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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 2024; 196:4049-4066. [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] [MESH Headings] [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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Wu Y, Guo J, Li W, Xiu X, Thirunavukarasu D, Wang Y, Wang K, Chen W, Yu Zhang D, Yang X, Fan C, Song P. Enhanced Detection of Novel Low-Frequency Gene Fusions via High-Yield Ligation and Multiplexed Enrichment Sequencing. Angew Chem Int Ed Engl 2024; 63:e202316484. [PMID: 38494435 DOI: 10.1002/anie.202316484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Panel-based methods are commonly employed for the analysis of novel gene fusions in precision diagnostics and new drug development in cancer. However, these methods are constrained by limitations in ligation yield and the enrichment of novel gene fusions with low variant allele frequencies. In this study, we conducted a pioneering investigation into the stability of double-stranded adapter DNA, resulting in improved ligation yield and enhanced conversion efficiency. Additionally, we implemented blocker displacement amplification, achieving a remarkable 7-fold enrichment of novel gene fusions. Leveraging the pre-enrichment achieved with this approach, we successfully applied it to Nanopore sequencing, enabling ultra-fast analysis of novel gene fusions within one hour with high sensitivity. This method offers a robust and remarkably sensitive mean of analyzing novel gene fusions, promising the discovery of pivotal biomarkers that can significantly improve cancer diagnostics and the development of new therapeutic strategies.
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Affiliation(s)
- Yi Wu
- School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinxiao Guo
- Shanghai Sixth People's Hospital Affiliated to, Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Wenjun Li
- NuProbe USA, Inc., 2575 West Bellfort Avenue, Ste. 200 Houston, TX 77054, USA
| | - Xuehao Xiu
- School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | | | - Yudong Wang
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Kai Wang
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 322000, China
| | - Weiyu Chen
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 322000, China
| | - David Yu Zhang
- NuProbe USA, Inc., 2575 West Bellfort Avenue, Ste. 200 Houston, TX 77054, USA
| | - Xiurong Yang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ping Song
- School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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3
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Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology. Diagnostics (Basel) 2022; 12:diagnostics12071539. [PMID: 35885445 PMCID: PMC9318977 DOI: 10.3390/diagnostics12071539] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022] Open
Abstract
Screening for genomic sequence variants in genes of predictive and prognostic significance is an integral part of precision medicine. Next-generation sequencing (NGS) technologies are progressively becoming platforms of choice to facilitate this, owing to their massively parallel sequencing capability, which can be used to simultaneously screen multiple markers in multiple samples for a variety of variants (single nucleotide and multi nucleotide variants, insertions and deletions, gene copy number variations, and fusions). A crucial step in the workflow of targeted NGS is the enrichment of the genomic regions of interest to be sequenced, against the whole genomic background. This ensures that the NGS effort is focused to predominantly screen target regions of interest with minimal off-target sequencing, making it more accurate and economical. Polymerase chain reaction-based (PCR, or amplicon-based) and hybridization capture-based methodologies are the two prominent approaches employed for target enrichment. This review summarizes the basic principles of target enrichment utilized by these methods, their multiple variations that have evolved over time, automation approaches, overall comparison of their advantages and drawbacks, and commercially available choices for these methodologies.
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4
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Darbeheshti F, Yu F, Ahmed F, Adalsteinsson VA, Makrigiorgos GM. Recent Developments in Mutation Enrichment and Detection Technologies. Clin Chem 2022; 68:1250-1260. [PMID: 35716101 DOI: 10.1093/clinchem/hvac093] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Presence of excess unaltered, wild-type DNA (wtDNA) providing information of little clinical value may often mask low-level mutations containing important diagnostic or therapeutic clues. This is a recurring hurdle in biotechnology and medicine, including cancer, prenatal diagnosis, infectious diseases, and organ transplantation. Mutation enrichment techniques that allow reduction of unwanted DNA to enable the detection of low-level mutations have emerged since the early 1990s. They are continuously being refined and updated with new technologies. The burgeoning interest in liquid biopsies for residual cancer monitoring, detection of resistance to therapy, and early cancer detection has driven an expanded interest in new and improved methodologies for practical and effective mutation enrichment and detection of low-level mutations of clinical relevance. CONTENT Newly developed mutation enrichment technologies are described and grouped according to the main principle of operation, PCR-blocking technologies, enzymatic methods, and physicochemical approaches. Special emphasis is given to technologies enabling pre-PCR blockage of wtDNA to bypass PCR errors [nuclease-assisted minor-allele enrichment assay with overlapping probes (NaME-PrO) and UV-mediated cross-linking minor allele enrichment (UVME)] or providing high multiplexity followed by next-generation sequencing [Minor allele enriched sequencing through recognition oligonucleotides (MAESTRO)]. SUMMARY This review summarizes technological developments in rare mutation enrichment over the last 12 years, complementing pre-2010 reviews on this topic. The expanding field of liquid biopsy calls for improved limits of detection (LOD) and highly parallel applications, along with the traditional requirements for accuracy, speed, and cost-effectiveness. The current technologies are reviewed with regards to these new requirements.
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Affiliation(s)
- Farzaneh Darbeheshti
- Department of Radiation Oncology, Dana Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Fangyan Yu
- Department of Radiation Oncology, Dana Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Farzana Ahmed
- Department of Radiation Oncology, Dana Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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5
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Song P, Wu LR, Yan YH, Zhang JX, Chu T, Kwong LN, Patel AA, Zhang DY. Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics. Nat Biomed Eng 2022; 6:232-245. [PMID: 35102279 PMCID: PMC9336539 DOI: 10.1038/s41551-021-00837-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/27/2021] [Indexed: 12/15/2022]
Abstract
Cell-free DNA (cfDNA) in the circulating blood plasma of patients with cancer contains tumour-derived DNA sequences that can serve as biomarkers for guiding therapy, for the monitoring of drug resistance, and for the early detection of cancers. However, the analysis of cfDNA for clinical diagnostic applications remains challenging because of the low concentrations of cfDNA, and because cfDNA is fragmented into short lengths and is susceptible to chemical damage. Barcodes of unique molecular identifiers have been implemented to overcome the intrinsic errors of next-generation sequencing, which is the prevailing method for highly multiplexed cfDNA analysis. However, a number of methodological and pre-analytical factors limit the clinical sensitivity of the cfDNA-based detection of cancers from liquid biopsies. In this Review, we describe the state-of-the-art technologies for cfDNA analysis, with emphasis on multiplexing strategies, and discuss outstanding biological and technical challenges that, if addressed, would substantially improve cancer diagnostics and patient care.
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Affiliation(s)
- Ping Song
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Lucia Ruojia Wu
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | | | - Tianqing Chu
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
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6
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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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7
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Li M, Yin F, Song L, Mao X, Li F, Fan C, Zuo X, Xia Q. Nucleic Acid Tests for Clinical Translation. Chem Rev 2021; 121:10469-10558. [PMID: 34254782 DOI: 10.1021/acs.chemrev.1c00241] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.
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Affiliation(s)
- Min Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fangfei Yin
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Song
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Xia
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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8
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Song P, Chen SX, Yan YH, Pinto A, Cheng LY, Dai P, Patel AA, Zhang DY. Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing. Nat Biomed Eng 2021; 5:690-701. [PMID: 33941896 PMCID: PMC9631981 DOI: 10.1038/s41551-021-00713-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/09/2021] [Indexed: 02/02/2023]
Abstract
DNA sequence variants with allele fractions below 1% are difficult to detect and quantify by sequencing owing to intrinsic errors in sequencing-by-synthesis methods. Although molecular-identifier barcodes can detect mutations with a variant-allele frequency (VAF) as low as 0.1% using next-generation sequencing (NGS), sequencing depths of over 25,000× are required, thus hampering the detection of mutations at high sensitivity in patient samples and in most samples used in research. Here we show that low-frequency DNA variants can be detected via low-depth multiplexed NGS after their amplification, by a median of 300-fold, using polymerase chain reaction and rationally designed 'blocker' oligonucleotides that bind to the variants. Using an 80-plex NGS panel and a sequencing depth of 250×, we detected single nucleotide polymorphisms with a VAF of 0.019% and contamination in human cell lines at a VAF as low as 0.07%. With a 16-plex NGS panel covering 145 mutations across 9 genes involved in melanoma, we detected low-VAF mutations (0.2-5%) in 7 out of the 19 samples of freshly frozen tumour biopsies, suggesting that tumour heterogeneity could be notably higher than previously recognized.
