1
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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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2
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Jeanjean SI, Renault V, Daunay A, Shen Y, Hardy LM, Deleuze JF, How-Kit A. LT-RPA: An Isothermal DNA Amplification Approach for Improved Microsatellite Genotyping and Microsatellite Instability Detection. Methods Mol Biol 2023; 2621:91-109. [PMID: 37041442 DOI: 10.1007/978-1-0716-2950-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Microsatellites are short tandem repeats of one to six nucleotides that are highly polymorphic and extensively used as genetic markers in numerous biomedical applications, including the detection of microsatellite instability (MSI) in cancer. The standard analytical method for microsatellite analysis relies on PCR amplification followed by capillary electrophoresis or, more recently, next-generation sequencing (NGS). However, their amplification during PCR generates undesirable frameshift products known as stutter peaks caused by polymerase slippage, complicating data analysis and interpretation, while very few alternative methods for microsatellite amplification have been developed to reduce the formation of these artifacts. In this context, the recently developed low-temperature recombinase polymerase amplification (LT-RPA) is an isothermal DNA amplification method at low temperature (32 °C) that drastically reduces and sometimes completely abolishes the formation of stutter peaks. LT-RPA greatly simplifies the genotyping of microsatellites and improves the detection of MSI in cancer. In this chapter, we describe in detail all the experimental steps necessary for the development of LT-RPA simplex and multiplex assays for microsatellite genotyping and MSI detection, including the design, optimization, and validation of the assays combined with capillary electrophoresis or NGS.
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Affiliation(s)
- Sophie I Jeanjean
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Victor Renault
- Laboratoire de Bio-informatique Clinique, Institut Curie, Paris, France
| | - Antoine Daunay
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Yimin Shen
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Lise M Hardy
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
- Laboratory of Excellence GenMed, Paris, France
| | - Jean-François Deleuze
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
- Laboratory of Excellence GenMed, Paris, France
- Centre National de Recherche en Génomique Humaine, CEA- Institut François Jacob, Evry, France
| | - Alexandre How-Kit
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand.
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3
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Daunay A, Hardy LM, Bouyacoub Y, Sahbatou M, Touvier M, Blanché H, Deleuze JF, How-Kit A. Centenarians consistently present a younger epigenetic age than their chronological age with four epigenetic clocks based on a small number of CpG sites. Aging (Albany NY) 2022; 14:7718-7733. [PMID: 36202132 PMCID: PMC9596211 DOI: 10.18632/aging.204316] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022]
Abstract
Aging is a progressive time-dependent biological process affecting differentially individuals, who can sometimes present exceptional longevity. Epigenetic alterations are one of the hallmarks of aging, which comprise the epigenetic drift and clock at DNA methylation level. In the present study, we estimated the DNA methylation-based age (DNAmage) using four epigenetic clocks based on a small number of CpGs in French centenarians and semi-supercentenarians (CSSC, n=214) as well as nonagenarians' and centenarians' offspring (NCO, n=143) compared to individuals from the French general population (CG, n=149). DNA methylation analysis of the nine CpGs included in the epigenetic clocks showed high correlation with chronological age (-0.66>R>0.54) and also the presence of an epigenetic drift for four CpGs that was only visible in CSSC. DNAmage analysis showed that CSSC and to a lesser extend NCO present a younger DNAmage than their chronological age (15-28.5 years for CSSC, 4.4-11.5 years for NCO and 4.2-8.2 years for CG), which were strongly significant in CSSC compared to CG (p-values<2.2e-16). These differences suggest that epigenetic aging and potentially biological aging are slowed in exceptionally long-lived individuals and that epigenetic clocks based on a small number of CpGs are sufficient to reveal alterations of the global epigenetic clock.
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Affiliation(s)
- Antoine Daunay
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France
| | - Lise M Hardy
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France.,Laboratory of Excellence GenMed, Paris, France
| | - Yosra Bouyacoub
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France.,Laboratory of Excellence GenMed, Paris, France
| | - Mourad Sahbatou
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France
| | - Mathilde Touvier
- Sorbonne Paris Nord University, Nutritional Epidemiology Research Team (EREN), Epidemiology and Statistics Research Center Inserm U1153, Inrae U1125, Cnam, University of Paris (CRESS), Bobigny, France
| | - Hélène Blanché
- Laboratory of Excellence GenMed, Paris, France.,Centre de Ressources Biologiques, CEPH Biobank, Foundation Jean Dausset - CEPH, Paris, France
| | - Jean-François Deleuze
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France.,Laboratory of Excellence GenMed, Paris, France.,Centre de Ressources Biologiques, CEPH Biobank, Foundation Jean Dausset - CEPH, Paris, France.,Centre National de Recherche en Génomique Humaine, CEA, Institut François Jacob, Evry, France
| | - Alexandre How-Kit
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France
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4
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A high-throughput real-time PCR tissue-of-origin test to distinguish blood from lymphoblastoid cell line DNA for (epi)genomic studies. Sci Rep 2022; 12:4684. [PMID: 35304543 PMCID: PMC8933453 DOI: 10.1038/s41598-022-08663-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
Lymphoblastoid cell lines (LCLs) derive from blood infected in vitro by Epstein–Barr virus and were used in several genetic, transcriptomic and epigenomic studies. Although few changes were shown between LCL and blood genotypes (SNPs) validating their use in genetics, more were highlighted for other genomic features and/or in their transcriptome and epigenome. This could render them less appropriate for these studies, notably when blood DNA could still be available. Here we developed a simple, high-throughput and cost-effective real-time PCR approach allowing to distinguish blood from LCL DNA samples based on the presence of EBV relative load and rearranged T-cell receptors γ and β. Our approach was able to achieve 98.5% sensitivity and 100% specificity on DNA of known origin (458 blood and 316 LCL DNA). It was further applied to 1957 DNA samples from the CEPH Aging cohort comprising DNA of uncertain origin, identifying 784 blood and 1016 LCL DNA. A subset of these DNA was further analyzed with an epigenetic clock indicating that DNA extracted from blood should be preferred to LCL for DNA methylation-based age prediction analysis. Our approach could thereby be a powerful tool to ascertain the origin of DNA in old collections prior to (epi)genomic studies.
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5
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Garali I, Sahbatou M, Daunay A, Baudrin LG, Renault V, Bouyacoub Y, Deleuze JF, How-Kit A. Improvements and inter-laboratory implementation and optimization of blood-based single-locus age prediction models using DNA methylation of the ELOVL2 promoter. Sci Rep 2020; 10:15652. [PMID: 32973211 PMCID: PMC7515898 DOI: 10.1038/s41598-020-72567-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 09/02/2020] [Indexed: 01/21/2023] Open
Abstract
Several blood-based age prediction models have been developed using less than a dozen to more than a hundred DNA methylation biomarkers. Only one model (Z-P1) based on pyrosequencing has been developed using DNA methylation of a single locus located in the ELOVL2 promoter, which is considered as one of the best age-prediction biomarker. Although multi-locus models generally present better performances compared to the single-locus model, they require more DNA and present more inter-laboratory variations impacting the predictions. Here we developed 17,018 single-locus age prediction models based on DNA methylation of the ELOVL2 promoter from pooled data of four different studies (training set of 1,028 individuals aged from 0 and 91 years) using six different statistical approaches and testing every combination of the 7 CpGs, aiming to improve the prediction performances and reduce the effects of inter-laboratory variations. Compared to Z-P1 model, three statistical models with the optimal combinations of CpGs presented improved performances (MAD of 4.41–4.77 in the testing set of 385 individuals) and no age-dependent bias. In an independent testing set of 100 individuals (19–65 years), we showed that the prediction accuracy could be further improved by using different CpG combinations and increasing the number of technical replicates (MAD of 4.17).
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Affiliation(s)
- Imene Garali
- Laboratory for Bioinformatics, Foundation Jean Dausset-CEPH, Paris, France.,Laboratory of Excellence GenMed, Paris, France
| | - Mourad Sahbatou
- Laboratory for Human Genetics, Foundation Jean Dausset-CEPH, Paris, France
| | - Antoine Daunay
- Laboratory for Genomics, Foundation Jean Dausset-CEPH, 75010, Paris, France
| | - Laura G Baudrin
- Laboratory of Excellence GenMed, Paris, France.,Laboratory for Genomics, Foundation Jean Dausset-CEPH, 75010, Paris, France
| | - Victor Renault
- Laboratory for Bioinformatics, Foundation Jean Dausset-CEPH, Paris, France
| | - Yosra Bouyacoub
- Laboratory of Excellence GenMed, Paris, France.,Laboratory for Genomics, Foundation Jean Dausset-CEPH, 75010, Paris, France
| | - Jean-François Deleuze
- Laboratory for Bioinformatics, Foundation Jean Dausset-CEPH, Paris, France.,Laboratory of Excellence GenMed, Paris, France.,Laboratory for Human Genetics, Foundation Jean Dausset-CEPH, Paris, France.,Laboratory for Genomics, Foundation Jean Dausset-CEPH, 75010, Paris, France.,Centre National de Recherche en Génomique Humaine, CEA, Institut François Jacob, Evry, France
| | - Alexandre How-Kit
- Laboratory for Genomics, Foundation Jean Dausset-CEPH, 75010, Paris, France.
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6
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Jouenne F, Sadoux A, Lorillon G, Louveau B, Bugnet E, Meignin V, Mourah S, Tazi A. Custom pyrosequencing assay to detect short BRAF deletions in Langerhans cell histiocytic lesions. J Clin Pathol 2020; 74:533-536. [PMID: 32873703 DOI: 10.1136/jclinpath-2020-206974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 11/04/2022]
Abstract
Langerhans cell histiocytosis (LCH) is a rare inflammatory myeloid neoplastic disease driven by activating mutations in the mitogen-activating protein kinase signalling pathway, including the BRAF V600E mutation and BRAF deletions (BRAFdel). Next-generation sequencing and whole exome sequencing (WES) are valuable and powerful approaches for BRAFdel identification, but these techniques are costly and time consuming. Pyrosequencing is an alternative method that has the potential to rapidly and reliably identify gene deletions. We developed a custom pyrosequencing assay to detect the exon-12 BRAFdel in 18 biopsies from adult patients with LCH, which were all genotyped in parallel using Sanger sequencing and WES. A BRAFdel was detected in 7/18 (39%), 6/18 (33%) and 3/18 (17%) LCH lesions using WES, pyrosequencing and Sanger, respectively, with good concordance between the WES and pyrosequencing results (Kappa-coefficient=0.88). Therefore, our pyrosequencing assay is reliable and useful for detecting BRAFdel, particularly in BRAF V600E-negative LCH lesions, for which targeted treatment is indicated.
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Affiliation(s)
- Fanélie Jouenne
- Pharmacogenomics Department, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, Île-de-France, France.,INSERM U976, Université de Paris, Paris, Île-de-France, France
| | - Aurélie Sadoux
- Pharmacogenomics Department, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, Île-de-France, France.,INSERM U976, INSERM, Paris, Île-de-France, France
| | - Gwenaël Lorillon
- National Reference Centre for Histiocytoses, Pulmonology Department, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, Île-de-France, France
| | - Baptiste Louveau
- Pharmacogenomics Department, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, Île-de-France, France.,INSERM U976, INSERM, Paris, Île-de-France, France
| | - Emmanuelle Bugnet
- National Reference Centre for Histiocytoses, Pulmonology Department, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, Île-de-France, France
| | - Veronique Meignin
- Pathology Department, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, Île-de-France, France
| | - Samia Mourah
- Pharmacogenomics Department, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, Île-de-France, France.,INSERM U976, Université de Paris, Paris, Île-de-France, France
| | - Abdellatif Tazi
- INSERM U976, Université de Paris, Paris, Île-de-France, France .,National Reference Centre for Histiocytoses, Pulmonology Department, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, Île-de-France, France
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7
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Mauger F, Tost J. Enhanced- ice-COLD-PCR for the Sensitive Detection of Rare DNA Methylation Patterns in Liquid Biopsies. Bio Protoc 2019; 9:e3452. [PMID: 33654946 DOI: 10.21769/bioprotoc.3452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 11/18/2019] [Accepted: 11/18/2019] [Indexed: 11/02/2022] Open
Abstract
