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Liu Q, Jiang X, Tu W, Liu L, Huang Y, Xia Y, Xia X, Shi Y. Comparative efficiency of differential diagnostic methods for the identification of BRAF V600E gene mutation in papillary thyroid cancer (Review). Exp Ther Med 2024; 27:149. [PMID: 38476918 PMCID: PMC10928970 DOI: 10.3892/etm.2024.12437] [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: 07/13/2023] [Accepted: 02/02/2024] [Indexed: 03/14/2024] Open
Abstract
V-Raf murine sarcoma viral oncogene homolog B1 (BRAF) encodes a serine-threonine kinase. The V600E point mutation in the BRAF gene is the most common mutation, predominantly occurring in melanoma, and colorectal, thyroid and non-small cell lung cancer. Particularly in the context of thyroid cancer research, it is routinely employed as a molecular biomarker to assist in diagnosing and predicting the prognosis of papillary thyroid cancer (PTC), and to formulate targeted therapeutic strategies. Currently, several methods are utilized in clinical settings to detect BRAF V600E mutations in patients with PTC. However, the sensitivity and specificity of various detection techniques vary significantly, resulting in diverse detection outcomes. The present review highlights the advantages and disadvantages of the methods currently employed in medical practice, with the aim of guiding clinicians and researchers in selecting the most suitable detection approach for its high sensitivity, reproducibility and potential to develop targeted therapeutic regimens for patients with BRAF gene mutation-associated PTC.
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Affiliation(s)
- Qian Liu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Xue Jiang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Wenling Tu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Lina Liu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Ying Huang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Yuxiao Xia
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Xuliang Xia
- Department of General Surgery, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Yuhong Shi
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
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Aran V, Lyra Miranda R, Heringer M, Carvalho da Fonseca AC, Andreiuolo F, Chimelli L, Devalle S, Niemeyer Filho P, Moura-Neto V. Liquid biopsy evaluation of circulating tumor DNA, miRNAs, and cytokines in meningioma patients. Front Neurol 2024; 14:1321895. [PMID: 38259646 PMCID: PMC10800936 DOI: 10.3389/fneur.2023.1321895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Liquid biopsy is a non-invasive method used to detect cancer and monitor treatment responses by analyzing blood or other bodily fluids for cancer biomarkers. Meningiomas are the most common primary central nervous system tumors, and biomarkers play a crucial role in their diagnosis, prognosis, and treatment monitoring. The World Health Organization (WHO) classifies meningiomas based on tumor grades and molecular alterations in genes such as in NF2, AKT1, TRAF7, SMO, PIK3CA, KLF4, SMARCE1, BAP1, H3K27me3, TERT promoter, and CDKN2A/B. Liquid biopsy, specifically cell-free DNA (cfDNA) analysis, has shown potential for monitoring meningiomas as it can detect ctDNA release in the blood, unaffected by the blood-brain barrier. MicroRNAs (miRNAs) have also been found to be deregulated in various cancers, including meningiomas, presenting potential as diagnostic biomarkers. Additionally, studying cytokines in the tumor microenvironment may aid in establishing prognostic or diagnostic panels for meningiomas. Methods In the present study we analyzed the DNA coming from both the plasma and tumor samples, in addition to analyze miRNA-21 and cytokines in the plasma of 28 meningioma patients. Discussion and Conclusion Our findings indicate that the detection of ctDNA in the plasma of meningioma patients is feasible. However, it's important to note that certain challenges persist when comparing plasma DNA analysis to that of tumor tissues. In our study, we observed a paired identification of mutations in only one patient, highlighting the complexities involved. Furthermore, we successfully identified miR-21 and cytokines in the plasma samples. Notably, our analysis of Interleukin 6 (IL-6) unveiled higher expression in the clear cell subtype compared to the other types. Despite the ongoing research, the clinical implementation of liquid biopsy in meningiomas remains somewhat limited. Nevertheless, our promising results underscore the need for further investigation.
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Affiliation(s)
- Veronica Aran
- Laboratório de Biomedicina do Cérebro, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | - Renan Lyra Miranda
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | - Manoela Heringer
- Laboratório de Biomedicina do Cérebro, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | | | - Felipe Andreiuolo
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
- Rede D'Or, IDOR - Instituto D'Or de Pesquisa e Ensino, Rio de Janeiro, Brazil
| | - Leila Chimelli
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | - Sylvie Devalle
- Laboratório de Biomedicina do Cérebro, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | - Paulo Niemeyer Filho
- Neurosurgery Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | - Vivaldo Moura-Neto
- Laboratório de Biomedicina do Cérebro, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
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Tak LJ, Shin MK, Yoo JI, Cho MC, Kim W. Development of droplet digital PCR-based detection of bacterial pathogens in prosthetic joint infection: a preliminary study using a synthesized model plasmid. Front Cell Infect Microbiol 2023; 13:1301446. [PMID: 38029245 PMCID: PMC10651726 DOI: 10.3389/fcimb.2023.1301446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Periprosthetic joint infection (PJI) can be diagnosed to characterize the microorganisms constituting a biofilm, which is an essential procedure for proper treatment. The gold standard method for detecting and identifying the causative microorganism is culture of microorganisms from patients-derived sample.; however, this method takes a long time and has low sensitivity. To compensate for these limitations, identification methods based on real-time PCR (RT-PCR) have been widely used. However, RT-PCR also has limitations, including low sensitivity and the requirement of a standard curve for quantification. Therefore, to prevent significant proliferation of pathogenic bacteria, it is important to detect a limited number of infectious bacteria during early stages of PJI. In the present study, we developed droplet digital PCR-based detection of bacterial pathogens in PJI. And we evaluated the analytical performance of the assay using a model plasmid, based on the 16S ribosomal DNA sequence of target bacteria commonly found in PJI. We also prepared genomic DNA extracted from E. coli, S. aureus, and S. epidermidis to test whether ddPCR provides better sensitivity and quantification of the target sequences. ddPCR detected 400 attograms of target DNA, which was more than 10 times less than that detected by real-time PCR using synthesized plasmid. In addition, ddPCR detected target regions from genomic DNA of 50 femtograms for E. coli, 70 femtograms for S. epidermidis, and 90 femtograms for S. aureus. The results indicate that ddPCR has the potential to decrease the microbial detection limit and provide precise detection, signifying its effectiveness for early PJI.
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Affiliation(s)
- Lee-Jung Tak
- Department of Convergence Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Min-Kyoung Shin
- Department of Microbiology, Department of Convergence Medical Science, and Institute of Health Sciences, School of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Jun-Il Yoo
- Department of Orthopedic Surgery, Inha University Hospital, Incheon, Republic of Korea
| | - Min-Chul Cho
- Departments of Laboratory Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Wanil Kim
- Department of Biochemistry, Department of Convergence Medical Science, and Institute of Health Sciences, School of Medicine, Gyeongsang National University, Jinju, Republic of Korea
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Salman P, de Melo AC, Rico-Restrepo M, Rodriguez J, Russi A, Schmerling RA, Zambrano A, Cinat G. Addressing the unmet needs of patients with BRAF-mutated melanoma in Latin America: Expert perspective. Front Oncol 2023; 13:1032300. [PMID: 36998456 PMCID: PMC10043339 DOI: 10.3389/fonc.2023.1032300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/27/2023] [Indexed: 03/16/2023] Open
Abstract
Melanoma represents an increasing public health burden with extensive unmet needs in Latin America (LA). A mutation in the BRAF gene is present in approximately 50% of all melanomas in White populations and is a target of precision medicine, with the potential to dramatically improve patient outcomes. Thus, increased access to BRAF testing and therapy is LA must be explored. At a multi-day conference, a panel of Latin American experts in oncology and dermatology were provided with questions to address the barriers limiting access to testing for BRAF mutation in patients with melanoma in LA, who may be eligible for targeted therapy to improve their prognosis. During the conference, responses were discussed and edited until a consensus on addressing the barriers was achieved. Identified challenges included ignorance of BRAF-status implications, limited human and infrastructural resources, affordability and reimbursement, fragmented care delivery, pitfalls in the sample journey, and lack of local data. Despite the clear benefits of targeted therapies for BRAF-mutated melanoma in other regions, there is no clear path to prepare LA for a sustainable personalized medicine approach to this disease. Due to melanoma’s time-sensitive nature, LA must aim to provide early access to BRAF testing and consider mutational status within treatment decision making. To this end, recommendations are provided and include establishing multidisciplinary teams and melanoma referral centers and improving access to diagnosis and treatment.