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Affiliation(s)
- Ping Song
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Sherry X Chen
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Yan Helen Yan
- Department of Bioengineering, Rice University, Houston, TX, USA.,Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | | | - Lauren Y Cheng
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Peng Dai
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, TX, USA. .,Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA.
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9
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Enhanced asymmetric blocked qPCR method for affordable detection of point mutations in KRAS oncogene. Anal Bioanal Chem 2021; 413:2961-2969. [PMID: 33619642 DOI: 10.1007/s00216-021-03229-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 10/22/2022]
Abstract
An accurate genetic diagnostic is key for adequate patient management and the suitability of healthcare systems. The scientific challenge lies in developing methods to discriminate those patients with certain genetic variations present in tumor cells at low concentrations. We report a method called enhanced asymmetric blocked qPCR (EAB-qPCR) that promotes the blocker annealing against the primer-template hybrid controlling thermal cycling and reaction conditions with nonmodified oligonucleotides. Real-time fluorescent amplification curves of wild-type alleles were delayed by about eight cycles for EAB-qPCR, compared to conventional blocked qPCR approaches. This method reduced the amplification of native DNA variants (blocking percentage 99.7%) and enabled the effective enrichment of low-level DNA mutations. Excellent performance was estimated for the detection of mutated alleles in sensitivity (up to 0.5% mutant/total DNA) and reproducibility terms, with a relative standard deviation below 2.8%. The method was successfully applied to the mutational analysis of metastatic colorectal carcinoma from biopsied tissues. The determined single-nucleotide mutations in the KRAS oncogene (codon 12-13) totally agreed with those obtained from next-generation sequencing. EAB-qPCR is an accurate cheap method and can be easily incorporated into daily routine to detect mutant alleles. Hence, these features are especially interesting to facilitate the diagnosis and prognosis of several clinical diseases.
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10
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Chen H, Zhang J, Chen HY, Su B, Lu D. Establishment of multiplex allele-specific blocker PCR for enrichment and detection of 4 common EGFR mutations in non-small cell lung cancer. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1509. [PMID: 33313254 PMCID: PMC7729377 DOI: 10.21037/atm-20-6754] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Background Lung cancer is one of the most severe cancers and the majority of patients miss the best timing for surgery when diagnosed, thus having to rely on radiotherapy, chemotherapy or target therapy. Epidermal growth factor receptor (EGFR) upregulation occurs in a large percentage of patients, who can then benefit from tyrosine kinase inhibitors (TKI). However, the EGFR mutations they carry will vary the effectiveness of TKI. Circulating tumor DNA (ctDNA) contains genetic information from cancer tissue that can be used as a liquid biopsy by non-invasive sampling. This study aimed to provide a solution for minor allele detection from ctDNA. Methods Our novel method, named multiplex allele-specific blocker PCR (MAB PCR), combines amplification refractory mutation system (ARMS), blocker PCR and fluorescent-labeled probes for better discrimination and higher throughput. MAB PCR was specially designed for low-quality samples such as ctDNA. A sensitive assay based on MAB PCR was developed for enriching and detecting four common EGFR mutations. This assay was optimized and evaluated with manufactured plasmids, and validated with 34 tissue samples and 94 plasma samples. Results The limit of detection of this assay was 102 copies and the detection sensitivity reached 0.1% mutant allele fraction (MAF). The results of clinical sample testing had 100% accordance with sequencing, which proved that this assay was accurate and applicable in clinical settings. Conclusions This assay could accomplish low-cost and rapid detection of 4 common EGFR mutations sensitively and accurately, which has huge potential in clinical usage for guiding medication. Furthermore, this design could be used to detect other mutations.
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Affiliation(s)
- Hongyuan Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jie Zhang
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hong-Yan Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Bo Su
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
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11
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Pan X, Zhang X. Utility of circulating tumor cells and DNA in the management of advanced colorectal cancer. Future Oncol 2020; 16:1289-1299. [PMID: 32379501 DOI: 10.2217/fon-2020-0073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aim: Clinical management of colorectal cancer is challenging. Circulating tumor cells (CTCs) and DNA (ctDNA) are investigated to detect key KRAS mutation and for prognosis for risk stratifications. Materials & methods: 200 advance-stage patients with metastatic disease were selected and followed-up. Serial blood draws were used to quantify CTCs and ctDNA. Results: Both CTCs and ctDNA are strongly associated with colorectal cancer patients. The positive predictive values were 96.5 and 96.3% among CTCs and ctDNA, respectively, for all 200 patients using KRAS mutation. Specificity for healthy controls was 100%. As a prognosis indicator, results demonstrated that patients who had positive CTCs and plasma DNA had worse outcomes. Conclusion: Blood-based assessment of colorectal cancer shows promising results in early-risk stratifications.
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Affiliation(s)
- Xiaohong Pan
- Department of Gastrointestinal Surgery, Jingzhou Central Hospital, the Clinical Second Clinical Medical College of Yangtze University, Jingzhou, Hubei, Renmin Road 1, Jingzhou, 434020, PR China
| | - Xiaoli Zhang
- Department of Gastrointestinal Surgery, Jingzhou Central Hospital, the Clinical Second Clinical Medical College of Yangtze University, Jingzhou, Hubei, Renmin Road 1, Jingzhou, 434020, PR China
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12
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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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13
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Leong KW, Yu F, Adalsteinsson VA, Reed S, Gydush G, Ladas I, Li J, Tantisira KG, Makrigiorgos GM. A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment. Nucleic Acids Res 2019; 47:e147. [PMID: 31598677 PMCID: PMC6902007 DOI: 10.1093/nar/gkz870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 09/06/2019] [Accepted: 10/01/2019] [Indexed: 11/13/2022] Open
Abstract
DNA target enrichment via hybridization capture is a commonly adopted approach which remains expensive due in-part to using biotinylated-probe panels. Here we provide a novel isothermal amplification reaction to amplify rapidly existing probe panels without knowledge of the sequences involved, thereby decreasing a major portion of the overall sample preparation cost. The reaction employs two thermostable enzymes, BST-polymerase and duplex-specific nuclease DSN. DSN initiates random ‘nicks’ on double-stranded-DNA which enable BST to polymerize DNA by displacing the nicked-strand. Displaced strands re-hybridize and the process leads to an exponential chain-reaction generating biotinylated DNA fragments within minutes. When starting from single-stranded-DNA, DNA is first converted to double-stranded-DNA via terminal-deoxynucleotidyl-transferase (TdT) prior to initiation of BST–DSN reaction. Biotinylated probes generated by TdT–BST–DSN (TBD) reactions using panels of 33, 190 or 7186 DNA targets are used for hybrid-capture-based target enrichment from amplified circulating-DNA, followed by targeted re-sequencing. Polymerase-nuclease isothermal-chain-reactions generate random amplified probes with no apparent sequence dependence. One round of target-capture using TBD probes generates a modest on-target sequencing ratio, while two successive rounds of capture generate >80% on-target reads with good sequencing uniformity. TBD-reactions generate enough capture-probes to increase by approximately two to three orders-of-magnitude the target-enrichment experiments possible from an initial set of probes.
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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, Boston, MA 02115, USA
| | - Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Sarah Reed
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gregory Gydush
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jiang Li
- The Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medicine School, Boston, MA 02142, USA
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medicine School, Boston, MA 02142, USA
| | - Gerassimos Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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14
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van der Pol Y, Mouliere F. Toward the Early Detection of Cancer by Decoding the Epigenetic and Environmental Fingerprints of Cell-Free DNA. Cancer Cell 2019; 36:350-368. [PMID: 31614115 DOI: 10.1016/j.ccell.2019.09.003] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/18/2019] [Accepted: 09/06/2019] [Indexed: 12/15/2022]
Abstract
Widespread adaptation of liquid biopsy for the early detection of cancer has yet to reach clinical utility. Circulating tumor DNA is commonly detected though the presence of genetic alterations, but only a minor fraction of tumor-derived cell-free DNA (cfDNA) fragments exhibit mutations. The cellular processes occurring in cancer development mark the chromatin. These epigenetic marks are reflected by modifications in the cfDNA methylation, fragment size, and structure. In this review, we describe how going beyond DNA sequence information alone, by analyzing cfDNA epigenetic and immune signatures, boosts the potential of liquid biopsy for the early detection of cancer.