In the context of precision medicine, the identification of novel biomarkers for the diagnosis of disease, prognosis, predicting treatment outcome and monitoring of treatment success is of great importance. The analysis of methylated circulating-cell free DNA provides great promise to complement or replace genetic markers for these applications, but is associated with substantial challenges. This is particularly true for the detection of rare methylated DNA molecules in a limited amount of sample such as tumor released hypermethylated molecules in the background of DNA fragments from normal cells, especially lymphocytes. Technologies for the sensitive detection of DNA methylation have been developed to enrich specifically methylated DNA or unmethylated DNA using among other methods: enzymatic digestion, methylation-specific PCR (often combined with TaqMan like oligonucleotide probes (MethyLight)) and co-amplification at lower denaturation temperature PCR (COLD-PCR). E-ice-COLD-PCR (Enhanced-improved and complete enrichment-COLD-PCR) is a sensitive method that takes advantage of a Locked Nucleic Acid (LNA)-containing oligonucleotide probe to block specifically unmethylated CpG sites allowing the strong enrichment of low-abundant methylated CpG sites from a limited quantity of input. E-ice-COLD-PCRs are performed on bisulfite-converted DNA followed by Pyrosequencing analysis. The quantification of the initially present DNA methylation level is obtained using calibration curves of methylated and unmethylated DNA. The E-ice-COLD-PCR reactions can be multiplexed, allowing the analysis and quantification of the DNA methylation level of several target genes. In contrast to the above-mentioned assays, E-ice-COLD-PCR will also perform in the presence of frequently occurring heterogeneous DNA methylation patterns at the target sites. The presented protocol describes the development of an E-ice-COLD-PCR assay including assay design, optimization of E-ice-COLD-PCR conditions including annealing temperature, critical temperature and concentration of LNA blocker probe followed by Pyrosequencing analysis.
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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
| | - 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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8
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Evaluation of six blood-based age prediction models using DNA methylation analysis by pyrosequencing. Sci Rep 2019; 9:8862. [PMID: 31222117 PMCID: PMC6586942 DOI: 10.1038/s41598-019-45197-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/22/2019] [Indexed: 01/08/2023] Open
Abstract
DNA methylation has been identified as the most promising molecular biomarker for the prediction of age. Several DNA methylation-based models have been proposed for age prediction based on blood samples, using mainly pyrosequencing. These methods present different performances for age prediction and have rarely, if ever, been evaluated and intercompared in an independent validation study. Here, for the first time, we evaluate and compare six blood-based age prediction models (Bekaert1, Park2, Thong3, Weidner4, and the Zbiec-Piekarska 15 and Zbiec-Piekarska 26), using DNA methylation analysis by pyrosequencing on 100 blood samples from French individuals aged between 19–65 years. For each model, we perform correlation analysis and evaluate age-prediction performance (mean absolute deviation (MAD) and standard error of the estimate (SEE)). The best age-prediction performances were found with the Bekaert and Thong models (MAD of 4.5–5.2, SEE of 6.8–7.2), followed by the Zbiec-Piekarska 1 model (MAD of 6.8 and SEE of 9.2), while the Park, Weidner and Zbiec-Piekarska 2 models presented lower performances (MAD of 7.2–8.7 and SEE of 9.2–10.3). Given these results, we recommend performing systematic, independent evaluation of all age prediction models on a same cohort to validate the different models and compare their performance.
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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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10
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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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11
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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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12
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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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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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Whale AS, Fernandez-Gonzalez A, Gutteridge A, Devonshire AS. Control Materials and Digital PCR Methods for Evaluation of Circulating Cell-Free DNA Extractions from Plasma. Methods Mol Biol 2018; 1768:45-65. [PMID: 29717437 DOI: 10.1007/978-1-4939-7778-9_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Cell-free DNA is an accessible source of genetic material found naturally in plasma that could be used in many diagnostic applications. Translation of cfDNA analysis methods from research laboratories into the clinic would benefit from controls for monitoring the efficiency of patient sample purification and for quality control of the whole workflow from extraction through to analysis. Here we describe two types of control materials that can be "spiked" into plasma samples to monitor and evaluate different aspects of the workflow. The first control material is an internal control that enables evaluation of extraction efficiency, fragment size bias, and sample inhibition. The second control material serves as a parallel quality control material for measurement of specific genetic targets such as tumor mutations.
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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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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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