1
|
Mirlohi MS, Pishbin E, Dezhkam R, Kiani MJ, Shamloo A, Salami S. Innovative PNA-LB mediated allele-specific LAMP for KRAS mutation profiling on a compact lab-on-a-disc device. Talanta 2024; 276:126224. [PMID: 38772176 DOI: 10.1016/j.talanta.2024.126224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/24/2024] [Accepted: 05/05/2024] [Indexed: 05/23/2024]
Abstract
Tailored healthcare, an approach focused on individual patients, requires integrating emerging interdisciplinary technologies to develop accurate and user-friendly diagnostic tools. KRAS mutations, prevalent in various common cancers, are crucial determinants in selecting patients for novel KRAS inhibitor therapies. This study presents a novel state-of-the-art Lab-on-a-Disc system utilizing peptide nucleic acids-loop backward (PNA-LB) mediated allele-specific loop-mediated isothermal amplification (LAMP) for detecting the frequent G12D KRAS mutation, signifying its superiority over alternative mutation detection approaches. The designed Lab-on-a-Disc system demonstrated exceptional preclinical and technical precision, accuracy, and versatility. By applying varying cutoff values to PNA- LB LAMP reactions, the assay's sensitivity and specificity were increased by 80 % and 90 %, respectively. The device's key advantages include a robust microfluidic Lab-on-a-Disc design, precise rotary control, and a cutting-edge induction heating module. These features enable multiplexing of LAMP reactions with high reproducibility and repeatability, with CV% values less than 3.5 % and 5.5 %, respectively. The device offers several methods for accurate endpoint result detection, including naked-eye observation, RGB image analysis using Python code, and time of fluorescence (Tf) values. Preclinical specificity and sensitivity, assessed using different cutoffs for Eva-Green fluorescence Tf values and pH-sensitive dyes, demonstrated comparable performance to the best standard methods. Overall, this study represents a significant step towards tailoring treatment strategies for cancer patients through precise and efficient mutation detection technologies.
Collapse
Affiliation(s)
- Maryam Sadat Mirlohi
- Clinical Biochemistry Department, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Esmail Pishbin
- Bio-microfluidics Laboratory, Department of Electrical Engineering and Information Technology, Iranian Research Organization for Science and Technology, Tehran, Iran.
| | - Rasool Dezhkam
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran; Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Mohammad Javad Kiani
- School of Mechanical Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Amir Shamloo
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran
| | - Siamak Salami
- Clinical Biochemistry Department, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
2
|
Saito Y, Takahashi N, Matsui A, Michiyuki S, Yamauchi Y, Shimizu Y, Hoshi E, Sakao Y, Kawamura M. Comparative study of the loop-mediated isothermal amplification method and the QIAGEN therascreen PCR kit for the detection of EGFR mutations in non-small cell lung cancer. J Thorac Dis 2021; 13:743-753. [PMID: 33717546 PMCID: PMC7947485 DOI: 10.21037/jtd-20-2642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Epidermal growth factor receptor (EGFR) mutations are important biomarkers in the treatment of patients with advanced or metastatic diseases. The therascreen EGFR Rotor-Gene Q (RGQ) PCR Kit® (Qiagen, Inc.) is an approved diagnostic test for EGFR mutations in non-small cell lung cancer (NSCLC). This study aims to investigate the diagnostic capability of a loop-mediated isothermal amplification (LAMP) assay as an accurate, efficient, and cost-effective alternative to the therascreen assay. Methods EGFR mutations were investigated by LAMP and therascreen assays using tissue samples that were surgically resected or biopsied from 117 consecutive patients with NSCLC tumors. The EGFR status from the LAMP assay was compared with that of the therascreen assay. Next-generation sequencing (NGS) was performed to confirm EGFR status of tumors that did not match in both assays. To establish an optimal LAMP AUC value, receiver operating characteristics (ROC) curve analysis was performed within tumors with exon 19 deletion or L858R point mutation. Results Of the 117 tumors assayed, 45 tumors with EGFR mutations and 68 tumors with EGFR wild type were matched in both assays, four tumors having mismatched EGFR statuses. NGS further confirmed that two of the four discordant tumors had the same EGFR status that was determined by the LAMP assay. The AUC values were 0.973 (95% CI: 0.929–1.00) in exon 19 deletion, and 0.952 (95% CI: 0.885–1.00) in L858R point mutation. In exon 19 deletion, sensitivity, specificity, and accuracy were 89.3%, 98.9%, and 96.6%, respectively, and 94.7%, 95.9%, and 95.7%, respectively, in L858R using AUC value of 0.222. Conclusions The LAMP assay compared favorably with the therascreen assay and has potential as an effective, simple, rapid, and low-cost diagnostic alternative. Based on these results, a liquid biopsy LAMP system should be developed for point-of-care testing of oncogenes in the near future.
Collapse
Affiliation(s)
- Yuichi Saito
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan.,Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Nobumasa Takahashi
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Atsuka Matsui
- Fundamental Research Laboratory, Fundamental Technology Research Department, Eiken Chemical Co., Ltd., Tochigi, Japan
| | - Satoru Michiyuki
- Fundamental Research Laboratory, Fundamental Technology Research Department, Eiken Chemical Co., Ltd., Tochigi, Japan
| | - Yoshikane Yamauchi
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Yoshihiko Shimizu
- Department of Pathology, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Eishin Hoshi
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Yukinori Sakao
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Masafumi Kawamura
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| |
Collapse
|
3
|
Gits-Muselli M, Campagne P, Desnos-Ollivier M, Le Pape P, Bretagne S, Morio F, Alanio A. Comparison of MultiLocus Sequence Typing (MLST) and Microsatellite Length Polymorphism (MLP) for Pneumocystis jirovecii genotyping. Comput Struct Biotechnol J 2020; 18:2890-2896. [PMID: 33163149 PMCID: PMC7593342 DOI: 10.1016/j.csbj.2020.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/28/2020] [Accepted: 10/02/2020] [Indexed: 01/02/2023] Open
Abstract
Pneumocystis jirovecii is an atypical fungus responsible for severe respiratory infections, often reported as local outbreaks in immunocompromised patients. Epidemiology of this infection, and transmission risk emphasises the need for developing genotyping techniques. Currently, two methods have emerged: Multilocus Sequence typing (MLST) and microsatellite length polymorphism (MLP). Here we compare an MLST strategy, including 2 nuclear loci and 2 mitochondrial loci, with an MLP strategy including 6 nuclear markers using 37 clinical PCR-positive respiratory samples from two French hospitals. Pneumocystis jirovecii MLST and MLP provided 30 and 35 different genotypes respectively. A higher number of mixed infections was detected using MLP (48.6% vs. 13.5% respectively; p = 0.002). Only one MLP marker (STR279) was statistically associated with the geographical origin of samples. Haplotype network inferred using the available genotypes yielded expanded network for MLP, characterized by more mutational steps as compared to MLST, suggesting that the MLP approach is more resolutive to separate genotypes. The correlation between genetic distances calculated based on MLST and MLP was modest with a R2 value = 0.32 (p < 0.001). Finally, both genotyping methods fulfilled important criteria: (i) a discriminatory power from 97.5% to 99.5% and (ii) being quick and convenient genotyping tools. While MLP appeared highly resolutive regarding genotypes mixture within samples, using one genotyping method rather than the other may also depend on the context (i.e., MLST for investigation of suspected clonal outbreaks versus MLP for population structure study) as well as local facilities.
Collapse
Affiliation(s)
- Maud Gits-Muselli
- Laboratoire de Parasitologie-Mycologie; AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France.,Institut Pasteur, CNRS, unité de Mycologie Moléculaire, Centre National de référence Mycoses invasives et Antifongiques (CNRMA), UMR2000, Paris, France
| | - Pascal Campagne
- Hub of Bioinformatics and Biostatistics - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Marie Desnos-Ollivier
- Institut Pasteur, CNRS, unité de Mycologie Moléculaire, Centre National de référence Mycoses invasives et Antifongiques (CNRMA), UMR2000, Paris, France
| | - Patrice Le Pape
- Laboratoire de Parasitologie-Mycologie, Institut de Biologie, CHU Nantes, Nantes, France.,Département de Parasitologie et Mycologie Médicale, EA1155 IICiMed, Institut de Recherche en Santé 2, Université de Nantes, Nantes Atlantique Universités, Nantes, France
| | - Stéphane Bretagne
- Laboratoire de Parasitologie-Mycologie; AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France.,Institut Pasteur, CNRS, unité de Mycologie Moléculaire, Centre National de référence Mycoses invasives et Antifongiques (CNRMA), UMR2000, Paris, France
| | - Florent Morio
- Laboratoire de Parasitologie-Mycologie, Institut de Biologie, CHU Nantes, Nantes, France.,Département de Parasitologie et Mycologie Médicale, EA1155 IICiMed, Institut de Recherche en Santé 2, Université de Nantes, Nantes Atlantique Universités, Nantes, France
| | - Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie; AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France.,Institut Pasteur, CNRS, unité de Mycologie Moléculaire, Centre National de référence Mycoses invasives et Antifongiques (CNRMA), UMR2000, Paris, France
| |
Collapse
|
4
|
Joy RA, Thelakkattusserry SK, Vikkath N, Bhaskaran R, Krishnan S, Vasudevan D, Ariyannur PS. Somatic mutation detection efficiency in EGFR: a comparison between high resolution melting analysis and Sanger sequencing. BMC Cancer 2020; 20:902. [PMID: 32962681 PMCID: PMC7510081 DOI: 10.1186/s12885-020-07411-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/14/2020] [Indexed: 11/21/2022] Open
Abstract
Background High resolution melting curve analysis is a cost-effective rapid screening method for detection of somatic gene mutation. The performance characteristics of this technique has been explored previously, however, analytical parameters such as limit of detection of mutant allele fraction and total concentration of DNA, have not been addressed. The current study focuses on comparing the mutation detection efficiency of High-Resolution Melt Analysis (HRM) with Sanger Sequencing in somatic mutations of the EGFR gene in non-small cell lung cancer. Methods The minor allele fraction of somatic mutations was titrated against total DNA concentration using Sanger sequencing and HRM to determine the limit of detection. The mutant and wildtype allele fractions were validated by multiplex allele-specific real-time PCR. Somatic mutation detection efficiency, for exons 19 & 21 of the EGFR gene, was compared in 116 formalin fixed paraffin embedded tumor tissues, after screening 275 tumor tissues by Sanger sequencing. Results The limit of detection of minor allele fraction of exon 19 mutation was 1% with sequencing, and 0.25% with HRM, whereas for exon 21 mutation, 0.25% MAF was detected using both methods. Multiplex allele-specific real-time PCR revealed that the wildtype DNA did not impede the amplification of mutant allele in mixed DNA assays. All mutation positive samples detected by Sanger sequencing, were also detected by HRM. About 28% cases in exon 19 and 40% in exon 21, detected as mutated in HRM, were not detected by sequencing. Overall, sensitivity and specificity of HRM were found to be 100 and 67% respectively, and the negative predictive value was 100%, while positive predictive value was 80%. Conclusion The comparative series study suggests that HRM is a modest initial screening test for somatic mutation detection of EGFR, which must further be confirmed by Sanger sequencing. With the modification of annealing temperature of initial PCR, the limit of detection of Sanger sequencing can be improved.