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Affiliation(s)
- Ymke van der Pol
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
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15
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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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16
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Buono G, Gerratana L, Bulfoni M, Provinciali N, Basile D, Giuliano M, Corvaja C, Arpino G, Del Mastro L, De Placido S, De Laurentiis M, Cristofanilli M, Puglisi F. Circulating tumor DNA analysis in breast cancer: Is it ready for prime-time? Cancer Treat Rev 2019; 73:73-83. [PMID: 30682661 DOI: 10.1016/j.ctrv.2019.01.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 01/06/2023]
Abstract
Precision Medicine is becoming the new paradigm in healthcare as it enables better resources allocation, treatment optimization with a potential side-effects reduction and consequent impact on quality of life and survival. This revolution is being catalyzed by liquid biopsy technologies, which provide prognostic and predictive information for advanced cancer patients, without the analytical and procedural drawbacks of tissue-biopsy. In particular, circulating tumor DNA (ctDNA) is gaining momentum as a clinically feasible option capable to capture both spatial and temporal tumor heterogeneity. Several techniques are currently available for ctDNA extraction and analysis, each with its preferential case scenarios and preanalytical implications which must be taken into consideration to effectively support clinical decision-making and to better highlight its clinical utility. Aim of this review is to summarize both analytical developments and clinical evidences to offer a comprehensive update on the deployment of ctDNA in breast cancer's (BC) characterization and treatment.
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Affiliation(s)
- Giuseppe Buono
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | - Lorenzo Gerratana
- Department of Medicine (DAME), University of Udine, Italy; Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Michela Bulfoni
- Department of Pathology, ASUIUD University Hospital, Udine, Italy
| | | | - Debora Basile
- Department of Medicine (DAME), University of Udine, Italy
| | - Mario Giuliano
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy; Lester and Sue Smith Breast Center at Baylor College of Medicine, Houston, TX, USA
| | - Carla Corvaja
- Department of Medicine (DAME), University of Udine, Italy
| | - Grazia Arpino
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | - Lucia Del Mastro
- Department of Medical Oncology, IRCCS AOU San Martino-IST, National Cancer Institute, Genova, Italy
| | - Sabino De Placido
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | | | - Massimo Cristofanilli
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Fabio Puglisi
- Department of Medicine (DAME), University of Udine, Italy; Department of Medical Oncology, Centro di Riferimento Oncologico (CRO), IRCCS, Aviano, PN, Italy
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17
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Kim MJ, Kim SC, Kim YJ. A Universal Analysis Pipeline of Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes (UMIs). Genomics Inform 2018; 16:e29. [PMID: 30602090 PMCID: PMC6440665 DOI: 10.5808/gi.2018.16.4.e29] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 12/18/2018] [Indexed: 01/20/2023] Open
Abstract
Hybrid capture-based targeted sequencing is increasingly used for genomic variants profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy of variant calling by minimizing PCR biases and sequencing errors. However, UMI-adopted targeted sequencing data analysis is slightly different from the methods for other types of omics data, and its pipeline for variant calling is still being optimized in various studying groups for their own purpose. Due to this provincial usage range of tools, our group built an analysis pipeline for global application to many studies of targeted sequencing generated with different methods. First, we generated hybrid capture-based data using genomic DNA extracted from tumor tissues of colorectal cancer patients. Sequencing libraries were prepared, pooled together and an 8-plexed capture library was processed to the enrichment step before 150bp paired-end (PE) sequencing with Illumina Hiseq series. For the analysis, we evaluated several different tools published. We mainly focused on the compatibility of input and output of each tool. Finally, our laboratory built an analysis pipeline specialized for UMI-adopted data. Through this pipeline, we were able to estimate the even on-target rates and filtered consensus reads for more accurate variant calling. These results suggest the potential of our analysis pipeline in the precise examination of quality and efficiency of conducted experiments.
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Affiliation(s)
- Min-Jung Kim
- Department of Integrated Omics and Biomedical Science, Yonsei University, Seoul 03722, Korea
| | - Si-Cho Kim
- Department of Biochemistry, Yonsei University 03722, Seoul, Korea
| | - Young-Joon Kim
- Department of Integrated Omics and Biomedical Science, Yonsei University, Seoul 03722, Korea.,Department of Biochemistry, Yonsei University 03722, Seoul, Korea
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18
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Galbiati S, Damin F, Burgio V, Brisci A, Soriani N, Belcastro B, Di Resta C, Gianni L, Chiari M, Ronzoni M, Ferrari M. Evaluation of three advanced methodologies, COLD-PCR, microarray and ddPCR, for identifying the mutational status by liquid biopsies in metastatic colorectal cancer patients. Clin Chim Acta 2018; 489:136-143. [PMID: 30550935 DOI: 10.1016/j.cca.2018.12.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/27/2018] [Accepted: 12/07/2018] [Indexed: 01/22/2023]
Abstract
A major effort has been focused on the detection of oncogenes' mutations in diverse types of clinical specimens including formalin-fixed and paraffin embedded tissues, presently the gold-standard samples, up to plasma, that constitute a noninvasive alternative source of tumor DNA. The reliable detection of mutations in circulating tumor DNA requires a high analytical sensitivity. Here, we applied three different highly sensitive methodologies (COLD-PCR, a microarray-based approach and the droplet digital PCR, ddPCR) to identify mutations in the plasma of 30 metastatic colorectal cancer patients previously genotyped on tissue biopsy. The methods showed a modest concordance rate with respect to the results obtained on tissue biopsies: 63.3% by ddPCR, 63% by microarray and 55.6% by COLD-PCR. This could be ascribed either to the different timing between tissue and liquid biopsy collection, which could reflect a different stage of disease progression or to the diverse sensitivity of the methodologies applied. Indeed, if we compare the results obtained on plasma samples, the concordance rates were higher especially by comparing ddPCR versus COLD-PCR (92.6%). Thus, we consider both methodologies as useful procedures easily transferable in a clinical setting. Notably, the ddPCR allows a quantitative assessment of the fractional abundance of the mutation.
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Affiliation(s)
- Silvia Galbiati
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy.
| | - Francesco Damin
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare, Milano, Italy
| | - Valentina Burgio
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Angela Brisci
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nadia Soriani
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bernadette Belcastro
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Di Resta
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Gianni
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare, Milano, Italy
| | - Monica Ronzoni
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Maurizio Ferrari
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Milan, Italy; Università Vita-Salute San Raffaele, Milano, Italy
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19
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Dong L, Wang S, Fu B, Wang J. Evaluation of droplet digital PCR and next generation sequencing for characterizing DNA reference material for KRAS mutation detection. Sci Rep 2018; 8:9650. [PMID: 30504843 PMCID: PMC6269532 DOI: 10.1038/s41598-018-27368-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 05/23/2018] [Indexed: 01/05/2023] Open
Abstract
KRAS gene mutations are predictive markers of non-response to anti-epidermal growth factor receptor. An increasing number of techniques are being developed to detect KRAS mutations. To obtain consistent and comparable results, a traceable reference material (RM) is necessary for validation the routinely used method. However, a lack of reference methods is a main impediment for deriving traceability and measurement comparability. In this study, droplet digital PCR (ddPCR) and next generation sequencing (NGS) were evaluated. No cross- reactivity was detected with any of the probe by ddPCR. The measured fraction of KRAS mutant allele by ddPCR and NGS agreed with the prepared value by gravimetrical dilution (concordance (k) >0.95 and >0.93 for ddPCR and NGS, respectively). The reliable limit of quantification (LOQ) was 0.1% and 1% for ddPCR and NGS, respectively. In conclusion, the validated ddPCR and NGS are suitable to characterize the KRAS RM due to the high specificity and accuracy. Verification of the LOD of three commercial kits by using the NIM-KRAS-8 RM showed that the LOD was inconsistent with the claimed LOD of the kits (1%) for some assays. This indicates a traceable RM was important for setting up the criteria regarding the LOD for the commercial kit.
