assay (AmoyDx, Xiamen, China), which detects the 21 most common fusion transcripts of the chimeric EML4-ALK gene. Fifty samples were analyzed following the manufacturer's instructions. The same statistical metrics were estimated for the concordance analysis. A post hoc statistical power analysis of the concordance metrics for the sample size was performed following the Bland-Altman method.20Lu M.-J. Zhong W.-H. Liu Y.-X. Miao H.-Z. Li Y.-C. Ji M.-H. Sample size for assessing agreement between two methods of measurement by Bland-Altman method.Int J Biostat. 2016; 12Crossref PubMed Scopus (108) Google Scholar The relationship of clinical and demographic covariates over the results of the SofC ALK and OFA assays was calculated. Univariate and multivariate regression analyses was used with the testing result of each method as a response variable. The following covariates were evaluated: sex, age at diagnostics, histology, cancer stage, sample strata (retrospective or prospective), the clinical procedure to obtain the biopsy, and the country and city of subject's recruitment. Covariates were considered statistically significant at P < 0.05. These analyses were implemented with the python package Statsmodels version 0.10.1 (University of North Carolina at Chapel Hill, Chapel Hill, NC). This study recruited and tested 4240 lung cancer patients (52.6% male, 47.4% female) with ages ranging from 23 to 94 years (mean, 66 years). Chilean subjects contributed half of the whole cohort, followed by Brazil (27.6%) and Peru (20.9%) (Figure 1 and Table 1). Most of the patients had adenocarcinoma (82%), followed by squamous cell carcinoma (12.5%). Smoking behavior was reported for 3515 patients. Never smokers included 35.3% of all cases, and former and current smokers accounted for 56% and 8.7%, respectively. Quantitative tobacco use information was available for 1755 patients; on average, they reported the consumption of 58 packs per year. Disease stage information (according to the eighth edition of the TNM classification for lung cancer23Rami-Porta R. Bolejack V. Giroux D.J. Chansjy K. Crowley J. Asamura H. Goldstraw P. International Association for the Study of Lung Cancer Staging and Prognostic Factors Committee Advisory Board Members and Participating Institutions The IASLC lung cancer staging project: the new database to inform the eighth edition of the TNM classification of lung cancer.J Thorac Oncol. 2014; 9: 1618-1624Abstract Full Text Full Text PDF PubMed Scopus (211) Google Scholar) was available for 3320 patients (69% stage IV, 18% stage III, 6% stage II, and 7% stage I).Table 1NIRVANA Cohort DescriptionCharacteristicsAge at diagnosis, years (n = 4240) Mean66.0 SD11.5 Range23–94Sex (n = 4240)n% Female201147.4 Male222952.6NSCLC histology (n = 4240) LUAD347682 LUSC53012.5 Others1242.9 NSCLC NOS621.5 NEC NOS240.6 LUPC240.6Country (n = 4240) Chile218451.5 Brazil117027.6 Peru88620.9Tobacco use (n = 3515) Former196856 Never124235.3 Current3058.7Tobacco use, packs per year (n = 1755) Mean58.43 SD47.83 Range0–346.5Lung cancer stage (n = 3320)n% I2327 II2006 III59418 IV229469Biopsy procedure (n = 3946) Fibrobronchoscopy146637.1 Percutaneous puncture62215.8 Tumor resection60315.3 Surgical biopsy112128.4 Transthoracic pleura biopsy1343.4ALK standard-of-care testing type (n = 4240) Ventana ALK (D5f3)373988.2 Vysis ALK Break-Apart FISH2315.4 Not tested/not informed2706.4ALK standard-of-care testing results (n = 3730) Positive1473.9 Negative358396.1ALK standard-of-care testing results on adenocarcinomas (n = 3064) Positive1334.3 Negative293195.7 Chile (n = 1636)Positive654Negative157196 Brazil (n = 824)Positive384.6Negative78695.4 Peru (n = 604)Positive305Negative57495Clinical, demographic, and pathologic aspects of the subjects are given. The table shows the most relevant clinical aspects collected in the NIRVANA cohort. Histologic classifications according to Memorial Sloan Kettering Cancer Center Oncotree (http://oncotree.mskcc.org, last accessed December 21, 2019): LUAD, LUSC, LUPC, NEC, and NOS. For the ALK standard-of-care result, 510 subjects, which represents 12% of the total recruitment, have an invalid outcome because of insufficient tissue, not tested/not informed, or others.ALK, anaplastic lymphoma kinase; FISH, fluorescent in situ hybridization; LUAD, lung adenocarcinoma; LUPC, pleomorphic carcinoma of the lung; LUSC, lung squamous cell carcinoma; NEC, neuroendocrine carcinoma; NIRVANA, Validation of Molecular Diagnostic Technologies for Lung Cancer Patients; NOS, not otherwise specified; NSCLC, non–small-cell lung cancer. Open table in a new tab Clinical, demographic, and pathologic aspects of the subjects are given. The table shows the most relevant clinical aspects collected in the NIRVANA cohort. Histologic classifications according to Memorial Sloan Kettering Cancer Center Oncotree (http://oncotree.mskcc.org, last accessed December 21, 2019): LUAD, LUSC, LUPC, NEC, and NOS. For the ALK standard-of-care result, 510 subjects, which represents 12% of