Collapse
Affiliation(s)
- Reenu Anne Joy
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India
| | | | - Narendranath Vikkath
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India
| | - Renjitha Bhaskaran
- Department of Biostatistics, Amrita School of Medicine, Amrita Vishwa Vidyapeetham, Kochi, 682041, India
| | - Sajitha Krishnan
- Department of Biochemistry, Amrita School of Medicine, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Ponekkara P.O., Kochi, Kerala, 682041, India
| | - Damodaran Vasudevan
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India.,Department of Biochemistry, Amrita School of Medicine, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Ponekkara P.O., Kochi, Kerala, 682041, India
| | - Prasanth S Ariyannur
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India. .,Department of Biochemistry, Amrita School of Medicine, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Ponekkara P.O., Kochi, Kerala, 682041, India.
| |
Collapse
|
5
|
Horiuchi S, Saito Y, Matsui A, Takahashi N, Ikeya T, Hoshi E, Shimizu Y, Yasuda M. A novel loop‑mediated isothermal amplification method for efficient and robust detection of EGFR mutations. Int J Oncol 2020; 56:743-749. [PMID: 32124949 PMCID: PMC7010225 DOI: 10.3892/ijo.2020.4961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/12/2019] [Indexed: 12/23/2022] Open
Abstract
The activation of somatic mutations conferring sensitivity to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors has been widely used in the development of advanced or metastatic primary lung cancer therapy. Therefore, identification of EGFR mutations is essential. In the present study, a loop-mediated isothermal amplification (LAMP) method was used to identify EGFR mutations, and its efficiency was compared with the Therascreen quantitative PCR assay. Using LAMP and Therascreen to analyze surgically resected tissue samples from patients with pulmonary adenocarcinoma, EGFR mutations were observed in 32/59 tumor samples (LAMP) and 33/59 tumor samples (Therascreen). Notably, the LAMP assay identified one tumor as wild-type, which had previously been identified as a deletion mutation in exon 19 via the Therascreen assay (Case X). However, the direct sequencing to confirm the EGFR status of the Case X adhered to the results of the LAMP assay. Further experiments using Case X DNA identified this exon 19 deletion mutation using both methods. In addition, a novel deletion mutation in exon 19 of the EGFR was identified. Overall, the present study shows that the LAMP method may serve as a valuable alternative for the identification oncogene mutations.
Collapse
Affiliation(s)
- Sho Horiuchi
- Department of Pathology, Saitama Medical University International Medical Center, Hidaka 350‑1298, Japan
| | - Yuichi Saito
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, Kumagaya, Saitama 360‑0197, Japan
| | - Atsuka Matsui
- Fundamental Research Laboratory, Fundamental Technology Research Department, Eiken Chemical Co., Ltd., Otawara, Tochigi 324‑0036, Japan
| | - Nobumasa Takahashi
- Department of Surgery, Teikyo University School of Medicine, Tokyo 173‑8605, Japan
| | - Tomohiko Ikeya
- Department of Surgery, Teikyo University School of Medicine, Tokyo 173‑8605, Japan
| | - Eishin Hoshi
- Department of Surgery, Teikyo University School of Medicine, Tokyo 173‑8605, Japan
| | - Yoshihiko Shimizu
- Department of Pathology, Saitama Cardiovascular and Respiratory Center, Kumagaya, Saitama 360‑0197, Japan
| | - Masanori Yasuda
- Department of Pathology, Saitama Medical University International Medical Center, Hidaka 350‑1298, Japan
| |
Collapse
|
6
|
Kim YJ, Chambers AG, Cecchi F, Hembrough T. Targeted data-independent acquisition for mass spectrometric detection of RAS mutations in formalin-fixed, paraffin-embedded tumor biopsies. J Proteomics 2018; 189:91-96. [DOI: 10.1016/j.jprot.2018.04.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/13/2018] [Accepted: 04/14/2018] [Indexed: 01/14/2023]
|
7
|
Gray PN, Vuong H, Tsai P, Lu HM, Mu W, Hsuan V, Hoo J, Shah S, Uyeda L, Fox S, Patel H, Janicek M, Brown S, Dobrea L, Wagman L, Plimack E, Mehra R, Golemis EA, Bilusic M, Zibelman M, Elliott A. TumorNext: A comprehensive tumor profiling assay that incorporates high resolution copy number analysis and germline status to improve testing accuracy. Oncotarget 2018; 7:68206-68228. [PMID: 27626691 PMCID: PMC5356550 DOI: 10.18632/oncotarget.11910] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/26/2016] [Indexed: 01/08/2023] Open
Abstract
The development of targeted therapies for both germline and somatic DNA mutations has increased the need for molecular profiling assays to determine the mutational status of specific genes. Moreover, the potential of off-label prescription of targeted therapies favors classifying tumors based on DNA alterations rather than traditional tissue pathology. Here we describe the analytical validation of a custom probe-based NGS tumor panel, TumorNext, which can detect single nucleotide variants, small insertions and deletions in 142 genes that are frequently mutated in somatic and/or germline cancers. TumorNext also detects gene fusions and structural variants, such as tandem duplications and inversions, in 15 frequently disrupted oncogenes and tumor suppressors. The assay uses a matched control and custom bioinformatics pipeline to differentiate between somatic and germline mutations, allowing precise variant classification. We tested 170 previously characterized samples, of which > 95% were formalin-fixed paraffin embedded tissue from 8 different cancer types, and highlight examples where lack of germline status may have led to the inappropriate prescription of therapy. We also describe the validation of the Affymetrix OncoScan platform, an array technology for high resolution copy number variant detection for use in parallel with the NGS panel that can detect single copy amplifications and hemizygous deletions. We analyzed 80 previously characterized formalin-fixed paraffin-embedded specimens and provide examples of hemizygous deletion detection in samples with known pathogenic germline mutations. Thus, the TumorNext combined approach of NGS and OncoScan potentially allows for the identification of the “second hit” in hereditary cancer patients.
Collapse
Affiliation(s)
| | - Huy Vuong
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | - Pei Tsai
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | | | - Wenbo Mu
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | | | - Jayne Hoo
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | - Swati Shah
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | - Lisa Uyeda
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | | | | | | | | | | | | | | | - Ranee Mehra
- Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | | | | | | | | |
Collapse
|
8
|
Mauger F, How-Kit A, Tost J. COLD-PCR Technologies in the Area of Personalized Medicine: Methodology and Applications. Mol Diagn Ther 2018; 21:269-283. [PMID: 28101802 DOI: 10.1007/s40291-016-0254-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Somatic mutations bear great promise for use as biomarkers for personalized medicine, but are often present only in low abundance in biological material and are therefore difficult to detect. Many assays for mutation analysis in cancer-related genes (hotspots) have been developed to improve diagnosis, prognosis, prediction of drug resistance, and monitoring of the response to treatment. Two major approaches have been developed: mutation-specific amplification methods and methods that enrich and detect mutations without prior knowledge on the exact location and identity of the mutation. CO-amplification at Lower Denaturation temperature Polymerase Chain Reaction (COLD-PCR) methods such as full-, fast-, ice- (improved and complete enrichment), enhanced-ice, and temperature-tolerant COLD-PCR make use of a critical temperature in the polymerase chain reaction to selectively denature wild-type-mutant heteroduplexes, allowing the enrichment of rare mutations. Mutations can subsequently be identified using a variety of laboratory technologies such as high-resolution melting, digital polymerase chain reaction, pyrosequencing, Sanger sequencing, or next-generation sequencing. COLD-PCR methods are sensitive, specific, and accurate if appropriately optimized and have a short time to results. A large variety of clinical samples (tumor DNA, circulating cell-free DNA, circulating cell-free fetal DNA, and circulating tumor cells) have been studied using COLD-PCR in many different applications including the detection of genetic changes in cancer and infectious diseases, non-invasive prenatal diagnosis, detection of microorganisms, or DNA methylation analysis. In this review, we describe in detail the different COLD-PCR approaches, highlighting their specificities, advantages, and inconveniences and demonstrating their use in different fields of biological and biomedical research.
Collapse
Affiliation(s)
- Florence Mauger
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Alexandre How-Kit
- Laboratory for Genomics, Fondation Jean Dausset-CEPH, 75010, Paris, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
| |
Collapse
|
9
|
Sutton BC, Birse RT, Maggert K, Ray T, Hobbs J, Ezenekwe A, Kazmierczak J, Mosko M, Kish J, Bullock A, Shi Z, Stack MS, Irwin D. Assessment of common somatic mutations of EGFR, KRAS, BRAF, NRAS in pulmonary non-small cell carcinoma using iPLEX® HS, a new highly sensitive assay for the MassARRAY® System. PLoS One 2017; 12:e0183715. [PMID: 28926605 PMCID: PMC5604939 DOI: 10.1371/journal.pone.0183715] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/09/2017] [Indexed: 11/19/2022] Open
Abstract
Increased early detection and personalized therapy for lung cancer have coincided with greater use of minimally invasive sampling techniques such as endobronchial ultrasound-guided biopsy (EBUS), endoscopic ultrasound-guided biopsy (EUS), and navigational biopsy, as well as thin needle core biopsies. As many lung cancer patients have late stage disease and other comorbidities that make open surgical procedures hazardous, the least invasive biopsy technique with the highest potential specimen yield is now the preferred first diagnostic study. However, use of these less invasive procedures generates significant analytical challenges for the laboratory, such as a requirement for robust detection of low level somatic mutations, particularly when the starting sample is very small or demonstrates few intact tumor cells. In this study, we assessed 179 clinical cases of non-small cell lung carcinoma (NSCLC) that had been previously tested for EGFR, KRAS, NRAS, and BRAF mutations using a novel multiplexed analytic approach that reduces wild-type signal and allows for detection of low mutation load approaching 1%, iPLEX® HS panel for the MassARRAY® System (Agena Bioscience, San Diego, CA). This highly sensitive system identified approximately 10% more KRAS, NRAS, EGFR and BRAF mutations than were detected by the original test platform, which had a sensitivity range of 5-10% variant allele frequency (VAF).
Collapse
Affiliation(s)
- Bobbie C. Sutton
- Pathology Department, South Bend Medical Foundation, South Bend, IN, United States of America
| | - Ryan T. Birse
- Agena Bioscience, San Diego, CA, United States of America
| | - Kevin Maggert
- Pathology Department, South Bend Medical Foundation, South Bend, IN, United States of America
| | - Tammy Ray
- Pathology Department, South Bend Medical Foundation, South Bend, IN, United States of America
| | - Jessica Hobbs
- Pathology Department, South Bend Medical Foundation, South Bend, IN, United States of America
| | - Amobi Ezenekwe
- Pathology Department, South Bend Medical Foundation, South Bend, IN, United States of America
| | | | - Michael Mosko
- Agena Bioscience, San Diego, CA, United States of America
| | - Joan Kish
- Pathology Department, South Bend Medical Foundation, South Bend, IN, United States of America
| | - Andrew Bullock
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States of America
| | - Zonggao Shi
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States of America
| | - M. Sharon Stack
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States of America
| | - Darryl Irwin
- Agena Bioscience, San Diego, CA, United States of America
| |
Collapse
|
10
|
Emelyanova M, Ghukasyan L, Abramov I, Ryabaya O, Stepanova E, Kudryavtseva A, Sadritdinova A, Dzhumakova C, Belysheva T, Surzhikov S, Lyubchenko L, Zasedatelev A, Nasedkina T. Detection of BRAF, NRAS, KIT, GNAQ, GNA11 and MAP2K1/2 mutations in Russian melanoma patients using LNA PCR clamp and biochip analysis. Oncotarget 2017; 8:52304-52320. [PMID: 28881731 PMCID: PMC5581030 DOI: 10.18632/oncotarget.17014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 03/30/2017] [Indexed: 12/19/2022] Open
Abstract
Target inhibitors are used for melanoma treatment, and their effectiveness depends on the tumor genotype. We developed a diagnostic biochip for the detection of 39 clinically relevant somatic mutations in the BRAF, NRAS, KIT, GNAQ, GNA11, MAP2K1 and MAP2K2 genes. We used multiplex locked nucleic acid (LNA) PCR clamp for the preferable amplification of mutated over wild type DNA. The amplified fragments were labeled via the incorporation of fluorescently labeled dUTP during PCR and were hybridized with specific oligonucleotides immobilized on a biochip. This approach could detect 0.5% of mutated DNA in the sample analyzed. The method was validated on 253 clinical samples and six melanoma cell lines. Among 253 melanomas, 129 (51.0%) BRAF, 45 (17.8%) NRAS, 6 (2.4%) KIT, 4 (1.6%) GNAQ, 2 (0.8%) GNA11, 2 (0.8%) MAP2K1 and no MAP2K2 gene mutations were detected by the biochip assay. The results were compared with Sanger sequencing, next generation sequencing and ARMS/Scorpion real-time PCR. The specimens with discordant results were subjected to LNA PCR clamp followed by sequencing. The results of this analysis were predominantly identical to the results obtained by the biochip assay. Infrequently, we identified rare somatic mutations. In the present study we demonstrate that the biochip-based assay can effectively detect somatic mutations in approximately 70% of melanoma patients, who may require specific targeted therapy.