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Affiliation(s)
- Lianhua Dong
- National Institute of Metrology, Beijing, 100013, P. R. China.
| | - Shangjun Wang
- Nanjing Institute of Measurement and Testing Technology, Nanjing, 210049, P. R. China
| | - Boqiang Fu
- National Institute of Metrology, Beijing, 100013, P. R. China
| | - Jing Wang
- National Institute of Metrology, Beijing, 100013, P. R. China
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20
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Fitarelli-Kiehl M, Yu F, Ashtaputre R, Leong KW, Ladas I, Supplee J, Paweletz C, Mitra D, Schoenfeld JD, Parangi S, Makrigiorgos GM. Denaturation-Enhanced Droplet Digital PCR for Liquid Biopsies. Clin Chem 2018; 64:1762-1771. [PMID: 30274976 DOI: 10.1373/clinchem.2018.293845] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/04/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Although interest in droplet-digital PCR technology (ddPCR) for cell-free circulating DNA (cfDNA) analysis is burgeoning, the technology is compromised by subsampling errors and the few clinical targets that can be analyzed from limited input DNA. The paucity of starting material acts as a "glass ceiling" in liquid biopsies because, irrespective how analytically sensitive ddPCR techniques are, detection limits cannot be improved past DNA input limitations. METHODS We applied denaturation-enhanced ddPCR (dddPCR) using fragmented genomic DNA (gDNA) with defined mutations. We then tested dddPCR on cfDNA from volunteers and patients with cancer for commonly-used mutations. gDNA and cfDNA were tested with and without end repair before denaturation and digital PCR. RESULTS By applying complete denaturation of double-stranded DNA before ddPCR droplet formation the number of positive droplets increased. dddPCR using gDNA resulted in a 1.9-2.0-fold increase in data-positive droplets, whereas dddPCR applied on highly-fragmented cfDNA resulted in a 1.6-1.7-fold increase. End repair of cfDNA before denaturation enabled cfDNA to display a 1.9-2.0-fold increase in data-positive signals, similar to gDNA. Doubling of data-positive droplets doubled the number of potential ddPCR assays that could be conducted from a given DNA input and improved ddPCR precision for cfDNA mutation detection. CONCLUSIONS dddPCR is a simple and useful modification in ddPCR that enables extraction of more information from low-input clinical samples with minor change in protocols. It should be applicable to all ddPCR platforms for mutation detection and, potentially, for gene copy-number analysis in cancer and prenatal screening.
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Affiliation(s)
- Mariana Fitarelli-Kiehl
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Ravina Ashtaputre
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Julianna Supplee
- Department of Medical Oncology and Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Cloud Paweletz
- Department of Medical Oncology and Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Devarati Mitra
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Jonathan D Schoenfeld
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Sareh Parangi
- Department of General & Gastrointestinal Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA;
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21
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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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22
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Rodda AE, Parker BJ, Spencer A, Corrie SR. Extending Circulating Tumor DNA Analysis to Ultralow Abundance Mutations: Techniques and Challenges. ACS Sens 2018; 3:540-560. [PMID: 29441780 DOI: 10.1021/acssensors.7b00953] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liquid biopsies that analyze circulating tumor DNA (ctDNA) hold great promise in the guidance of clinical treatment for various cancers. However, the innate characteristics of ctDNA make it a difficult target: ctDNA is highly fragmented, and found at very low concentrations, both in absolute terms and relative to wildtype species. Clinically relevant target sequences often differ from the wildtype species by a single DNA base pair. These characteristics make analyzing mutant ctDNA a uniquely difficult process. Despite this, techniques have recently emerged for analyzing ctDNA, and have been used in pilot studies that showed promising results. These techniques each have various drawbacks, either in their analytical capabilities or in practical considerations, which restrict their application to many clinical situations. Many of the most promising potential applications of ctDNA require assay characteristics that are not currently available, and new techniques with these properties could have benefits in companion diagnostics, monitoring response to treatment and early detection. Here we review the current state of the art in ctDNA detection, with critical comparison of the analytical techniques themselves. We also examine the improvements required to expand ctDNA diagnostics to more advanced applications and discuss the most likely pathways for these improvements.
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Affiliation(s)
| | | | - Andrew Spencer
- Myeloma Research Group, Australian Center for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
- Malignant Haematology & Stem Cell Transplantation Service, Alfred Hospital, Melbourne, Victoria 3004, Australia
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23
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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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24
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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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25
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Variations in transrenal DNA and comparison with plasma DNA as a diagnostic marker for colorectal cancer. Int J Biol Markers 2017; 32:e434-e440. [PMID: 28708207 DOI: 10.5301/ijbm.5000288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND Transrenal DNA can potentially be useful in the disease management of colorectal cancer (CRC) and has potential diagnostic utility. Our study aimed to conduct preoperative and postoperative analysis of KRAS-positive patients, using transrenal DNA compared with plasma DNA. This is critically needed for disease diagnostics and treatment response monitoring. METHODS CRC patients at different stages of the disease and with different molecular profiles were recruited for serial time-point analysis. Preoperative and postoperative urine specimens were extracted and compared with tumor tissues and plasma DNA. RESULTS Our analysis demonstrated that transrenal DNA offered comparable sensitivity and specificity to plasma DNA analysis. Collection of transrenal DNA, being noninvasive, is an attractive assay and easily allows serial monitoring of the disease. Results from preoperative detection showed a close correlation to tumor tissue profiling and demonstrated close associations to the disease. We also observed significant decreases in mutant KRAS DNA concentration after surgery, which confirmed transrenal DNA's sensitivity to treatment response. CONCLUSIONS The use of transrenal DNA offers a possible alternative method of disease profiling, detection and tracking. Our study is one of the first to systematically analyze a relatively large number of different CRC patients using transrenal DNA. The positive correlation with disease demonstrates the assay's viability in the clinical setting, and our method further opens up the possibility to use transrenal DNA for clinical intervention investigations.
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Ladas I, Fitarelli-Kiehl M, Song C, Adalsteinsson VA, Parsons HA, Lin NU, Wagle N, Makrigiorgos GM. Multiplexed Elimination of Wild-Type DNA and High-Resolution Melting Prior to Targeted Resequencing of Liquid Biopsies. Clin Chem 2017; 63:1605-1613. [PMID: 28679646 PMCID: PMC5914173 DOI: 10.1373/clinchem.2017.272849] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/12/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The use of clinical samples and circulating cell-free DNA (cfDNA) collected from liquid biopsies for diagnostic and prognostic applications in cancer is burgeoning, and improved methods that reduce the influence of excess wild-type (WT) portion of the sample are desirable. Here we present enrichment of mutation-containing sequences using enzymatic degradation of WT DNA. Mutation enrichment is combined with high-resolution melting (HRM) performed in multiplexed closed-tube reactions as a rapid, cost-effective screening tool before targeted resequencing. METHODS We developed a homogeneous, closed-tube approach to use a double-stranded DNA-specific nuclease for degradation of WT DNA at multiple targets simultaneously. The No Denaturation Nuclease-assisted Minor Allele Enrichment with Probe Overlap (ND-NaME-PrO) uses WT oligonucleotides overlapping both strands on putative DNA targets. Under conditions of partial denaturation (DNA breathing), the oligonucleotide probes enhance double-stranded DNA-specific nuclease digestion at the selected targets, with high preference toward WT over mutant DNA. To validate ND-NaME-PrO, we used multiplexed HRM, digital PCR, and MiSeq targeted resequencing of mutated genomic DNA and cfDNA. RESULTS Serial dilution of KRAS mutation-containing DNA shows mutation enrichment by 10- to 120-fold and detection of allelic fractions down to 0.01%. Multiplexed ND-NaME-PrO combined with multiplexed PCR-HRM showed mutation scanning of 10-20 DNA amplicons simultaneously. ND-NaME-PrO applied on cfDNA from clinical samples enables mutation enrichment and HRM scanning over 10 DNA targets. cfDNA mutations were enriched up to approximately 100-fold (average approximately 25-fold) and identified via targeted resequencing. CONCLUSIONS Closed-tube homogeneous ND-NaME-PrO combined with multiplexed HRM is a convenient approach to efficiently enrich for mutations on multiple DNA targets and to enable prescreening before targeted resequencing.
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Affiliation(s)
- Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Mariana Fitarelli-Kiehl
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Chen Song
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | | | - Heather A. Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Nancy U. Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - G. Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA,Correspondence: G. Mike Makrigiorgos, Ph.D., Brigham and Women’s Hospital, Level L2, Radiation Therapy, 75 Francis Street, Boston, MA 02115., Tel: 617-525-7122. Fax: 617-582-6037,
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Wu LR, Chen SX, Wu Y, Patel AA, Zhang DY. Multiplexed enrichment of rare DNA variants via sequence-selective and temperature-robust amplification. Nat Biomed Eng 2017; 1:714-723. [PMID: 29805844 DOI: 10.1038/s41551-017-0126-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Rare DNA-sequence variants hold important clinical and biological information, but existing detection techniques are expensive, complex, allele-specific, or don't allow for significant multiplexing. Here, we report a temperature-robust polymerase-chain-reaction method, which we term blocker displacement amplification (BDA), that selectively amplifies all sequence variants, including single-nucleotide variants (SNVs), within a roughly 20-nucleotide window by 1,000-fold over wild-type sequences. This allows for easy detection and quantitation of hundreds of potential variants originally at ≤0.1% in allele frequency. BDA is compatible with inexpensive thermocycler instrumentation and employs a rationally designed competitive hybridization reaction to achieve comparable enrichment performance across annealing temperatures ranging from 56 °C to 64 °C. To show the sequence generality of BDA, we demonstrate enrichment of 156 SNVs and the reliable detection of single-digit copies. We also show that the BDA detection of rare driver mutations in cell-free DNA samples extracted from the blood plasma of lung-cancer patients is highly consistent with deep sequencing using molecular lineage tags, with a receiver operator characteristic accuracy of 95%.
