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Xu B, Lan Y, Luo D, Zheng Y, Ni R, Su G, Huang Q, Li Q. Highly Sensitive Detection of PIK3CA Mutations by Looping-Out Probes-Based Melting Curve Analysis. Biochem Genet 2024; 62:77-94. [PMID: 37249716 DOI: 10.1007/s10528-023-10408-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 05/19/2023] [Indexed: 05/31/2023]
Abstract
PIK3CA mutations have important therapeutic and prognostic implications in various cancer types. However, highly sensitive detection of PIK3CA hotspot mutations in heterogeneous tumor samples remains a challenge in clinical settings. To establish a rapid PCR assay for highly sensitive detection of multiple PIK3CA hotspot mutations. We described a novel melting curve analysis-based assay using looping-out probes that can enrich target mutations in the background of excess wild-type and concurrently reveal the presence of mutations. The analytical and clinical performance of the assay were evaluated. The developed assay could detect 10 PIK3CA hotspot mutations at a mutant allele fraction of 0.05-0.5% within 2 h in a single step. Analysis of 82 breast cancer tissue samples revealed 43 samples with PIK3CA mutations, 28 of which were confirmed by Sanger sequencing. Further testing of 175 colorectal cancer tissue samples showed that 24 samples contained PIK3CA mutations and 19 samples were confirmed by Sanger sequencing. Droplet digital PCR supported that all mutation-containing samples undetected by sequencing contained mutations with a low allele fraction. The rapidity, ease of use, high sensitivity and accuracy make the new assay a potential screening tool for PIK3CA mutations in clinical laboratories.
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Affiliation(s)
- Boheng Xu
- Department of Molecular Diagnostics, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong, China
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yanping Lan
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Danjiao Luo
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yangsi Zheng
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Runfang Ni
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Guoqiang Su
- The First Affiliated Hospital of Xiamen University, Xiamen, 361003, Fujian, China
| | - Qiuying Huang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
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2
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Lan Y, Xu B, Xi Y, Luo Y, Guo X, Huang Z, Luo D, Zhu A, He P, Li C, Huang Q, Li Q. Accurate Detection of Multiple Tumor Mutations in Formalin-Fixed Paraffin-Embedded Tissues by Coupling Sequence Artifacts Elimination and Mutation Enrichment With MeltArray. J Transl Med 2024; 104:100300. [PMID: 38042496 DOI: 10.1016/j.labinv.2023.100300] [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: 09/07/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are the primary source of DNA for companion diagnostics (CDx) of cancers. Degradation of FFPE tissue DNA and inherent tumor heterogeneity constitute serious challenges in current CDx assays. To address these limitations, we introduced sequence artifact elimination and mutation enrichment to MeltArray, a highly multiplexed PCR approach, to establish an integrated protocol that provides accuracy, ease of use, and rapidness. Using PIK3CA mutations as a model, we established a MeltArray protocol that could eliminate sequence artifacts completely and enrich mutations from 23.5- to 59.4-fold via a single-reaction pretreatment step comprising uracil-DNA-glycosylase excision and PCR clamping. The entire protocol could identify 13 PIK3CA hotspot mutations of 0.05% to 0.5% mutant allele fractions within 5 hours. Evaluation of 106 breast cancer and 40 matched normal FFPE tissue samples showed that all 47 PIK3CA mutant samples were from the cancer tissue, and no false-positive results were detected in the normal samples. Further evaluation of 105 colorectal and 40 matched normal FFPE tissue samples revealed that 11 PIK3CA mutants were solely from the cancer sample. The detection results of our protocol were consistent with those of the droplet digital PCR assays that underwent sequence artifact elimination. Of the 60 colorectal samples with next-generation sequencing results, the MeltArray protocol detected 2 additional mutant samples with low mutant allele fractions. We conclude that the new protocol provides an improved alternative to current CDx assays for detecting tumor mutations in FFPE tissue DNA.
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Affiliation(s)
- Yanping Lan
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Boheng Xu
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, China
| | - Yuxin Xi
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yi Luo
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China; School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiaoxia Guo
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Zhibin Huang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Danjiao Luo
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Anqi Zhu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Pujing He
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Changxing Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China; School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Qiuying Huang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China.
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China.
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3
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Pablo-Fontecha V, Hernández-Illán E, Reparaz A, Asensio E, Morata J, Tonda R, Lahoz S, Parra C, Lozano JJ, García-Heredia A, Martínez-Roca A, Beltran S, Balaguer F, Jover R, Castells A, Trullàs R, Podlesniy P, Camps J. Quantification of rare somatic single nucleotide variants by droplet digital PCR using SuperSelective primers. Sci Rep 2023; 13:18997. [PMID: 37923774 PMCID: PMC10624686 DOI: 10.1038/s41598-023-39874-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/01/2023] [Indexed: 11/06/2023] Open
Abstract
Somatic single-nucleotide variants (SNVs) occur every time a cell divides, appearing even in healthy tissues at low frequencies. These mutations may accumulate as neutral variants during aging, or eventually, promote the development of neoplasia. Here, we present the SP-ddPCR, a droplet digital PCR (ddPCR) based approach that utilizes customized SuperSelective primers aiming at quantifying the proportion of rare SNVs. For that purpose, we selected five potentially pathogenic variants identified by whole-exome sequencing (WES) occurring at low variant allele frequency (VAF) in at-risk colon healthy mucosa of patients diagnosed with colorectal cancer or advanced adenoma. Additionally, two APC SNVs detected in two cancer lesions were added to the study for WES-VAF validation. SuperSelective primers were designed to quantify SNVs at low VAFs both in silico and in clinical samples. In addition to the two APC SNVs in colonic lesions, SP-ddPCR confirmed the presence of three out of five selected SNVs in the normal colonic mucosa with allelic frequencies ≤ 5%. Moreover, SP-ddPCR showed the presence of two potentially pathogenic variants in the distal normal mucosa of patients with colorectal carcinoma. In summary, SP-ddPCR offers a rapid and feasible methodology to validate next-generation sequencing data and accurately quantify rare SNVs, thus providing a potential tool for diagnosis and stratification of at-risk patients based on their mutational profiling.
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Affiliation(s)
- Verónica Pablo-Fontecha
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
| | - Eva Hernández-Illán
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain
| | - Andrea Reparaz
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona (IIBB-CSIC), Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
| | - Elena Asensio
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain
| | - Jordi Morata
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Raúl Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Sara Lahoz
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029, Madrid, Spain
| | - Carolina Parra
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain
| | - Juan José Lozano
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029, Madrid, Spain
| | - Anabel García-Heredia
- Servicio de Medicina Digestiva, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010, Alicante, Spain
| | - Alejandro Martínez-Roca
- Servicio de Medicina Digestiva, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010, Alicante, Spain
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Francesc Balaguer
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029, Madrid, Spain
| | - Rodrigo Jover
- Servicio de Medicina Digestiva, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010, Alicante, Spain
| | - Antoni Castells
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029, Madrid, Spain
| | - Ramon Trullàs
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona (IIBB-CSIC), Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
| | - Petar Podlesniy
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona (IIBB-CSIC), Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
| | - Jordi Camps
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029, Madrid, Spain.
- Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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4
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Zhang S, Chen X, Lin Z, Tan Y, Liang B, Pan Y, Huang M, Su B, Hu X, Xu Y, Li Q. Quantification of Isoniazid-Heteroresistant Mycobacterium tuberculosis Using Droplet Digital PCR. J Clin Microbiol 2023; 61:e0188422. [PMID: 37195177 PMCID: PMC10281145 DOI: 10.1128/jcm.01884-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/04/2023] [Indexed: 05/18/2023] Open
Abstract
The quantitative detection of drug-resistance mutations in Mycobacterium tuberculosis (MTB) is critical for determining the drug resistance status of a sample. We developed a drop-off droplet digital PCR (ddPCR) assay targeting all major isoniazid (INH)-resistant mutations. The ddPCR assay consisted of three reactions: reaction A detects mutations at katG S315; reaction B detects inhA promoter mutations; and reaction C detects ahpC promoter mutations. All reactions could quantify 1%-50% of mutants in the presence of the wild-type, ranging from 100 to 50,000 copies/reaction. Clinical evaluation with 338 clinical isolates yielded clinical sensitivity of 94.5% (95% confidence interval [CI] = 89.1%-97.3%) and clinical specificity of 97.6% (95% CI = 94.6%-99.0%) compared with the traditional drug susceptibility testing (DST). Further clinical evaluation using 194 nucleic acid-positive MTB sputum samples revealed clinical sensitivity of 87.8% (95% CI = 75.8%-94.3%) and clinical specificity of 96.5% (95% CI = 92.2%-98.5%) in comparison with DST. All the mutant and heteroresistant samples detected by the ddPCR assay but susceptible by DST were confirmed by combined molecular assays, including Sanger sequencing, mutant-enriched Sanger sequencing and a commercial melting curve analysis-based assay. Finally, the ddPCR assay was used to monitor longitudinally the INH-resistance status and the bacterial load in nine patients undergoing treatment. Overall, the developed ddPCR assay could be an indispensable tool for quantification of INH-resistant mutations in MTB and bacterial loads in patients.
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Affiliation(s)
- Siqi Zhang
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaohong Chen
- The Pulmonary Hospital of Fuzhou in Fujian Province, Fuzhou, Fujian, China
| | - Zhonghui Lin
- The Pulmonary Hospital of Fuzhou in Fujian Province, Fuzhou, Fujian, China
| | - Yaoju Tan
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, China
| | - Bin Liang
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuying Pan
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mingxiang Huang
- The Pulmonary Hospital of Fuzhou in Fujian Province, Fuzhou, Fujian, China
| | - Biyi Su
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, China
| | - Xiaoman Hu
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
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5
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Luigi M, Manglli A, Corrado CL, Tiberini A, Costantini E, Ferretti L, Tomassoli L, Bertin S. Development, Validation, and Application of Reverse Transcription Real-Time and Droplet Digital PCR Assays for the Detection of the Potyviruses Watermelon Mosaic Virus and Zucchini Yellow Mosaic Virus in Cucurbits. PLANTS (BASEL, SWITZERLAND) 2023; 12:2364. [PMID: 37375989 DOI: 10.3390/plants12122364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/29/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Among the cucurbit-infecting viruses, watermelon mosaic virus (WMV) and zucchini yellow mosaic virus (ZYMV) (Potyvirus: Potyviridae) are responsible for severe symptoms on cucumber, melon, watermelon, and zucchini cultivations worldwide. In this study, reverse transcription real-time PCR (real-time RT-PCR) and droplet-digital PCR (RT-ddPCR) assays targeting the coat protein (CP) genes of WMV and ZYMV were developed and validated according to the international standards of plant pest diagnosis (EPPO PM 7/98 (5)). First, the diagnostic performance of WMV-CP and ZYMV-CP real-time RT-PCRs was evaluated, and the assays displayed an analytical sensitivity of 10-5 and 10-3, respectively. The tests also showed an optimal repeatability, reproducibility and analytical specificity, and were reliable for the virus detection in naturally infected samples and across a wide range of cucurbit hosts. Based on these results, the real-time RT-PCR reactions were adapted to set up RT-ddPCR assays. These were the first RT-ddPCR assays aiming at the detection and quantification of WMV and ZYMV and showed a high sensitivity, being able to detect until 9 and 8 copies/µL of WMV or ZYMV, respectively. The RT-ddPCRs allowed the direct estimation of the virus concentrations and opened to a broad range of applications in disease management, such as the evaluation of partial resistance in breeding processes, identification of antagonistic/synergistic events, and studies on the implementation of natural compounds in the integrated management strategies.
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Affiliation(s)
- Marta Luigi
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Ariana Manglli
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Carla Libia Corrado
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Antonio Tiberini
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Elisa Costantini
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Luca Ferretti
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Laura Tomassoli
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Sabrina Bertin
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
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Yu Q, Jiang H, Su X, Jiang Z, Liang X, Zhang C, Shang W, Zhang Y, Chen H, Yang Z, Shen M, Huang F, Chen X, Yang Y, Pan B, Wang B, Lu D, Guo W. Development of multiplex drop-off digital PCR assays for hotspot mutation detection of KRAS, NRAS, BRAF and PIK3CA in the plasma of colorectal cancer patients. J Mol Diagn 2023; 25:388-402. [PMID: 36963484 DOI: 10.1016/j.jmoldx.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/30/2022] [Accepted: 03/08/2023] [Indexed: 03/26/2023] Open
Abstract
The detection of mutations in KRAS, NRAS, BRAF and PIK3CA has become essential in treatment management of metastatic colorectal cancer (mCRC), with the approval of new targeted therapies. We developed novel multiplex drop-off digital PCR (MDO-dPCR) assays, by combining amplitude-/ratio-based multiplexing with drop-off/double drop-off strategies, which allow for detection of at least 69 most frequent hotspot mutations in all four genes with only three reactions. We assessed the analytical performance of the assays using synthetic oligonucleotides, further validated on plasma cfDNA samples from a large cohort of CRC patients and compared with next generation sequencing (NGS) data. The MDO-dPCR assays showed a high sensitivity with a limit of detection (LOD) ranging from 0.084 to 0.182% in mutant allelic frequency (MAF). The screening of plasma cfDNAs from 106 CRC patients identified mutations in 42.45% of them, with a sensitivity of 95.24%, a specificity of 98.53% and an accuracy of 96.98% for mutation detection and a strong correlation of measured MAFs as compared to NGS results. The high sensitivity and comprehensive mutation coverage of the MDO-dPCR assays make them suitable for rapid and cost-effective detection of KRAS, NRAS, BRAF and PIK3CA mutations in the plasma of CRC patients, and could be useful in early response assessment and longitudinal disease monitoring.
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Affiliation(s)
- Qian Yu
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China
| | - Huiqin Jiang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xi Su
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | | | - Xue Liang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Chunyan Zhang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China
| | - Wu Shang
- Nanjing Pregene Biotechnology, Nanjing, China
| | | | - Hao Chen
- Nanjing Pregene Biotechnology, Nanjing, China
| | - Zhijie Yang
- Nanjing Pregene Biotechnology, Nanjing, China
| | - Minna Shen
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fei Huang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinning Chen
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yihui Yang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Baishen Pan
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Beili Wang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China.
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7
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Ahmad E, Ali A, Nimisha, Kumar Sharma A, Ahmed F, Mehdi Dar G, Mohan Singh A, Apurva, Kumar A, Athar A, Parveen F, Mahajan B, Singh Saluja S. Molecular approaches in cancer. Clin Chim Acta 2022; 537:60-73. [DOI: https:/doi.org/10.1016/j.cca.2022.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
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8
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Ahmad E, Ali A, Nimisha, Kumar Sharma A, Ahmed F, Mehdi Dar G, Mohan Singh A, Apurva, Kumar A, Athar A, Parveen F, Mahajan B, Singh Saluja S. Molecular approaches in cancer. Clin Chim Acta 2022; 537:60-73. [DOI: 10.1016/j.cca.2022.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/03/2022]
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9
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Rosvall BR, Kostiuk M, Williams J, Matkin A, Harris J, Seikaly H, O'Connell DA, Biron VL. Utility of droplet digital polymerase chain reaction for TERT and BRAF mutational profiling of thyroid nodules. BMC Cancer 2021; 21:1142. [PMID: 34702207 PMCID: PMC8547072 DOI: 10.1186/s12885-021-08810-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/22/2021] [Indexed: 12/07/2022] Open
Abstract
Background Mutations involving BRAF and TERT are important predictors of disease severity in thyroid cancer, but molecular testing is limited by cost and lack of adequate tissue sample. This study aimed to assess the utility of BRAFV600E and TERT testing using droplet digital PCR (ddPCR) as a diagnostic and prognostic tool for thyroid fine needle aspirate biopsy (FNAB). Methods Patients with thyroid nodules were prospectively enrolled from March 2015 to September 2018. Pre-operative FNAB was collected for standard cytology and molecular testing. BRAFV600E and TERT levels were analyzed by ddPCR. Cytology (Bethesda system) and ddPCR results were correlated to surgical pathology. Results A total of 222 patients were enrolled, of which 124 received thyroid surgery. Pre-operative cytology alone with Bethesda ≥5 was 100% specific and 70% sensitive for malignancy on final surgical pathology. BRAFV600E positivity or TERT overexpression was 100% specific and 60.0% sensitive. Combining cytology (Bethesda ≥5) with BRAFV600E and TERT testing increased the sensitivity of a malignant diagnosis to 80.0%. High TERT levels and/or BRAFV600E was associated with aggressive or advanced stage pathology. Conclusions Combining cytology with ddPCR analysis of BRAFV600E and TERT can improve the diagnostic accuracy of thyroid FNAB, and help predict aggressive pathology. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08810-8.