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Affiliation(s)
- Pamela Salman
- Oncology Department, Oncovida Cancer Center, Santiago, Chile
- *Correspondence: Pamela Salman,
| | | | | | | | - Andrea Russi
- Departamento de Oncología, Hospital Universitario San Ignacio, Centro Javeriano de Oncología, Bogotá, Colombia
| | | | - Angela Zambrano
- Departamento de Oncología, Fundación Valle del Lili, Cali, Colombia
| | - Gabriela Cinat
- Instituto de Oncología Ángel Roffo, Universidad de Buenos Aires, Fundación CIDEA, Buenos Aires, Argentina
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Wang Z, Weller C, Pinto A, Zhang DY, Mularo F, Tu ZJ, Cheng YW. Highly Sensitive Blocker Displacement Amplification for Detection of Low-Level JAK2V617F Variant. J Appl Lab Med 2023; 8:479-490. [PMID: 36759689 DOI: 10.1093/jalm/jfac130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/02/2022] [Indexed: 02/11/2023]
Abstract
BACKGROUND Key criteria in the diagnostic workup and risk stratification for myeloproliferative neoplasms (MPN) include molecular testing for JAK2V617F and other mutant alleles. Multiple methods for quantitatively detecting nucleotide sequence changes exist, but the lower limit of detection can limit identification of the low-level allele fraction of a variant. We evaluated a recently developed blocker displacement amplification (BDA)-based quantitative PCR platform for detection and quantitation of JAK2V617F variant allele fraction (VAF). METHODS Clinical samples were tested using BDA, next-generation sequencing (NGS), and droplet digital PCR (ddPCR) in a head-to-head comparison of sensitivity and specificity in detecting the JAK2V617F variant. In total, 112 human genomic DNA specimens previously tested for JAK2V617F gene mutation status with NGS were analyzed, including 12 samples with low-level variants with VAF ≤2%, 6 samples with VAF >2%, and 94 samples with no variant previously identified by NGS. RESULTS BDA and ddPCR results correlated well across a range of VAFs, with both methods identifying the JAK2V617F variant down to at least 0.05% VAF. NGS of routine sequencing depth was less sensitive, identifying JAK2V617F only at 0.6% VAF. CONCLUSIONS BDA can provide a cost-effective alternative means to identify low-level variants using instrumentation commonly found in laboratories.
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Affiliation(s)
- Zhen Wang
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | | | | | - Frank Mularo
- Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Zheng Jin Tu
- Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yu-Wei Cheng
- Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
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O'Hern K, Barney R, Chambers M, Baker C, Stevanovic M, Tsongalis GJ, Hughes E, Sriharan A. A novel method to assess copy number variation in melanoma: Droplet digital PCR for precise quantitation of the RREB1 gene in formalin-fixed, paraffin-embedded melanocytic neoplasms, a proof-of-concept study. J Cutan Pathol 2023; 50:169-177. [PMID: 36325821 DOI: 10.1111/cup.14352] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/11/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Melanocytic neoplasms can be challenging to diagnose. One well-established diagnostic aid is the detection of copy number variation (CNV) in a few key genetic loci using conventional methods such as fluorescence in situ hybridization (FISH) and chromosomal microarray (CMA). Droplet digital polymerase chain reaction (ddPCR) is a novel, cost-effective, rapid, and automated method to detect CNV. METHODS We perform the first investigation of ddPCR to assay Ras-responsive element-binding protein-1 (RREB1), the most common CNV in melanoma using formalin-fixed, paraffin-embedded (FFPE) melanocytic lesion samples; CMA data are used as the gold standard. Archival samples from 2013 to 2021 were analyzed, including 153 data points from 39 FFPE samples representing 34 patients. Benign, borderline, malignant, and metastatic melanocytic neoplasms were examined. RESULTS ddPCR showed a sensitivity and specificity of 93.8% and 95.7% using one reference gene, and 87.5% and 100% using a different reference gene for RREB1 gain detection. CONCLUSIONS Here we show that ddPCR can provide inexpensive, rapid, and robust data on the commonest copy number alteration in melanoma. Future development and validation could provide a useful ancillary tool in the diagnosis of challenging melanocytic lesions.
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Affiliation(s)
- Keegan O'Hern
- Dartmouth Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Rachael Barney
- Clinical Genomics and Advanced Technology Laboratory, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Meagan Chambers
- Dartmouth Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Catherine Baker
- Dartmouth Geisel School of Medicine, Hanover, New Hampshire, USA
| | | | - Gregory J Tsongalis
- Clinical Genomics and Advanced Technology Laboratory, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Edward Hughes
- Clinical Genomics and Advanced Technology Laboratory, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Aravindhan Sriharan
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
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Emerging digital PCR technology in precision medicine. Biosens Bioelectron 2022; 211:114344. [DOI: 10.1016/j.bios.2022.114344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/23/2022] [Accepted: 05/03/2022] [Indexed: 12/20/2022]
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Dobre EG, Constantin C, Neagu M. Skin Cancer Research Goes Digital: Looking for Biomarkers within the Droplets. J Pers Med 2022; 12:jpm12071136. [PMID: 35887633 PMCID: PMC9323323 DOI: 10.3390/jpm12071136] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 12/24/2022] Open
Abstract
Skin cancer, which includes the most frequent malignant non-melanoma carcinomas (basal cell carcinoma, BCC, and squamous cell carcinoma, SCC), along with the difficult to treat cutaneous melanoma (CM), pose important worldwide issues for the health care system. Despite the improved anti-cancer armamentarium and the latest scientific achievements, many skin cancer patients fail to respond to therapies, due to the remarkable heterogeneity of cutaneous tumors, calling for even more sophisticated biomarker discovery and patient monitoring approaches. Droplet digital polymerase chain reaction (ddPCR), a robust method for detecting and quantifying low-abundance nucleic acids, has recently emerged as a powerful technology for skin cancer analysis in tissue and liquid biopsies (LBs). The ddPCR method, being capable of analyzing various biological samples, has proved to be efficient in studying variations in gene sequences, including copy number variations (CNVs) and point mutations, DNA methylation, circulatory miRNome, and transcriptome dynamics. Moreover, ddPCR can be designed as a dynamic platform for individualized cancer detection and monitoring therapy efficacy. Here, we present the latest scientific studies applying ddPCR in dermato-oncology, highlighting the potential of this technology for skin cancer biomarker discovery and validation in the context of personalized medicine. The benefits and challenges associated with ddPCR implementation in the clinical setting, mainly when analyzing LBs, are also discussed.