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Affiliation(s)
- Lucia R Wu
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Sherry X Chen
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Yalei Wu
- Thermo Fisher, San Francisco, CA, 94080, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA.
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Jackson JM, Witek MA, Kamande JW, Soper SA. Materials and microfluidics: enabling the efficient isolation and analysis of circulating tumour cells. Chem Soc Rev 2017; 46:4245-4280. [PMID: 28632258 PMCID: PMC5576189 DOI: 10.1039/c7cs00016b] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present a critical review of microfluidic technologies and material effects on the analyses of circulating tumour cells (CTCs) selected from the peripheral blood of cancer patients. CTCs are a minimally invasive source of clinical information that can be used to prognose patient outcome, monitor minimal residual disease, assess tumour resistance to therapeutic agents, and potentially screen individuals for the early diagnosis of cancer. The performance of CTC isolation technologies depends on microfluidic architectures, the underlying principles of isolation, and the choice of materials. We present a critical review of the fundamental principles used in these technologies and discuss their performance. We also give context to how CTC isolation technologies enable downstream analysis of selected CTCs in terms of detecting genetic mutations and gene expression that could be used to gain information that may affect patient outcome.
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Efficient identification of SNPs in pooled DNA samples using a dual mononucleotide addition-based sequencing method. Mol Genet Genomics 2017; 292:1069-1081. [PMID: 28612167 PMCID: PMC5594057 DOI: 10.1007/s00438-017-1332-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 06/02/2017] [Indexed: 11/18/2022]
Abstract
Identifying single nucleotide polymorphism (SNPs) from pooled samples is critical for many studies and applications. SNPs determined by next-generation sequencing results may suffer from errors in both base calling and read mapping. Taking advantage of dual mononucleotide addition-based pyrosequencing, we present Epds, a method to efficiently identify SNPs from pooled DNA samples. On the basis of only five patterns of non-synchronistic extensions between the wild and mutant sequences using dual mononucleotide addition-based pyrosequencing, we employed an enumerative algorithm to infer the mutant locus and estimate the proportion of mutant sequence. According to the profiles resulting from three runs with distinct dual mononucleotide additions, Epds could recover the mutant bases. Results showed that our method had a false-positive rate of less than 3%. Series of simulations revealed that Epds outperformed the current method (PSM) in many situations. Finally, experiments based on profiles produced by real sequencing proved that our method could be successfully applied for the identification of mutants from pooled samples. The software for implementing this method and the experimental data are available at http://bioinfo.seu.edu.cn/Epds.
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Liu Y, Song C, Ladas I, Fitarelli-Kiehl M, Makrigiorgos GM. Methylation-sensitive enrichment of minor DNA alleles using a double-strand DNA-specific nuclease. Nucleic Acids Res 2017; 45:e39. [PMID: 27903892 PMCID: PMC5389605 DOI: 10.1093/nar/gkw1166] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/08/2016] [Indexed: 02/06/2023] Open
Abstract
Aberrant methylation changes, often present in a minor allelic fraction in clinical samples such as plasma-circulating DNA (cfDNA), are potentially powerful prognostic and predictive biomarkers in human disease including cancer. We report on a novel, highly-multiplexed approach to facilitate analysis of clinically useful methylation changes in minor DNA populations. Methylation Specific Nuclease-assisted Minor-allele Enrichment (MS-NaME) employs a double-strand-specific DNA nuclease (DSN) to remove excess DNA with normal methylation patterns. The technique utilizes oligonucleotide-probes that direct DSN activity to multiple targets in bisulfite-treated DNA, simultaneously. Oligonucleotide probes targeting unmethylated sequences generate local double stranded regions resulting to digestion of unmethylated targets, and leaving methylated targets intact; and vice versa. Subsequent amplification of the targeted regions results in enrichment of the targeted methylated or unmethylated minority-epigenetic-alleles. We validate MS-NaME by demonstrating enrichment of RARb2, ATM, MGMT and GSTP1 promoters in multiplexed MS-NaME reactions (177-plex) using dilutions of methylated/unmethylated DNA and in DNA from clinical lung cancer samples and matched normal tissue. MS-NaME is a highly scalable single-step approach performed at the genomic DNA level in solution that combines with most downstream detection technologies including Sanger sequencing, methylation-sensitive-high-resolution melting (MS-HRM) and methylation-specific-Taqman-based-digital-PCR (digital Methylight) to boost detection of low-level aberrant methylation-changes.
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Affiliation(s)
- Yibin Liu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chen Song
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mariana Fitarelli-Kiehl
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - G. Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA,To whom correspondence should be addressed. Tel: +1 617 525 7122; Fax: +1 617 582 6037;
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Pu D, Pan R, Liu W, Xiao P. Quantitative analysis of single-nucleotide polymorphisms by pyrosequencing with di-base addition. Electrophoresis 2017; 38:876-885. [PMID: 27957738 DOI: 10.1002/elps.201600430] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/24/2016] [Accepted: 12/01/2016] [Indexed: 02/06/2023]
Abstract
We have developed and validated a novel method for quantitative detection of SNPs by using pyrosequencing with di-base addition (PDBA). Based on the principle that the signal intensity is proportional to the template concentration within a linear concentration range, linear formula (Y = AX + B) for each genotype is established, and the relationship between two genotypes of a single SNP can be resolved by corresponding linear formulas. Here, PDBA assays were developed to detect variants rs6717546 and rs4148324, and the linear formulas for each genotype of rs6717546 and rs4148324 were established. The method allowed to quantitatively determine each genotype and showed 100% accordant results against a panel of defined mixtures. A set of 24 template fragments containing variants rs6717546 or rs4148324 was tested to evaluate the method. Our results showed that allele frequency of each genotype was accurately quantified, with results comparable to those of conventional pyrosequencing. Furthermore, this method was capable of detecting alleles with frequencies as low as 3%, which was more sensitive than ∼5 to ∼7% level detected by conventional pyrosequencing. This method offers high sensitivity, reproducibility, and relatively low costs, and thus could provide a much-needed approach for quantitative analysis of SNPs in clinical samples.
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Affiliation(s)
- Dan Pu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China.,School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, P. R. China
| | - Rongfang Pan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Wenbin Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Pengfeng Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
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PCR-Based Detection Methods for Single-Nucleotide Polymorphism or Mutation: Real-Time PCR and Its Substantial Contribution Toward Technological Refinement. Adv Clin Chem 2017; 80:45-72. [PMID: 28431642 DOI: 10.1016/bs.acc.2016.11.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) and single-nucleotide mutations result from the substitution of only a single base. The SNP or mutation can be relevant to disease susceptibility, pathogenesis of disease, and efficacy of specific drugs. It is important to detect SNPs or mutations clinically. Methods to distinguish/detect SNPs or mutations should be highly specific and sensitive. In this regard, polymerase chain reaction (PCR) has provided the necessary analytical performance for many molecular analyses. PCR-based methods for SNP/mutation detection are broadly categorized into two types-(1) polymorphic or mutant allele-directed specific analysis using primers matched with substituted nucleotide or using oligonucleotides to block or clamp the nontargeted template, and (2) melting curve analysis, which is combined with the real-time PCR techniques using hydrolysis probes, hybridization probes, or double-stranded DNA-binding fluorescent dyes. Innovative and novel approaches as well as technical improvements have made SNP- or mutation-detection methods increasingly more sophisticated. These advances include DNA/RNA preparation and subsequent amplification steps, and miniaturization of PCR instruments such that testing may be performed with relative ease in clinical laboratories or as a point-of-care test in clinical settings.