Collapse
Affiliation(s)
- Marina Emelyanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Lilit Ghukasyan
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ivan Abramov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
- Blokhin Cancer Research Center, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Oxana Ryabaya
- Blokhin Cancer Research Center, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Evgenia Stepanova
- Blokhin Cancer Research Center, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
- P. Hertsen Moscow Oncology Research Institute, Moscow, Russian Federation
| | - Asiya Sadritdinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
- P. Hertsen Moscow Oncology Research Institute, Moscow, Russian Federation
| | - Cholpon Dzhumakova
- Blokhin Cancer Research Center, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Tatiana Belysheva
- Blokhin Cancer Research Center, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Sergey Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Lyudmila Lyubchenko
- Blokhin Cancer Research Center, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Alexander Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
- Blokhin Cancer Research Center, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Tatiana Nasedkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
- Blokhin Cancer Research Center, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| |
Collapse
|
11
|
Rapid and accurate detection of KRAS mutations in colorectal cancers using the isothermal-based optical sensor for companion diagnostics. Oncotarget 2017; 8:83860-83871. [PMID: 29137388 PMCID: PMC5663560 DOI: 10.18632/oncotarget.20038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/25/2017] [Indexed: 01/23/2023] Open
Abstract
Although KRAS mutational status testing is becoming a companion diagnostic tool for managing patients with colorectal cancer (CRC), there are still several difficulties when analyzing KRAS mutations using the existing assays, particularly with regard to low sensitivity, its time-consuming, and the need for large instruments. We developed a rapid, sensitive, and specific mutation detection assay based on the bio-photonic sensor termed ISAD (isothermal solid-phase amplification/detection), and used it to analyze KRAS gene mutations in human clinical samples. To validate the ISAD-KRAS assay for use in clinical diagnostics, we examined for hotspot KRAS mutations (codon 12 and codon 13) in 70 CRC specimens using PCR and direct sequencing methods. In a serial dilution study, ISAD-KRAS could detect mutations in a sample containing only 1% of the mutant allele in a mixture of wild-type DNA, whereas both PCR and direct sequencing methods could detect mutations in a sample containing approximately 30% of mutant cells. The results of the ISAD-KRAS assay from 70 clinical samples matched those from PCR and direct sequencing, except in 5 cases, wherein ISAD-KRAS could detect mutations that were not detected by PCR and direct sequencing. We also found that the sensitivity and specificity of ISAD-KRAS were 100% within 30 min. The ISAD-KRAS assay provides a rapid, highly sensitive, and label-free method for KRAS mutation testing, and can serve as a robust and near patient testing approach for the rapid detection of patients most likely to respond to anti-EGFR drugs.
Collapse
|
12
|
Phase II Trial of Target-guided Personalized Chemotherapy in First-line Metastatic Colorectal Cancer. Am J Clin Oncol 2017; 39:236-42. [PMID: 24517959 DOI: 10.1097/coc.0000000000000045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE The aim of this study was to investigate the feasibility and efficacy of personalizing treatment of patients with advanced untreated colorectal cancer (CRC). PATIENTS AND METHODS Patients with untreated metastatic CRC, performance status 0-1, and candidates for systemic chemotherapy were eligible. Tumor tissues were analyzed for KRAS, BRAF, and PI3K mutations and expression of topoisomerase-1 (Topo-1), excision repair cross-complementing gene 1 (ERCC1), thymidylate synthase (TS), and thymidine phosphorylase (TP). Patients with Topo-1 expression received irinotecan, whereas patients with negative Topo-1 and ERCC1 expression received oxaliplatin. Otherwise, patients received physician's choice of treatment. If TS was positive, no fluoropyrimidine was administered and if negative, 5-flurorouracil if TP was negative, or capecitabine if TP was positive. KRAS-mutated patients were treated with bevacizumab, whereas KRAS-native received cetuximab. The primary endpoint of the study was progression-free survival (PFS). RESULTS A total of 74 patients were enrolled and 67 received personalized treatment including irinotecan (n=27), oxaliplatin (n=16), FOLFIRI (n=12), and FOLFOX (n=12). Thirty-eight patients received cetuximab and 29 bevacizumab. With a median follow-up time of 18.3 months (95% confidence interval [CI], 4-36), the overall median PFS was 8.3 months (95% CI, 6.9-9.7), representing a 12-month PFS rate of 36.5% (95% CI, 25-48). Overall clinical benefit, including response rate and disease stabilization, was 86% (95% CI, 73%-97%). The overall median survival was 21 months (95% CI, 11-40). CONCLUSIONS Real-time target-guided personalized first-line treatment of patients with advanced CRC is feasible but, with the approached used, did not result in a clear improvement in PFS to warrant phase III testing.
Collapse
|
13
|
Loopback rolling circle amplification for ultrasensitive detection of Kras gene. Talanta 2017; 164:511-517. [DOI: 10.1016/j.talanta.2016.12.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/02/2016] [Accepted: 12/06/2016] [Indexed: 02/06/2023]
|
14
|
Loree JM, Kopetz S, Raghav KPS. Current companion diagnostics in advanced colorectal cancer; getting a bigger and better piece of the pie. J Gastrointest Oncol 2017; 8:199-212. [PMID: 28280626 PMCID: PMC5334060 DOI: 10.21037/jgo.2017.01.01] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/18/2016] [Indexed: 12/19/2022] Open
Abstract
While the treatment of colorectal cancer continues to rely heavily on conventional cytotoxic therapy, an increasing number of targeted agents are under development. Many of these treatments require companion diagnostic tests in order to define an appropriate population that will derive benefit. In addition, a growing number of biomarkers provide prognostic information about a patient's malignancy. As we learn more about these biomarkers and their assays, selecting the appropriate companion diagnostic becomes increasingly important. In the case of many biomarkers, there are numerous assays which could provide the same information to a treating physician, however each assay has strengths and weaknesses. Institutions must balance cost, assay sensitivity, turn-around time, and labor resources when selecting which assay to offer. In this review we will discuss the current state of companion diagnostics available in metastatic colorectal cancer and explore emerging biomarkers and their assays. We will focus on KRAS, BRAF, HER2, and PIK3CA testing, as well as microsatellite stability assessment and multigene panels.
Collapse
Affiliation(s)
- Jonathan M Loree
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kanwal P S Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
15
|
Pekin D, Taly V. Droplet-Based Microfluidics Digital PCR for the Detection of KRAS Mutations. Methods Mol Biol 2017; 1547:143-164. [PMID: 28044294 DOI: 10.1007/978-1-4939-6734-6_12] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We demonstrate an accurate and sensitive quantification of mutated KRAS oncogene in genomic DNA, using droplet-based microfluidics and digital PCR.
Collapse
Affiliation(s)
- Deniz Pekin
- CNRS, Univ. Bordeaux, CRPP, UPR 8641, 115 Avenue Schweitzer, F-33600, Pessac, France
| | - Valerie Taly
- INSERM UMRS1147, CNRS SNC 5014, Université Paris Descartes, 45 rue des Saints-Pères, 75270, ParisCedex 06, France.
| |
Collapse
|
16
|
Lee SH, Chung AM, Lee A, Oh WJ, Choi YJ, Lee YS, Jung ES. KRAS Mutation Test in Korean Patients with Colorectal Carcinomas: A Methodological Comparison between Sanger Sequencing and a Real-Time PCR-Based Assay. J Pathol Transl Med 2016; 51:24-31. [PMID: 28013534 PMCID: PMC5267542 DOI: 10.4132/jptm.2016.10.03] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/23/2016] [Accepted: 10/02/2016] [Indexed: 12/19/2022] Open
Abstract
Background Mutations in the KRAS gene have been identified in approximately 50% of colorectal cancers (CRCs). KRAS mutations are well established biomarkers in anti–epidermal growth factor receptor therapy. Therefore, assessment of KRAS mutations is needed in CRC patients to ensure appropriate treatment. Methods We compared the analytical performance of the cobas test to Sanger sequencing in 264 CRC cases. In addition, discordant specimens were evaluated by 454 pyrosequencing. Results KRAS mutations for codons 12/13 were detected in 43.2% of cases (114/264) by Sanger sequencing. Of 257 evaluable specimens for comparison, KRAS mutations were detected in 112 cases (43.6%) by Sanger sequencing and 118 cases (45.9%) by the cobas test. Concordance between the cobas test and Sanger sequencing for each lot was 93.8% positive percent agreement (PPA) and 91.0% negative percent agreement (NPA) for codons 12/13. Results from the cobas test and Sanger sequencing were discordant for 20 cases (7.8%). Twenty discrepant cases were subsequently subjected to 454 pyrosequencing. After comprehensive analysis of the results from combined Sanger sequencing–454 pyrosequencing and the cobas test, PPA was 97.5% and NPA was 100%. Conclusions The cobas test is an accurate and sensitive test for detecting KRAS-activating mutations and has analytical power equivalent to Sanger sequencing. Prescreening using the cobas test with subsequent application of Sanger sequencing is the best strategy for routine detection of KRAS mutations in CRC.
Collapse
Affiliation(s)
- Sung Hak Lee
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Arthur Minwoo Chung
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahwon Lee
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Woo Jin Oh
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeong Jin Choi
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Youn-Soo Lee
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eun Sun Jung
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| |
Collapse
|
17
|
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.
Collapse
|
18
|
Luquain A, Arbez-Gindre F, Bedgedjian I, Felix S, Harimenshi JM, Mihai IM, Monnien F, Singeorzan C, Valmary-Degano S. Habilitation des pathologistes pour l’évaluation du pourcentage de cellules tumorales lors du contrôle morphologique avant extraction d’acides nucléiques. Ann Pathol 2016; 36:268-74. [DOI: 10.1016/j.annpat.2016.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/12/2016] [Accepted: 06/15/2016] [Indexed: 01/17/2023]
|
19
|
Alanio A, Gits-Muselli M, Mercier-Delarue S, Dromer F, Bretagne S. Diversity of Pneumocystis jirovecii during Infection Revealed by Ultra-Deep Pyrosequencing. Front Microbiol 2016; 7:733. [PMID: 27252684 PMCID: PMC4877386 DOI: 10.3389/fmicb.2016.00733] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/02/2016] [Indexed: 01/05/2023] Open
Abstract
Pneumocystis jirovecii is an uncultivable fungal pathogen responsible for Pneumocystis pneumonia (PCP) in immunocompromised patients, the physiopathology of which is only partially understood. The diversity of the Pneumocystis strains associated with acute infection has mainly been studied by Sanger sequencing techniques precluding any identification of rare genetic events (< 20% frequency). We used next-generation sequencing to detect minority variants causing infection, and analyzed the complexity of the genomes of infection-causing P. jirovecii. Ultra-deep pyrosequencing (UDPS) of PCR amplicons of two nuclear target region [internal transcribed spacer 2 (ITS2) and dihydrofolate reductase (DHFR)] and one mitochondrial DNA target region [the mitochondrial ribosomal RNA large subunit gene (mtLSU)] was performed on 31 samples from 25 patients. UDPS revealed that almost all patients (n = 23/25, 92%) were infected with mixtures of strains. An analysis of repeated samples from six patients showed that the proportion of each variant change significantly (by up to 30%) over time on treatment in three of these patients. A comparison of mitochondrial and nuclear UDPS data revealed heteroplasmy in P. jirovecii. The recognition site for the homing endonuclease I-SceI was recovered from the mtLSU gene, whereas its two conserved motifs of the enzyme were not. This suggests that heteroplasmy may result from recombination induced by unidentified homing endonucleases. This study sheds new light on the biology of P. jirovecii during infection. PCP results from infection not with a single microorganism, but with a complex mixture of different genotypes, the proportions of which change over time due to intricate selection and reinfection mechanisms that may differ between patients, treatments, and predisposing diseases.