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Affiliation(s)
- Elena-Georgiana Dobre
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Correspondence:
| | - Carolina Constantin
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Monica Neagu
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
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Multivariate Risk Analysis of RAS, BRAF and EGFR Mutations Allelic Frequency and Coexistence as Colorectal Cancer Predictive Biomarkers. Cancers (Basel) 2022; 14:cancers14112792. [PMID: 35681771 PMCID: PMC9179415 DOI: 10.3390/cancers14112792] [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: 05/02/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary The colorectal cancer (CRC) stage and evolution should be described by biomarker profiles. In 60 CRC cases, KRAS, NRAS, BRAF, and EGFR mutations were analyzed by droplet digital PCR (ddPCR). KRAS G12/G13 mutation was present in all patients with variable allelic frequencies. KRAS Q61 mutation was correlated with tumor invasion beyond the subserosa and poor differentiation, both associated with worst prognosis. Tumors with NRAS and BRAF mutations were prevalently localized on the right segment colon. The discovery of the KRAS Q61 role in tumor phenotypes provides the foundation for new therapeutic strategies and perspectives on molecular subtypes classification of CRC. Abstract Background: Biomarker profiles should represent a coherent description of the colorectal cancer (CRC) stage and its predicted evolution. Methods: Using droplet digital PCR, we detected the allelic frequencies (AF) of KRAS, NRAS, BRAF, and EGFR mutations from 60 tumors. We employed a pair-wise association approach to estimate the risk involving AF mutations as outcome variables for clinical data and as predicting variables for tumor-staging. We evaluated correlations between mutations of AFs and also between the mutations and histopathology features (tumor staging, inflammation, differentiation, and invasiveness). Results: KRAS G12/G13 mutations were present in all patients. KRAS Q61 was significantly associated with poor differentiation, high desmoplastic reaction, invasiveness (ypT4), and metastasis (ypM1). NRAS and BRAF were associated with the right-side localization of tumors. Diabetic patients had a higher risk to exhibit NRAS G12/G13 mutations. BRAF and NRAS G12/G13 mutations co-existed in tumors with invasiveness limited to the submucosa. Conclusions: The associations we found and the mutational AF we reported may help to understand disease processes and may be considered as potential CCR biomarker candidates. In addition, we propose representative mutation panels associated with specific clinical and histopathological features of CRC, as a unique opportunity to refine the degree of personalization of CRC treatment.
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Wolter M, Felsberg J, Malzkorn B, Kaulich K, Reifenberger G. Droplet digital PCR-based analyses for robust, rapid, and sensitive molecular diagnostics of gliomas. Acta Neuropathol Commun 2022; 10:42. [PMID: 35361262 PMCID: PMC8973808 DOI: 10.1186/s40478-022-01335-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/20/2022] [Indexed: 11/10/2022] Open
Abstract
Classification of gliomas involves the combination of histological features with molecular biomarkers to establish an integrated histomolecular diagnosis. Here, we report on the application and validation of a set of molecular assays for glioma diagnostics based on digital PCR technology using the QX200™ Droplet Digital™ PCR (ddPCR) system. The investigated ddPCR-based assays enable the detection of diagnostically relevant glioma-associated mutations in the IDH1, IDH2, H3-3A, BRAF, and PRKCA genes, as well as in the TERT promoter. In addition, ddPCR-based assays assessing diagnostically relevant copy number alterations were studied, including 1p/19q codeletion, gain of chromosome 7 and loss of chromosome 10 (+ 7/-10), EGFR amplification, duplication of the BRAF locus, and CDKN2A homozygous deletion. Results obtained by ddPCR were validated by other methods, including immunohistochemistry, Sanger sequencing, pyrosequencing, microsatellite analyses for loss of heterozygosity, as well as real-time PCR- or microarray-based copy number assays. Particular strengths of the ddPCR approach are (1) its high analytical sensitivity allowing for reliable detection of mutations even with low mutant allele frequencies, (2) its quantitative determination of mutant allele frequencies and copy number changes, and (3) its rapid generation of results within a single day. Thus, in line with other recent studies our findings support ddPCR analysis as a valuable approach for molecular glioma diagnostics in a fast, quantitative and highly sensitive manner.
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Sorokina A, Artyuhov A, Goltsova A, Dashinimaev E. Detection of CCR5Δ32 Mutant Alleles in Heterogeneous Cell Mixtures Using Droplet Digital PCR. Front Mol Biosci 2022; 9:805931. [PMID: 35265670 PMCID: PMC8898955 DOI: 10.3389/fmolb.2022.805931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/10/2022] [Indexed: 01/05/2023] Open
Abstract
The C-C chemokine receptor type 5 (CCR5 or CD195) is one of the co-receptor binding sites of the human immunodeficiency virus (HIV). Transplantations of hematopoietic stem cells with the CCR5Δ32 knockout mutation could represent an effective tool for the complete cure of HIV; these methods having passed the stage of proof-of-principle. At the same time, using the modern CRISPR/Cas9 genome editing method, we can effectively reproduce the CCR5Δ32 mutation in any wild-type cells. Thus, the task of searching for and accurately quantifying the content of mutant CCR5Δ32 alleles in heterogeneous cell mixtures becomes relevant. In this study, we describe the generation of an artificial CCR5Δ32 mutation using CRISPR/Cas9 followed by multiplex droplet digital polymerase chain reaction (ddPCR) to quantify its content in cell mixtures. The system we have developed allows us to quickly and accurately measure the content of cells with the CCR5Δ32 mutation, down to 0.8%.
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Affiliation(s)
- Alyona Sorokina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexander Artyuhov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Erdem Dashinimaev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
- *Correspondence: Erdem Dashinimaev,
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Neagu M, Constantin C, Surcel M. Testing Antigens, Antibodies, and Immune Cells in COVID-19 as a Public Health Topic—Experience and Outlines. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182413173. [PMID: 34948782 PMCID: PMC8700871 DOI: 10.3390/ijerph182413173] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 12/14/2022]
Abstract
The current COVID-19 pandemic has triggered an accelerated pace in all research domains, including reliable diagnostics methodology. Molecular diagnostics of the virus and its presence in biological samples relies on the RT-PCR method, the most used and validated worldwide. Nonconventional tests with improved parameters that are in the development stages will be presented, such as droplet digital PCR or CRISPR-based assays. These molecular tests were followed by rapid antigen testing along with the development of antibody tests, whether based on ELISA platform or on a chemiluminescent microparticle immunoassay. Less-conventional methods of testing antibodies (e.g., lateral flow immunoassay) are presented as well. Left somewhere in the backstage of COVID-19 research, immune cells and, furthermore, immune memory cells, are gaining the spotlight, more so in the vaccination context. Recently, methodologies using flow-cytometry evaluate circulating immune cells in infected/recovered patients. The appearance of new virus variants has triggered a surge for tests improvement. As the pandemic has entered an ongoing or postvaccination era, all methodologies that are used to monitor public health focus on diagnostic strategies and this review points out where gaps should be filled in both clinical and research settings.
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Affiliation(s)
- Monica Neagu
- Immunology Laboratory, Victor Babes National Institute of Pathology, 99-101 Splaiul Independentei, 050096 Bucharest, Romania; (M.N.); (M.S.)
- Pathology Department, Colentina University Hospital, 19-21 Șoseaua Ștefan cel Mare, 020125 Bucharest, Romania
- Doctoral School of Biology, Faculty of Biology, University of Bucharest, 91-93 Splaiul Independentei, 050095 Bucharest, Romania
| | - Carolina Constantin
- Immunology Laboratory, Victor Babes National Institute of Pathology, 99-101 Splaiul Independentei, 050096 Bucharest, Romania; (M.N.); (M.S.)
- Pathology Department, Colentina University Hospital, 19-21 Șoseaua Ștefan cel Mare, 020125 Bucharest, Romania
- Correspondence:
| | - Mihaela Surcel
- Immunology Laboratory, Victor Babes National Institute of Pathology, 99-101 Splaiul Independentei, 050096 Bucharest, Romania; (M.N.); (M.S.)