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Zischewski J, Fischer R, Bortesi L. Detection of on-target and off-target mutations generated by CRISPR/Cas9 and other sequence-specific nucleases. Biotechnol Adv 2017; 35:95-104. [DOI: 10.1016/j.biotechadv.2016.12.003] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/18/2016] [Accepted: 12/19/2016] [Indexed: 12/17/2022]
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Khodakov D, Wang C, Zhang DY. Diagnostics based on nucleic acid sequence variant profiling: PCR, hybridization, and NGS approaches. Adv Drug Deliv Rev 2016; 105:3-19. [PMID: 27089811 DOI: 10.1016/j.addr.2016.04.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/21/2016] [Accepted: 04/06/2016] [Indexed: 12/22/2022]
Abstract
Nucleic acid sequence variations have been implicated in many diseases, and reliable detection and quantitation of DNA/RNA biomarkers can inform effective therapeutic action, enabling precision medicine. Nucleic acid analysis technologies being translated into the clinic can broadly be classified into hybridization, PCR, and sequencing, as well as their combinations. Here we review the molecular mechanisms of popular commercial assays, and their progress in translation into in vitro diagnostics.
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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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Azuara D, Santos C, Lopez-Doriga A, Grasselli J, Nadal M, Sanjuan X, Marin F, Vidal J, Montal R, Moreno V, Bellosillo B, Argiles G, Elez E, Dienstmann R, Montagut C, Tabernero J, Capellá G, Salazar R. Nanofluidic Digital PCR and Extended Genotyping of RAS and BRAF for Improved Selection of Metastatic Colorectal Cancer Patients for Anti-EGFR Therapies. Mol Cancer Ther 2016; 15:1106-12. [PMID: 27037411 DOI: 10.1158/1535-7163.mct-15-0820] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/17/2016] [Indexed: 11/16/2022]
Abstract
The clinical significance of low-frequent RAS pathway-mutated alleles and the optimal sensitivity cutoff value in the prediction of response to anti-EGFR therapy in metastatic colorectal cancer (mCRC) patients remains controversial. We aimed to evaluate the added value of genotyping an extended RAS panel using a robust nanofluidic digital PCR (dPCR) approach. A panel of 34 hotspots, including RAS (KRAS and NRAS exons 2/3/4) and BRAF (V600E), was analyzed in tumor FFPE samples from 102 mCRC patients treated with anti-EGFR therapy. dPCR was compared with conventional quantitative PCR (qPCR). Response rates, progression-free survival (PFS), and overall survival (OS) were correlated to the mutational status and the mutated allele fraction. Tumor response evaluations were not available in 9 patients and were excluded for response rate analysis. Twenty-two percent of patients were positive for one mutation with qPCR (mutated alleles ranged from 2.1% to 66.6%). Analysis by dPCR increased the number of positive patients to 47%. Mutated alleles for patients only detected by dPCR ranged from 0.04% to 10.8%. An inverse correlation between the fraction of mutated alleles and radiologic response was observed. ROC analysis showed that a fraction of 1% or higher of any mutated alleles offered the best predictive value for all combinations of RAS and BRAF analysis. In addition, this threshold also optimized prediction both PFS and OS. We conclude that mutation testing using an extended gene panel, including RAS and BRAF with a threshold of 1% improved prediction of response to anti-EGFR therapy. Mol Cancer Ther; 15(5); 1106-12. ©2016 AACR.
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Affiliation(s)
- Daniel Azuara
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Santos
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Adriana Lopez-Doriga
- Unit of Biomarkers and Susceptibility, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Julieta Grasselli
- Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marga Nadal
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Xavier Sanjuan
- Department of Pathology, University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Fátima Marin
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Joana Vidal
- Department of Medical Oncology, Hospital Universitari del Mar, Barcelona, Spain
| | - Robert Montal
- Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Beatriz Bellosillo
- Department of Pathology, Hospital Universitari del Mar, Barcelona, Spain
| | - Guillem Argiles
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elena Elez
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rodrigo Dienstmann
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Clara Montagut
- Department of Medical Oncology, Hospital Universitari del Mar, Barcelona, Spain
| | - Josep Tabernero
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Gabriel Capellá
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.
| | - Ramon Salazar
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.
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How-Kit A, Tost J. Pyrosequencing®-Based Identification of Low-Frequency Mutations Enriched Through Enhanced-ice-COLD-PCR. Methods Mol Biol 2016; 1315:83-101. [PMID: 26103893 DOI: 10.1007/978-1-4939-2715-9_7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A number of molecular diagnostic assays have been developed in the last years for mutation detection. Although these methods have become increasingly sensitive, most of them are incompatible with a sequencing-based readout and require prior knowledge of the mutation present in the sample. Consequently, coamplification at low denaturation (COLD)-PCR-based methods have been developed and combine a high analytical sensitivity due to mutation enrichment in the sample with the identification of known or unknown mutations by downstream sequencing experiments. Among these methods, the recently developed Enhanced-ice-COLD-PCR appeared as the most powerful method as it outperformed the other COLD-PCR-based methods in terms of the mutation enrichment and due to the simplicity of the experimental setup of the assay. Indeed, E-ice-COLD-PCR is very versatile as it can be used on all types of PCR platforms and is applicable to different types of samples including fresh frozen, FFPE, and plasma samples. The technique relies on the incorporation of an LNA containing blocker probe in the PCR reaction followed by selective heteroduplex denaturation enabling amplification of the mutant allele while amplification of the wild-type allele is prevented. Combined with Pyrosequencing(®), which is a very quantitative high-resolution sequencing technology, E-ice-COLD-PCR can detect and identify mutations with a limit of detection down to 0.01 %.
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Affiliation(s)
- Alexandre How-Kit
- Laboratory for Functional Genomics, Fondation Jean Dausset-CEPH, 27 rue Juliette Dodu, 75010, Paris, France
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Song C, Castellanos-Rizaldos E, Bejar R, Ebert BL, Makrigiorgos GM. DMSO Increases Mutation Scanning Detection Sensitivity of High-Resolution Melting in Clinical Samples. Clin Chem 2015; 61:1354-62. [PMID: 26432802 DOI: 10.1373/clinchem.2015.245357] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/17/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND Mutation scanning provides the simplest, lowest-cost method for identifying DNA variations on single PCR amplicons, and it may be performed before sequencing to avoid screening of noninformative wild-type samples. High-resolution melting (HRM) is the most commonly used method for mutation scanning. With PCR-HRM, however, mutations less abundant than approximately 3%-10% that can still be clinically significant may often be missed. Therefore, enhancing HRM detection sensitivity is important for mutation scanning and its clinical application. METHODS We used serial dilution of cell lines containing the TP53 exon 8 mutation to demonstrate the improvement in detection sensitivity for conventional-PCR-HRM in the presence of DMSO. We also conducted coamplification at lower denaturation temperature (COLD)-PCR with an extra step for cross-hybridization, followed by preferential denaturation and amplification at optimized critical temperature (full-COLD-PCR), to further enrich low-level mutations before HRM with or without DMSO, and we used droplet-digital PCR to derive the optimal conditions for mutation enrichment. Both conventional PCR-HRM and full-COLD-PCR-HRM with and without DMSO were used for mutation scanning of TP53 exon 8 in cancer samples containing known mutations and myelodysplastic syndrome samples with unknown mutations. Mutations in other genes were also examined. RESULTS The detection sensitivity of PCR-HRM scanning increases 2- to 5-fold in the presence of DMSO, depending on mutation type and sequence context, and can typically detect mutation abundance of approximately 1%. When mutation enrichment is applied during amplification with full-COLD-PCR followed by HRM in the presence of DMSO, mutations with 0.2%-0.3% abundance in TP53 exon 8 can be detected. CONCLUSIONS DMSO improves HRM mutation scanning sensitivity with saturating dyes. When full-COLD-PCR is used, followed by DMSO-HRM, the overall improvement is about 20-fold compared with conventional PCR-HRM.