Collapse
Affiliation(s)
- Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique Hôpitaux de Paris, Hôpital Saint-LouisParis, France; Université Paris Diderot, Sorbonne Paris CitéParis, France; Unité de Mycologie Moléculaire, Département de Mycologie, Centre National de Référence Mycoses Invasives et Antifongiques, Institut PasteurParis, France; Centre National de la Recherche Scientifique CNRS URA3012Paris, France
| | - Maud Gits-Muselli
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique Hôpitaux de Paris, Hôpital Saint-LouisParis, France; Université Paris Diderot, Sorbonne Paris CitéParis, France
| | - Séverine Mercier-Delarue
- Laboratoire de Microbiologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique Hôpitaux de Paris, Hôpital Saint-Louis Paris, France
| | - Françoise Dromer
- Unité de Mycologie Moléculaire, Département de Mycologie, Centre National de Référence Mycoses Invasives et Antifongiques, Institut PasteurParis, France; Centre National de la Recherche Scientifique CNRS URA3012Paris, France
| | - Stéphane Bretagne
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique Hôpitaux de Paris, Hôpital Saint-LouisParis, France; Université Paris Diderot, Sorbonne Paris CitéParis, France; Unité de Mycologie Moléculaire, Département de Mycologie, Centre National de Référence Mycoses Invasives et Antifongiques, Institut PasteurParis, France; Centre National de la Recherche Scientifique CNRS URA3012Paris, France
| |
Collapse
|
20
|
Matsunaga M, Kaneta T, Miwa K, Ichikawa W, Fujita KI, Nagashima F, Furuse J, Kage M, Akagi Y, Sasaki Y. A comparison of four methods for detecting KRAS mutations in formalin-fixed specimens from metastatic colorectal cancer patients. Oncol Lett 2016; 12:150-156. [PMID: 27347117 DOI: 10.3892/ol.2016.4576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 04/29/2016] [Indexed: 12/24/2022] Open
Abstract
There is currently no standard method for the detection of Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation status in colorectal tumors. In the present study, we compared the KRAS mutation detection ability of four methods: direct sequencing, Scorpion-ARMS assaying, pyrosequencing and multi-analyte profiling (Luminex xMAP). We evaluated 73 cases of metastatic colorectal cancer (mCRC) resistant to irinotecan, oxaliplatin and fluoropyrimidine that were enrolled in an all-case study of cetuximab. The KRAS mutation detection capacity of the four analytical methods was compared using DNA samples extracted from tumor tissue, and the detection success rate and concordance of the detection results were evaluated. KRAS mutations were detected by direct sequencing, Scorpion-ARMS assays, pyrosequencing and Luminex xMAP at success rates of 93.2%, 97.3%, 95.9% and 94.5%, respectively. The concordance rates of the detection results by Scorpion-ARMS, pyrosequencing and Luminex xMAP with those of direct sequencing were 0.897, 0.923 and 0.900 (κ statistics), respectively. The direct sequencing method could not determine KRAS mutation status in five DNA samples. Of these, Scorpion-ARMS, pyrosequencing and Luminex xMAP successfully detected three, two and one KRAS mutation statuses, respectively. Three cases demonstrated inconsistent results, whereby Luminex xMAP detected mutated KRAS in two samples while wild-type KRAS was detected by the other methods. In the remaining case, direct sequencing detected wild-type KRAS, which was identified as mutated KRAS by the other methods. In conclusion, we confirmed that Scorpion-ARMS, pyrosequencing and Luminex xMAP were equally reliable in detecting KRAS mutation status in mCRC. However, in rare cases, the KRAS status was differentially diagnosed using these methods.
Collapse
Affiliation(s)
- Mototsugu Matsunaga
- Multidisciplinary Treatment Cancer Center, Kurume University Hospital, Kurume, Fukuoka 830-0011, Japan
| | - Toshikado Kaneta
- Division of Medical Oncology, Department of Internal Medicine, Showa University Hospital, Hatanodai, Shinagawa, Tokyo 142-8666, Japan
| | - Keisuke Miwa
- Multidisciplinary Treatment Cancer Center, Kurume University Hospital, Kurume, Fukuoka 830-0011, Japan
| | - Wataru Ichikawa
- Division of Medical Oncology, Department of Internal Medicine, Showa University Hospital, Hatanodai, Shinagawa, Tokyo 142-8666, Japan
| | - Ken-Ichi Fujita
- Division of Medical Oncology, Department of Internal Medicine, Showa University Hospital, Hatanodai, Shinagawa, Tokyo 142-8666, Japan
| | - Fumio Nagashima
- Department of Medical Oncology, Kyorin University School of Medicine, Hinkawa, Mitaka, Tokyo 181-8611, Japan
| | - Junji Furuse
- Department of Medical Oncology, Kyorin University School of Medicine, Hinkawa, Mitaka, Tokyo 181-8611, Japan
| | - Masayoshi Kage
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Fukuoka 830-0011, Japan
| | - Yoshito Akagi
- Department of Surgery, Kurume University Hospital, Kurume, Fukuoka 830-0011, Japan
| | - Yasutsuna Sasaki
- Division of Medical Oncology, Department of Internal Medicine, Showa University Hospital, Hatanodai, Shinagawa, Tokyo 142-8666, Japan
| |
Collapse
|
21
|
Gao J, Wu H, Wang L, Zhang H, Duan H, Lu J, Liang Z. Validation of targeted next-generation sequencing for RAS mutation detection in FFPE colorectal cancer tissues: comparison with Sanger sequencing and ARMS-Scorpion real-time PCR. BMJ Open 2016; 6:e009532. [PMID: 26747035 PMCID: PMC4716245 DOI: 10.1136/bmjopen-2015-009532] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE To validate the targeted next-generation sequencing (NGS) platform-Ion Torrent PGM for KRAS exon 2 and expanded RAS mutations detection in formalin-fixed paraffin-embedded (FFPE) colorectal cancer (CRC) specimens, with comparison of Sanger sequencing and ARMS-Scorpion real-time PCR. SETTING Beijing, China. PARTICIPANTS 51 archived FFPE CRC samples (36 men, 15 women) were retrospectively randomly selected and then checked by an experienced pathologist for sequencing based on histological confirmation of CRC and availability of sufficient tissue. METHODS RAS mutations were detected in the 51 FFPE CRC samples by PGM analysis, Sanger sequencing and the Therascreen KRAS assay, respectively. Agreement among the 3 methods was assessed. Assay sensitivity was further determined by sequencing serially diluted DNA from FFPE cell lines with known mutation statuses. RESULTS 13 of 51 (25.5%) cases had a mutation in KRAS exon 2, as determined by PGM analysis. PGM analysis showed 100% (51/51) concordance with Sanger sequencing (κ=1.000, 95% CI 1 to 1) and 98.04% (50/51) agreement with the Therascreen assay (κ=0.947, 95% CI 0.844 to 1) for detecting KRAS exon 2 mutations, respectively. The only discrepant case harboured a KRAS exon 2 mutation (c.37G>T) that was not covered by the Therascreen kit. The dilution series experiment results showed that PGM was able to detect KRAS mutations at a frequency of as low as 1%. Importantly, RAS mutations other than KRAS exon 2 mutations were also detected in 10 samples by PGM. Furthermore, mutations in other CRC-related genes could be simultaneously detected in a single test by PGM. CONCLUSIONS The targeted NGS platform is specific and sensitive for KRAS exon 2 mutation detection and is appropriate for use in routine clinical testing. Moreover, it is sample saving and cost-efficient and time-efficient, and has great potential for clinical application to expand testing to include mutations in RAS and other CRC-related genes.
Collapse
Affiliation(s)
- Jie Gao
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Li Wang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Hui Zhang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Huanli Duan
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Junliang Lu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| |
Collapse
|
22
|
Taylor SC, Carbonneau J, Shelton DN, Boivin G. Optimization of Droplet Digital PCR from RNA and DNA extracts with direct comparison to RT-qPCR: Clinical implications for quantification of Oseltamivir-resistant subpopulations. J Virol Methods 2015; 224:58-66. [PMID: 26315318 DOI: 10.1016/j.jviromet.2015.08.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 07/21/2015] [Accepted: 08/19/2015] [Indexed: 01/21/2023]
Abstract
The recent introduction of Droplet Digital PCR (ddPCR) has provided researchers with a tool that permits direct quantification of nucleic acids from a wide range of samples with increased precision and sensitivity versus RT-qPCR. The sample interdependence of RT-qPCR stemming from the measurement of Cq and ΔCq values is eliminated with ddPCR which provides an independent measure of the absolute nucleic acid concentration for each sample without standard curves thereby reducing inter-well and inter-plate variability. Well-characterized RNA purified from H275-wild type (WT) and H275Y-point mutated (MUT) neuraminidase of influenza A (H1N1) pandemic 2009 virus was used to demonstrate a ddPCR optimization workflow to assure robust data for downstream analysis. The ddPCR reaction mix was also tested with RT-qPCR and gave excellent reaction efficiency (between 90% and 100%) with the optimized MUT/WT duplexed assay thus enabling the direct comparison of the two platforms from the same reaction mix and thermal cycling protocol. ddPCR gave a marked improvement in sensitivity (>30-fold) for mutation abundance using a mixture of purified MUT and WT RNA and increased precision (>10 fold, p<0.05 for both inter- and intra-assay variability) versus RT-qPCR from patient samples to accurately identify residual mutant viral population during recovery.
Collapse
Affiliation(s)
- Sean C Taylor
- Bio-Rad Laboratories Canada, Inc., 1329 Meyerside Drive, Mississauga, ON, Canada L5T1C9.
| | | | - Dawne N Shelton
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, CA, USA
| | - Guy Boivin
- CHU of Quebec and Laval University, Quebec City, QC, Canada
| |
Collapse
|
23
|
Kriegsmann M, Arens N, Endris V, Weichert W, Kriegsmann J. Detection of KRAS, NRAS and BRAF by mass spectrometry - a sensitive, reliable, fast and cost-effective technique. Diagn Pathol 2015; 10:132. [PMID: 26220423 PMCID: PMC4518505 DOI: 10.1186/s13000-015-0364-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/09/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND According to current clinical guidelines mutational analysis for KRAS and NRAS is recommended prior to EGFR-directed therapy of colorectal cancer (CRC) in the metastatic setting. Therefore, reliable, fast, sensitive and cost-effective methods for routine tissue based molecular diagnostics are required that allow the assessment of the CRC mutational status in a high throughput fashion. METHODS We have developed a custom designed assay for routine mass-spectrometric (MS) (MassARRAY, Agena Bioscience) analysis to test the presence/absence of 18 KRAS, 14 NRAS and 4 BRAF mutations. We have applied this assay to 93 samples from patients with CRC and have compared the results with Sanger sequencing and a chip hybridization assay (KRAS LCD-array Kit, Chipron). In cases with discordant results, next-generation sequencing (NGS) was performed. RESULTS MS detected a KRAS mutation in 46/93 (49%), a NRAS mutation in 2/93 (2%) and a BRAF mutation in 1/93 (1%) of the cases. MS results were in agreement with results obtained by combination of the two other methods in 92 (99%) of 93 cases. In 1/93 (1%) of the cases a G12V mutation has been detected by Sanger sequencing and MS, but not by the chip assay. In this case, NGS has confirmed the G12V mutation in KRAS. CONCLUSIONS Mutational analysis by MS is a reliable method for routine diagnostic use, which can be easily extended for testing of additional mutations.
Collapse
Affiliation(s)
- Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, INF 224, Heidelberg, Germany.
| | | | - Volker Endris
- Institute of Pathology, University of Heidelberg, INF 224, Heidelberg, Germany.
| | - Wilko Weichert
- Institute of Pathology, University of Heidelberg, INF 224, Heidelberg, Germany.