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Affiliation(s)
- Brandon R Rosvall
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4 Walter Mackenzie Center, 8440 112 St, Edmonton, Alberta, T6G 2B7, Canada
| | - Morris Kostiuk
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4 Walter Mackenzie Center, 8440 112 St, Edmonton, Alberta, T6G 2B7, Canada
| | - Jordana Williams
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4 Walter Mackenzie Center, 8440 112 St, Edmonton, Alberta, T6G 2B7, Canada
| | - Ashlee Matkin
- Division of Plastic and Reconstructive Surgery, Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Jeffrey Harris
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4 Walter Mackenzie Center, 8440 112 St, Edmonton, Alberta, T6G 2B7, Canada
| | - Hadi Seikaly
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4 Walter Mackenzie Center, 8440 112 St, Edmonton, Alberta, T6G 2B7, Canada
| | - Daniel A O'Connell
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4 Walter Mackenzie Center, 8440 112 St, Edmonton, Alberta, T6G 2B7, Canada
| | - Vincent L Biron
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4 Walter Mackenzie Center, 8440 112 St, Edmonton, Alberta, T6G 2B7, Canada.
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10
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Bidshahri R, Fakhfakh K, McNeil K, Won JR, Wolber R, Hughesman C, Haynes C. Analysis of
KRAS
G12
/
G13
in colorectal cancer using an economical digital
PCR
assay that unequivocally differentiates missense and synonymous alleles. CAN J CHEM ENG 2021. [DOI: 10.1002/cjce.24243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Roza Bidshahri
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Biomedical Engineering Program University of British Columbia Vancouver British Columbia Canada
| | - Kareem Fakhfakh
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Department of Chemical and Biological Engineering University of British Columbia Vancouver British Columbia Canada
| | - Kelly McNeil
- Department of Genetics and Molecular Diagnostics British Columbia Cancer Agency Vancouver British Columbia Canada
| | - Jennifer R. Won
- Canadian Immunohistochemistry Quality Control, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver British Columbia Canada
| | - Robert Wolber
- Canadian Immunohistochemistry Quality Control, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver British Columbia Canada
- Department of Pathology Lion's Gate Hospital North Vancouver British Columbia Canada
| | - Curtis Hughesman
- Cancer Genetics and Genomics Lab British Columbia Cancer Agency Vancouver British Columbia Canada
| | - Charles Haynes
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Biomedical Engineering Program University of British Columbia Vancouver British Columbia Canada
- Department of Chemical and Biological Engineering University of British Columbia Vancouver British Columbia Canada
- Genome Sciences and Technology Program Vancouver British Columbia Canada
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11
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Rausch C, Rothenberg-Thurley M, Buerger SA, Tschuri S, Dufour A, Neusser M, Schneider S, Spiekermann K, Metzeler KH, Ziemann F. Double Drop-Off Droplet Digital PCR: A Novel, Versatile Tool for Mutation Screening and Residual Disease Monitoring in Acute Myeloid Leukemia Using Cellular or Cell-Free DNA. J Mol Diagn 2021; 23:975-985. [PMID: 34020042 DOI: 10.1016/j.jmoldx.2021.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022] Open
Abstract
In acute myeloid leukemia (AML), somatic gene mutations are important prognostic markers and increasingly constitute therapeutic targets. Therefore, robust, sensitive, and fast diagnostic assays are needed. Current techniques for mutation screening and quantification, including next-generation sequencing and quantitative PCR, each have weaknesses that leave a need for novel diagnostic tools. We established double drop-off digital droplet PCR (DDO-ddPCR) assays for gene mutations in NPM1, IDH2, and NRAS, which can detect and quantify diverse alterations at two nearby hotspot regions present in these genes. These assays can be used for mutation screening as well as quantification and sequential monitoring. The assays were validated against next-generation sequencing and existing ddPCR assays and achieved high concordance with an overall sensitivity comparable to conventional digital PCR. In addition, the feasibility of detecting and monitoring genetic alterations in peripheral blood cell-free DNA (cfDNA) of patients with AML by DDO-ddPCR was studied. cfDNA analysis was found to have similar sensitivity compared to quantitative PCR-based analysis of peripheral blood. Finally, the cfDNA-based digital PCR in several clinical scenarios was found to be useful in long-term monitoring of target-specific therapy, early response assessment during induction chemotherapy, and identification of mutations in patients with extramedullary disease. Thus, DDO-ddPCR-based cfDNA analysis may complement existing genetic tools for diagnosis and disease monitoring in AML.
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Affiliation(s)
- Christian Rausch
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Maja Rothenberg-Thurley
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Simon A Buerger
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Sebastian Tschuri
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Annika Dufour
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Michaela Neusser
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany; Institute of Human Genetics, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Stephanie Schneider
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany; Institute of Human Genetics, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Karsten Spiekermann
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Klaus H Metzeler
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany; Department of Hematology, Cellular Therapy, and Hemostaseology, University of Leipzig, Leipzig, Germany.
| | - Frank Ziemann
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
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12
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Cusenza VY, Bisagni A, Rinaldini M, Cattani C, Frazzi R. Copy Number Variation and Rearrangements Assessment in Cancer: Comparison of Droplet Digital PCR with the Current Approaches. Int J Mol Sci 2021; 22:ijms22094732. [PMID: 33946969 PMCID: PMC8124143 DOI: 10.3390/ijms22094732] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
The cytogenetic and molecular assessment of deletions, amplifications and rearrangements are key aspects in the diagnosis and therapy of cancer. Not only the initial evaluation and classification of the disease, but also the follow-up of the tumor rely on these laboratory approaches. The therapeutic choice can be guided by the results of the laboratory testing. Genetic deletions and/or amplifications directly affect the susceptibility or the resistance to specific therapies. In an era of personalized medicine, the correct and reliable molecular characterization of the disease, also during the therapeutic path, acquires a pivotal role. Molecular assays like multiplex ligation-dependent probe amplification and droplet digital PCR represent exceptional tools for a sensitive and reliable detection of genetic alterations and deserve a role in molecular oncology. In this manuscript we provide a technical comparison of these two approaches with the golden standard represented by fluorescence in situ hybridization. We also describe some relevant targets currently evaluated with these techniques in solid and hematologic tumors.