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Machine learning algorithm improved automated droplet classification of ddPCR for detection of BRAF V600E in paraffin-embedded samples. Sci Rep 2021; 11:12648. [PMID: 34135377 PMCID: PMC8209227 DOI: 10.1038/s41598-021-92014-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/25/2021] [Indexed: 12/17/2022] Open
Abstract
Somatic mutations in cancer driver genes can help diagnosis, prognosis and treatment decisions. Formalin-fixed paraffin-embedded (FFPE) specimen is the main source of DNA for somatic mutation detection. To overcome constraints of DNA isolated from FFPE, we compared pyrosequencing and ddPCR analysis for absolute quantification of BRAF V600E mutation in the DNA extracted from FFPE specimens and compared the results to the qualitative detection information obtained by Sanger Sequencing. Sanger sequencing was able to detect BRAF V600E mutation only when it was present in more than 15% total alleles. Although the sensitivity of ddPCR is higher than that observed for Sanger, it was less consistent than pyrosequencing, likely due to droplet classification bias of FFPE-derived DNA. To address the droplet allocation bias in ddPCR analysis, we have compared different algorithms for automated droplet classification and next correlated these findings with those obtained from pyrosequencing. By examining the addition of non-classifiable droplets (rain) in ddPCR, it was possible to obtain better qualitative classification of droplets and better quantitative classification compared to no rain droplets, when considering pyrosequencing results. Notable, only the Machine learning k-NN algorithm was able to automatically classify the samples, surpassing manual classification based on no-template controls, which shows promise in clinical practice.
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Abarna R, Nancy R, Chacko A, Chacko G, Pai R. Diagnostic utility of droplet digital PCR to detect TERT promoter mutations among glioblastoma samples using 7-deaza-dGTP. J Clin Pathol 2021; 75:140-142. [PMID: 33766956 DOI: 10.1136/jclinpath-2021-207402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/18/2021] [Accepted: 03/01/2021] [Indexed: 11/03/2022]
Affiliation(s)
- Rajadurai Abarna
- Pathology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Rachel Nancy
- Pathology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Ari Chacko
- Division of Neurosciences, Christian Medical College, Vellore, Tamil Nadu, India
| | - Geeta Chacko
- Pathology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Rekha Pai
- Pathology, Christian Medical College, Vellore, Tamil Nadu, India
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Enhanced asymmetric blocked qPCR method for affordable detection of point mutations in KRAS oncogene. Anal Bioanal Chem 2021; 413:2961-2969. [PMID: 33619642 DOI: 10.1007/s00216-021-03229-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 10/22/2022]
Abstract
An accurate genetic diagnostic is key for adequate patient management and the suitability of healthcare systems. The scientific challenge lies in developing methods to discriminate those patients with certain genetic variations present in tumor cells at low concentrations. We report a method called enhanced asymmetric blocked qPCR (EAB-qPCR) that promotes the blocker annealing against the primer-template hybrid controlling thermal cycling and reaction conditions with nonmodified oligonucleotides. Real-time fluorescent amplification curves of wild-type alleles were delayed by about eight cycles for EAB-qPCR, compared to conventional blocked qPCR approaches. This method reduced the amplification of native DNA variants (blocking percentage 99.7%) and enabled the effective enrichment of low-level DNA mutations. Excellent performance was estimated for the detection of mutated alleles in sensitivity (up to 0.5% mutant/total DNA) and reproducibility terms, with a relative standard deviation below 2.8%. The method was successfully applied to the mutational analysis of metastatic colorectal carcinoma from biopsied tissues. The determined single-nucleotide mutations in the KRAS oncogene (codon 12-13) totally agreed with those obtained from next-generation sequencing. EAB-qPCR is an accurate cheap method and can be easily incorporated into daily routine to detect mutant alleles. Hence, these features are especially interesting to facilitate the diagnosis and prognosis of several clinical diseases.
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Vanni I, Casula M, Pastorino L, Manca A, Dalmasso B, Andreotti V, Pisano M, Colombino M, Pfeffer U, Tanda ET, Rozzo C, Paliogiannis P, Cossu A, Ghiorzo P, Palmieri G. Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI). Diagn Pathol 2020; 15:143. [PMID: 33317587 PMCID: PMC7737361 DOI: 10.1186/s13000-020-01052-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/04/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Identification of somatic mutations in key oncogenes in melanoma is important to lead the effective and efficient use of personalized anticancer treatment. Conventional methods focus on few genes per run and, therefore, are unable to screen for multiple genes simultaneously. The use of Next-Generation Sequencing (NGS) technologies enables sequencing of multiple cancer-driving genes in a single assay, with reduced costs and DNA quantity needed and increased mutation detection sensitivity. METHODS We designed a customized IMI somatic gene panel for targeted sequencing of actionable melanoma mutations; this panel was tested on three different NGS platforms using 11 metastatic melanoma tissue samples in blinded manner between two EMQN quality certificated laboratory. RESULTS The detection limit of our assay was set-up to a Variant Allele Frequency (VAF) of 10% with a coverage of at least 200x. All somatic variants detected by all NGS platforms with a VAF ≥ 10%, were also validated by an independent method. The IMI panel achieved a very good concordance among the three NGS platforms. CONCLUSION This study demonstrated that, using the main sequencing platforms currently available in the diagnostic setting, the IMI panel can be adopted among different centers providing comparable results.
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Affiliation(s)
- Irene Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Milena Casula
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Lorenza Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Antonella Manca
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Bruna Dalmasso
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Virginia Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Marina Pisano
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Maria Colombino
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Ulrich Pfeffer
- Tumor Epigenetics, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Carla Rozzo
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Panagiotis Paliogiannis
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Antonio Cossu
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy.
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy.
| | - Giuseppe Palmieri
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
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Hosen MI, Forey N, Durand G, Voegele C, Bilici S, Avogbe PH, Delhomme TM, Foll M, Manel A, Vian E, Meziani S, De Tilly B, Polo G, Lole O, Francois P, Boureille A, Pisarev E, Salas AROSE, Monteiro-Reis S, Henrique R, Byrnes G, Jeronimo C, Scelo G, McKay JD, Calvez-Kelm FL, Zvereva M. Development of Sensitive Droplet Digital PCR Assays for Detecting Urinary TERT Promoter Mutations as Non-Invasive Biomarkers for Detection of Urothelial Cancer. Cancers (Basel) 2020; 12:E3541. [PMID: 33260905 PMCID: PMC7761513 DOI: 10.3390/cancers12123541] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/18/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022] Open
Abstract
Somatic mutations in the telomerase reverse transcriptase (TERT) promoter regions are frequent events in urothelial cancer (UC) and their detection in urine (supernatant cell-free DNA or DNA from exfoliated cells) could serve as putative non-invasive biomarkers for UC detection and monitoring. However, detecting these tumor-borne mutations in urine requires highly sensitive methods, capable of measuring low-level mutations. In this study, we developed sensitive droplet digital PCR (ddPCR) assays for detecting TERT promoter mutations (C228T, C228A, CC242-243TT, and C250T). We tested the C228T and C250T ddPCR assays on all samples with sufficient quantity of urinary DNA (urine supernatant cell-free DNA (US cfDNA) or urine pellet cellular DNA (UP cellDNA)) from the DIAGURO (n = 89/93 cases and n = 92/94 controls) and from the IPO-PORTO (n = 49/50 cases and n = 50/50 controls) series that were previously screened with the UroMuTERT assay and compared the performance of the two approaches. In the DIAGURO series, the sensitivity and specificity of the ddPCR assays for detecting UC using either US cfDNA or UP cellDNA were 86.8% and 92.4%. The sensitivity was slightly higher than that of the UroMuTERT assay in the IPO-PORTO series (67.4% vs. 65.3%, respectively), but not in the DIAGURO series (86.8% vs. 90.7%). The specificity was 100% in the IPO-PORTO controls for both the UroMuTERT and ddPCR assays, whereas in the DIAGURO series, the specificity dropped for ddPCR (92.4% versus 95.6%). Overall, an almost perfect agreement between the two methods was observed for both US cfDNA (n = 164; kappa coefficient of 0.91) and UP cellDNA (n = 280; kappa coefficient of 0.94). In a large independent series of serial urine samples from DIAGURO follow-up BC cases (n = 394), the agreement between ddPCR and UroMuTERT was (i) strong (kappa coefficient of 0.87), regardless of urine DNA types (kappa coefficient 0.89 for US cfDNA and 0.85 for UP cellDNA), (ii) the highest for samples with mutant allelic fractions (MAFs) > 2% (kappa coefficient of 0.99) and (iii) only minimal for the samples with the lowest MAFs (< 0.5%; kappa coefficient 0.32). Altogether, our results indicate that the two methods (ddPCR and UroMuTERT) for detecting urinary TERT promoter mutations are comparable and that the discrepancies relate to the detection of low-allelic fraction mutations. The simplicity of the ddPCR assays makes them suitable for implementation in clinical settings.