- National Center of Tumor Diseases, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Jörg Kriegsmann
- Institute of Molecular Pathology, Trier, Germany.
- MVZ for Histology, Cytology and Molecular Diagnostics, Trier, Germany.
| |
Collapse
|
24
|
Sinicrope FA, Mahoney MR, Yoon HH, Smyrk TC, Thibodeau SN, Goldberg RM, Nelson GD, Sargent DJ, Alberts SR. Analysis of Molecular Markers by Anatomic Tumor Site in Stage III Colon Carcinomas from Adjuvant Chemotherapy Trial NCCTG N0147 (Alliance). Clin Cancer Res 2015; 21:5294-304. [PMID: 26187617 DOI: 10.1158/1078-0432.ccr-15-0527] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/30/2015] [Indexed: 12/16/2022]
Abstract
PURPOSE To determine the frequency and prognostic association of molecular markers by anatomic tumor site in patients with stage III colon carcinomas. EXPERIMENTAL DESIGN In a randomized trial of adjuvant FOLFOX ± cetuximab, BRAF(V600E) and KRAS (exon 2) mutations and DNA mismatch repair (MMR) proteins were analyzed in tumors (N = 3,018) in relationship to tumor location, including subsite. Cox models were used to assess clinical outcome, including overall survival (OS). RESULTS KRAS codon 12 mutations were most frequent at the splenic flexure and cecum; codon 13 mutations were evenly distributed. BRAF mutation frequency sharply increased from transverse colon to cecum in parallel with deficient (d) MMR. Nonmutated BRAF and KRAS tumors progressively decreased from sigmoid to transverse (all P < 0.0001). Significantly, poorer OS was found for mutant KRAS in distal [HR, 1.98; 95% confidence interval (CI), 1.49-2.63; P < 0.0001] versus proximal (1.25; 95% CI, 0.97-1.60; P = 0.079) cancers. BRAF status and outcome were not significantly associated with tumor site. Proximal versus distal dMMR tumors had significantly better outcome. An interaction test was significant for tumor site by KRAS (P(adjusted) = 0.043) and MMR (P(adjusted) = 0.010) for OS. Significant prognostic differences for biomarkers by tumor site were maintained in the FOLFOX arm. Tumor site was independently prognostic with a stepwise improvement from cecum to sigmoid (OS: P(adjusted) = 0.001). CONCLUSIONS Mutation in BRAF or KRAS codon 12 was enriched in proximal cancers whereas nonmutated BRAF/KRAS was increased in distal tumors. Significant differences in outcome for KRAS mutations and dMMR were found by tumor site, indicating that their interpretation should occur in the context of tumor location.
Collapse
Affiliation(s)
- Frank A Sinicrope
- Department of Medicine, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota. Department of Oncology, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota.
| | - Michelle R Mahoney
- Alliance Statistics and Data Center, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota
| | - Harry H Yoon
- Department of Oncology, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota
| | - Thomas C Smyrk
- Laboratory Medicine and Pathology, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota
| | - Stephen N Thibodeau
- Laboratory Medicine and Pathology, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota
| | | | - Garth D Nelson
- Alliance Statistics and Data Center, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota
| | - Daniel J Sargent
- Alliance Statistics and Data Center, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota
| | - Steven R Alberts
- Department of Oncology, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota
| | | |
Collapse
|
25
|
Not All Next Generation Sequencing Diagnostics are Created Equal: Understanding the Nuances of Solid Tumor Assay Design for Somatic Mutation Detection. Cancers (Basel) 2015; 7:1313-32. [PMID: 26193321 PMCID: PMC4586770 DOI: 10.3390/cancers7030837] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 06/30/2015] [Accepted: 07/10/2015] [Indexed: 01/15/2023] Open
Abstract
The molecular characterization of tumors using next generation sequencing (NGS) is an emerging diagnostic tool that is quickly becoming an integral part of clinical decision making. Cancer genomic profiling involves significant challenges including DNA quality and quantity, tumor heterogeneity, and the need to detect a wide variety of complex genetic mutations. Most available comprehensive diagnostic tests rely on primer based amplification or probe based capture methods coupled with NGS to detect hotspot mutation sites or whole regions implicated in disease. These tumor panels utilize highly customized bioinformatics pipelines to perform the difficult task of accurately calling cancer relevant alterations such as single nucleotide variations, small indels or large genomic alterations from the NGS data. In this review, we will discuss the challenges of solid tumor assay design/analysis and report a case study that highlights the need to include complementary technologies (i.e., arrays) and germline analysis in tumor testing to reliably identify copy number alterations and actionable variants.
Collapse
|
26
|
Alanio A, Olivi M, Cabaret O, Foulet F, Bellanger AP, Millon L, Berceanu A, Cordonnier C, Costa JM, Bretagne S. Correlation Between Pneumocystis jirovecii Mitochondrial Genotypes and High and Low Fungal Loads Assessed by Single Nucleotide Primer Extension Assay and Quantitative Real-Time PCR. J Eukaryot Microbiol 2015; 62:650-6. [PMID: 25940946 DOI: 10.1111/jeu.12222] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 02/06/2015] [Accepted: 02/06/2015] [Indexed: 12/12/2022]
Abstract
We designed a single nucleotide primer extension (SNaPshot) assay for Pneumocystis jirovecii genotyping, targeting mt85 SNP of the mitochondrial large subunit ribosomal RNA locus, to improve minority allele detection. We then analyzed 133 consecutive bronchoalveolar lavage (BAL) fluids tested positive for P. jirovecii DNA by quantitative real-time PCR, obtained from two hospitals in different locations (Hospital 1 [n = 95] and Hospital 2 [n = 38]). We detected three different alleles, either singly (mt85C: 39.1%; mt85T: 24.1%; mt85A: 9.8%) or together (27%), and an association between P. jirovecii mt85 genotype and the patient's place of hospitalization (p = 0.011). The lowest fungal loads (median = 0.82 × 10(3) copies/μl; range: 15-11 × 10(3) ) were associated with mt85A and the highest (median = 1.4 × 10(6) copies/μl; range: 17 × 10(3) -1.3 × 10(7) ) with mt85CTA (p = 0.010). The ratios of the various alleles differed between the 36 mixed-genotype samples. In tests of serial BALs (median: 20 d; range 4-525) from six patients with mixed genotypes, allele ratio changes were observed five times and genotype replacement once. Therefore, allele ratio changes seem more frequent than genotype replacement when using a SNaPshot assay more sensitive for detecting minority alleles than Sanger sequencing. Moreover, because microscopy detects only high fungal loads, the selection of microscopy-positive samples may miss genotypes associated with low loads.
Collapse
Affiliation(s)
- Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.,Université Paris-Diderot, Sorbonne Cité, Paris, France.,Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycologie et Antifongiques, Paris, France.,CNRS URA3012, Paris, France
| | - Martine Olivi
- Laboratoire Cerba, Cergy-Pontoise, Saint-Ouen-l'Aumône, France
| | - Odile Cabaret
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe hospitalier Chenevier-Mondor, Créteil, France.,Université Paris-Est-Créteil, Créteil, France
| | - Françoise Foulet
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe hospitalier Chenevier-Mondor, Créteil, France.,Université Paris-Est-Créteil, Créteil, France
| | - Anne-Pauline Bellanger
- Laboratoire de Parasitologie-Mycologie, Centre hospitalier universitaire, Besançon, France.,Laboratoire Chrono-Environnement, Université Franche-Comté, UMR CNRS 6249, Besançon, France
| | - Laurence Millon
- Laboratoire de Parasitologie-Mycologie, Centre hospitalier universitaire, Besançon, France.,Laboratoire Chrono-Environnement, Université Franche-Comté, UMR CNRS 6249, Besançon, France
| | - Ana Berceanu
- Service d'Hématologie, Centre Hospitalier Universitaire, Besançon, France
| | - Catherine Cordonnier
- Université Paris-Est-Créteil, Créteil, France.,Département d'Hématologie, APHP, Groupe Hospitalier Albert Chenevier-Henri Mondor, Creteil, France
| | - Jean-Marc Costa
- Laboratoire Cerba, Cergy-Pontoise, Saint-Ouen-l'Aumône, France.,Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe hospitalier Chenevier-Mondor, Créteil, France
| | - Stéphane Bretagne
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.,Université Paris-Diderot, Sorbonne Cité, Paris, France.,Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycologie et Antifongiques, Paris, France.,CNRS URA3012, Paris, France
| |
Collapse
|
27
|
Serizawa M, Yokota T, Hosokawa A, Kusafuka K, Sugiyama T, Tsubosa Y, Yasui H, Nakajima T, Koh Y. The efficacy of uracil DNA glycosylase pretreatment in amplicon-based massively parallel sequencing with DNA extracted from archived formalin-fixed paraffin-embedded esophageal cancer tissues. Cancer Genet 2015; 208:415-27. [PMID: 26194062 DOI: 10.1016/j.cancergen.2015.05.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 04/10/2015] [Accepted: 05/01/2015] [Indexed: 12/21/2022]
Abstract
Advances in mutation testing for molecular-targeted cancer therapies have led to the increased use of archived formalin-fixed paraffin-embedded (FFPE) tumors. However, DNA extracted from FFPE tumors (FFPE DNA) is problematic for mutation testing, especially for amplicon-based massively parallel sequencing (MPS), owing to DNA fragmentation and artificial C:G > T:A single nucleotide variants (SNVs) caused by deamination of cytosine to uracil. Therefore, to reduce artificial C:G > T:A SNVs in amplicon-based MPS using FFPE DNA, we evaluated the efficacy of uracil DNA glycosylase (UDG) pretreatment, which can eliminate uracil-containing DNA molecules, with 126 archived FFPE esophageal cancer specimens. We also examined the association between the frequency of C:G > T:A SNVs and DNA quality, as assessed by a quantitative PCR (qPCR)-based assay. UDG pretreatment significantly lowered the frequency of C:G > T:A SNVs in highly fragmented DNA (by approximately 60%). This effect was not observed for good- to moderate-quality DNA, suggesting that a predictive assay (i.e., DNA quality assessment) needs to be performed prior to UDG pretreatment. These results suggest that UDG pretreatment is efficacious for mutation testing by amplicon-based MPS with fragmented DNA from FFPE samples.
Collapse
Affiliation(s)
- Masakuni Serizawa
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Japan
| | - Tomoya Yokota
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Japan; Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Sunto-gun, Japan
| | - Ayumu Hosokawa
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Toyama, Toyama, Japan
| | | | - Toshiro Sugiyama
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Yasuhiro Tsubosa
- Division of Esophageal Surgery, Shizuoka Cancer Center, Sunto-gun, Japan
| | - Hirofumi Yasui
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Sunto-gun, Japan
| | | | - Yasuhiro Koh
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Japan; Third Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan.
| |
Collapse
|
28
|
Gits-Muselli M, Peraldi MN, de Castro N, Delcey V, Menotti J, Guigue N, Hamane S, Raffoux E, Bergeron A, Valade S, Molina JM, Bretagne S, Alanio A. New Short Tandem Repeat-Based Molecular Typing Method for Pneumocystis jirovecii Reveals Intrahospital Transmission between Patients from Different Wards. PLoS One 2015; 10:e0125763. [PMID: 25933203 PMCID: PMC4416908 DOI: 10.1371/journal.pone.0125763] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/26/2015] [Indexed: 12/26/2022] Open
Abstract
Pneumocystis pneumonia is a severe opportunistic infection in immunocompromised patients caused by the unusual fungus Pneumocystis jirovecii. Transmission is airborne, with both immunocompromised and immunocompetent individuals acting as a reservoir for the fungus. Numerous reports of outbreaks in renal transplant units demonstrate the need for valid genotyping methods to detect transmission of a given genotype. Here, we developed a short tandem repeat (STR)-based molecular typing method for P. jirovecii. We analyzed the P. jirovecii genome and selected six genomic STR markers located on different contigs of the genome. We then tested these markers in 106 P. jirovecii PCR-positive respiratory samples collected between October 2010 and November 2013 from 91 patients with various underlying medical conditions. Unique (one allele per marker) and multiple (more than one allele per marker) genotypes were observed in 34 (32%) and 72 (68%) samples, respectively. A genotype could be assigned to 55 samples (54 patients) and 61 different genotypes were identified in total with a discriminatory power of 0.992. Analysis of the allelic distribution of the six markers and minimum spanning tree analysis of the 61 genotypes identified a specific genotype (Gt21) in our hospital, which may have been transmitted between 10 patients including six renal transplant recipients. Our STR-based molecular typing method is a quick, cheap and reliable approach to genotype Pneumocystis jirovecii in hospital settings and is sensitive enough to detect minor genotypes, thus enabling the study of the transmission and pathophysiology of Pneumocystis pneumonia.