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Affiliation(s)
- Chen Song
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Elena Castellanos-Rizaldos
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Rafael Bejar
- Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, CA
| | - Benjamin L Ebert
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA;
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Freidin MB, Freydina DV, Leung M, Montero Fernandez A, Nicholson AG, Lim E. Circulating tumor DNA outperforms circulating tumor cells for KRAS mutation detection in thoracic malignancies. Clin Chem 2015; 61:1299-304. [PMID: 26272233 DOI: 10.1373/clinchem.2015.242453] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/09/2015] [Indexed: 01/05/2023]
Abstract
BACKGROUND Circulating biomarkers, such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), are both considered for blood-based mutation detection, but limited studies have compared them in a head-to-head manner. Using KRAS (Kirsten rat sarcoma viral oncogene homolog), we performed such a comparison in patients who underwent surgery for suspected lung cancer. METHODS We recruited 93 patients, including 82 with lung cancer and 11 with benign diseases of the lung. Mutations were detected in codons 12 and 13 of KRAS in DNA extracted from CTCs, plasma, and matched tumors or lung tissues with custom-designed coamplification at lower denaturation temperature (COLD)-PCR assays, high-resolution melt analysis (HRM), and commercial assays (Roche Cobas(®) KRAS mutation test and Qiagen Therascreen(®) pyrosequencing KRAS kit). RESULTS With the Cobas mutation test, we identified KRAS mutations in 21.3% of tumors. Mutation analysis in matched CTC DNA and ctDNA samples by COLD-PCR/HRM assay revealed mutations in 30.5% (ctDNA) and 23.2% (CTC DNA) of patients with lung cancer. Combined results of different tests revealed KRAS-positive cases for 28% of tumors. The diagnostic sensitivity and specificity of KRAS mutation detection in tumors achieved with ctDNA was 0.96 (95% CI 0.81-1.00) and 0.95 (0.85-0.99), respectively. The diagnostic test performance was lower for CTC DNA, at 0.52 (0.34-0.73) and 0.88 (0.79-0.95). CONCLUSIONS Our results support ctDNA as a preferential specimen type for mutation screening in thoracic malignancies vs CTC DNA, achieving greater mutation detection than either CTCs or limited amounts of tumor tissue alone.
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Affiliation(s)
- Maxim B Freidin
- Royal Brompton and Harefield National Health Service Foundation Trust, London, UK; National Heart and Lung Institute, Imperial College London, London, UK
| | - Dasha V Freydina
- Royal Brompton and Harefield National Health Service Foundation Trust, London, UK; National Heart and Lung Institute, Imperial College London, London, UK
| | - Maria Leung
- Royal Brompton and Harefield National Health Service Foundation Trust, London, UK
| | | | - Andrew G Nicholson
- Royal Brompton and Harefield National Health Service Foundation Trust, London, UK; National Heart and Lung Institute, Imperial College London, London, UK
| | - Eric Lim
- Royal Brompton and Harefield National Health Service Foundation Trust, London, UK; National Heart and Lung Institute, Imperial College London, London, UK.
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Contini E, Paganini I, Sestini R, Candita L, Capone GL, Barbetti L, Falconi S, Frusconi S, Giotti I, Giuliani C, Torricelli F, Benelli M, Papi L. A Systematic Assessment of Accuracy in Detecting Somatic Mosaic Variants by Deep Amplicon Sequencing: Application to NF2 Gene. PLoS One 2015; 10:e0129099. [PMID: 26066488 PMCID: PMC4466335 DOI: 10.1371/journal.pone.0129099] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/05/2015] [Indexed: 11/18/2022] Open
Abstract
The accurate detection of low-allelic variants is still challenging, particularly for the identification of somatic mosaicism, where matched control sample is not available. High throughput sequencing, by the simultaneous and independent analysis of thousands of different DNA fragments, might overcome many of the limits of traditional methods, greatly increasing the sensitivity. However, it is necessary to take into account the high number of false positives that may arise due to the lack of matched control samples. Here, we applied deep amplicon sequencing to the analysis of samples with known genotype and variant allele fraction (VAF) followed by a tailored statistical analysis. This method allowed to define a minimum value of VAF for detecting mosaic variants with high accuracy. Then, we exploited the estimated VAF to select candidate alterations in NF2 gene in 34 samples with unknown genotype (30 blood and 4 tumor DNAs), demonstrating the suitability of our method. The strategy we propose optimizes the use of deep amplicon sequencing for the identification of low abundance variants. Moreover, our method can be applied to different high throughput sequencing approaches to estimate the background noise and define the accuracy of the experimental design.
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Affiliation(s)
- Elisa Contini
- Diagnostic Genetics Unit, Careggi University Hospital, Florence, Italy
| | - Irene Paganini
- Department of Biomedical Experimental and Clinical Sciences, Medical Genetics, University of Florence, Florence, Italy
| | - Roberta Sestini
- Department of Biomedical Experimental and Clinical Sciences, Medical Genetics, University of Florence, Florence, Italy
| | - Luisa Candita
- Department of Biomedical Experimental and Clinical Sciences, Medical Genetics, University of Florence, Florence, Italy
| | - Gabriele Lorenzo Capone
- Department of Biomedical Experimental and Clinical Sciences, Medical Genetics, University of Florence, Florence, Italy
| | - Lorenzo Barbetti
- Department of Biomedical Experimental and Clinical Sciences, Medical Genetics, University of Florence, Florence, Italy
| | - Serena Falconi
- Diagnostic Genetics Unit, Careggi University Hospital, Florence, Italy
| | - Sabrina Frusconi
- Diagnostic Genetics Unit, Careggi University Hospital, Florence, Italy
| | - Irene Giotti
- Diagnostic Genetics Unit, Careggi University Hospital, Florence, Italy
| | - Costanza Giuliani
- Diagnostic Genetics Unit, Careggi University Hospital, Florence, Italy
| | | | - Matteo Benelli
- Diagnostic Genetics Unit, Careggi University Hospital, Florence, Italy
- * E-mail:
| | - Laura Papi
- Department of Biomedical Experimental and Clinical Sciences, Medical Genetics, University of Florence, Florence, Italy
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Huang MMC, Leong SM, Chua HW, Tucker S, Cheong WC, Chiu L, Li MH, Koay ESC. Highly sensitive KRAS mutation detection from formalin-fixed paraffin-embedded biopsies and circulating tumour cells using wild-type blocking polymerase chain reaction and Sanger sequencing. Mol Diagn Ther 2015; 18:459-68. [PMID: 24664550 DOI: 10.1007/s40291-014-0098-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND OBJECTIVES Among patients with colorectal cancer (CRC), KRAS mutations were reported to occur in 30-51 % of all cases. CRC patients with KRAS mutations were reported to be non-responsive to anti-epidermal growth factor receptor (EGFR) monoclonal antibody (MoAb) treatment in many clinical trials. Hence, accurate detection of KRAS mutations would be critical in guiding the use of anti-EGFR MoAb therapies in CRC. METHODS In this study, we carried out a detailed investigation of the efficacy of a wild-type (WT) blocking real-time polymerase chain reaction (PCR), employing WT KRAS locked nucleic acid blockers, and Sanger sequencing, for KRAS mutation detection in rare cells. Analyses were first conducted on cell lines to optimize the assay protocol which was subsequently applied to peripheral blood and tissue samples from patients with CRC. RESULTS The optimized assay provided a superior sensitivity enabling detection of as little as two cells with mutated KRAS in the background of 10(4) WT cells (0.02 %). The feasibility of this assay was further investigated to assess the KRAS status of 45 colorectal tissue samples, which had been tested previously, using a conventional PCR sequencing approach. The analysis showed a mutational discordance between these two methods in 4 of 18 WT cases. CONCLUSION Our results present a simple, effective, and robust method for KRAS mutation detection in both paraffin embedded tissues and circulating tumour cells, at single-cell level. The method greatly enhances the detection sensitivity and alleviates the need of exhaustively removing co-enriched contaminating lymphocytes.
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Affiliation(s)
- Meggie Mo Chao Huang
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Hospital, 5 Lower Kent Ridge Road, 119074, Singapore, Singapore
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Enhanced ratio of signals enables digital mutation scanning for rare allele detection. J Mol Diagn 2015; 17:284-92. [PMID: 25772705 DOI: 10.1016/j.jmoldx.2014.12.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 12/12/2014] [Accepted: 12/19/2014] [Indexed: 12/23/2022] Open
Abstract
The use of droplet digital PCR (ddPCR) for low-level DNA mutation detection in cancer, prenatal diagnosis, and infectious diseases is growing rapidly. However, although ddPCR has been implemented successfully for detection of rare mutations at pre-determined positions, no ddPCR adaptation for mutation scanning exists. Yet, frequently, clinically relevant mutations reside on multiple sequence positions in tumor suppressor genes or complex hotspot mutations in oncogenes. Here, we describe a combination of coamplification at lower denaturation temperature PCR (COLD-PCR) with ddPCR that enables digital mutation scanning within approximately 50-bp sections of a target amplicon. Two FAM/HEX-labeled hydrolysis probes matching the wild-type sequence are used during ddPCR. The ratio of FAM/HEX-positive droplets is constant when wild-type amplicons are amplified but deviates when mutations anywhere under the FAM or HEX probes are present. To enhance the change in FAM/HEX ratio, we employed COLD-PCR cycling conditions that enrich mutation-containing amplicons anywhere on the sequence. We validated COLD-ddPCR on multiple mutations in TP53 and in EGFR using serial mutation dilutions and cell-free circulating DNA samples, and demonstrate detection down to approximately 0.2% to 1.2% mutation abundance. COLD-ddPCR enables a simple, rapid, and robust two-fluorophore detection method for the identification of multiple mutations during ddPCR and potentially can identify unknown DNA variants present in the target sequence.