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Affiliation(s)
- Md Ismail Hosen
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka 1000, Bangladesh
| | - Nathalie Forey
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Geoffroy Durand
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Catherine Voegele
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Selin Bilici
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Patrice Hodonou Avogbe
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Tiffany Myriam Delhomme
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Matthieu Foll
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | | | - Emmanuel Vian
- Department of Urology, Protestant Clinic of Lyon, 69300 Caluire-et-Cuire, France; (E.V.); (B.D.T.); (G.P.)
| | - Sonia Meziani
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Berengere De Tilly
- Department of Urology, Protestant Clinic of Lyon, 69300 Caluire-et-Cuire, France; (E.V.); (B.D.T.); (G.P.)
| | - Gilles Polo
- Department of Urology, Protestant Clinic of Lyon, 69300 Caluire-et-Cuire, France; (E.V.); (B.D.T.); (G.P.)
| | - Olesia Lole
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Pauline Francois
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Antoine Boureille
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Eduard Pisarev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Andrei R. O. S. E. Salas
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
- Santa Casa de Sao Paulo School of Medical Sciences, Sao Paulo 01221-020, Brazil
| | - Sara Monteiro-Reis
- Portuguese Oncology Institute of Porto, Research Center (CI-IPOP), 4200-072 Porto, Portugal; (S.M.-R.); (R.H.); (C.J.)
| | - Rui Henrique
- Portuguese Oncology Institute of Porto, Research Center (CI-IPOP), 4200-072 Porto, Portugal; (S.M.-R.); (R.H.); (C.J.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), 4200-072 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4099-002 Porto, Portugal
| | - Graham Byrnes
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Carmen Jeronimo
- Portuguese Oncology Institute of Porto, Research Center (CI-IPOP), 4200-072 Porto, Portugal; (S.M.-R.); (R.H.); (C.J.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), 4200-072 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4099-002 Porto, Portugal
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
- Department of Medical Sciences, University of Turin, 8-10124 Turin, Italy
| | - James D. McKay
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Florence Le Calvez-Kelm
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Maria Zvereva
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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Michaelidou K, Koutoulaki C, Mavridis K, Vorrias E, Papadaki MA, Koutsopoulos AV, Mavroudis D, Agelaki S. Detection of KRAS G12/G13 Mutations in Cell Free-DNA by Droplet Digital PCR, Offers Prognostic Information for Patients with Advanced Non-Small Cell Lung Cancer. Cells 2020; 9:cells9112514. [PMID: 33233668 PMCID: PMC7699710 DOI: 10.3390/cells9112514] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022] Open
Abstract
KRAS mutations are found in approximately one third of non-small cell lung cancer (NSCLC) patients. In this study, we aim to investigate whether KRAS G12/G13 mutant allele fraction (MAF) in cell-free DNA (cfDNA) can provide meaningful prognostic information in NSCLC. Multiplex droplet-digital PCR was used to quantitatively assess KRAS G12/G13 MAF in cfDNA from 114 pre-treated advanced disease NSCLC patients. In 14 patients, changes in KRAS G12/G13 MAF were longitudinally monitored during treatment. Plasma KRAS G12/G13 status was associated with poor patients’ outcome in terms of progression-free survival (PFS) (p < 0.001) and overall survival (OS) (p < 0.001). In multivariate analysis, the detection of plasma KRAS mutations was an independent predictor of adverse PFS (HR = 3.12; p < 0.001) and OS (HR = 2.53; p = 0.002). KRAS G12/G13 MAF at first treatment evaluation (T1) was higher (p = 0.013) among patients experiencing progressive disease compared to those with disease control, and increased KRAS MAF at T1 was associated (p = 0.005) with shorter PFS. On the contrary, no association was observed between tissue KRAS mutation status and patients’ prognosis. Our results show that ddPCR-based detection of KRAS G12/G13 mutations in plasma could serve as an independent biomarker of unfavorable prognosis in NSCLC patients. Changes in KRAS MAF can provide valuable information for monitoring patient outcome during treatment.
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Affiliation(s)
- Kleita Michaelidou
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 71110 Heraklion, Crete, Greece; (K.M.); (C.K.); (M.A.P.); (D.M.)
| | - Chara Koutoulaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 71110 Heraklion, Crete, Greece; (K.M.); (C.K.); (M.A.P.); (D.M.)
| | - Konstantinos Mavridis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Crete, Greece;
| | - Eleftherios Vorrias
- Department of Medical Oncology, University General Hospital of Heraklion, 71110 Heraklion, Crete, Greece;
| | - Maria A. Papadaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 71110 Heraklion, Crete, Greece; (K.M.); (C.K.); (M.A.P.); (D.M.)
| | - Anastasios V. Koutsopoulos
- Department of Pathology, University General Hospital of Heraklion, University of Crete, Medical School, 71110 Heraklion, Crete, Greece;
| | - Dimitrios Mavroudis
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 71110 Heraklion, Crete, Greece; (K.M.); (C.K.); (M.A.P.); (D.M.)
- Department of Medical Oncology, University General Hospital of Heraklion, 71110 Heraklion, Crete, Greece;
| | - Sofia Agelaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 71110 Heraklion, Crete, Greece; (K.M.); (C.K.); (M.A.P.); (D.M.)
- Department of Medical Oncology, University General Hospital of Heraklion, 71110 Heraklion, Crete, Greece;
- Correspondence: ; Tel.: +30-281-039-2438
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Otsuji K, Sasaki T, Tanabe M, Seto Y. Droplet-digital PCR reveals frequent mutations in TERT promoter region in breast fibroadenomas and phyllodes tumours, irrespective of the presence of MED12 mutations. Br J Cancer 2020; 124:466-473. [PMID: 33046803 PMCID: PMC7852881 DOI: 10.1038/s41416-020-01109-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Breast fibroadenoma (FA) and phyllodes tumour (PT) often have variations of gene mediator complex subunit 12 (MED12) and mutations in the telomerase reverse transcriptase promoter region (TERTp). TERTp mutation is usually tested by Sanger sequencing. In this study, we compared Sanger sequencing and droplet-digital PCR (ddPCR) to measure TERTp mutations in FA and PT samples. METHODS FA and PT samples were collected from 82 patients who underwent surgery at our institution from 2005 to 2016. MED12 mutations for all cases and TERTp mutations for 17 tumours were detected by Sanger sequencing. ddPCR was performed to analyse TERTp mutation in all cases. RESULTS A total of 75 samples were eligible for analysis. Sanger sequencing detected MED12 mutations in 19/44 FA (42%) and 21/31 PT (68%). Among 17 Sanger sequencing-tested samples, 2/17 (12%) were TERTp mutation-positive. In ddPCR analyses, a significantly greater percentage of PT (19/31, 61%) was TERTp mutation-positive than was FA (13/44, 30%; P = 0.0046). The mutation positivity of TERTp and MED12 did not correlate, in either FA or PT. CONCLUSIONS ddPCR was more sensitive for detecting TERTp mutation than Sanger sequencing, being able to elucidate tumorigenesis in FA and PT.