Collapse
Affiliation(s)
- Maud Gits-Muselli
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France
| | - Marie-Noelle Peraldi
- Service de transplantation rénale, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France
- Université Paris-Diderot, Sorbonne Cité, Paris, France
| | - Nathalie de Castro
- Service de Maladie Infectieuses et tropicales, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France
| | - Véronique Delcey
- Service de Médecine interne, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Hôpital Lariboisière, Paris, France
| | - Jean Menotti
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France
- Université Paris-Diderot, Sorbonne Cité, Paris, France
- Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses invasives et Antifongiques, Paris, France
- CNRS URA3012, Paris, France
| | - Nicolas Guigue
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France
- Université Paris-Diderot, Sorbonne Cité, Paris, France
| | - Samia Hamane
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France
| | - Emmanuel Raffoux
- Service d’Hématologie adulte, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France
| | - Anne Bergeron
- Université Paris-Diderot, Sorbonne Cité, Paris, France
- Service de Pneumologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France
| | - Sandrine Valade
- Service de Réanimation, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France
| | - Jean-Michel Molina
- Université Paris-Diderot, Sorbonne Cité, Paris, France
- Service de Maladie Infectieuses et tropicales, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France
| | - Stéphane Bretagne
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France
- Université Paris-Diderot, Sorbonne Cité, Paris, France
- Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses invasives et Antifongiques, Paris, France
- CNRS URA3012, Paris, France
| | - Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France
- Université Paris-Diderot, Sorbonne Cité, Paris, France
- Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses invasives et Antifongiques, Paris, France
- CNRS URA3012, Paris, France
- * E-mail:
| |
Collapse
|
29
|
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.
Collapse
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)
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection. Biotechniques 2015; 58:126-34. [DOI: 10.2144/000114264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 12/17/2014] [Indexed: 11/23/2022] Open
Abstract
The detection of KRAS mutations in codons 12 and 13 is critical for anti-EGFR therapy strategies; however, only those methodologies with high sensitivity, specificity, and accuracy as well as the best cost and turnaround balance are suitable for routine daily testing. Here we compared the performance of compact sequencing using the novel hybcell technology with 454 next-generation sequencing (454-NGS), Sanger sequencing, and pyrosequencing, using an evaluation panel of 35 specimens. A total of 32 mutations and 10 wild-type cases were reported using 454-NGS as the reference method. Specificity ranged from 100% for Sanger sequencing to 80% for pyrosequencing. Sanger sequencing and hybcell-based compact sequencing achieved a sensitivity of 96%, whereas pyrosequencing had a sensitivity of 88%. Accuracy was 97% for Sanger sequencing, 85% for pyrosequencing, and 94% for hybcell-based compact sequencing. Quantitative results were obtained for 454-NGS and hybcell-based compact sequencing data, resulting in a significant correlation (r = 0.914). Whereas pyrosequencing and Sanger sequencing were not able to detect multiple mutated cell clones within one tumor specimen, 454-NGS and the hybcell-based compact sequencing detected multiple mutations in two specimens. Our comparison shows that the hybcell-based compact sequencing is a valuable alternative to state-of-the-art methodologies used for detection of clinically relevant point mutations.
Collapse
|
31
|
Zhang Y, Fang W, Yan Y, Wang M, Kang S, Sheng J, Zhan J, Chen N, Hong S, Yang Y, Ma Y, He D, Qin T, Zhou T, Tang Y, He X, Liang W, Zhang L. The efficacy of first-line chemotherapy is associated with KRAS mutation status in patients with advanced non-small cell lung cancer: a meta-analysis. Med Oncol 2015; 32:61. [DOI: 10.1007/s12032-015-0489-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 01/23/2015] [Indexed: 01/07/2023]
|
32
|
Sinicrope FA, Shi Q, Smyrk TC, Thibodeau SN, Dienstmann R, Guinney J, Bot BM, Tejpar S, Delorenzi M, Goldberg RM, Mahoney M, Sargent DJ, Alberts SR. Molecular markers identify subtypes of stage III colon cancer associated with patient outcomes. Gastroenterology 2015; 148:88-99. [PMID: 25305506 PMCID: PMC4274188 DOI: 10.1053/j.gastro.2014.09.041] [Citation(s) in RCA: 252] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Categorization of colon cancers into distinct subtypes using a combination of pathway-based biomarkers could provide insight into stage-independent variability in outcomes. METHODS We used a polymerase chain reaction-based assay to detect mutations in BRAF (V600E) and in KRAS in 2720 stage III cancer samples, collected prospectively from patients participating in an adjuvant chemotherapy trial (NCCTG N0147). Tumors deficient or proficient in DNA mismatch repair (MMR) were identified based on detection of MLH1, MSH2, and MSH6 proteins and methylation of the MLH1 promoter. Findings were validated using tumor samples from a separate set of patients with stage III cancer (n = 783). Association with 5-year disease-free survival was evaluated using Cox proportional hazards models. RESULTS Tumors were categorized into 5 subtypes based on MMR status and detection of BRAF or KRAS mutations which were mutually exclusive. Three subtypes were MMR proficient: those with mutations in BRAF (6.9% of samples), mutations in KRAS (35%), or tumors lacking either BRAF or KRAS mutations (49%). Two subtypes were MMR deficient: the sporadic type (6.8%) with BRAF mutation and/or or hypermethylation of MLH1 and the familial type (2.6%), which lacked BRAF(V600E) or hypermethylation of MLH1. A higher percentage of MMR-proficient tumors with BRAF(V600E) were proximal (76%), high-grade (44%), N2 stage (59%), and detected in women (59%), compared with MMR-proficient tumors without BRAF(V600E) or KRAS mutations (33%, 19%, 41%, and 42%, respectively; all P < .0001). A significantly lower proportion of patients with MMR-proficient tumors with mutant BRAF (hazard ratio = 1.43; 95% confidence interval: 1.11-1.85; Padjusted = .0065) or mutant KRAS (hazard ratio = 1.48; 95% confidence interval: 1.27-1.74; Padjusted < .0001) survived disease-free for 5 years compared with patients whose MMR-proficient tumors lacked mutations in either gene. Disease-free survival rates of patients with MMR-deficient sporadic or familial subtypes was similar to those of patients with MMR-proficient tumors without BRAF or KRAS mutations. The observed differences in survival rates of patients with different tumor subtypes were validated in an independent cohort. CONCLUSIONS We identified subtypes of stage III colon cancer, based on detection of mutations in BRAF (V600E) or KRAS, and MMR status that show differences in clinical and pathologic features and disease-free survival. Patients with MMR-proficient tumors and BRAF or KRAS mutations had statistically shorter survival times than patients whose tumors lacked these mutations. The tumor subtype found in nearly half of the study cohort (MMR-proficient without BRAF(V600E) or KRAS mutations) had similar outcomes to those of patients with MMR-deficient cancers.
Collapse
Affiliation(s)
- Frank A. Sinicrope
- Department of Medicine, Mayo Clinic, Rochester, MN,Department of Oncology, Mayo Clinic, Rochester, MN
| | - Qian Shi
- Alliance Statistics and Data Center, Mayo Clinic, Rochester, MN
| | - Thomas C. Smyrk
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | | | | | | | - Sabine Tejpar
- Molecular Digestive Oncology, KU Leuven, The Netherlands
| | - Mauro Delorenzi
- Swiss Institute of Bioinformatics, University Lausanne, Switzerland
| | - Richard M. Goldberg
- Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH
| | | | | | | |
Collapse
|
33
|
Anti-EGFR Resistance in Colorectal Cancer: Current Knowledge and Future Perspectives. CURRENT COLORECTAL CANCER REPORTS 2014. [DOI: 10.1007/s11888-014-0242-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
34
|
Immunohistochemistry with a novel mutation-specific monoclonal antibody as a screening tool for the EGFR L858R mutational status in primary lung adenocarcinoma. Tumour Biol 2014; 36:693-700. [DOI: 10.1007/s13277-014-2643-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 11/28/2013] [Indexed: 12/29/2022] Open
|
35
|
Laurent-Puig P, Pekin D, Normand C, Kotsopoulos SK, Nizard P, Perez-Toralla K, Rowell R, Olson J, Srinivasan P, Le Corre D, Hor T, El Harrak Z, Li X, Link DR, Bouché O, Emile JF, Landi B, Boige V, Hutchison JB, Taly V. Clinical relevance of KRAS-mutated subclones detected with picodroplet digital PCR in advanced colorectal cancer treated with anti-EGFR therapy. Clin Cancer Res 2014; 21:1087-97. [PMID: 25248381 DOI: 10.1158/1078-0432.ccr-14-0983] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE KRAS mutations are predictive of nonresponse to anti-EGFR therapies in metastatic colorectal cancer (mCRC). However, only 50% of nonmutated patients benefit from them. KRAS-mutated subclonal populations nondetectable by conventional methods have been suggested as the cause of early progression. Molecular analysis technology with high sensitivity and precision is required to test this hypothesis. EXPERIMENTAL DESIGN From two cohorts of patients with mCRC, 136 KRAS, NRAS, and BRAF wild-type tumors with sufficient tumor material to perform highly sensitive picodroplet digital PCR (dPCR) and 41 KRAS-mutated tumors were selected. All these patients were treated by anti-EGFR therapy. dPCR was used for KRAS or BRAF mutation screening and compared with qPCR. Progression-free survival (PFS) and overall survival (OS) were analyzed according to the KRAS-mutated allele fraction. RESULTS In addition to the confirmation of the 41 patients with KRAS-mutated tumors, dPCR also identified KRAS mutations in 22 samples considered as KRAS wild-type by qPCR. The fraction of KRAS-mutated allele quantified by dPCR was inversely correlated with anti-EGFR therapy response rate (P < 0.001). In a Cox model, the fraction of KRAS-mutated allele was associated with worse PFS and OS. Patients with less than 1% of mutant KRAS allele have similar PFS and OS than those with wild-type KRAS tumors. CONCLUSIONS This study suggests that patients with mCRC with KRAS-mutated subclones (at least those with a KRAS-mutated subclones fraction lower or equal to 1%) had a benefit from anti-EGFR therapies.