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Ho TH, Dang KX, Lintula S, Hotakainen K, Feng L, Olkkonen VM, Verschuren EW, Tenkanen T, Haglund C, Kolho KL, Stenman UH, Stenman J. Extendable blocking probe in reverse transcription for analysis of RNA variants with superior selectivity. Nucleic Acids Res 2015; 43:e4. [PMID: 25378315 PMCID: PMC4288146 DOI: 10.1093/nar/gku1048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 10/09/2014] [Accepted: 10/13/2014] [Indexed: 12/16/2022] Open
Abstract
Here we provide the first strategy to use a competitive Extendable Blocking Probe (ExBP) for allele-specific priming with superior selectivity at the stage of reverse transcription. In order to analyze highly similar RNA variants, a reverse-transcriptase primer whose sequence matches a specific variant selectively primes only that variant, whereas mismatch priming to the alternative variant is suppressed by virtue of hybridization and subsequent extension of the perfectly matched ExBP on that alternative variant template to form a cDNA-RNA hybrid. This hybrid will render the alternative RNA template unavailable for mismatch priming initiated by the specific primer in a hot-start protocol of reverse transcription when the temperature decreases to a level where such mismatch priming could occur. The ExBP-based reverse transcription assay detected BRAF and KRAS mutations in at least 1000-fold excess of wild-type RNA and detection was linear over a 4-log dynamic range. This novel strategy not only reveals the presence or absence of rare mutations with an exceptionally high selectivity, but also provides a convenient tool for accurate determination of RNA variants in different settings, such as quantification of allele-specific expression.
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Affiliation(s)
- Tho H Ho
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Kien X Dang
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Susanna Lintula
- Haartman Institute, Department of Clinical Chemistry, Biomedicum Helsinki, University of Helsinki and Helsinki University Central Hospital, Helsinki, FI-00029 HUS, Finland
| | - Kristina Hotakainen
- Haartman Institute, Department of Clinical Chemistry, Biomedicum Helsinki, University of Helsinki and Helsinki University Central Hospital, Helsinki, FI-00029 HUS, Finland Helsinki University Central Hospital, HUSLAB, Helsinki, 00029 HUS, Finland
| | - Lin Feng
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Vesa M Olkkonen
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, FI-00014, Finland
| | | | - Caj Haglund
- Department of Surgery, Helsinki University Central Hospital, Helsinki, 00029 HUS, Finland Research Program Unit, Translational Cancer Biology, University of Helsinki, Helsinki, FI-00014, Finland Haartman Institute, Department of Pathology, University of Helsinki, Helsinki, FI-00014, Finland
| | - Kaija-Leena Kolho
- Children's Hospital, University of Helsinki, Helsinki, FI-00014, Finland
| | - Ulf-Hakan Stenman
- Haartman Institute, Department of Clinical Chemistry, Biomedicum Helsinki, University of Helsinki and Helsinki University Central Hospital, Helsinki, FI-00029 HUS, Finland
| | - Jakob Stenman
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, FI-00014, Finland Department of Women's and Children's Health, Karolinska Institutet, Stockholm, SE-17176, Sweden
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Castellanos-Rizaldos E, Richardson K, Lin R, Wu G, Makrigiorgos MG. Single-tube, highly parallel mutation enrichment in cancer gene panels by use of temperature-tolerant COLD-PCR. Clin Chem 2015; 61:267-77. [PMID: 25297854 PMCID: PMC4281501 DOI: 10.1373/clinchem.2014.228361] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Multiplexed detection of low-level mutations presents a technical challenge for many technologies, including cancer gene panels used for targeted-resequencing. Analysis of mutations below approximately 2%-5% abundance in tumors with heterogeneity, samples with stromal contamination, or biofluids is problematic owing to increased noise from sequencing errors. Technologies that reduce noise via deep sequencing unavoidably reduce throughput and increase cost. Here we provide proof of principle that coamplification at lower denaturation temperature (COLD)-PCR technology enables multiplex low-level mutation detection in cancer gene panels while retaining throughput. METHODS We have developed a multiplex temperature-tolerant COLD-PCR (fast-TT-COLD-PCR) approach that uses cancer gene panels developed for massively parallel sequencing. After multiplex preamplification from genomic DNA, we attach tails to all amplicons and perform fast-TT-COLD-PCR. This approach gradually increases denaturation temperatures in a step-wise fashion, such that all possible denaturation temperatures are encompassed. By introducing modified nucleotides, fast-COLD-PCR is adapted to enrich for melting temperature (Tm)-increasing mutations over all amplicons, in a single tube. Therefore, in separate reactions, both Tm-decreasing and Tm-increasing mutations are enriched. RESULTS Using custom-made and commercial gene panels containing 8, 50, 190, or 16 000 amplicons, we demonstrate that fast-TT-COLD-PCR enriches mutations on all examined targets simultaneously. Incorporation of deoxyinosine triphosphate (dITP)/2,6-diaminopurine triphosphate (dDTP) in place of deoxyguanosine triphosphate (dGTP)/deoxyadenosine triphosphate (dATP) enables enrichment of Tm-increasing mutations. Serial dilution experiments demonstrate a limit of detection of approximately 0.01%-0.1% mutation abundance by use of Ion-Torrent and 0.1%-0.3% by use of Sanger sequencing. CONCLUSIONS Fast-TT-COLD-PCR improves the limit of detection of cancer gene panels by enabling mutation enrichment in multiplex, single-tube reactions. This novel adaptation of COLD-PCR converts subclonal mutations to clonal, thereby facilitating detection and subsequent mutation sequencing.
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Affiliation(s)
| | | | - Rui Lin
- Transgenomic Inc., Omaha, NE
| | | | - Mike G Makrigiorgos
- Division of DNA Repair and Genome Stability and Division of Medical Physics and Biophysics, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA;
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Walsh K, Wallace WA. Molecular pathology in lung cancer: a guide to the techniques used in clinical practice. Histopathology 2014; 65:731-41. [PMID: 25130601 DOI: 10.1111/his.12505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Five year survival rates for lung cancer patients are poor; however the development of new therapeutic options, which benefit subsets of the population, offer hope of improvement. These novel therapies frequently rely upon the analysis of biomarkers in pathology samples; in lung cancer patients, testing is now routinely carried out to identify small mutations and chromosomal rearrangements in order to predict response to treatment. The recent increase in biomarker analyses in pathology samples has lead to the development of a new specialty, molecular pathology. The use of molecular pathology assays in clinical samples is largely under the control of the histopathologist; who is likely to be asked, as a minimum, to select tissue sections for molecular analysis and mark areas of H&E stained slides for macro or microdissection. Many histopathologists will also be involved in the sourcing and implementation of new assays. This review aims to provide a guide to some of the most commonly used molecular pathology methods - their advantages and their limitations.
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Affiliation(s)
- Kathy Walsh
- Pathology, Division of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK
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Mairinger FD, Vollbrecht C, Streubel A, Roth A, Landt O, Walter HFR, Kollmeier J, Mairinger T. The "COLD-PCR approach" for early and cost-effective detection of tyrosine kinase inhibitor resistance mutations in EGFR-positive non-small cell lung cancer. Appl Immunohistochem Mol Morphol 2014; 22:114-8. [PMID: 24517913 DOI: 10.1097/pdm.0b013e31829a638d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Activating epidermal growth factor receptor (EGFR) gene mutations can be successfully treated by EGFR tyrosine kinase inhibitors (EGFR-TKIs), but nearly 50% of all patients' exhibit progression of the disease until treatment because of T790M mutations. It is proposed that this is mostly caused by therapy-resistant tumor clones harboring a T790M mutation. Until now no cost-effective routine-diagnostic method for EGFR-resistance mutation status analysis is available leaving long-time response to TKI treatment to chance. Unambiguous identification of T790M EGFR mutations is mandatory to optimize initial treatment strategies. MATERIALS AND METHODS Artificial EGFR T790M mutations and human wild-type gDNA were prepared in several dilution series. