1
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Liu Z, Li X, Zhang R, Ji L, Gong L, Ji Y, Zhou F, Yin Y, Li K, Sun P, Pu Z, Wang Q, Zou J. Identification of DNA variants at ultra-low variant allele frequencies via Taq polymerase cleavage of wild-specific blockers. Anal Bioanal Chem 2023; 415:6537-6549. [PMID: 37702773 DOI: 10.1007/s00216-023-04931-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/27/2023] [Accepted: 08/29/2023] [Indexed: 09/14/2023]
Abstract
Detecting mutations related to tumors holds immense clinical significance for cancer diagnosis and treatment. However, the presence of highly redundant wild DNA poses a challenge for the advancement of low-copy mutant ctDNA genotyping in cancer cases. To address this, a Taqman qPCR strategy to identify rare mutations at low variant allele fractions (VAFs) has been developed. This strategy combines mutant-specific primers with wild-specific blockers. Diverging from other blocker-mediated PCRs, which rely on primer-induced strand displacement or the use of modified oligos resistant to Taq polymerase, our innovation is built upon the cleavage of specific blockers by Taq polymerase. Given its unique design, which does not hinge on strand displacement or base modification, we refer to this novel method as unmodified-blocker cleavage PCR (UBC-PCR). Multiple experiments consistently confirmed that variant distinction was improved significantly by introduction of 5' unmatched blockers into the reaction. Moreover, UBC-PCR successfully detected mutant DNA at VAFs as low as 0.01% across six different variant contexts. Multiplex UBC-PCR was also performed to identify a reference target and three mutations with a sensitivity of 0.01% VAFs in one single tube. In profiling the gene status from 12 lung cancer ctDNA samples and 22 thyroid cancer FNA DNA samples, UBC-PCR exhibited a 100% concordance rate with ddPCR and a commercial ARMS kit, respectively. Our work demonstrates that UBC-PCR can identify low-abundance variants with high sensitivity in multiplex reactions, independent of strand displacement and base modification. This strategy holds the potential to significantly impact clinical practice and precision medicine.
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Affiliation(s)
- Zhaocheng Liu
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Xiushuai Li
- Department of Neurosurgery, The Affiliated Wuxi Second Hospital of Nanjing Medical University, 68 Zhongshan Road, Wuxi, 214122, Jiangsu Province, China
| | - Rui Zhang
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Li Ji
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Lingli Gong
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Yong Ji
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Fengsheng Zhou
- Department of Ultrasound, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Ying Yin
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Koukou Li
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Ping Sun
- Department of Pathology, Jiangnan University Medical Center, Wuxi, 214023, Jiangsu, China
| | - Zhening Pu
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Qing Wang
- Department of Neurosurgery, The Affiliated Wuxi Second Hospital of Nanjing Medical University, 68 Zhongshan Road, Wuxi, 214122, Jiangsu Province, China.
| | - Jian Zou
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China.
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China.
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2
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Pu D, Chen H, Fu W, Cui Y, Shu K. Combining E-ice-COLD-PCR and Pyrosequencing with Di-Base Addition (PDBA) Enables Sensitive Detection of Low-Abundance Mutations. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04718-0. [PMID: 37864708 DOI: 10.1007/s12010-023-04718-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2023] [Indexed: 10/23/2023]
Abstract
Detecting low-abundance mutations is of particular interest in the fields of biology and medical science. However, most currently available molecular assays have limited sensitivity for the detection of low-abundance mutations. Here, we established a platform for detecting low-level DNA mutations with high sensitivity and accuracy by combining enhanced-ice-COLD-PCR (E-ice-COLD-PCR) and pyrosequencing with di-base addition (PDBA). The PDBA assay was performed by selectively adding one di-base (AG, CT, AC, GT, AT, or GC) instead of one base (A, T, C, or G) into the reaction at a time during sequencing primer extension and thus enabling to increase the sequencing intensity. A specific E-ice-COLD-PCR/PDBA assay was developed for the detection of the most frequent BRAF V600E mutation to verify the feasibility of our method. E-ice-COLD-PCR/PDBA assay permitted the reliable detection of down to 0.007% of mutant alleles in a wild-type background. Furthermore, it required only a small amount of starting material (20 pg) to sensitively detect and identify low-abundance mutations, thus increasing the screening capabilities in limited DNA material. The E-ice-COLD-PCR/PDBA assay was applied in the current study to clinical formalin-fixed paraffin-embedded (FFPE) and plasma samples, and it enabled the detection of BRAF V600E mutations in samples that appeared as a wild type using PCR/conventional pyrosequencing (CP) and E-ice-COLD-PCR/CP. E-ice-COLD-PCR/PDBA assay is a rapid, cost-effective, and highly sensitive method that could improve the detection of low-abundance mutations in routine clinical use.
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Affiliation(s)
- Dan Pu
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Huimin Chen
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Wenjuan Fu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Youhong Cui
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China.
| | - Kunxian Shu
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
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3
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Tébar-Martínez R, Martín-Arana J, Gimeno-Valiente F, Tarazona N, Rentero-Garrido P, Cervantes A. Strategies for improving detection of circulating tumor DNA using next generation sequencing. Cancer Treat Rev 2023; 119:102595. [PMID: 37390697 DOI: 10.1016/j.ctrv.2023.102595] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/02/2023]
Abstract
Cancer has become a global health issue and liquid biopsy has emerged as a non-invasive tool for various applications. In cancer, circulating tumor DNA (ctDNA) can be detected from cell-free DNA (cfDNA) obtained from plasma and has potential for early diagnosis, treatment, resistance, minimal residual disease detection, and tumoral heterogeneity identification. However, the low frequency of ctDNA requires techniques for accurate analysis. Multitarget assay such as Next Generation Sequencing (NGS) need improvement to achieve limits of detection that can identify the low frequency variants present in the cfDNA. In this review, we provide a general overview of the use of cfDNA and ctDNA in cancer, and discuss techniques developed to optimize NGS as a tool for ctDNA detection. We also summarize the results obtained using NGS strategies in both investigational and clinical contexts.