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Affiliation(s)
- Vincenza Ylenia Cusenza
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy;
| | - Alessandra Bisagni
- Pathology Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy;
| | - Monia Rinaldini
- Medical Genetics Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (M.R.); (C.C.)
| | - Chiara Cattani
- Medical Genetics Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (M.R.); (C.C.)
| | - Raffaele Frazzi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy;
- Correspondence:
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13
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Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients. Genes (Basel) 2021; 12:genes12020289. [PMID: 33669856 PMCID: PMC7923234 DOI: 10.3390/genes12020289] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/12/2021] [Accepted: 02/16/2021] [Indexed: 02/07/2023] Open
Abstract
Liquid biopsy and cell-free DNA (cfDNA) show great promise in cancer diagnostics. In this study, we designed a custom droplet digital PCR (ddPCR) assay for the quantification and quality control of cfDNA isolated from serum. The assay was validated on a group of locally advanced colorectal cancer (CRC) patients and two control groups-patients with hemorrhoids and healthy individuals. The assay shows a high correlation with Qubit measurement (r = 0.976) but offers a higher dynamic range. Mean concentrations of cfDNA were 12.36 ng/µL, 5.17 ng/µL, and 0.29 ng/µL for CRC, hemorrhoid patients, and healthy controls, respectively. The quality of cfDNA was assessed with the measurement of B-cell DNA contamination. On a subset of CRC patients, we compared the mutation status on KRAS (G12A, G12D, G12V, G13D) and BRAF (V600E) genes in the primary tumor and cfDNA isolated from the serum. A total of 70.6% of primary tumor samples were mutated, and the mean fractional abundance of mutations was 9.50%. The matching serum samples were mutated in 38% cases with an average fractional abundance of 0.23%. We conclude that any decisions based solely on the amount of cfDNA present in patient serum must be interpreted carefully and in the context of co-morbidities. This study explores the potential of ddPCR somatic mutations detection from liquid biopsy as a supplement to tissue biopsy in targeted personalized CRC patient management.
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14
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Silveira AB, Bidard FC, Kasperek A, Melaabi S, Tanguy ML, Rodrigues M, Bataillon G, Cabel L, Buecher B, Pierga JY, Proudhon C, Stern MH. High-Accuracy Determination of Microsatellite Instability Compatible with Liquid Biopsies. Clin Chem 2020; 66:606-613. [PMID: 32176763 DOI: 10.1093/clinchem/hvaa013] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/30/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Microsatellite instability (MSI) has recently emerged as a predictive pan-tumor biomarker of immunotherapy efficacy, stimulating the development of diagnostic tools compatible with large-scale screening of patients. In this context, noninvasive detection of MSI from circulating tumor DNA stands as a promising diagnostic and posttreatment monitoring tool. METHODS We developed drop-off droplet-digital PCR (ddPCR) assays targeting BAT-26, activin A receptor type 2A (ACVR2A), and defensin beta 105A/B (DEFB105A/B) microsatellite markers. Performances of the assays were measured on reconstitution experiments of various mutant allelic fractions, on 185 tumor samples with known MSI status, and on 72 blood samples collected from 42 patients with advanced colorectal or endometrial cancers before and/or during therapy. RESULTS The 3 ddPCR assays reached analytical sensitivity <0.1% variant allelic frequency and could reliably detect and quantify MSI in both tumor and body fluid samples. High concordance between MSI status determination by the three-marker ddPCR test and the reference pentaplex method were observed (100% for colorectal tumors and 93% for other tumor types). Moreover, the 3 assays showed correlations with r ≥ 0.99 with other circulating tumor DNA markers and their dynamic during treatment correlated well with clinical response. CONCLUSIONS This innovative approach for MSI detection provides a noninvasive, cost-effective, and fast diagnostic tool, well suited for large-scale screening of patients that may benefit from immunotherapy agents, as well as for monitoring treatment responses.
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Affiliation(s)
- Amanda Bortolini Silveira
- Circulating Tumor Biomarkers Laboratory, Institut Curie, PSL Research University, INSERM CIC 1428, Paris, France
| | - François-Clément Bidard
- Circulating Tumor Biomarkers Laboratory, Institut Curie, PSL Research University, INSERM CIC 1428, Paris, France.,Department of Medical Oncology, Institut Curie, Paris, France.,Versailles Saint Quentin en Yvelines University, Paris Saclay University, Saint Cloud, Paris, France
| | - Amélie Kasperek
- Circulating Tumor Biomarkers Laboratory, Institut Curie, PSL Research University, INSERM CIC 1428, Paris, France
| | - Samia Melaabi
- Department of Biopathology, Institut Curie, Paris, France
| | | | - Manuel Rodrigues
- Department of Medical Oncology, Institut Curie, Paris, France.,Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.) team, Equipe labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, Paris, France
| | | | - Luc Cabel
- Department of Medical Oncology, Institut Curie, Paris, France.,Versailles Saint Quentin en Yvelines University, Paris Saclay University, Saint Cloud, Paris, France
| | - Bruno Buecher
- Department of Medical Oncology, Institut Curie, Paris, France
| | - Jean-Yves Pierga
- Circulating Tumor Biomarkers Laboratory, Institut Curie, PSL Research University, INSERM CIC 1428, Paris, France.,Department of Medical Oncology, Institut Curie, Paris, France.,Paris University, Paris, France
| | - Charlotte Proudhon
- Circulating Tumor Biomarkers Laboratory, Institut Curie, PSL Research University, INSERM CIC 1428, Paris, France
| | - Marc-Henri Stern
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.) team, Equipe labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, Paris, France
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15
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Evaluating the quantity, quality and size distribution of cell-free DNA by multiplex droplet digital PCR. Sci Rep 2020; 10:12564. [PMID: 32724107 PMCID: PMC7387491 DOI: 10.1038/s41598-020-69432-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/07/2020] [Indexed: 01/06/2023] Open
Abstract
Cell-free DNA (cfDNA) has become a comprehensive biomarker in the fields of non-invasive cancer detection and monitoring, organ transplantation, prenatal genetic testing and pathogen detection. While cfDNA samples can be obtained using a broad variety of approaches, there is an urgent need to standardize analytical tools aimed at assessing its basic properties. Typical methods to determine the yield and fragment size distribution of cfDNA samples are usually either blind to genomic DNA contamination or the presence of enzymatic inhibitors, which can confound and undermine downstream analyses. Here, we present a novel droplet digital PCR assay to identify suboptimal samples and aberrant cfDNA size distributions, the latter typically associated with high levels of circulating tumour DNA (ctDNA). Our assay was designed to promiscuously cross-amplify members of the human olfactory receptor (OR) gene family and includes a customizable diploid locus for the determination of absolute cfDNA concentrations. We demonstrate here the utility of our assay to estimate the yield and quality of cfDNA extracts and deduce fragment size distributions that correlate well with those inferred by capillary electrophoresis and high throughput sequencing. The assay described herein is a powerful tool to establish quality controls and stratify cfDNA samples based on presumed ctDNA levels, then facilitating the implementation of robust, cost-effective and standardized analytical workflows into clinical practice.
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16
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Tang Y, Zou B, Wang R, Luo N, Qi X, Zhou G, Song Q. Multiplex-invasive reaction-assisted qPCR for quantitatively detecting the abundance of EGFR exon 19 deletions in cfDNA. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3344-3350. [PMID: 32930221 DOI: 10.1039/d0ay00897d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Exon 19 deletions (19-Del) on the epidermal growth factor receptor (EGFR) gene are vital biomarkers for guiding tyrosine kinase inhibitor (TKI) treatment and the diagnosis of non-small cell lung cancer (NSCLC). However, it is difficult for conventional qPCR to quantitatively detect all 19-Del targets of EGFR, especially for cfDNA samples. Herein, a multiplex invasive reaction-assisted qPCR was proposed by employing a multiplex invasive reaction to distinguish 19-Del DNA targets from wild DNA targets and report them with different fluorescence signals in each PCR cycle. As all 19-Del targets have the same amplification efficiency and very similar invasive reaction efficiencies, the 19-Del abundance in a sample could be quantified by using the difference between the Ct values (ΔCt) of the deletion targets and the wild targets without the requirement of a standard calibration curve. Combining the high sensitivity of PCR and the high specificity of the invasive reaction, this method can detect 10 copies of the deletion targets and lower than 0.1% deletion abundance. The results were 100% consistent with ARMS-PCR for the 38 tumor tissues tested and were in good agreement with next-generation sequencing for quantifying the abundance of EGFR 19-Del in 15 cfDNA samples, showing the great potential of the method for liquid biopsies.
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Affiliation(s)
- Yunmei Tang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Bingjie Zou
- Department of Clinical Pharmacy, Jinling Hospital, School of Medicine, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210002, China.
| | - Runyuan Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Nan Luo
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Xiemin Qi
- Department of Clinical Pharmacy, Jinling Hospital, School of Medicine, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210002, China.
| | - Guohua Zhou
- Department of Clinical Pharmacy, Jinling Hospital, School of Medicine, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210002, China.
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Qinxin Song
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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17
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Jeannot E, Darrigues L, Michel M, Stern MH, Pierga JY, Rampanou A, Melaabi S, Benoist C, Bièche I, Vincent-Salomon A, El Ayachy R, Noret A, Epaillard N, Cabel L, Bidard FC, Proudhon C. A single droplet digital PCR for ESR1 activating mutations detection in plasma. Oncogene 2020; 39:2987-2995. [PMID: 32042112 DOI: 10.1038/s41388-020-1174-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/07/2020] [Accepted: 01/20/2020] [Indexed: 11/09/2022]
Abstract
Activating mutations in the estrogen receptor 1 (ESR1) gene confer resistance to aromatase inhibitors (AI), and may be targeted by selective estrogen receptor downregulators. We designed a multiplex droplet digital PCR (ddPCR), which combines a drop-off assay, targeting the clustered hotspot mutations found in exon 8, with an unconventional assay interrogating the E380Q mutation in exon 5. We assessed its sensitivity in vitro using synthetic oligonucleotides, harboring E380Q, L536R, Y537C, Y537N, Y537S, or D538G mutations. Further validation was performed on plasma samples from a prospective study and compared with next generation sequencing (NGS) data. The multiplex ESR1-ddPCR showed a high sensitivity with a limit of detection ranging from 0.07 to 0.19% in mutant allele frequency. The screening of plasma samples from patients with AI-resistant metastatic breast cancer identified ESR1 mutations in 29% of them, all mutations being confirmed by NGS. In addition, this test identifies patients harboring polyclonal alterations. Furthermore, the monitoring of circulating tumor DNA using this technique during treatment follow-up predicts the clinical benefit of palbociclib-fulvestrant. The multiplex ESR1-ddPCR detects, in a single reaction, the most frequent ESR1 activating mutations with good sensitivity. This method allows real-time liquid biopsy for ESR1 mutation monitoring in large cohorts of patients.
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Affiliation(s)
- Emmanuelle Jeannot
- Circulating tumor biomarkers laboratory, Inserm CIC 1428, Institut Curie, PSL Research University, Paris, France.,Department of Biopathology and Genetics, Institut Curie, PSL Research University, Paris, France
| | - Lauren Darrigues
- Circulating tumor biomarkers laboratory, Inserm CIC 1428, Institut Curie, PSL Research University, Paris, France
| | - Marc Michel
- Circulating tumor biomarkers laboratory, Inserm CIC 1428, Institut Curie, PSL Research University, Paris, France
| | - Marc-Henri Stern
- INSERM U830, Institut Curie, PSL Research University, Paris, France
| | - Jean-Yves Pierga
- Circulating tumor biomarkers laboratory, Inserm CIC 1428, Institut Curie, PSL Research University, Paris, France.,Department of Medical Oncology, Institut Curie, PSL Research University, Paris & Saint Cloud, France.,Université de Paris, Paris, France.,Medical Oncology, Department of the Institut Curie, Paris, France
| | - Aurore Rampanou
- Circulating tumor biomarkers laboratory, Inserm CIC 1428, Institut Curie, PSL Research University, Paris, France
| | - Samia Melaabi
- Department of Biopathology and Genetics, Institut Curie, PSL Research University, Paris, France
| | - Camille Benoist
- Department of Biopathology and Genetics, Institut Curie, PSL Research University, Paris, France
| | - Ivan Bièche
- Department of Biopathology and Genetics, Institut Curie, PSL Research University, Paris, France
| | - Anne Vincent-Salomon
- Department of Biopathology and Genetics, Institut Curie, PSL Research University, Paris, France
| | - Radouane El Ayachy
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris & Saint Cloud, France
| | - Aurélien Noret
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris & Saint Cloud, France
| | - Nicolas Epaillard
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris & Saint Cloud, France
| | - Luc Cabel
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris & Saint Cloud, France.,Versailles Saint Quentin University, Paris Saclay University, Saint Cloud, France
| | - François-Clément Bidard
- Circulating tumor biomarkers laboratory, Inserm CIC 1428, Institut Curie, PSL Research University, Paris, France.,Department of Medical Oncology, Institut Curie, PSL Research University, Paris & Saint Cloud, France.,Versailles Saint Quentin University, Paris Saclay University, Saint Cloud, France
| | - Charlotte Proudhon
- Circulating tumor biomarkers laboratory, Inserm CIC 1428, Institut Curie, PSL Research University, Paris, France.
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18
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Syeda MM, Wiggins JM, Corless B, Spittle C, Karlin-Neumann G, Polsky D. Validation of Circulating Tumor DNA Assays for Detection of Metastatic Melanoma. Methods Mol Biol 2020; 2055:155-180. [PMID: 31502151 DOI: 10.1007/978-1-4939-9773-2_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The detection of cell-free, circulating tumor DNA (ctDNA) in the blood of patients with solid tumors is often referred to as "liquid biopsy." ctDNA is particularly attractive as a candidate biomarker in the blood. It is relatively stable after blood collection, can be easily purified, and can be quantitatively measured with high sensitivity and specificity using advanced technologies. Current liquid biopsy research has focused on detecting and quantifying ctDNA to (1) diagnose and characterize mutations in a patient's cancer to help select the appropriate treatment; (2) predict clinical outcomes associated with different treatments; and (3) monitor the response and/or progression of a patient's disease. The diagnostic use of liquid biopsies is probably greatest in tumors where the difficulty and/or risk of obtaining a tissue specimen for molecular diagnostics is high (e.g., lung, colon). In metastatic melanoma, however, obtaining a tissue sample for molecular diagnostics is not typically a major obstacle to patient care plans; rather predicting treatment outcomes and monitoring a patient's disease course during therapy are considered the current priorities for this cancer type. In this chapter we describe an approach to the validation of ctDNA detection assays for melanoma, focusing primarily on analytical validation, and provide methods to guide the use of droplet digital PCR assays for measuring ctDNA levels in plasma samples.
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Affiliation(s)
- Mahrukh M Syeda
- The Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, NY, USA
| | - Jennifer M Wiggins
- The Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, NY, USA
| | - Broderick Corless
- The Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, NY, USA
| | | | | | - David Polsky
- The Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, NY, USA.
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19
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Zhu X, Su S, Fu M, Peng Z, Wang D, Rui X, Wang F, Liu X, Liu B, Zhu L, Yang W, Gao N, Huang G, Jing G, Guo Y. A density-watershed algorithm (DWA) method for robust, accurate and automatic classification of dual-fluorescence and four-cluster droplet digital PCR data. Analyst 2019; 144:4757-4771. [PMID: 31290860 DOI: 10.1039/c9an00637k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Droplet digital PCR (ddPCR) is a single-molecule amplification technology with broad applications in precision medicine and clinical diagnosis. Dual-fluorescence and four-cluster ddPCR (two/four-ddPCR) assay is an effective way to quantify copy numbers. Currently, two/four-ddPCR data are usually classified with manual thresholds. For clinical applications, automatic and accurate methods are required to avoid subjectivity in diagnosis. Although there are some automatic classification algorithms, their accuracy and robustness still need to be improved to meet the needs of clinical diagnosis. Therefore, a new method is in high demand to automatically classify two/four-ddPCR data in an accurate and robust way. Here, a novel density-watershed algorithm (DWA) method was developed for the accurate, automatic and unsupervised classification of two/four-ddPCR data. First, data gridding was applied to a scatter plot of the fluorescence signal intensity to calculate data densities. Based on the data densities, the watershed algorithm was used to divide the gridded scatter plot into isolated regions automatically. Next, an optimal cluster pattern was determined based on these isolated regions, and excess regions were merged. Finally, the two/four-ddPCR data were classified based on the merged regions, and DNA template copy numbers were calculated accordingly. Using the DWA method for the quantification of both wild types and mutants of epidermal growth factor receptor (EGFR) L858R and T790M, the classification results were highly consistent with expectations, and significantly better than commonly-used automatic algorithms for now. The computed template copy numbers scaled proportionally to the relative concentration of input templates (r2 > 0.998) in four orders of magnitude with a good reproducibility, and achieved a limit of detection over 40 times lower than the commonly-used automatic algorithms. Furthermore, the DWA method was validated on 254 clinical DNA samples derived from frozen tissues, formalin-fixed paraffin-embedded tissues and peripheral blood. In most cases, the DWA method derived accurate and valid classification results. This highly effective DWA method may be widely used for automatically classifying two/four-ddPCR data, and it will greatly promote the application of ddPCR in clinical diagnosis.
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Affiliation(s)
- Xiurui Zhu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China.
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20
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Fu X, Huang Y, Fan X, Deng Y, Liu H, Zou H, Wu P, Chen Z, Huang J, Wang J, Lin H, Huang S, Tan X, Lan P, Wang L, Wang JP. Demographic trends and KRAS/BRAF V600E mutations in colorectal cancer patients of South China: A single-site report. Int J Cancer 2019; 144:2109-2117. [PMID: 30414169 DOI: 10.1002/ijc.31973] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022]
Abstract
The incidence of colorectal cancer (CRC) is increasing in China. Here, we aimed to evaluate the latest demographic trends and KRAS/BRAF mutations status of Chinese CRC. Five thousand five hundred and forty-six CRC patients diagnosed from 2010 to 2017 were involved. KRAS exon 2 and BRAFV600E mutations were detected by Sanger sequencing and high-resolution melting analysis or allelic-specific probe method. Gene mutation profiles and clinicopathologic characteristics of 5495 patients were analyzed. The joinpoint regression model was used to predict the demographic data in 2018. We found KRAS exon 2 and BRAFV600E mutation rates were 37.7 and 2.8% in CRC patients. Tumors with KRAS exon 2 mutations were more likely to be present in female and patients aged older than 75 years, right colon and have well-differentiated histology. Tumors with BRAFV600E mutations were more likely to be present in the female, right colon and have poorly differentiated histology. From 2010 to 2017, the percentage of colon cancer and tubular adenocarcinoma in CRC increased substantially (from 39.3 to 51.8%, from 78.6 to 93.4%, respectively). The percentage of right colon cancer increased from 18.3 to 20.5%, which predictively may keep at 22.6% in 2018. The rise trends for patients with moderate differentiation tumor or KRAS exon 2 mutated tumor were apparent (from 50.3 to 78.6%, from 32.8 to 39.7%, respectively). In conclusion, in recent 8 years, there is a shift to the colon, especially right colon in the incidence of Chinese CRC. Moreover tubular adenocarcinoma is becoming the primary histology type.
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Affiliation(s)
- Xinhui Fu
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yan Huang
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xinjuan Fan
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanhong Deng
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huanliang Liu
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hongzhi Zou
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Peihuang Wu
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhiting Chen
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jinglin Huang
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jingxuan Wang
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hanjie Lin
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shuhui Huang
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoli Tan
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ping Lan
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of GI Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lei Wang
- Department of GI Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jian-Ping Wang
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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21
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Decraene C, Bortolini Silveira A, Michel M, Bidard FC, Pierga JY, Stern MH, Proudhon C. Single Droplet Digital Polymerase Chain Reaction for Comprehensive and Simultaneous Detection of Mutations in Hotspot Regions. J Vis Exp 2018. [PMID: 30320738 DOI: 10.3791/58051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Droplet digital polymerase chain reaction (ddPCR) is a highly sensitive quantitative polymerase chain reaction (PCR) method based on sample fractionation into thousands of nano-sized water-in-oil individual reactions. Recently, ddPCR has become one of the most accurate and sensitive tools for circulating tumor DNA (ctDNA) detection. One of the major limitations of the standard ddPCR technique is the restricted number of mutations that can be screened per reaction, as specific hydrolysis probes recognizing each possible allelic version are required. An alternative methodology, the drop-off ddPCR, increases throughput, since it requires only a single pair of probes to detect and quantify potentially all genetic alterations in the targeted region. Drop-off ddPCR displays comparable sensitivity to conventional ddPCR assays with the advantage of detecting a greater number of mutations in a single reaction. It is cost-effective, conserves precious sample material, and can also be used as a discovery tool when mutations are not known a priori.
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Affiliation(s)
- Charles Decraene
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University; CNRS UMR144, Institut Curie, PSL Research University
| | - Amanda Bortolini Silveira
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University
| | - Marc Michel
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University
| | - François-Clément Bidard
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University; Department of Medical Oncology, Institut Curie, PSL Research University; University Versailles Saint-Quentin-en-Yvelines
| | - Jean-Yves Pierga
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University; Department of Medical Oncology, Institut Curie, PSL Research University; University Paris Descartes
| | - Marc-Henri Stern
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University; Inserm U830, Institut Curie, PSL Research University
| | - Charlotte Proudhon
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University;
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22
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Biron VL, Matkin A, Kostiuk M, Williams J, Cote DW, Harris J, Seikaly H, O'Connell DA. Analytic and clinical validity of thyroid nodule mutational profiling using droplet digital polymerase chain reaction. J Otolaryngol Head Neck Surg 2018; 47:60. [PMID: 30249281 PMCID: PMC6154415 DOI: 10.1186/s40463-018-0299-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/26/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Recent guidelines for the management of thyroid nodules incorporate mutation testing as an adjunct for surgical decision-making, however current tests are costly with limited accuracy. Droplet digital PCR (ddPCR) is an ultrasensitive method of nucleic acid detection that is particularly useful for identifying gene mutations. This study aimed to assess the analytic and clinical validity of RAS and BRAF ddPCR mutational testing as a diagnostic tool for thyroid fine needle aspirate biopsy (FNAB). METHODS Patients with thyroid nodules meeting indication for FNAB were prospectively enrolled from March 2015 to September 2017. In addition to clinical protocol, an additional FNAB was obtained for ddPCR. Optimized ddPCR probes were used to detect mutations including HRASG12 V, HRASQ61K, HRASQ61R, NRASQ61R, NRASQ61K and BRAFV600E. The diagnostic performance of BRAF and RAS mutations was assessed individually or in combination with Bethesda classification against final surgical pathology. RESULTS A total of 208 patients underwent FNAB and mutational testing with the following Bethesda cytologic classification: 26.9% non-diagnostic, 55.2% benign, 5.3% FLUS/AUS, 2.9% FN/SPN, 2.4% SFM and 7.2% malignant. Adequate RNA was obtained from 91.3% (190) FNABs from which mutations were identified in 21.1% of HRAS, 11.5% of NRAS and 7.4% of BRAF. Malignant cytology or BRAFV600E was 100% specific for malignancy. Combining cytology with ddPCR BRAF600E mutations testing increased the sensitivity of Bethesda classification from 41.7 to 75%. Combined BRAFV600E and Bethesda results had a positive predictive value (PPV) of 100% and negative predictive value (NPV) of 89.7% for thyroid malignancy in our cohort. CONCLUSIONS DdPCR offers a novel and ultrasensitive method of detecting RAS and BRAF mutations from thyroid FNABs. BRAFV600E mutation testing by ddPCR may serve as a useful adjunct to increase sensitivity and specificity of thyroid FNAB.
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Affiliation(s)
- Vincent L Biron
- Division of Otolaryngology-Head and Neck Surgery, University of Alberta, 8440-112 st, 1E4 Walter Mackenzie Centre, Edmonton, AB, T6G 2B7, Canada. .,Alberta Head and Neck Centre for Oncology and Reconstruction, Walter MacKenzie Health Sciences Centre, Edmonton, AB, Canada. .,Otolaryngology-Head and Neck Surgery Research Laboratory of Alberta, University of Alberta, Edmonton, AB, Canada.
| | - Ashlee Matkin
- Alberta Head and Neck Centre for Oncology and Reconstruction, Walter MacKenzie Health Sciences Centre, Edmonton, AB, Canada.,Faculty of Medicine and Dentistry, Undergraduate Medical Education, University of Alberta, Edmonton, AB, Canada
| | - Morris Kostiuk
- Alberta Head and Neck Centre for Oncology and Reconstruction, Walter MacKenzie Health Sciences Centre, Edmonton, AB, Canada.,Otolaryngology-Head and Neck Surgery Research Laboratory of Alberta, University of Alberta, Edmonton, AB, Canada
| | - Jordana Williams
- Otolaryngology-Head and Neck Surgery Research Laboratory of Alberta, University of Alberta, Edmonton, AB, Canada
| | - David W Cote
- Division of Otolaryngology-Head and Neck Surgery, University of Alberta, 8440-112 st, 1E4 Walter Mackenzie Centre, Edmonton, AB, T6G 2B7, Canada
| | - Jeffrey Harris
- Division of Otolaryngology-Head and Neck Surgery, University of Alberta, 8440-112 st, 1E4 Walter Mackenzie Centre, Edmonton, AB, T6G 2B7, Canada.,Alberta Head and Neck Centre for Oncology and Reconstruction, Walter MacKenzie Health Sciences Centre, Edmonton, AB, Canada
| | - Hadi Seikaly
- Division of Otolaryngology-Head and Neck Surgery, University of Alberta, 8440-112 st, 1E4 Walter Mackenzie Centre, Edmonton, AB, T6G 2B7, Canada.,Alberta Head and Neck Centre for Oncology and Reconstruction, Walter MacKenzie Health Sciences Centre, Edmonton, AB, Canada
| | - Daniel A O'Connell
- Division of Otolaryngology-Head and Neck Surgery, University of Alberta, 8440-112 st, 1E4 Walter Mackenzie Centre, Edmonton, AB, T6G 2B7, Canada.,Alberta Head and Neck Centre for Oncology and Reconstruction, Walter MacKenzie Health Sciences Centre, Edmonton, AB, Canada
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23
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Decraene C, Silveira AB, Bidard FC, Vallée A, Michel M, Melaabi S, Vincent-Salomon A, Saliou A, Houy A, Milder M, Lantz O, Ychou M, Denis MG, Pierga JY, Stern MH, Proudhon C. Multiple Hotspot Mutations Scanning by Single Droplet Digital PCR. Clin Chem 2018; 64:317-328. [DOI: 10.1373/clinchem.2017.272518] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 10/10/2017] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Progress in the liquid biopsy field, combined with the development of droplet digital PCR (ddPCR), has enabled noninvasive monitoring of mutations with high detection accuracy. However, current assays detect a restricted number of mutations per reaction. ddPCR is a recognized method for detecting alterations previously characterized in tumor tissues, but its use as a discovery tool when the mutation is unknown a priori remains limited.
METHODS
We established 2 ddPCR assays detecting all genomic alterations within KRAS exon 2 and EGFR exon 19 mutation hotspots, which are of clinical importance in colorectal and lung cancer, with use of a unique pair of TaqMan® oligoprobes. The KRAS assay scanned for the 7 most common mutations in codons 12/13 but also all other mutations found in that region. The EGFR assay screened for all in-frame deletions of exon 19, which are frequent EGFR-activating events.
RESULTS
The KRAS and EGFR assays were highly specific and both reached a limit of detection of <0.1% in mutant allele frequency. We further validated their performance on multiple plasma and formalin-fixed and paraffin-embedded tumor samples harboring a panel of different KRAS or EGFR mutations.
CONCLUSIONS
This method presents the advantage of detecting a higher number of mutations with single-reaction ddPCRs while consuming a minimum of patient sample. This is particularly useful in the context of liquid biopsy because the amount of circulating tumor DNA is often low. This method should be useful as a discovery tool when the tumor tissue is unavailable or to monitor disease during therapy.
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Affiliation(s)
- Charles Decraene
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- CNRS UMR144, Institut Curie, PSL Research University, Paris, France
| | - Amanda B Silveira
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
| | - François-Clément Bidard
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Audrey Vallée
- Department of Biochemistry and INSERM U1232, Nantes University Hospital, Nantes, France
| | - Marc Michel
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
| | - Samia Melaabi
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Anne Vincent-Salomon
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
- Inserm U934, Institut Curie, PSL Research University, Paris, France
| | - Adrien Saliou
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
| | - Alexandre Houy
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Inserm U830, Institut Curie, PSL Research University, Paris, France
| | - Maud Milder
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Inserm CIC BT 1418, Institut Curie, PSL Research University, Paris, France
| | - Olivier Lantz
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Inserm CIC BT 1418, Institut Curie, PSL Research University, Paris, France
- Inserm U932, Institut Curie, PSL Research University, Paris, France
| | - Marc Ychou
- Department of Medical Oncology, Montpellier Cancer Institute, Montpellier, France
| | - Marc G Denis
- Department of Biochemistry and INSERM U1232, Nantes University Hospital, Nantes, France
| | - Jean-Yves Pierga
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
- University Paris Descartes, Paris, France
| | - Marc-Henri Stern
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Inserm U830, Institut Curie, PSL Research University, Paris, France
| | - Charlotte Proudhon
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
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24
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Lau BT, Wood-Bouwens C, Ji HP. Robust Multiplexed Clustering and Denoising of Digital PCR Assays by Data Gridding. Anal Chem 2017; 89:11913-11917. [PMID: 29083143 DOI: 10.1021/acs.analchem.7b02688] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Digital PCR (dPCR) relies on the analysis of individual partitions to accurately quantify nucleic acid species. The most widely used analysis method requires manual clustering through individual visual inspection. Some automated analysis methods have emerged but do not robustly account for multiplexed targets, low target concentration, and assay noise. In this study, we describe an open source analysis software called Calico that uses "data gridding" to increase the sensitivity of clustering toward small clusters. Our workflow also generates quality score metrics in order to gauge and filter individual assay partitions by how well they were classified. We applied our analysis algorithm to multiplexed droplet-based digital PCR data sets in both EvaGreen and probes-based schemes, and targeted the oncogenic BRAF V600E and KRAS G12D mutations. We demonstrate an automated clustering sensitivity of down to 0.1% mutant fraction and filtering of artifactual assay partitions from low quality DNA samples. Overall, we demonstrate a vastly improved approach to analyzing ddPCR data that can be applied to clinical use, where automation and reproducibility are critical.
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Affiliation(s)
- Billy T Lau
- Stanford Genome Technology Center, Stanford University , Palo Alto, California 94304, United States
| | - Christina Wood-Bouwens
- Division of Oncology, Stanford School of Medicine , Stanford, California 94305, United States
| | - Hanlee P Ji
- Division of Oncology, Stanford School of Medicine , Stanford, California 94305, United States
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25
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26
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Sho S, Court CM, Kim S, Braxton DR, Hou S, Muthusamy VR, Watson RR, Sedarat A, Tseng HR, Tomlinson JS. Digital PCR Improves Mutation Analysis in Pancreas Fine Needle Aspiration Biopsy Specimens. PLoS One 2017; 12:e0170897. [PMID: 28125707 PMCID: PMC5268428 DOI: 10.1371/journal.pone.0170897] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 01/11/2017] [Indexed: 12/27/2022] Open
Abstract
Applications of precision oncology strategies rely on accurate tumor genotyping from clinically available specimens. Fine needle aspirations (FNA) are frequently obtained in cancer management and often represent the only source of tumor tissues for patients with metastatic or locally advanced diseases. However, FNAs obtained from pancreas ductal adenocarcinoma (PDAC) are often limited in cellularity and/or tumor cell purity, precluding accurate tumor genotyping in many cases. Digital PCR (dPCR) is a technology with exceptional sensitivity and low DNA template requirement, characteristics that are necessary for analyzing PDAC FNA samples. In the current study, we sought to evaluate dPCR as a mutation analysis tool for pancreas FNA specimens. To this end, we analyzed alterations in the KRAS gene in pancreas FNAs using dPCR. The sensitivity of dPCR mutation analysis was first determined using serial dilution cell spiking studies. Single-cell laser-microdissection (LMD) was then utilized to identify the minimal number of tumor cells needed for mutation detection. Lastly, dPCR mutation analysis was performed on 44 pancreas FNAs (34 formalin-fixed paraffin-embedded (FFPE) and 10 fresh (non-fixed)), including samples highly limited in cellularity (100 cells) and tumor cell purity (1%). We found dPCR to detect mutations with allele frequencies as low as 0.17%. Additionally, a single tumor cell could be detected within an abundance of normal cells. Using clinical FNA samples, dPCR mutation analysis was successful in all preoperative FNA biopsies tested, and its accuracy was confirmed via comparison with resected tumor specimens. Moreover, dPCR revealed additional KRAS mutations representing minor subclones within a tumor that were not detected by the current clinical gold standard method of Sanger sequencing. In conclusion, dPCR performs sensitive and accurate mutation analysis in pancreas FNAs, detecting not only the dominant mutation subtype, but also the additional rare mutation subtypes representing tumor heterogeneity.
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Affiliation(s)
- Shonan Sho
- Department of Surgery, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Surgery, Greater Los Angeles Veteran’s Affairs Administration, Los Angeles, California, United States of America
- * E-mail:
| | - Colin M. Court
- Department of Surgery, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Surgery, Greater Los Angeles Veteran’s Affairs Administration, Los Angeles, California, United States of America
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Stephen Kim
- UCLA Center for Pancreatic Diseases, University of California Los Angeles, Los Angeles, California, United States of America
- Division of Digestive Diseases, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, United States of America
| | - David R. Braxton
- Department of Pathology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Shuang Hou
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America
| | - V. Raman Muthusamy
- UCLA Center for Pancreatic Diseases, University of California Los Angeles, Los Angeles, California, United States of America
- Division of Digestive Diseases, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, United States of America
| | - Rabindra R. Watson
- UCLA Center for Pancreatic Diseases, University of California Los Angeles, Los Angeles, California, United States of America
- Division of Digestive Diseases, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, United States of America
| | - Alireza Sedarat
- UCLA Center for Pancreatic Diseases, University of California Los Angeles, Los Angeles, California, United States of America
- Division of Digestive Diseases, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, United States of America
| | - Hsian-Rong Tseng
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America
| | - James S. Tomlinson
- Department of Surgery, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Surgery, Greater Los Angeles Veteran’s Affairs Administration, Los Angeles, California, United States of America
- UCLA Center for Pancreatic Diseases, University of California Los Angeles, Los Angeles, California, United States of America
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27
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Hughesman CB, Lu XJD, Liu KYP, Zhu Y, Poh CF, Haynes C. A Robust Protocol for Using Multiplexed Droplet Digital PCR to Quantify Somatic Copy Number Alterations in Clinical Tissue Specimens. PLoS One 2016; 11:e0161274. [PMID: 27537682 PMCID: PMC4990255 DOI: 10.1371/journal.pone.0161274] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 06/25/2016] [Indexed: 12/24/2022] Open
Abstract
The ability of droplet digital PCR (ddPCR) to accurately determine the concentrations of amplifiable targets makes it a promising platform for measuring copy number alterations (CNAs) in genomic biomarkers. However, its application to clinical samples, particularly formalin-fixed paraffin-embedded specimens, will require strategies to reliably determine CNAs in DNA of limited quantity and quality. When applied to cancerous tissue, those methods must also account for global genetic instability and the associated probability that the abundance(s) of one or more chosen reference loci do not represent the average ploidy of cells comprising the specimen. Here we present an experimental design strategy and associated data analysis tool that enables accurate determination of CNAs in a panel of biomarkers using multiplexed ddPCR. The method includes strategies to optimize primer and probes design to cleanly segregate droplets in the data output from reaction wells amplifying multiple independent templates, and to correct for bias from artifacts such as DNA fragmentation. We demonstrate how a panel of reference loci can be used to determine a stable CNA-neutral benchmark. These innovations, when taken together, provide a comprehensive strategy that can be used to reliably detect biomarker CNAs in DNA extracted from either frozen or FFPE tissue biopsies.
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Affiliation(s)
- Curtis B. Hughesman
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - X. J. David Lu
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Kelly Y. P. Liu
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Yuqi Zhu
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Catherine F. Poh
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 2B5, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
- * E-mail: (CH); (CP)
| | - Charles Haynes
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- RES’EAU NSERC Research Network, Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- * E-mail: (CH); (CP)
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Attali D, Bidshahri R, Haynes C, Bryan J. ddpcr: an R package and web application for analysis of droplet digital PCR data. F1000Res 2016; 5:1411. [PMID: 27703666 PMCID: PMC5031129 DOI: 10.12688/f1000research.9022.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/15/2016] [Indexed: 12/14/2022] Open
Abstract
Droplet digital polymerase chain reaction (ddPCR) is a novel platform for exact quantification of DNA which holds great promise in clinical diagnostics. It is increasingly popular due to its digital nature, which provides more accurate quantification and higher sensitivity than traditional real-time PCR. However, clinical adoption has been slowed in part by the lack of software tools available for analyzing ddPCR data. Here, we present
ddpcr – a new R package for ddPCR visualization and analysis. In addition,
ddpcr includes a web application (powered by the Shiny R package) that allows users to analyze ddPCR data using an interactive graphical interface.
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Affiliation(s)
- Dean Attali
- Bioinformatics Training Program, University of British Columbia, Vancouver, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Roza Bidshahri
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, Canada
| | - Charles Haynes
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, Canada
| | - Jennifer Bryan
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Statistics, University of British Columbia, Vancouver, Canada
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Lund HL, Hughesman CB, Fakhfakh K, McNeil K, Clemens S, Hocken K, Pettersson R, Karsan A, Foster LJ, Haynes C. Initial Diagnosis of ALK-Positive Non-Small-Cell Lung Cancer Based on Analysis of ALK Status Utilizing Droplet Digital PCR. Anal Chem 2016; 88:4879-85. [PMID: 27043019 DOI: 10.1021/acs.analchem.6b00707] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We describe a novel droplet digital PCR (ddPCR) assay capable of detecting genomic alterations associated with inversion translocations. It is applied here to detection of rearrangements in the anaplastic lymphoma kinase (ALK) gene associated with ALK-positive non-small-cell lung cancer (NSCLC). NSCLC patients may carry a nonreciprocal translocation on human chromosome 2, in which synchronized double stranded breaks (DSB) within the echinoderm microtubule-associated protein-like 4 (EML4) gene and ALK lead to an inversion of genetic material that forms the non-natural gene fusion EML4-ALK encoding a constitutively active tyrosine kinase that is associated with 3 to 7% of all NSCLCs. Detection of ALK rearrangements is currently achieved in clinics through direct visualization via a fluorescent in situ hybridization (FISH) assay, which can detect those rearrangements to a limit of detection (LOD) of ca. 15%. We show that the ddPCR assay presented here provides a LOD of 0.25% at lower cost and with faster turnaround times.
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Affiliation(s)
- H Louise Lund
- Michael Smith Laboratories, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada.,Genomic Science and Technology, University of British Columbia , Vancouver, British Columbia V5Z 4S6, Canada
| | - Curtis B Hughesman
- Michael Smith Laboratories, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada.,Department of Chemical and Biological Engineering, University of British Columbia , Vancouver, British Columbia V6T 1Z3, Canada
| | - Kareem Fakhfakh
- Michael Smith Laboratories, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada.,Department of Chemical and Biological Engineering, University of British Columbia , Vancouver, British Columbia V6T 1Z3, Canada
| | - Kelly McNeil
- Cancer Genetics Testing Laboratory, Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
| | - Shahira Clemens
- Cancer Genetics Testing Laboratory, Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
| | - Kimberly Hocken
- Cancer Genetics Testing Laboratory, Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
| | - Ryan Pettersson
- Cancer Genetics Testing Laboratory, Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
| | - Aly Karsan
- Cancer Genetics Testing Laboratory, Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z3, Canada
| | - Charles Haynes
- Michael Smith Laboratories, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada.,Genomic Science and Technology, University of British Columbia , Vancouver, British Columbia V5Z 4S6, Canada.,Department of Chemical and Biological Engineering, University of British Columbia , Vancouver, British Columbia V6T 1Z3, Canada
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