Collapse
Affiliation(s)
- Pierre Laurent-Puig
- Université Paris Sorbonne Cité; INSERM UMR-S1147; Centre Universitaire des Saints-Pères, Paris, France. Departement of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.
| | - Deniz Pekin
- Université Paris Sorbonne Cité; INSERM UMR-S1147; Centre Universitaire des Saints-Pères, Paris, France
| | - Corinne Normand
- Université Paris Sorbonne Cité; INSERM UMR-S1147; Centre Universitaire des Saints-Pères, Paris, France
| | | | - Philippe Nizard
- Université Paris Sorbonne Cité; INSERM UMR-S1147; Centre Universitaire des Saints-Pères, Paris, France
| | - Karla Perez-Toralla
- Université Paris Sorbonne Cité; INSERM UMR-S1147; Centre Universitaire des Saints-Pères, Paris, France
| | | | - Jeff Olson
- RainDance Technologies, Billerica, Massachusetts
| | | | - Delphine Le Corre
- Université Paris Sorbonne Cité; INSERM UMR-S1147; Centre Universitaire des Saints-Pères, Paris, France
| | - Thevy Hor
- Université Paris Sorbonne Cité; INSERM UMR-S1147; Centre Universitaire des Saints-Pères, Paris, France
| | - Zakaria El Harrak
- Université Paris Sorbonne Cité; INSERM UMR-S1147; Centre Universitaire des Saints-Pères, Paris, France
| | - Xinyu Li
- RainDance Technologies, Billerica, Massachusetts
| | | | - Olivier Bouché
- Service d'hépatogastroentérologie et de Cancérologie Digestive, CHU de Reims, Hôpital Robert-Debré, Reims, France
| | - Jean-François Emile
- Department of Pathology, Hôpital Ambroise Paré, AP-HP, Université de Versailles St Quentin en Yvelines, Boulogne-Billancourt, France
| | - Bruno Landi
- Department of Oncology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | | | | | - Valerie Taly
- Université Paris Sorbonne Cité; INSERM UMR-S1147; Centre Universitaire des Saints-Pères, Paris, France.
| |
Collapse
|
36
|
Patton S, Normanno N, Blackhall F, Murray S, Kerr KM, Dietel M, Filipits M, Benlloch S, Popat S, Stahel R, Thunnissen E. Assessing standardization of molecular testing for non-small-cell lung cancer: results of a worldwide external quality assessment (EQA) scheme for EGFR mutation testing. Br J Cancer 2014; 111:413-20. [PMID: 24983368 PMCID: PMC4102953 DOI: 10.1038/bjc.2014.353] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The external quality assurance (EQA) process aims at establishing laboratory performance levels. Leading European groups in the fields of EQA, Pathology, and Medical and Thoracic Oncology collaborated in a pilot EQA scheme for somatic epidermal growth factor receptor (EGFR) gene mutational analysis in non-small-cell lung cancer (NSCLC). METHODS EQA samples generated from cell lines mimicking clinical samples were provided to participating laboratories, each with a mock clinical case. Participating laboratories performed the analysis using their usual method(s). Anonymous results were assessed and made available to all participants. Two subsequent EQA rounds followed the pilot scheme. RESULTS One hundred and seventeen labs from 30 countries registered and 91 returned results. Sanger sequencing and a commercial kit were the main methodologies used. The standard of genotyping was suboptimal, with a significant number of genotyping errors made. Only 72 out of 91 (72%) participants passed the EQA. False-negative and -positive results were the main sources of error. The quality of reports submitted was acceptable; most were clear, concise and easy to read. However, some participants reported the genotyping result in the absence of any interpretation and many obscured the interpretation required for clinical care. CONCLUSIONS Even in clinical laboratories, the technical performance of genotyping in EGFR mutation testing for NSCLC can be improved, evident from a high level of diagnostic errors. Robust EQA can contribute to global optimisation of EGFR testing for NSCLC patients.
Collapse
Affiliation(s)
- S Patton
- EMQN, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester M13 9WL, UK
| | - N Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori ‘Fondazione Giovanni Pascale'—IRCCS, 80131 Naples, Italy
| | | | - S Murray
- Biomarker Solutions Ltd, London EC1V 2NX, UK
| | - K M Kerr
- Department of Pathology, Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - M Dietel
- Charité, Humboldt-Universität zu Berlin, Berlin 10117, Germany
| | - M Filipits
- Medical University of Vienna, 1010 Vienna, Austria
| | - S Benlloch
- Pangaea Biotech, USP Dexeus University Institute, Barcelona 08028, Spain
| | - S Popat
- Royal Marsden Hospital, London SW3 6JJ, UK
| | - R Stahel
- University Hospital Zürich, CH-8091 Zürich, Switzerland
| | - E Thunnissen
- Department of Pathology, VU University Medical Center, Amsterdam 1081 HZ, The Netherlands
| |
Collapse
|
37
|
Sherwood JL, Müller S, Orr MCM, Ratcliffe MJ, Walker J. Panel based MALDI-TOF tumour profiling is a sensitive method for detecting mutations in clinical non small cell lung cancer tumour. PLoS One 2014; 9:e100566. [PMID: 24956168 PMCID: PMC4067351 DOI: 10.1371/journal.pone.0100566] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 05/23/2014] [Indexed: 02/07/2023] Open
Abstract
Background Analysis of tumour samples for mutations is becoming increasingly important in driving personalised therapy in cancer. As more targeted therapies are developed, options to survey mutations in multiple genes in a single tumour sample will become ever more attractive and are expected to become the mainstay of molecular diagnosis in non-small cell lung cancer (NSCLC) in the future. Materials and Methods 238 non-small cell lung cancer (NSCLC) tumour samples were analysed using a custom panel of 82 mutation assays across 14 oncogenes including KRAS and EGFR using Sequenom iPlex Matrix Assisted Laser Desorption/Ionisation Time of Flight Mass Spectrometry (MALDI-TOF). We compared the data generated for KRAS mutations to those detected by Amplification Refractory Mutation System (ARMS) based DxS TheraScreen K-RAS Mutation Kit. Results The ARMS detected mutations in 46/238 tumour samples. For samples with mutations detected by both approaches, 99.1% overall agreement was observed. The MALDI-TOF method detected an additional 6 samples as KRAS mutation positive and also provided data on concomitant mutations including PIK3CA and TP53. Conclusions The Sequenom MALDI-TOF method provides a sensitive panel-based approach which makes efficient use of patient diagnostic samples. This technology could provide an opportunity to deliver comprehensive screening of relevant biomarkers to the clinic earlier in disease management, without the need for repeat biopsy and allow for additional downstream analysis in NSCLC where available tissue may have been exhausted.
Collapse
Affiliation(s)
- James L. Sherwood
- Personalised Healthcare & Biomarkers, AstraZeneca, Macclesfield, United Kingdom
- * E-mail:
| | | | - Maria C. M. Orr
- Personalised Healthcare & Biomarkers, AstraZeneca, Macclesfield, United Kingdom
| | | | - Jill Walker
- Personalised Healthcare & Biomarkers, AstraZeneca, Macclesfield, United Kingdom
| |
Collapse
|
38
|
A new sensitive PCR assay for one-step detection of 12 IDH1/2 mutations in glioma. Acta Neuropathol Commun 2014; 2:58. [PMID: 24889502 PMCID: PMC4229941 DOI: 10.1186/2051-5960-2-58] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/23/2014] [Indexed: 01/13/2023] Open
Abstract
INTRODUCTION Mutations in isocitrate dehydrogenase genes IDH1 or IDH2 are frequent in glioma, and IDH mutation status is a strong diagnostic and prognostic marker. Current IDH mutation screening is performed with an immunohistochemistry (IHC) assay specific for IDH1 R132H, the most common mutation. Sequencing is recommended as a second-step test for IHC-negative or -equivocal cases. We developed and validated a new real-time quantitative polymerase chain reaction (PCR) assay for single-step detection of IDH1 R132H and 11 rare IDH1/2 mutations in formalin-fixed paraffin-embedded (FFPE) glioma samples. Performance of the IDH1/2 PCR assay was compared to IHC and Sanger sequencing. RESULTS The IDH1/2 PCR assay combines PCR clamping for detection of 7 IDH1 and 5 IDH2 mutations, and Amplification Refractory Mutation System technology for specific identification of the 3 most common mutations (IDH1 R132H, IDH1 R132C, IDH2 R172K). Analytical sensitivity of the PCR assay for mutation detection was <5% for 11/12 mutations (mean: 3.3%), and sensitivity for mutation identification was very high (0.8% for IDH1 R132H; 1.2% for IDH1 R132C; 0.6% for IDH2 R172K). Assay performance was further validated on 171 clinical glioma FFPE samples; of these, 147 samples met the selection criteria and 146 DNA samples were successfully extracted. IDH1/2 status was successfully obtained in 91% of cases. All but one positive IDH1 R132H-IHC cases were concordantly detected by PCR and 3 were not detected by sequencing. Among the IHC-negative cases (n = 72), PCR detected 12 additional rare mutations (10 IDH1, 2 IDH2). All mutations detected by sequencing (n = 67) were concordantly detected by PCR and 5/66 sequencing-negative cases were PCR-positive (overall concordance: 96%). Analysis of synthetic samples representative of the 11 rare IDH1/2 mutations detected by the assay produced 100% correct results. CONCLUSIONS The new IDH1/2 PCR assay has a high technical success rate and is more sensitive than Sanger sequencing. Positive concordance was 98% with IHC for IDH1 R132H detection and 100% with sequencing. The PCR assay can reliably be performed on FFPE samples and has a faster turnaround time than current IDH mutation detection algorithms. The assay should facilitate implementation of a comprehensive IDH1/2 testing protocol in routine clinical practice.
Collapse
|
39
|
Real-time bidirectional pyrophosphorolysis-activated polymerization for quantitative detection of somatic mutations. PLoS One 2014; 9:e96420. [PMID: 24769870 PMCID: PMC4000192 DOI: 10.1371/journal.pone.0096420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/07/2014] [Indexed: 12/24/2022] Open
Abstract
Detection of somatic mutations for targeted therapy is increasingly used in clinical settings. However, due to the difficulties of detecting rare mutations in excess of wild-type DNA, current methods often lack high sensitivity, require multiple procedural steps, or fail to be quantitative. We developed real-time bidirectional pyrophosphorolysis-activated polymerization (real-time Bi-PAP) that allows quantitative detection of somatic mutations. We applied the method to quantify seven mutations at codons 12 and 13 in KRAS, and 2 mutations (L858R, and T790M) in EGFR in clinical samples. The real-time Bi-PAP could detect 0.01% mutation in the presence of 100 ng template DNA. Of the 34 samples from the colon cancer patients, real-time Bi-PAP detected 14 KRAS mutant samples whereas the traditional real-time allele-specific PCR missed two samples with mutation abundance <1% and DNA sequencing missed nine samples with mutation abundance <10%. The detection results of the two EGFR mutations in 45 non-small cell lung cancer samples further supported the applicability of the real-time Bi-PAP. The real-time Bi-PAP also proved to be more efficient than the real-time allele-specific PCR in the detection of templates prepared from formalin-fixed paraffin-embedded samples. Thus, real-time Bi-PAP can be used for rapid and accurate quantification of somatic mutations. This flexible approach could be widely used for somatic mutation detection in clinical settings.
Collapse
|
40
|
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.
Collapse
Affiliation(s)
- Bryce P Portier
- Dept of Hematopathology, MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 149, Houston, TX 77030; e-mail:
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Clinical validation of a PCR assay for the detection of EGFR mutations in non-small-cell lung cancer: retrospective testing of specimens from the EURTAC trial. PLoS One 2014; 9:e89518. [PMID: 24586842 PMCID: PMC3934888 DOI: 10.1371/journal.pone.0089518] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 01/21/2014] [Indexed: 01/21/2023] Open
Abstract
The EURTAC trial demonstrated that the tyrosine kinase inhibitor (TKI) erlotinib was superior to chemotherapy as first-line therapy for advanced non-small cell lung cancers (NSCLC) that harbor EGFR activating mutations in a predominantly Caucasian population. Based on EURTAC and several Asian trials, anti-EGFR TKIs are standard of care for EGFR mutation-positive NSCLC. We sought to validate a rapid multiplex EGFR mutation assay as a companion diagnostic assay to select patients for this therapy. Samples from the EURTAC trial were prospectively screened for EGFR mutations using a combination of laboratory-developed tests (LDTs), and tested retrospectively with the cobas EGFR mutation test (EGFR PCR test). The EGFR PCR test results were compared to the original LDT results and to Sanger sequencing, using a subset of specimens from patients screened for the trial. Residual tissue was available from 487 (47%) of the 1044 patients screened for the trial. The EGFR PCR test showed high concordance with LDT results with a 96.3% overall agreement. The clinical outcome of patients who were EGFR-mutation detected by the EGFR PCR test was very similar to the entire EURTAC cohort. The concordance between the EGFR PCR test and Sanger sequencing was 90.6%. In 78.9% of the discordant samples, the EGFR PCR test result was confirmed by a sensitive deep sequencing assay. This retrospective study demonstrates the clinical utility of the EGFR PCR test in the accurate selection of patients for anti-EGFR TKI therapy. The EGFR PCR test demonstrated improved performance relative to Sanger sequencing.
Collapse
|
42
|
KRAS mutations: analytical considerations. Clin Chim Acta 2014; 431:211-20. [PMID: 24534449 DOI: 10.1016/j.cca.2014.01.049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/20/2014] [Accepted: 01/22/2014] [Indexed: 12/27/2022]
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second most common cause of cancer death globally. Significant improvements in survival have been made in patients with metastasis by new therapies. For example, Cetuximab and Panitumumab are monoclonal antibodies that inhibit the epidermal growth receptor (EGFR). KRAS mutations in codon 12 and 13 are the recognized biomarkers that are analyzed in clinics before the administration of anti-EGFR therapy. Genetic analyses have revealed that mutations in KRAS predict a lack of response to Panitumumab and Cetuximab in patients with metastatic CRC (mCRC). Notably, it is estimated that 35-45% of CRC patients harbor KRAS mutations. Therefore, KRAS mutation testing should be performed in all individuals with the advanced CRC in order to identify the patients who will not respond to the monoclonal EGFR antibody inhibitors. New techniques for KRAS testing have arisen rapidly, and each technique has advantages and disadvantages. Herein, we review the latest published literature specific to KRAS mutation testing techniques. Since reliability and feasibility are important issues in clinical analyses. Therefore, this review also summarizes the effectiveness and limitations of numerous KRAS mutation testing techniques.
Collapse
|
43
|
A Multicenter Blinded Study Evaluating EGFR and KRAS Mutation Testing Methods in the Clinical Non–Small Cell Lung Cancer Setting—IFCT/ERMETIC2 Project Part 1. J Mol Diagn 2014; 16:45-55. [DOI: 10.1016/j.jmoldx.2013.07.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 07/04/2013] [Accepted: 07/30/2013] [Indexed: 11/22/2022] Open
|
44
|
Mori N, Ohwashi M, Yoshinaga K, Mitsuhashi K, Tanaka N, Teramura M, Okada M, Shiseki M, Tanaka J, Motoji T. L265P mutation of the MYD88 gene is frequent in Waldenström's macroglobulinemia and its absence in myeloma. PLoS One 2013; 8:e80088. [PMID: 24224040 PMCID: PMC3818242 DOI: 10.1371/journal.pone.0080088] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 10/09/2013] [Indexed: 11/18/2022] Open
Abstract
L265P mutation in the MYD88 gene has recently been reported in Waldenström’s macroglobulinemia; however the incidence has been different according to the methods used. To determine the relevance and compare the incidence by different methods, we analyzed the L265P mutation in bone marrow mononuclear cells from lymphoid neoplasms. We first performed cloning and sequencing in 10 patients: 8 Waldenström’s macroglobulinemia; 1 non-IgM-secreting lymphoplasmacytic lymphoma; and 1 low grade B-cell lymphoma with monoclonal IgG protein. The L265P mutation was detected in only 1/8 Waldenström’s macroglobulinemia patients (2 of 9 clones). To confirm these results, direct sequencing was performed in the 10 patients and an additional 17 Waldenström’s macroglobulinemia patients and 1 lymphoplasmacytic lymphoma patient. Nine of 28 patients (7/25 Waldenström’s macroglobulinemia, 1/2 lymphoplasmacytic lymphoma, and B-cell lymphoma) harbored the mutation. We next tested for the mutation with BSiE1 digestion and allele-specific polymerase chain reaction in the 28 patients and 38 patients with myeloma. Aberrant bands corresponding to the mutation were detected by BSiE1 digestion in 19/25 patients with Waldenström’s macroglobulinemia (76%), 1/2 lymphoplasmacytic lymphoma and B-cell lymphoma, but not in the 38 myeloma patients. The L265P mutation was more frequent in patients with Waldenström’s macroglobulinemia than in those with myeloma (p=1.3x10-10). The mutation was detected by allele-specific polymerase chain reaction in 18/25 Waldenström’s macroglobulinemia patients (72%). In the 25 Waldenström’s macroglobulinemia patients, the L265P was more frequently detected by BSiE1 digestion than by direct sequencing (p=5.3x10-4), and in males (15/16, 94%) than in females (4/9, 44%) (p=1.2x10-2). No siginificant difference was observed in the incidence of the L265P mutation between BSiE1 digestion and allele-specific polymerase chain reaction (p=0.32). These results suggest that the L265P mutation is involved in the majority of Waldenström’s macroglobulinemia. BSiE1 digestion and allele-specific polymerase chain reaction may detect a small fraction of mutated cells in some cases.
Collapse
Affiliation(s)
- Naoki Mori
- Department of Hematology, Tokyo Women’s Medical University, Tokyo, Japan
- * E-mail:
| | - Mari Ohwashi
- Department of Hematology, Tokyo Women’s Medical University, Tokyo, Japan
| | - Kentaro Yoshinaga
- Department of Hematology, Tokyo Women’s Medical University, Tokyo, Japan
| | - Kenjiro Mitsuhashi
- Department of Hematology, Tokyo Women’s Medical University, Tokyo, Japan
| | - Norina Tanaka
- Department of Hematology, Tokyo Women’s Medical University, Tokyo, Japan
| | - Masanao Teramura
- Department of Hematology, Tokyo Women’s Medical University, Tokyo, Japan
| | - Michiko Okada
- Department of Hematology, Tokyo Women’s Medical University, Tokyo, Japan
| | - Masayuki Shiseki
- Department of Hematology, Tokyo Women’s Medical University, Tokyo, Japan
| | - Junji Tanaka
- Department of Hematology, Tokyo Women’s Medical University, Tokyo, Japan
| | - Toshiko Motoji
- Department of Hematology, Tokyo Women’s Medical University, Tokyo, Japan
| |
Collapse
|
45
|
Viray H, Li K, Long TA, Vasalos P, Bridge JA, Jennings LJ, Halling KC, Hameed M, Rimm DL. A Prospective, Multi-Institutional Diagnostic Trial to Determine Pathologist Accuracy in Estimation of Percentage of Malignant Cells. Arch Pathol Lab Med 2013; 137:1545-9. [DOI: 10.5858/arpa.2012-0561-cp] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
46
|
Martín-Algarra S, Fernández-Figueras MT, López-Martín JA, Santos-Briz A, Arance A, Lozano MD, Berrocal A, Ríos-Martín JJ, Espinosa E, Rodríguez-Peralto JL. Guidelines for biomarker testing in metastatic melanoma: a National Consensus of the Spanish Society of Pathology and the Spanish Society of Medical Oncology. Clin Transl Oncol 2013; 16:362-73. [DOI: 10.1007/s12094-013-1090-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 07/16/2013] [Indexed: 12/19/2022]
|
47
|
Beyond the standard of care: the role of cytopathology in molecular testing of cancer. Cancer Treat Res 2013. [PMID: 24092374 DOI: 10.1007/978-3-642-38850-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
48
|
How Kit A, Mazaleyrat N, Daunay A, Nielsen HM, Terris B, Tost J. Sensitive Detection of KRAS
Mutations Using Enhanced-ice
-COLD-PCR Mutation Enrichment and Direct Sequence Identification. Hum Mutat 2013; 34:1568-80. [DOI: 10.1002/humu.22427] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 08/02/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Alexandre How Kit
- Laboratory for Functional Genomics; Fondation Jean Dausset - CEPH, 27 rue Juliette Dodu; Paris 75010 France
| | - Nicolas Mazaleyrat
- Laboratory for Epigenetics and Environment; Centre National de Génotypage, CEA- Institut de Génomique; Evry 91000 France
| | - Antoine Daunay
- Laboratory for Functional Genomics; Fondation Jean Dausset - CEPH, 27 rue Juliette Dodu; Paris 75010 France
| | - Helene Myrtue Nielsen
- Laboratory for Functional Genomics; Fondation Jean Dausset - CEPH, 27 rue Juliette Dodu; Paris 75010 France
| | - Benoît Terris
- Service d'Anatomie et de Cytologie Pathologique; Hôpital Cochin, AP-HP, Université Paris Descartes; Paris 75014 France
- Institut Cochin de Génétique Moléculaire; Université Paris V René Descartes, CNRS (UMR8104); Paris 75014 France
- Institut National de la Santé et de la Recherche Médicale U567; Paris 75014 France
| | - Jörg Tost
- Laboratory for Functional Genomics; Fondation Jean Dausset - CEPH, 27 rue Juliette Dodu; Paris 75010 France
- Laboratory for Epigenetics and Environment; Centre National de Génotypage, CEA- Institut de Génomique; Evry 91000 France
| |
Collapse
|
49
|
Malapelle U, Carlomagno C, de Luca C, Bellevicine C, Troncone G. KRAS testing in metastatic colorectal carcinoma: challenges, controversies, breakthroughs and beyond. J Clin Pathol 2013; 67:1-9. [DOI: 10.1136/jclinpath-2013-201835] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
50
|
Sinicrope FA, Mahoney MR, Smyrk TC, Thibodeau SN, Warren RS, Bertagnolli MM, Nelson GD, Goldberg RM, Sargent DJ, Alberts SR. Prognostic impact of deficient DNA mismatch repair in patients with stage III colon cancer from a randomized trial of FOLFOX-based adjuvant chemotherapy. J Clin Oncol 2013; 31:3664-72. [PMID: 24019539 DOI: 10.1200/jco.2013.48.9591] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
PURPOSE The association of deficient DNA mismatch repair (dMMR) with prognosis in patients with colon cancer treated with adjuvant fluorouracil, leucovorin, and oxaliplatin (FOLFOX) chemotherapy remains unknown. PATIENTS AND METHODS Resected, stage III colon carcinomas from patients (N = 2,686) randomly assigned to FOLFOX ± cetuximab (North Central Cancer Treatment Group N0147 trial) were analyzed for mismatch repair (MMR) protein expression and mutations in BRAF(V600E) (exon 15) and KRAS (codons 12 and 13). Association of biomarkers with disease-free survival (DFS) was determined using Cox models. A validation cohort (Cancer and Leukemia Group B 88903 trial) was used. RESULTS dMMR was detected in 314 (12%) of 2,580 tumors, of which 49.3% and 10.6% had BRAF(V600E) or KRAS mutations, respectively. MMR status was not prognostic overall (adjusted hazard ratio [HR], 0.82; 95% CI, 0.64 to 1.07; P = .14), yet significant interactions were found between MMR and primary tumor site (P(interaction) = .009) and lymph node category (N1 v N2; P(interaction) = .014). Favorable DFS was observed for dMMR versus proficient MMR proximal tumors (HR, 0.71; 95% CI, 0.53 to 0.94; P = .018) but not dMMR distal tumors (HR, 1.71; 95% CI, 0.99 to 2.95; P = .056), adjusting for mutations and covariates. Any survival benefit of dMMR was lost in N2 tumors. Mutations in BRAF(V600E) (HR, 1.37; 95% CI, 1.08 to 1.70; P = .009) or KRAS (HR, 1.44; 95% CI, 1.21 to 1.70; P < .001) were independently associated with worse DFS. The observed MMR by tumor site interaction was validated in an independent cohort of stage III colon cancers (P(interaction) = .037). CONCLUSION The prognostic impact of MMR depended on tumor site, and this interaction was validated in an independent cohort. Among dMMR cancers, proximal tumors had favorable outcome, whereas distal or N2 tumors had poor outcome. BRAF or KRAS mutations were independently associated with adverse outcome.
Collapse
Affiliation(s)
- Frank A Sinicrope
- Frank A. Sinicrope, Michelle R. Mahoney, Thomas C. Smyrk, Stephen N. Thibodeau, Garth D. Nelson, Daniel J. Sargent, and Steven R. Alberts, Mayo Clinic, Mayo Cancer Center and the North Central Cancer Treatment Group, Rochester, MN; Robert S. Warren, University of California San Francisco, San Francisco, CA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; and Richard M. Goldberg, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | | | | | | | | | | | | | | | | | | |
Collapse
|