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Affiliation(s)
- Roberto Tébar-Martínez
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Precision Medicine Unit, INCLIVA Health Research Institute, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain.
| | - Jorge Martín-Arana
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Bioinformatics Unit, INCLIVA Health Research Institute, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain.
| | - Francisco Gimeno-Valiente
- Cancer Evolution and Genome Instability Laboratory, University College of London Cancer Institute, 72 Huntley St, WC1E 6DD London, United Kingdom.
| | - Noelia Tarazona
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Health Institute Carlos III, CIBERONC, C/ Sinesio Delgado, 4, 28029 Madrid, Spain.
| | - Pilar Rentero-Garrido
- Precision Medicine Unit, INCLIVA Health Research Institute, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain.
| | - Andrés Cervantes
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Health Institute Carlos III, CIBERONC, C/ Sinesio Delgado, 4, 28029 Madrid, Spain.
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4
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Leong KW, Yu F, Makrigiorgos GM. Mutation enrichment in human DNA samples via UV-mediated cross-linking. Nucleic Acids Res 2021; 50:e32. [PMID: 34904676 PMCID: PMC8989544 DOI: 10.1093/nar/gkab1222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/28/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
Detection of low-level DNA mutations can reveal recurrent, hotspot genetic changes of clinical relevance to cancer, prenatal diagnostics, organ transplantation or infectious diseases. However, the high excess of wild-type (WT) alleles, which are concurrently present, often hinders identification of salient genetic changes. Here, we introduce UV-mediated cross-linking minor allele enrichment (UVME), a novel approach that incorporates ultraviolet irradiation (∼365 nm UV) DNA cross-linking either before or during PCR amplification. Oligonucleotide probes matching the WT target sequence and incorporating a UV-sensitive 3-cyanovinylcarbazole nucleoside modification are employed for cross-linking WT DNA. Mismatches formed with mutated alleles reduce DNA binding and UV-mediated cross-linking and favor mutated DNA amplification. UV can be applied before PCR and/or at any stage during PCR to selectively block WT DNA amplification and enable identification of traces of mutated alleles. This enables a single-tube PCR reaction directly from genomic DNA combining optimal pre-amplification of mutated alleles, which then switches to UV-mediated mutation enrichment-based DNA target amplification. UVME cross-linking enables enrichment of mutated KRAS and p53 alleles, which can be screened directly via Sanger sequencing, high-resolution melting, TaqMan genotyping or digital PCR, resulting in the detection of mutation allelic frequencies of 0.001–0.1% depending on the endpoint detection method. UV-mediated mutation enrichment provides new potential for mutation enrichment in diverse clinical samples.
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Affiliation(s)
- Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
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5
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Ono Y, Hayashi A, Maeda C, Suzuki M, Wada R, Sato H, Kawabata H, Okada T, Goto T, Karasaki H, Mizukami Y, Okumura T. Time-saving method for directly amplifying and capturing a minimal amount of pancreatic tumor-derived mutations from fine-needle aspirates using digital PCR. Sci Rep 2020; 10:12332. [PMID: 32704002 PMCID: PMC7378187 DOI: 10.1038/s41598-020-69221-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/23/2020] [Indexed: 02/08/2023] Open
Abstract
It is challenging to secure a cytopathologic diagnosis using minute amounts of tumor fluids and tissue fragments. Hence, we developed a rapid, accurate, low-cost method for detecting tumor cell-derived DNA from limited amounts of specimens and samples with a low tumor cellularity, to detect KRAS mutations in pancreatic ductal carcinomas (PDA) using digital PCR (dPCR). The core invention is based on the suspension of tumor samples in pure water, which causes an osmotic burst; the crude suspension could be directly subjected to emulsion PCR in the platform. We examined the feasibility of this process using needle aspirates from surgically resected pancreatic tumor specimens (n = 12). We successfully amplified and detected mutant KRAS in 11 of 12 tumor samples harboring the mutation; the positive mutation frequency was as low as 0.8%. We used residual specimens from fine-needle aspiration/biopsy and needle flush processes (n = 10) for method validation. In 9 of 10 oncogenic KRAS pancreatic tumor samples, the "water-burst" method resulted in a positive mutation call. We describe a dPCR-based, super-sensitive screening protocol for determining KRAS mutation availability using tiny needle aspirates from PDAs processed using simple steps. This method might enable pathologists to secure a more accurate, minimally invasive diagnosis using minute tissue fragments.
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Affiliation(s)
- Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Akihiro Hayashi
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Chiho Maeda
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Mayumi Suzuki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Reona Wada
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Hiroki Sato
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Hidemasa Kawabata
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Tetsuhiro Okada
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Takuma Goto
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Hidenori Karasaki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan.
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan.
| | - Toshikatsu Okumura
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
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6
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Abstract
ctDNA provided by liquid biopsy offers a promising alternative to tumor biopsy as it gives a non-invasive and «real-time» access to the cancer genome and reflects tumor intra and extra heterogeneity. ctDNA has shown growing clinical interest for cancer diagnosis, prognosis, theragnostics, therapeutic monitoring, and clonal evolution tracking. A major technical limit for ctDNA analysis from body fluids is the extremely low proportion of ctDNA compared to non-malignant cell-free DNA, underscoring the need for highly sensitive and specific detection techniques. The control of pre-analytical procedures appears essential for optimal ctDNA analysis and need to be standardized for clinical research applications. This chapter provides insights into major current technologies for ctDNA detection. Overall, PCR-based techniques are able to detect limited molecular alterations and have a high sensitivity suitable for monitoring purposes while NGS-based approaches are broad range molecular screening assays more specifically indicated for treatment selection. We briefly reviewed new technical innovations that are now available for ctDNA detection.
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Affiliation(s)
- Pauline Gilson
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, 54000, Nancy, France.