the total recruitment, have an invalid outcome because of insufficient tissue, not tested/not informed, or others. ALK, anaplastic lymphoma kinase; FISH, fluorescent in situ hybridization; LUAD, lung adenocarcinoma; LUPC, pleomorphic carcinoma of the lung; LUSC, lung squamous cell carcinoma; NEC, neuroendocrine carcinoma; NIRVANA, Validation of Molecular Diagnostic Technologies for Lung Cancer Patients; NOS, not otherwise specified; NSCLC, non–small-cell lung cancer. SofC ALK test was possible in 3970 samples (94%), of which 3739 (88.2%) had Ventana-ALK test and 231 (11.8%) had FISH (Table 1). A negative or positive result was obtained in 3730 (95%) of the samples. The reasons to exclude the SofC ALK test were insufficient tissue (3.1%) and ambiguous results (2.5%). In Chile, the prevalence of ALK rearrangements was estimated at 3.67% (95% CI, 2.94%–4.58%); in Brazil, 4.05% (95% CI, 2.99%–5.46%); and in Peru, 4.59% (95% CI, 3.23%–6.47%). The prevalence of ALK-positive patients and the number of samples collected per city are shown in Figure 1A. An elevated prevalence was documented for the cities of Trujillo, Arequipa, and Rio de Janeiro (Figure 1A and Figure 2A); however, distortions cannot be excluded as these cities contributed with a small number of subjects (12, 15, and 15 patients, respectively). The age distribution (Figure 1B) was found to be similar between the countries, with a shifted distribution of ALK-positive cases toward younger subjects (14.8%, aged 18 to 33 years), followed by the next age bin (34 to 50 years) with a value of 9.8% (Figure 1B). ALK rearrangements were more frequent in females [odds ratio (OR), 1.02] as well as in younger patients from 18 to 50 years and never smokers (OR, 1.02) (Figure 2A). No significant differences were observed regarding biopsy procedures. Regarding histologies, adenocarcinoma tumors are more likely to be ALK positive than squamous cell carcinoma (OR, 1.02 versus 0.98). In adenocarcinoma only samples, SofC ALK+ prevalence in Chile is 4.3%; in Brazil, 4.6%; and in Peru, 5.0% (Table 1). Only 14 ALK+ samples were detected in nonadenocarcinoma samples, with 8 of them in squamous cell carcinoma (Supplemental Table S1). We analyzed a total of 1450 NSCLC tissue samples with valid results in SofC and OFA tests were analyzed. As described in Table 2, 45 samples were true positives, 21 samples were false positives, and 38 samples were false negatives. The statistical measures of concordance support the hypothesis that the detection of rearrangements using OFA is equivalent to the use of SofC ALK tests (κ, 0.583; P = 0.037) (Table 2). Regarding performance metrics, OFA displays a PPV of 68.2% and an NPV of 97.3% (Table 3). Age at diagnosis, sample strata, tobacco use, and country site were significant covariates for the rate of concordance between OFA and SofC ALK, but with a modest effect (OR, 0.98 to 1.03) (Figure 2B).Table 2Confusion Matrix and Statistical AnalysisContingency table for SofC ALK versus OFA resultsVariableSofC ALK positiveSofC ALK negativeOFA ALK positive4521OFA ALK negative381346OFA and SofC ALK hypothesis tests of concordanceStatistical testRank (value)P valueχ2 Independence testReal (4.339)0.037Cohen κ testModerate (0.583)NAContingency table for SofC ALK versus OFA results using data from 1450 patients who have met all of the quality criteria and OFA and SofC ALK hypothesis tests of concordance.ALK, anaplastic lymphoma kinase; NA, not applicale; OFA, Oncomine Focus Assay; SofC, standard of care. Open table in a new tab Table 3Concordance AnalysisIndex of concordanceEstimation, %95% CI, %OFA and SofC ALK (n = 1450) Sensitivity54.243.5–64.5 Specificity98.597.6–99.0 Accuracy95.994.8–96.8 Positive predictive value68.256.2–78.2 Negative predictive value97.396.2–98.0SofC ALK and qPCR (n = 44) Sensitivity78.956.1–92.0 Specificity88.069.2–96.7 Accuracy84.170.3–92.4 Positive predictive value83.360.0–95.0 Negative predictive value84.665.9–94.5OFA and qPCR (n = 44) Sensitivity63.240.9–81.0 Specificity100.084.2–100.0 Accuracy84.170.3–92.4 Positive predictive value100.071.8–100.0 Negative predictive value78.161.0–89.3Concordance analysis is given for OFA and SofC ALK, including all patients used on the confusion matrix. The indexes of concordance of an orthogonal analysis (n = 44) performed using qPCR as a reference standard are also provided.ALK, anaplastic lymphoma kinase; OFA, Oncomine Focus Assay; qPCR, real-time quantitative PCR; SofC, standard of care. Open table in a new tab Contingency table for SofC ALK versus OFA results using data from 1450 patients who have met all of the quality criteria and OFA and SofC ALK hypothesis tests of concordance. ALK, anaplastic lymphoma kinase; NA, not applicale; OFA, Oncomine Focus Assay; SofC, standard of care. Concordance analysis is given for OFA and SofC ALK, including all patients used on the confusion matrix. The indexes of concordance of an orthogonal analysis (n = 44) performed using qPCR as a r
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