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Affiliation(s)
- Kazutaka Otsuji
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeshi Sasaki
- Department of Next-Generation Pathology Information and Networking, Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Masahiko Tanabe
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Seto
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Minzenmayer AN, Miranda RN, Powell PR, Parekh PK. An unusual case of cutaneous Waldenström macroglobulinemia with the MYD88 L265P mutation. J Cutan Pathol 2020; 47:850-853. [PMID: 32335928 DOI: 10.1111/cup.13722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/13/2020] [Accepted: 04/20/2020] [Indexed: 12/12/2022]
Abstract
Waldenström macroglobulinemia is a lymphoplasmacytic lymphoma with bone marrow involvement and a monoclonal IgM gammopathy. Infiltration of the skin by neoplastic cells is very rare, and it can be difficult to distinguish from marginal zone lymphoma. The MYD88 L265P mutation is strongly associated with Waldenström macroglobulinemia, and it may be helpful in differentiating the two disorders, although the presence of this mutation is not specific, and other factors must be considered when making the final diagnosis. We present a diagnostically challenging case of cutaneous Waldenström macroglobulinemia in which the MYD88 L265P mutation was identified in the skin but not in the bone marrow, due to a low tumor burden.
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Affiliation(s)
- Andrew N Minzenmayer
- Department of Dermatology, Baylor Scott and White Central Texas, Temple, Texas, USA
| | - Roberto N Miranda
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Priscilla R Powell
- Department of Pathology, Baylor Scott and White Central Texas, Temple, Texas, USA
| | - Palak K Parekh
- Department of Dermatology, Baylor Scott and White Central Texas, Temple, Texas, USA
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21
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Vanni I, Tanda ET, Spagnolo F, Andreotti V, Bruno W, Ghiorzo P. The Current State of Molecular Testing in the BRAF-Mutated Melanoma Landscape. Front Mol Biosci 2020; 7:113. [PMID: 32695793 PMCID: PMC7338720 DOI: 10.3389/fmolb.2020.00113] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/13/2020] [Indexed: 01/19/2023] Open
Abstract
The incidence of melanoma, among the most lethal cancers, is widespread and increasing. Metastatic melanoma has a poor prognosis, representing about 90% of skin cancer mortality. The increased knowledge of tumor biology and the greater understanding of the immune system role in the anti-tumor response has allowed us to develop a more rational approach to systemic therapies. The discovery of activating BRAF mutations in half of all melanomas has led to the development of molecularly targeted therapy with BRAF and MEK inhibitors, which dramatically improved outcomes of patients with stage IV BRAF-mutant melanoma. More recently, the results of clinical phase III studies conducted in the adjuvant setting led to the combined administration of BRAF and MEK inhibitors also in patients with resected high-risk melanoma (stage III). Therefore, BRAF mutation testing has become a priority to determine the oncologist's choice and course of therapy. In this review, we will report the molecular biology-based strategies used for BRAF mutation detection with the main advantages and disadvantages of the most commonly used diagnostic strategies. The timing of such molecular assessment in patients with cutaneous melanoma will be discussed, and we will also examine considerations and approaches for accurate and effective BRAF testing.
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Affiliation(s)
- Irene Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | | | | | - Virginia Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
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22
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La Rocca F, Grieco V, Ruggieri V, Zifarone E, Villani O, Zoppoli P, Russi S, Laurino S, Falco G, Calice G, Marinaccio A, Natalicchio MI, Albano F, Musto P. Superiority of Droplet Digital PCR Over Real-Time Quantitative PCR for JAK2 V617F Allele Mutational Burden Assessment in Myeloproliferative Neoplasms: A Retrospective Study. Diagnostics (Basel) 2020; 10:diagnostics10030143. [PMID: 32150880 PMCID: PMC7151190 DOI: 10.3390/diagnostics10030143] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/11/2022] Open
Abstract
JAK2V617F mutational status is an essential diagnostic index in myeloproliferative neoplasms (MPNs). Although widely used for detection of JAK2 V617F mutation in peripheral blood (PB), sensitive real-time quantitative PCR (qPCR) presents some methodological limitations. Recently, emerging alternative technologies, like digital droplet PCR (ddPCR), have been reported to overcome some of qPCR’s technical drawbacks. The purpose of this study was to compare the diagnostic utility of ddPCR to qPCR for JAK2 V617F detection and quantification in samples from MPNs patients. Sensitivity and specificity of qPCR and ddPCR in the detection of the mutation were assessed by using a calibrator panel of mutated DNA on 195 JAK2 positive MPN samples. Based on our results, ddPCR proved to be a suitable, precise, and sensitive method for detection and quantification of the JAK2 V617F mutation.
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Affiliation(s)
- Francesco La Rocca
- Laboratory of Clinical Research and Advanced Diagnostics, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture (Pz), Italy; (F.L.R.); (V.G.)
| | - Vitina Grieco
- Laboratory of Clinical Research and Advanced Diagnostics, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture (Pz), Italy; (F.L.R.); (V.G.)
| | - Vitalba Ruggieri
- Laboratory of Preclinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata (CROB); 85028 Rionero in Vulture (Pz), Italy; (P.Z.); (S.R.); (S.L.); (G.C.)
- Correspondence:
| | - Emanuela Zifarone
- Trial Office, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture (Pz), Italy;
| | - Oreste Villani
- Hematology and Stem Cell Transplantation Unit, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture (Pz), Italy;
| | - Pietro Zoppoli
- Laboratory of Preclinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata (CROB); 85028 Rionero in Vulture (Pz), Italy; (P.Z.); (S.R.); (S.L.); (G.C.)
| | - Sabino Russi
- Laboratory of Preclinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata (CROB); 85028 Rionero in Vulture (Pz), Italy; (P.Z.); (S.R.); (S.L.); (G.C.)
| | - Simona Laurino
- Laboratory of Preclinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata (CROB); 85028 Rionero in Vulture (Pz), Italy; (P.Z.); (S.R.); (S.L.); (G.C.)
| | - Geppino Falco
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy;
- Biogem, Istituto di Biologia e Genetica Molecolare, Via Camporeale, 83031 Ariano Irpino (AV), Italy
| | - Giovanni Calice
- Laboratory of Preclinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata (CROB); 85028 Rionero in Vulture (Pz), Italy; (P.Z.); (S.R.); (S.L.); (G.C.)
| | - Anna Marinaccio
- Section of Clinic Pathology, OO.RR., 71122 Foggia, Italy; (A.M.); (M.I.N.)
| | | | - Francesco Albano
- Unit of Hematology and Stem Cell Transplantation, AOU Policlinico Consorziale “Giovanni XXIII”, “Aldo Moro” University, 70124 Bari, Italy; (F.A.); (P.M.)
| | - Pellegrino Musto
- Unit of Hematology and Stem Cell Transplantation, AOU Policlinico Consorziale “Giovanni XXIII”, “Aldo Moro” University, 70124 Bari, Italy; (F.A.); (P.M.)
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23
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Botezatu IV, Kondratova VN, Shelepov VP, Mazurenko NN, Tsyganova IV, Susova OY, Lichtenstein AV. Asymmetric mutant-enriched polymerase chain reaction and quantitative DNA melting analysis of KRAS mutation in colorectal cancer. Anal Biochem 2020; 590:113517. [PMID: 31782995 DOI: 10.1016/j.ab.2019.113517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/25/2019] [Accepted: 11/25/2019] [Indexed: 01/03/2023]
Abstract
Identification of mutant genes in tumor tissues and blood plasma (solid and liquid biopsy samples, respectively) is a necessity for individualized treatment of cancer patients. Here we report the use of a novel mutant-enriched PCR - quantitative DNA melting curve analysis (mePCR-qDMA) with TaqMan probes. The TaqMan probes served as blocking agents during PCR and as hybridization probes during DNA melting curve analyses. The end-point measurement of melt peaks areas by PeakFit software, a nonlinear iterative curve-fitting program, permitted quantification of the mutant/wild-type allele ratios. Approximately 6% and 0.1% of mutant KRAS allele in an excess of wild-type allele is detected with the standard and mePCR-qDMA processes, respectively. The application of the approach was tested for detecting the KRAS codon 12/13 mutation in paired tumor and blood plasma samples from 20 colorectal cancer patients. KRAS mutants were detected in 7 and 18 FFPE tumor samples, and in 3 and 7 plasma samples by the standard and mePCR-qDMA process, respectively. The results were confirmed by Sanger sequencing. This simple, rapid, cost-effective, and quantitative method carried out in a closed-tube format could be applied for the clinical analyses of other cancer genes.
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Affiliation(s)
- Irina V Botezatu
- Institute of Carcinogenesis, N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478, Moscow, Russia
| | - Valentina N Kondratova
- Institute of Carcinogenesis, N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478, Moscow, Russia
| | - Valery P Shelepov
- Institute of Carcinogenesis, N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478, Moscow, Russia
| | - Natalia N Mazurenko
- Institute of Carcinogenesis, N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478, Moscow, Russia
| | - Irina V Tsyganova
- Institute of Carcinogenesis, N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478, Moscow, Russia
| | - Olga Y Susova
- Institute of Carcinogenesis, N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478, Moscow, Russia
| | - Anatoly V Lichtenstein
- Institute of Carcinogenesis, N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478, Moscow, Russia.
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24
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Usefulness of droplet digital PCR and Sanger sequencing for detection of FGFR3 mutation in bladder cancer. Urol Oncol 2019; 37:907-915. [DOI: 10.1016/j.urolonc.2019.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 01/03/2023]
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25
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Lee KT, Park JE, Eom Y, Lim HS, Ki CS, Lim SY. Phenotypic association of presence of a somatic GNAQ mutation with port-wine stain distribution in capillary malformation. Head Neck 2019; 41:4143-4150. [PMID: 31532024 DOI: 10.1002/hed.25962] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 06/04/2019] [Accepted: 08/28/2019] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND A somatic mutation of GNAQ (c.548G>A, p.Arg183Gln) plays a key role in capillary malformation development. The present study aimed to evaluate clinical manifestations of port-win stain (PWS) associated with this genetic mutation. METHODS Skin tissue was obtained from 70 patients with capillary malformation who had been treated with excision for lesions. Droplet digital polymerase chain reaction was used to quantify the abundance of cells with the GNAQ mutation. RESULTS The GNAQ mutation was found in 50 patients. Patients with lesions involving upper facial region, which included forehead, eyebrow, and upper eyelid, showed a significantly higher rate of positive GNAQ mutation than those not involving it. Cases with facial PWS involving all three facial regions (upper, middle, and lower) showed significantly higher positive rate of GNAQ mutation compared to those involving one or two. CONCLUSIONS Presence of the somatic mutation GNAQ p.Arg183Gln might be associated with clinical manifestations of PWS.
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Affiliation(s)
- Kyeong-Tae Lee
- Department of Plastic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong Eun Park
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanynag University College of Medicine, Guri, Republic of Korea
| | - Yeseul Eom
- Department of Plastic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ha Seong Lim
- Areumdaunnara Dermatology Clinic, Sungnam-city, Kyunggido, Republic of Korea
| | - Chang-Seok Ki
- GC Genome, Yongin-si, Gyeonggi-do, Republic of Korea
| | - So Young Lim
- Department of Plastic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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26
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Wang Z, Sun K, Jing C, Cao H, Ma R, Wu J. Comparison of droplet digital PCR and direct Sanger sequencing for the detection of the BRAF V600E mutation in papillary thyroid carcinoma. J Clin Lab Anal 2019; 33:e22902. [PMID: 31021028 PMCID: PMC6642310 DOI: 10.1002/jcla.22902] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 12/19/2022] Open
Abstract
Background The BRAFV600E mutation status is a useful diagnostic and prognostic marker for papillary thyroid carcinoma (PTC). Although it is a commonly used method, Sanger sequencing has several limitations in detecting the BRAFV600E mutation. The aim of this study was to evaluate the efficiency of droplet digital PCR (ddPCR) as an alternative method for the detection of the BRAFV600E mutation in PTC patients. Methods Samples from a total of 120 patients with PTC and 30 patients with benign nodular thyroid disease who underwent thyroid surgery were collected. The BRAFV600E mutation status of the PTC patients was tested by Sanger sequencing and ddPCR. Results The BRAFV600E mutation was detected in 67 samples (44.67%) by Sanger sequencing and 92 samples (61.33%) by ddPCR. The detection of the mutation by the two methods was inconsistent in twenty‐five samples (16.67%). The sensitivity and specificity of the ddPCR method were 100% and 69.88%, respectively, and the positive predictive and negative predictive values were 72.83% and 100%, respectively. The concordance rate between the two methods in detecting the BRAFV600E mutation was 83.33%. Neither Sanger sequencing nor ddPCR detected BRAFV600E in 30 patients with benign nodular thyroid disease. The 92 samples with the BRAFV600E mutation were detected by ddPCR at a fractional abundance from 0.28% to 45.40% as follows: ≥10% (59 samples, 64.13%), 5%‐10% (8 samples, 8.70%), and ≤5% (25 samples, 27.17%). The BRAFV600E mutation was detected in all 59 samples at a fractional abundance ≥10% and in four samples at a fractional abundance from 5% to 10%, and no BRAFV600E mutation was detected at a fractional abundance ≤5% by Sanger sequencing. Conclusions ddPCR was a reliable, highly sensitive alternative method for the detection of the BRAFV600E mutation in PTC patients.
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Affiliation(s)
- Zhuo Wang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | | | - Changwen Jing
- Clinical Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Haixia Cao
- Clinical Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Rong Ma
- Clinical Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jianzhong Wu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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27
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Lee KS, Nam SK, Seo SH, Park KU, Oh HK, Kim DW, Kang SB, Kim WH, Lee HS. Digital polymerase chain reaction for detecting c-MYC copy number gain in tissue and cell-free plasma samples of colorectal cancer patients. Sci Rep 2019; 9:1611. [PMID: 30733532 PMCID: PMC6367402 DOI: 10.1038/s41598-018-38415-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 12/28/2018] [Indexed: 02/07/2023] Open
Abstract
We focused on the utility of the droplet digital polymerase chain reaction (ddPCR) for detecting c-MYC gene copy number (GCN) gain in cell-free plasma and tumor tissue of colorectal cancer (CRC) patients. c-MYC GCN status was determined using dual-color silver in situ hybridization (SISH) and ddPCR in retrospective cohort 1 (192 CRC patients) and prospective cohort 2 (64 CRC patients). In cohort 1, c-MYC GCN gain was observed in 34 (17.5%) patients by SISH, and in 7 (3.6%) patients by ddPCR. c-MYC GCN by SISH significantly correlated with ddPCR results (ρ = 0.532, P < 0.001). Although 40 cases (20.7%) showed intratumoral genetic heterogeneity, it did not cause discordance in results obtained by the two methods. c-MYC GCN gain, by both SISH and ddPCR was independently correlated with worst prognosis (P = 0.002). In cohort 2, c-MYC GCN estimation in tissue by ddPCR was also significantly associated with results obtained by SISH (ρ = 0.349, P = 0.005), but correlated with plasma ddPCR with borderline significance (ρ = 0.246, P = 0.050). Additionally, detecting c-MYC GCN gain in plasma with ddPCR might have relatively low sensitivity but high specificity. Our study suggests that ddPCR can be a useful tool for detecting c-MYC GCN gain as a potential prognostic biomarker in CRC tissue samples; however, this will need further verification in plasma samples.
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Affiliation(s)
- Kyu Sang Lee
- Department of Pathology, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Soo Kyung Nam
- Department of Pathology, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Heung-Kwon Oh
- Department of Surgery, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-707, Republic of Korea
| | - Duck-Woo Kim
- Department of Surgery, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-707, Republic of Korea
| | - Sung-Bum Kang
- Department of Surgery, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-707, Republic of Korea
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea. .,Department of Pathology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
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McEvoy AC, Pereira MR, Reid A, Pearce R, Cowell L, Al-Ogaili Z, Khattak MA, Millward M, Meniawy TM, Gray ES, Ziman M. Monitoring melanoma recurrence with circulating tumor DNA: a proof of concept from three case studies. Oncotarget 2019; 10:113-122. [PMID: 30719207 PMCID: PMC6349444 DOI: 10.18632/oncotarget.26451] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 11/26/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND A significant number of melanoma patients experience recurrence to distant sites, despite having had surgical treatment of the primary lesion, with curative intent. Monitoring of patients for early evidence of disease recurrence would significantly improve management of the disease, allowing timely therapeutic intervention. Circulating tumor DNA (ctDNA) is becoming a well-recognized biomarker for monitoring malignancies and has, in a few studies, been shown to signify disease recurrence earlier than conventional methods. METHODS We performed a retrospective analysis of plasma ctDNA using droplet digital PCR (ddPCR) in 30 primary melanoma patients with tumors harboring BRAF, NRAS or TERT promoter mutations. Mutant specific ctDNA, measured during clinical disease course, was compared with disease status in patients with confirmed disease recurrence (n = 3) and in those with no evidence of disease recurrence (n = 27). RESULTS Mutant specific ctDNA was detected in all three patients with disease recurrence at the time of clinically confirmed progression. In one case, plasma ctDNA detection preceded clinical identification of recurrence by an interval of 4 months. CtDNA was not detected in patients who were asymptomatic and had no radiological evidence of recurrence. CONCLUSIONS This study demonstrates promising results for the use of ctDNA as an informative monitoring tool for melanoma patients having undergone tumor resection of an early stage primary tumor. The clinical utility of ctDNA for monitoring disease recurrence warrants investigation in prospective studies as it may improve patient outcome.
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Affiliation(s)
- Ashleigh C. McEvoy
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia
| | - Michelle R. Pereira
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia
| | - Anna Reid
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia
| | - Robert Pearce
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia
| | - Lester Cowell
- Level1 Melanoma Clinic, Hamilton Hill, Western Australia 6163, Australia
| | - Zeyad Al-Ogaili
- Department of Molecular Imaging and Therapy Service, Fiona Stanley Hospital, Murdoch, Western Australia 6150, Australia
| | - Muhammad A. Khattak
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia
- Department of Medical Oncology, Fiona Stanley Hospital, Murdoch, Western Australia 6150, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Michael Millward
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia 6009, Australia
| | - Tarek M. Meniawy
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia 6009, Australia
| | - Elin S. Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia
- Centre for Ophthalmology and Visual Science, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Melanie Ziman
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
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Barcelos D, Neto RA, Cardili L, Fernandes M, Carapeto FCL, Comodo AN, Funabashi K, Iwamura ESM. KIT exon 11 and PDGFRA exon 18 gene mutations in gastric GIST: proposal of a short panel for predicting therapeutic response. SURGICAL AND EXPERIMENTAL PATHOLOGY 2018. [DOI: 10.1186/s42047-018-0021-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
GIST is the most common mesenchymal tumor of gastrointestinal tract and is more frequent in stomach. Its main mutations affect KIT and PDGFRA genes. Full genetic analysis panels are currently used to study mutations in GIST and other tumors. Considering that in gastric GIST KIT gene mutations in exon 11 are sensitive to IM whereas PDGFRΑ gene mutations in exon 18 (D842V) are resistant to the same drug, the aim of this study is to focus on these two molecular targets as a short alternative panel for predicting therapeutic response in gastric GIST which might optimize resources.
Methods
The genotypes of 38 cases of primary GIST were determined by performing bidirectional DNA sequencing.
Results
Exon 11 of KIT gene showed mutations in 65.3% and the exon 18 of PDGFRA gene showed 9% of cases. So it was possible to determine a subgroup of tumors which presented mutations in KIT exon 11 and PDGFRA exon 18.
Conclusion
Considering all of the foregoing analyzed globally, the application of short panel has impact on the cost and time of release of results to the physician, allowing a rapid approach to patients eligible for treatment with the target therapy.
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30
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McEvoy AC, Warburton L, Al-Ogaili Z, Celliers L, Calapre L, Pereira MR, Khattak MA, Meniawy TM, Millward M, Ziman M, Gray ES. Correlation between circulating tumour DNA and metabolic tumour burden in metastatic melanoma patients. BMC Cancer 2018; 18:726. [PMID: 29986670 PMCID: PMC6038195 DOI: 10.1186/s12885-018-4637-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/26/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Circulating tumour DNA (ctDNA) may serve as a measure of tumour burden and a useful tool for non-invasive monitoring of cancer. However, ctDNA is not always detectable in patients at time of diagnosis of metastatic disease. Therefore, there is a need to understand the correlation between ctDNA levels and the patients' overall metabolic tumour burden (MTB). METHODS Thirty-two treatment naïve metastatic melanoma patients were included in the study. MTB and metabolic tumour volume (MTV) was measured by 18F-fluoro-D-glucose positron emission tomography/computed tomography (FDG PET/CT). Plasma ctDNA was quantified using droplet digital PCR (ddPCR). RESULTS CtDNA was detected in 23 of 32 patients. Overall, a significant correlation was observed between ctDNA levels and MTB (p < 0.001). CtDNA was not detectable in patients with an MTB of ≤10, defining this value as the lower limit of tumour burden that can be detected through ctDNA analysis by ddPCR. CONCLUSIONS We showed that ctDNA levels measured by ddPCR correlate with MTB in treatment naïve metastatic melanoma patients and observed a limit in tumour size for which ctDNA cannot be detected in blood. Nevertheless, our findings support the use of ctDNA as a non-invasive complementary modality to functional imaging for monitoring tumour burden.
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Affiliation(s)
- Ashleigh C. McEvoy
- School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA 6027 Australia
| | - Lydia Warburton
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, WA 6009 Australia
| | - Zeyad Al-Ogaili
- Department of Molecular Imaging and Therapy Service, Fiona Stanley Hospital, Murdoch, WA 6150 Australia
| | - Liesl Celliers
- Department of Molecular Imaging and Therapy Service, Fiona Stanley Hospital, Murdoch, WA 6150 Australia
| | - Leslie Calapre
- School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA 6027 Australia
| | - Michelle R. Pereira
- School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA 6027 Australia
| | - Muhammad A. Khattak
- School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA 6027 Australia
- Department of Medical Oncology, Fiona Stanley Hospital, 11 Robin Warren Drive, Murdoch, WA 6150 Australia
- School of Medicine and Pharmacology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Tarek M. Meniawy
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, WA 6009 Australia
- School of Medicine and Pharmacology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Michael Millward
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, WA 6009 Australia
- School of Medicine and Pharmacology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Melanie Ziman
- School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA 6027 Australia
- School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Elin S. Gray
- School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA 6027 Australia
- Centre for Opthalmology and Visual Science, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009 Australia
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