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7
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Abstract
Breast cancer is a highly heterogeneous and dynamic disease, exhibiting unique somatic alterations that lead to disease recurrence and resistance. Tumor biopsy and conventional imaging approaches are not able to provide sufficient information regarding the early detection of recurrence and real time monitoring through tracking sensitive or resistance mechanisms to treatment. Circulating tumor DNA (ctDNA) analysis has emerged as an attractive noninvasive methodology to detect cancer-specific genetic aberrations in plasma including DNA mutations and DNA methylation patterns. Numerous studies have reported on the potential of ctDNA analysis in the management of early and advanced stages of breast cancer. Advances in high-throughput technologies, especially next generation sequencing and PCR-based assays, were highly important for the successful application of ctDNA analysis. However, before being integrated into clinical practice, ctDNA analysis needs to be standardized and validated through the performance of multicenter prospective and well-designed clinical studies. This review is focused on the clinical utility of ctDNA analysis, especially at the DNA mutation and methylation level, in breast cancer patients, incorporating the latest advances in technological approaches and involving key studies in the early and metastatic setting.
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Affiliation(s)
- Eleni Tzanikou
- Department of Chemistry, Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, University of Athens, Athens, Greece
| | - Evi Lianidou
- Department of Chemistry, Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, University of Athens, Athens, Greece
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8
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Steinfort DP, Kranz S, Dowers A, Leas L, Dimitriadis V, Pham K, Hsu A, Bozinovski S, Irving LB, Loveland P, Christie M. Sensitive molecular testing methods can demonstrate NSCLC driver mutations in malignant pleural effusion despite non-malignant cytology. Transl Lung Cancer Res 2019; 8:513-518. [PMID: 31555523 DOI: 10.21037/tlcr.2019.07.05] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Malignant pleural effusion (MPE) may be diagnosed by cytologic evaluation of pleural fluid, though false negative results can occur. Pleural effusions may provide a source of tumour material for genotyping in lung cancer patients. Detection of MPE may be improved through use of highly sensitive molecular techniques. We identified five patients with non-small cell lung cancer (NSCLC) with initial pleural fluid samples that were non-malignant on cytology, but were subsequently clinically confirmed to have MPE. Tumour mutation status was confirmed via routine testing of diagnostic clinical specimens. Cytologically negative pleural fluid cell-block specimens were analysed by amplicon-based parallel sequencing (APS) for somatic mutations commonly detected in NSCLC, and selected cases by improved and complete enrichment CO-amplification at lower denaturation temperature PCR (ICECOLD PCR) for known mutations. Mutations were detected in three out of three (sensitivity 100%) cytologically non-malignant pleural fluids from patients with a known mutation: two patients with known Kirsten rat sarcoma (KRAS) mutation demonstrated the same KRAS mutation in their pleural fluids by APS, both at approximately 2% mutant allele frequency. In one patient with a known KRAS mutation, ICECOLD PCR detected the same KRAS variant at 0.7% frequency. No mutations were detected in patients with wild-type findings from reference samples (specificity 100%). Sensitive DNA sequencing methods can detect cancer-driver mutations in cytologically non-malignant pleural fluid specimens from NSCLC patients with MPE. Our findings demonstrate the feasibility of sensitive molecular diagnostic techniques for improvement of diagnostic assessment of pleural effusions in patients with lung cancer.
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Affiliation(s)
- Daniel P Steinfort
- Department of Respiratory Medicine, Royal Melbourne Hospital, Parkville, Australia.,Department of Medicine, University of Melbourne, Parkville, Australia
| | - Sevastjan Kranz
- Department of Pathology, Royal Melbourne Hospital, Parkville, Australia
| | - Anthony Dowers
- Department of Pathology, University of Melbourne, Parkville, Australia
| | - Leakhena Leas
- Department of Pathology, University of Melbourne, Parkville, Australia
| | - Voula Dimitriadis
- Department of Pathology, University of Melbourne, Parkville, Australia
| | - Kym Pham
- Department of Pathology, University of Melbourne, Parkville, Australia
| | - Arthur Hsu
- Department of Pathology, University of Melbourne, Parkville, Australia
| | - Steven Bozinovski
- School of Health & Biomedical Sciences, RMIT University, Bundoora, Australia
| | - Louis B Irving
- Department of Respiratory Medicine, Royal Melbourne Hospital, Parkville, Australia
| | - Paula Loveland
- Department of Respiratory Medicine, Royal Melbourne Hospital, Parkville, Australia
| | - Michael Christie
- Department of Pathology, Royal Melbourne Hospital, Parkville, Australia.,Department of Pathology, University of Melbourne, Parkville, Australia
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9
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Louveau B, Delyon J, De Moura CR, Battistella M, Jouenne F, Golmard L, Sadoux A, Podgorniak MP, Chami I, Marco O, Caramel J, Dalle S, Feugeas JP, Dumaz N, Lebbe C, Mourah S. A targeted genomic alteration analysis predicts survival of melanoma patients under BRAF inhibitors. Oncotarget 2019; 10:1669-1687. [PMID: 30899440 PMCID: PMC6422198 DOI: 10.18632/oncotarget.26707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 01/31/2019] [Indexed: 11/25/2022] Open
Abstract
Several mechanisms have been described to elucidate the emergence of resistance to MAPK inhibitors in melanoma and there is a crucial need for biomarkers to identify patients who are likely to achieve a better and long-lasting response to BRAF inhibitors therapy. In this study, we developed a targeted approach combining both mRNA and DNA alterations analysis focusing on relevant gene alterations involved in acquired BRAF inhibitor resistance. We collected baseline tumor samples from 64 melanoma patients at BRAF inhibitor treatment initiation and showed that the presence, prior to treatment, of mRNA over-expression of genes' subset was significantly associated with improved progression free survival and overall survival. The presence of DNA alterations was in favor of better overall survival. The genomic analysis of relapsed-matched tumor samples from 20 patients allowed us to uncover the largest landscape of resistance mechanisms reported to date as at least one resistance mechanism was identified for each patient studied. Alterations in RB1 have been most frequent and hence represent an important additional acquired resistance mechanism. Our targeted genomic analysis emerges as a relevant tool in clinical practice to identify those patients who are more likely to achieve durable response to targeted therapies and to exhaustively describe the spectrum of resistance mechanisms. Our approach can be adapted to new targeted therapies by including newly identified genetic alterations.
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Affiliation(s)
- Baptiste Louveau
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Pharmacogenomics, Saint-Louis Hospital, AP-HP, Paris, France
| | - Julie Delyon
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Dermatology, Saint-Louis Hospital, AP-HP, Paris, France
| | - Coralie Reger De Moura
- Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Pharmacogenomics, Saint-Louis Hospital, AP-HP, Paris, France
| | - Maxime Battistella
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Department of Pathology, Saint-Louis Hospital, AP-HP, Paris, France.,Paris Diderot University, Inserm, UMR_S1165, Paris, France
| | - Fanelie Jouenne
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Pharmacogenomics, Saint-Louis Hospital, AP-HP, Paris, France
| | - Lisa Golmard
- Department of Genetics, Pôle de Médecine Diagnostique et Théranostique, Institut Curie, Paris, France
| | - Aurelie Sadoux
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Pharmacogenomics, Saint-Louis Hospital, AP-HP, Paris, France
| | - Marie-Pierre Podgorniak
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Pharmacogenomics, Saint-Louis Hospital, AP-HP, Paris, France
| | - Ichrak Chami
- Department of Dermatology, Saint-Louis Hospital, AP-HP, Paris, France
| | - Oren Marco
- Department of Plastic, Reconstructive and Esthetic Surgery, Saint-Louis Hospital, AP-HP, Paris, France
| | - Julie Caramel
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer, Lyon, France
| | - Stephane Dalle
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer, Lyon, France.,Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France
| | | | - Nicolas Dumaz
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France
| | - Celeste Lebbe
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Dermatology, Saint-Louis Hospital, AP-HP, Paris, France
| | - Samia Mourah
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Pharmacogenomics, Saint-Louis Hospital, AP-HP, Paris, France
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10
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Franczak C, Filhine-Tresarrieu P, Gilson P, Merlin JL, Au L, Harlé A. Technical considerations for circulating tumor DNA detection in oncology. Expert Rev Mol Diagn 2019; 19:121-135. [DOI: 10.1080/14737159.2019.1568873] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Claire Franczak
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy, France
| | | | - Pauline Gilson
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
| | - Jean-Louis Merlin
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
| | - Lewis Au
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Alexandre Harlé
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
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11
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Baudrin LG, Deleuze JF, How-Kit A. Molecular and Computational Methods for the Detection of Microsatellite Instability in Cancer. Front Oncol 2018; 8:621. [PMID: 30631754 PMCID: PMC6315116 DOI: 10.3389/fonc.2018.00621] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/30/2018] [Indexed: 12/31/2022] Open
Abstract
Microsatellite instability (MSI) is a genomic alteration in which microsatellites, usually of one to four nucleotide repeats, accumulate mutations corresponding to deletions/insertions of a few nucleotides. The MSI phenotype has been extensively characterized in colorectal cancer and is due to a deficiency of the DNA mismatch repair system. MSI has recently been shown to be present in most types of cancer with variable frequencies (from <1 to 30%). It correlates positively to survival outcome and predicts the response to immune checkpoint blockade therapy. The different methods developed for MSI detection in cancer require taking into consideration two critical parameters which influence method performance. First, the microsatellite markers used should be chosen carefully to ensure they are highly sensitive and specific for MSI detection. Second, the analytical method used should be highly resolute to allow clear identification of MSI and of the mutant allele genotype, and should present the lowest limit of detection possible for application in samples with low mutant allele frequency. In this review, we describe all the different molecular and computational methods developed to date for the detection of MSI in cancer, how they have evolved and improved over the years, and their advantages and drawbacks.
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Affiliation(s)
- Laura G Baudrin
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Paris, France.,Laboratoire d'Excellence GenMed Paris, Paris, France
| | - Jean-François Deleuze
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Paris, France.,Centre National de Recherche en Génomique Humaine, CEA-Institut François Jacob, Evry, France
| | - Alexandre How-Kit
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Paris, France
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12
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Mauger F, Kernaleguen M, Lallemand C, Kristensen VN, Deleuze JF, Tost J. Enrichment of methylated molecules using enhanced-ice-co-amplification at lower denaturation temperature-PCR (E-ice-COLD-PCR) for the sensitive detection of disease-related hypermethylation. Epigenomics 2018; 10:525-537. [PMID: 29697281 DOI: 10.2217/epi-2017-0166] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
AIM The detection of specific DNA methylation patterns bears great promise as biomarker for personalized management of cancer patients. Co-amplification at lower denaturation temperature-PCR (COLD-PCR) assays are sensitive methods, but have previously only been able to analyze loss of DNA methylation. MATERIALS & METHODS Enhanced (E)-ice-COLD-PCR reactions starting from 2 ng of bisulfite-converted DNA were developed to analyze methylation patterns in two promoters with locked nucleic acid (LNA) probes blocking amplification of unmethylated CpGs. The enrichment of methylated molecules was compared to quantitative (q)PCR and quantified using serial dilutions. RESULTS E-ice-COLD-PCR allowed the multiplexed enrichment and quantification of methylated DNA. Assays were validated in primary breast cancer specimens and circulating cell-free DNA from cancer patients. CONCLUSION E-ice-COLD-PCR could prove a useful tool in the context of DNA methylation analysis for personalized medicine.
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Affiliation(s)
- Florence Mauger
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Magali Kernaleguen
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Céline Lallemand
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Vessela N Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway.,Department of Clinical Molecular Biology & Laboratory Science (EpiGen), Akershus University Hospital, Division of Medicine, 1476 Lørenskog, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jean-François Deleuze
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France.,Centre d'Etudes du Polymorphisme Humain, CEPH-Fondation Jean Dausset, Paris, France.,Laboratoire d'Excellence GenMed, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
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13
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High-sensitivity assay for monitoring ESR1 mutations in circulating cell-free DNA of breast cancer patients receiving endocrine therapy. Sci Rep 2018. [PMID: 29531247 PMCID: PMC5847549 DOI: 10.1038/s41598-018-22312-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Approximately 70% of breast cancers (BCs) express estrogen receptor alpha (ERα) and are treated with endocrine therapy. However, the effectiveness of this therapy is limited by innate or acquired resistance in approximately one-third of patients. Activating mutations in the ESR1 gene that encodes ERα promote critical resistance mechanisms. Here, we developed a high sensitivity approach based on enhanced-ice-COLD-PCR for detecting ESR1 mutations. The method produced an enrichment up to 100-fold and allowed the unambiguous detection of ESR1 mutations even when they consisted of only 0.01% of the total ESR1 allelic fraction. After COLD-PCR enrichment, methods based on next-generation sequencing or droplet-digital PCR were employed to detect and quantify ESR1 mutations. We applied the method to detect ESR1 mutations in circulating free DNA from the plasma of 56 patients with metastatic ER-positive BC. Fifteen of these patients were found to have ESR1 mutations at codons 536-538. This study demonstrates the utility of the enhanced-ice-COLD-PCR approach for simplifying and improving the detection of ESR1 tumor mutations in liquid biopsies. Because of its high sensitivity, the approach may potentially be applicable to patients with non-metastatic disease.
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14
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Mauger F, How-Kit A, Tost J. COLD-PCR Technologies in the Area of Personalized Medicine: Methodology and Applications. Mol Diagn Ther 2018; 21:269-283. [PMID: 28101802 DOI: 10.1007/s40291-016-0254-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Somatic mutations bear great promise for use as biomarkers for personalized medicine, but are often present only in low abundance in biological material and are therefore difficult to detect. Many assays for mutation analysis in cancer-related genes (hotspots) have been developed to improve diagnosis, prognosis, prediction of drug resistance, and monitoring of the response to treatment. Two major approaches have been developed: mutation-specific amplification methods and methods that enrich and detect mutations without prior knowledge on the exact location and identity of the mutation. CO-amplification at Lower Denaturation temperature Polymerase Chain Reaction (COLD-PCR) methods such as full-, fast-, ice- (improved and complete enrichment), enhanced-ice, and temperature-tolerant COLD-PCR make use of a critical temperature in the polymerase chain reaction to selectively denature wild-type-mutant heteroduplexes, allowing the enrichment of rare mutations. Mutations can subsequently be identified using a variety of laboratory technologies such as high-resolution melting, digital polymerase chain reaction, pyrosequencing, Sanger sequencing, or next-generation sequencing. COLD-PCR methods are sensitive, specific, and accurate if appropriately optimized and have a short time to results. A large variety of clinical samples (tumor DNA, circulating cell-free DNA, circulating cell-free fetal DNA, and circulating tumor cells) have been studied using COLD-PCR in many different applications including the detection of genetic changes in cancer and infectious diseases, non-invasive prenatal diagnosis, detection of microorganisms, or DNA methylation analysis. In this review, we describe in detail the different COLD-PCR approaches, highlighting their specificities, advantages, and inconveniences and demonstrating their use in different fields of biological and biomedical research.
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Affiliation(s)
- Florence Mauger
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Alexandre How-Kit
- Laboratory for Genomics, Fondation Jean Dausset-CEPH, 75010, Paris, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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15
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How-Kit A, Daunay A, Buhard O, Meiller C, Sahbatou M, Collura A, Duval A, Deleuze JF. Major improvement in the detection of microsatellite instability in colorectal cancer using HSP110 T17 E-ice-COLD-PCR. Hum Mutat 2017; 39:441-453. [PMID: 29227006 DOI: 10.1002/humu.23379] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/13/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022]
Abstract
Every colorectal cancer (CRC) patient should be tested for microsatellite instability (MSI) to screen for Lynch syndrome. Evaluation of MSI status involves screening tumor DNA for the presence of somatic deletions in DNA repeats using PCR followed by fragment analysis. While this method may lack sensitivity due to the presence of a high level of germline DNA, which frequently contaminates the core of primary colon tumors, no other method developed to date is capable of modifying the standard PCR protocol to achieve improvement of MSI detection. Here, we describe a new approach developed for the ultra-sensitive detection of MSI in CRC based on E-ice-COLD-PCR, using HSP110 T17, a mononucleotide DNA repeat previously proposed as an optimal marker to detect MSI in tumor DNA, and an oligo(dT)16 LNA blocker probe complementary to wild-type genotypes. The HT17 E-ice-COLD-PCR assay improved MSI detection by 20-200-fold compared with standard PCR using HT17 alone. It presents an analytical sensitivity of 0.1%-0.05% of mutant alleles in wild-type background, thus greatly improving MSI detection in CRC samples highly contaminated with normal DNA. HT17 E-ice-COLD-PCR is a rapid, cost-effective, easy-to-implement, and highly sensitive method, which could significantly improve the detection of MSI in routine clinical testing.
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Affiliation(s)
- Alexandre How-Kit
- Laboratoire de Génomique, Fondation Jean Dausset - CEPH, Paris, France
| | - Antoine Daunay
- Laboratoire de Génomique, Fondation Jean Dausset - CEPH, Paris, France
| | - Olivier Buhard
- Sorbonne-Université, Université Pierre et Marie Curie - Paris 6, INSERM, UMRS 938-Centre de Recherche Saint-Antoine, Equipe 'Instabilité des Microsatellites et Cancers', Equipe labellisée par la Ligue Nationale contre le Cancer, France Université Pierre et Marie Curie, Paris, France
| | - Clément Meiller
- INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe labellisée Ligue Contre le Cancer, Paris, France
| | - Mourad Sahbatou
- Laboratoire de Biostatistique, Fondation Jean Dausset - CEPH, Paris, France
| | - Ada Collura
- Sorbonne-Université, Université Pierre et Marie Curie - Paris 6, INSERM, UMRS 938-Centre de Recherche Saint-Antoine, Equipe 'Instabilité des Microsatellites et Cancers', Equipe labellisée par la Ligue Nationale contre le Cancer, France Université Pierre et Marie Curie, Paris, France
| | - Alex Duval
- Sorbonne-Université, Université Pierre et Marie Curie - Paris 6, INSERM, UMRS 938-Centre de Recherche Saint-Antoine, Equipe 'Instabilité des Microsatellites et Cancers', Equipe labellisée par la Ligue Nationale contre le Cancer, France Université Pierre et Marie Curie, Paris, France
| | - Jean-François Deleuze
- Laboratoire de Génomique, Fondation Jean Dausset - CEPH, Paris, France.,Centre National de Recherche en Génomique Humaine, CEA-Institut François Jacob, Evry, France
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16
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Louveau B, Tost J, Mauger F, Sadoux A, Podgorniak MP, How-Kit A, Pages C, Roux J, Da Meda L, Lebbe C, Mourah S. Clinical value of early detection of circulating tumour DNA- BRAFV600mut in patients with metastatic melanoma treated with a BRAF inhibitor. ESMO Open 2017; 2:e000173. [PMID: 28761746 PMCID: PMC5519801 DOI: 10.1136/esmoopen-2017-000173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/09/2017] [Accepted: 03/11/2017] [Indexed: 02/05/2023] Open
Affiliation(s)
- Baptiste Louveau
- Assistance Publique-Hôpitaux de Paris, Laboratoire de Pharmacogénomique, Hôpital Saint-Louis, Paris, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France
| | - Florence Mauger
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France
| | - Aurélie Sadoux
- Assistance Publique-Hôpitaux de Paris, Laboratoire de Pharmacogénomique, Hôpital Saint-Louis, Paris, France
| | - Marie-Pierre Podgorniak
- Assistance Publique-Hôpitaux de Paris, Laboratoire de Pharmacogénomique, Hôpital Saint-Louis, Paris, France
| | | | - Cécile Pages
- Département de Dermatologie, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Jennifer Roux
- Département de Dermatologie, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Laetitia Da Meda
- Département de Dermatologie, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Céleste Lebbe
- Département de Dermatologie, Assistance publique-Hôpitaux de Paris, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,UMR-976, INSERM, Hôpital Saint-Louis, Paris, France
| | - Samia Mourah
- Assistance Publique-Hôpitaux de Paris, Laboratoire de Pharmacogénomique, Hôpital Saint-Louis, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,UMR-976, INSERM, Hôpital Saint-Louis, Paris, France
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17
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Sefrioui D, Mauger F, Leclere L, Beaussire L, Di Fiore F, Deleuze JF, Sarafan-Vasseur N, Tost J. Comparison of the quantification of KRAS mutations by digital PCR and E-ice-COLD-PCR in circulating-cell-free DNA from metastatic colorectal cancer patients. Clin Chim Acta 2016; 465:1-4. [PMID: 27940131 DOI: 10.1016/j.cca.2016.12.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 12/02/2016] [Accepted: 12/05/2016] [Indexed: 01/05/2023]
Abstract
Circulating cell-free DNA (ccfDNA) bears great promise as biomarker for personalized medicine, but ccfDNA is present only at low levels in the plasma or serum of cancer patients. E-ice-COLD-PCR is a recently developed enrichment method to detect and identify mutations present at low-abundance in clinical samples. However, recent studies have shown the importance to accurately quantify low-abundance mutations as clinically important decisions will depend on certain mutation thresholds. The possibility for an enrichment method to accurately quantify the mutation levels remains a point of concern and might limit its clinical applicability. In the present study, we compared the quantification of KRAS mutations in ccfDNA from metastatic colorectal cancer patients by E-ice-COLD-PCR with two digital PCR approaches. For the quantification of mutations by E-ice-COLD-PCR, cell lines with known mutations diluted into WT genomic DNA were used for calibration. E-ice-COLD-PCR and the two digital PCR approaches showed the same range of the mutation level and were concordant for mutation levels below the clinical relevant threshold. E-ice-COLD-PCR can accurately detect and quantify low-abundant mutations in ccfDNA and has a shorter time to results making it compatible with the requirements of analyses in a clinical setting without the loss of quantitative accuracy.
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Affiliation(s)
- David Sefrioui
- Digestive Oncology Unit, Rouen University Hospital, France; Inserm U1079, Iron group, IRIB, University of Rouen, Normandy University, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Florence Mauger
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France
| | - Laurence Leclere
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France
| | - Ludivine Beaussire
- Inserm U1079, Iron group, IRIB, University of Rouen, Normandy University, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Frédéric Di Fiore
- Digestive Oncology Unit, Rouen University Hospital, France; Inserm U1079, Iron group, IRIB, University of Rouen, Normandy University, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Jean-François Deleuze
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France
| | - Nasrin Sarafan-Vasseur
- Inserm U1079, Iron group, IRIB, University of Rouen, Normandy University, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France.
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18
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Guégan S, Kadlub N, Picard A, Rouillé T, Charbel C, Coulomb-L'Hermine A, How-Kit A, Fraitag S, Aractingi S, Fontaine RH. Varying proliferative and clonogenic potential inNRAS-mutated congenital melanocytic nevi according to size. Exp Dermatol 2016; 25:789-96. [DOI: 10.1111/exd.13073] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Sarah Guégan
- Institut National de la Santé et de la Recherche Médicale (INSERM), U938; Saint-Antoine Research Center; Paris France
- Université Pierre et Marie Curie-Paris VI; Paris France
- Department of Dermatology; Assistance Publique-Hôpitaux de Paris, Hôpital Tenon; Paris France
| | - Natacha Kadlub
- Université René Descartes-Paris V; Paris France
- Department of Maxillofacial and Plastic Surgery; Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants-Malades; Paris France
| | - Arnaud Picard
- Université René Descartes-Paris V; Paris France
- Department of Maxillofacial and Plastic Surgery; Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants-Malades; Paris France
| | - Thomas Rouillé
- Institut National de la Santé et de la Recherche Médicale (INSERM), U938; Saint-Antoine Research Center; Paris France
- Université Pierre et Marie Curie-Paris VI; Paris France
| | - Christelle Charbel
- Institut National de la Santé et de la Recherche Médicale (INSERM), U938; Saint-Antoine Research Center; Paris France
- Université Pierre et Marie Curie-Paris VI; Paris France
| | - Aurore Coulomb-L'Hermine
- Université Pierre et Marie Curie-Paris VI; Paris France
- Department of Pathology; Assistance Publique-Hôpitaux de Paris, Hôpital Trousseau; Paris France
| | - Alexandre How-Kit
- Laboratory for Functional Genomics; Fondation Jean Dausset - CEPH; Paris France
| | - Sylvie Fraitag
- Department of Pathology; Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants-Malades; Paris France
| | - Selim Aractingi
- Institut National de la Santé et de la Recherche Médicale (INSERM), U938; Saint-Antoine Research Center; Paris France
- Université René Descartes-Paris V; Paris France
- Department of Dermatology; Assistance Publique-Hôpitaux de Paris, Hôpital Cochin; Paris France
| | - Romain H. Fontaine
- Institut National de la Santé et de la Recherche Médicale (INSERM), U938; Saint-Antoine Research Center; Paris France
- Université Pierre et Marie Curie-Paris VI; Paris France
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19
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Bronte E, Bronte G, Novo G, Bronte F, Bavetta MG, Lo Re G, Brancatelli G, Bazan V, Natoli C, Novo S, Russo A. What links BRAF to the heart function? New insights from the cardiotoxicity of BRAF inhibitors in cancer treatment. Oncotarget 2016; 6:35589-601. [PMID: 26431495 PMCID: PMC4742127 DOI: 10.18632/oncotarget.5853] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/22/2015] [Indexed: 12/14/2022] Open
Abstract
The RAS-related signalling cascade has a fundamental role in cell. It activates differentiation and survival. It is particularly important one of its molecules, B-RAF. B-RAF has been a central point for research, especially in melanoma. Indeed, it lacked effective therapeutic weapons since the early years of its study. Molecules targeting B-RAF have been developed. Nowadays, two classes of molecules are approved by FDA. Multi-target molecules, such as Sorafenib and Regorafenib, and selective molecules, such as Vemurafenib and Dabrafenib. Many other molecules are still under investigation. Most of them are studied in phase 1 trials. Clinical studies correlate B-RAF inhibitors and QT prolongation. Though this cardiovascular side effect is not common using these drugs, it must be noticed early and recognize its signals. Indeed, Oncologists and Cardiologists should work in cooperation to prevent lethal events, such as fatal arrhythmias or sudden cardiac death. These events could originate from an uncontrolled QT prolongation.
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Affiliation(s)
- Enrico Bronte
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Giuseppe Bronte
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Giuseppina Novo
- Department of Internal Medicine and Cardiovascular Disease, University of Palermo, Palermo, Italy
| | - Fabrizio Bronte
- DiBiMIS, Section of Gastroenterology, University of Palermo, Palermo, Italy
| | | | - Giuseppe Lo Re
- Department of Radiology, University of Palermo, Palermo, Italy
| | | | - Viviana Bazan
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Clara Natoli
- Department of Medical, Oral and Biotechnological Sciences, University "G. D'Annunzio", Chieti, Italy
| | - Salvatore Novo
- Department of Internal Medicine and Cardiovascular Disease, University of Palermo, Palermo, Italy
| | - Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
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20
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Lorillon G, Mourah S, Vercellino L, de Margerie-Mellon C, Pagès C, Goldwirt L, Lebbe C, Tost J, Tazi A. Sustained response to salvage therapy for dabrafenib-resistant metastatic Langerhans cell sarcoma. Ann Oncol 2016; 27:2305-2307. [PMID: 27502715 DOI: 10.1093/annonc/mdw299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- G Lorillon
- Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, National Reference Center for Langerhans cell histiocytosis, Pulmonology Department, Paris, France
| | - S Mourah
- Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, Pharmacology and Genetic Department, Paris, France.,Univ Paris-Diderot, Sorbonne Paris Cité; INSERM U976, Paris, France
| | - L Vercellino
- Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, Nuclear Medicine Department, Paris, France
| | - C de Margerie-Mellon
- Univ. Paris-Diderot, Sorbonne Paris Cité; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, Radiology Department, Paris, France
| | - C Pagès
- Assistance Publique-Hôpitaux de Paris, Dermatology Department, Paris, France
| | - L Goldwirt
- Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, Pharmacology and Genetic Department, Paris, France
| | - C Lebbe
- Univ Paris-Diderot, Sorbonne Paris Cité; INSERM U976, Paris, France.,Assistance Publique-Hôpitaux de Paris, Dermatology Department, Paris, France
| | - J Tost
- Laboratory for Epigenetics and Environment, Genotyping National Center, CEA-Genomic Institute, Evry, France
| | - A Tazi
- Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, National Reference Center for Langerhans cell histiocytosis, Pulmonology Department, Paris, France .,Univ Paris-Diderot, Sorbonne Paris Cité; CRESS INSERM U1153, Biostatistics and Clinical Epidemiology Research Team, Paris, France
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21
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Mauger F, Daunay A, Deleuze JF, Tost J, How-Kit A. Multiplexing of E-ice-COLD-PCR Assays for Mutation Detection and Identification. Clin Chem 2016; 62:1155-8. [DOI: 10.1373/clinchem.2016.258830] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Florence Mauger
- Centre National de Génotypage CEA-Institut de Génomique Evry, France
| | - Antoine Daunay
- Laboratory for Genomics Fondation Jean Dausset–CEPH Paris, France
| | - Jean-François Deleuze
- Centre National de Génotypage CEA-Institut de Génomique Evry, France
- Laboratory for Genomics Fondation Jean Dausset–CEPH Paris, France
| | - Jörg Tost
- Centre National de Génotypage CEA-Institut de Génomique Evry, France
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Mourah S, How-Kit A, Meignin V, Gossot D, Lorillon G, Bugnet E, Mauger F, Lebbe C, Chevret S, Tost J, Tazi A. Recurrent NRAS mutations in pulmonary Langerhans cell histiocytosis. Eur Respir J 2016; 47:1785-96. [PMID: 27076591 DOI: 10.1183/13993003.01677-2015] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/11/2016] [Indexed: 02/06/2023]
Abstract
The mitogen-activated protein kinase (MAPK) pathway is constantly activated in Langerhans cell histiocytosis (LCH). Mutations of the downstream kinases BRAF and MAP2K1 mediate this activation in a subset of LCH lesions. In this study, we attempted to identify other mutations which may explain the MAPK activation in nonmutated BRAF and MAP2K1 LCH lesions.We analysed 26 pulmonary and 37 nonpulmonary LCH lesions for the presence of BRAF, MAP2K1, NRAS and KRAS mutations. Grossly normal lung tissue from 10 smoker patients was used as control. Patient spontaneous outcomes were concurrently assessed.BRAF(V600E) mutations were observed in 50% and 38% of the pulmonary and nonpulmonary LCH lesions, respectively. 40% of pulmonary LCH lesions harboured NRAS(Q61K) (/R) mutations, whereas no NRAS mutations were identified in nonpulmonary LCH biopsies or in lung tissue control. In seven out of 11 NRAS(Q61K) (/R)-mutated pulmonary LCH lesions, BRAF(V600) (E) mutations were also present. Separately genotyping each CD1a-positive area from the same pulmonary LCH lesion demonstrated that these concurrent BRAF and NRAS mutations were carried by different cell clones. NRAS(Q61K) (/R) mutations activated both the MAPK and AKT (protein kinase B) pathways. In the univariate analysis, the presence of concurrent BRAF(V600E) and NRAS(Q61K) (/R) mutations was significantly associated with patient outcome.These findings highlight the importance of NRAS genotyping of pulmonary LCH lesions because the use of BRAF inhibitors in this context may lead to paradoxical disease progression. These patients might benefit from MAPK kinase inhibitor-based treatments.
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Affiliation(s)
- Samia Mourah
- Assistance Publique - Hôpitaux de Paris, Laboratoire de Pharmacologie Biologique, Hôpital Saint-Louis; Université Paris-Diderot, Sorbonne Paris Cité; INSERM U976, Paris, France
| | - Alexandre How-Kit
- Laboratoire de Génomique fonctionnelle, Fondation Jean Dausset - CEPH, Paris, France
| | - Véronique Meignin
- Assistance Publique - Hôpitaux de Paris, Service de Pathologie, Hôpital Saint-Louis; INSERM UMR_S1165, Paris, France
| | - Dominique Gossot
- Département Thoracique, Institut Mutualiste Montsouris, Paris, France
| | - Gwenaël Lorillon
- Assistance Publique - Hôpitaux de Paris, Centre National de Référence de l'Histiocytose Langerhansienne, Service de Pneumologie, Hôpital Saint-Louis, Paris, France
| | - Emmanuelle Bugnet
- Assistance Publique - Hôpitaux de Paris, Centre National de Référence de l'Histiocytose Langerhansienne, Service de Pneumologie, Hôpital Saint-Louis, Paris, France
| | - Florence Mauger
- Laboratoire Epigénétique et Environnement, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France
| | - Celeste Lebbe
- Assistance Publique - Hôpitaux de Paris, Département de Dermatologie, Hôpital Saint-Louis; Université Paris-Diderot, Sorbonne Paris Cité; INSERM U976, Paris, France
| | - Sylvie Chevret
- Assistance Publique - Hôpitaux de Paris; Service de Biostatistique et Information Médicale, Hôpital Saint-Louis, Paris, France Université Paris-Diderot, Sorbonne Paris Cité; INSERM UMR 1153 CRESS, Equipe de Recherche en Biostatistiques et Epidémiologie Clinique, Paris, France
| | - Jörg Tost
- Laboratoire Epigénétique et Environnement, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France
| | - Abdellatif Tazi
- Assistance Publique - Hôpitaux de Paris, Centre National de Référence de l'Histiocytose Langerhansienne, Service de Pneumologie, Hôpital Saint-Louis, Paris, France Université Paris-Diderot, Sorbonne Paris Cité; INSERM UMR 1153 CRESS, Equipe de Recherche en Biostatistiques et Epidémiologie Clinique, Paris, France
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Bidshahri R, Attali D, Fakhfakh K, McNeil K, Karsan A, Won JR, Wolber R, Bryan J, Hughesman C, Haynes C. Quantitative Detection and Resolution of BRAF V600 Status in Colorectal Cancer Using Droplet Digital PCR and a Novel Wild-Type Negative Assay. J Mol Diagn 2016; 18:190-204. [PMID: 26762843 DOI: 10.1016/j.jmoldx.2015.09.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 08/25/2015] [Accepted: 09/17/2015] [Indexed: 12/21/2022] Open
Abstract
A need exists for robust and cost-effective assays to detect a single or small set of actionable point mutations, or a complete set of clinically informative mutant alleles. Knowledge of these mutations can be used to alert the clinician to a rare mutation that might necessitate more aggressive clinical monitoring or a personalized course of treatment. An example is BRAF, a (proto)oncogene susceptible to either common or rare mutations in codon V600 and adjacent codons. We report a diagnostic technology that leverages the unique capabilities of droplet digital PCR to achieve not only accurate and sensitive detection of BRAF(V600E) but also all known somatic point mutations within the BRAF V600 codon. The simple and inexpensive two-well droplet digital PCR assay uses a chimeric locked nucleic acid/DNA probe against wild-type BRAF and a novel wild-type-negative screening paradigm. The assay shows complete diagnostic accuracy when applied to formalin-fixed, paraffin-embedded tumor specimens from metastatic colorectal cancer patients deficient for Mut L homologue-1.
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Affiliation(s)
- Roza Bidshahri
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dean Attali
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kareem Fakhfakh
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kelly McNeil
- Department of Genetics and Molecular Diagnostics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Aly Karsan
- Department of Genetics and Molecular Diagnostics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Jennifer R Won
- Canadian Immunohistochemistry Quality Control Unit, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert Wolber
- Department of Pathology, Lion's Gate Hospital, North Vancouver, British Columbia, Canada
| | - Jennifer Bryan
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Curtis Hughesman
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Charles Haynes
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
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25
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Comprehensive evaluation of methods to isolate, quantify, and characterize circulating cell-free DNA from small volumes of plasma. Anal Bioanal Chem 2015; 407:6873-8. [DOI: 10.1007/s00216-015-8846-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/03/2015] [Accepted: 06/10/2015] [Indexed: 12/21/2022]
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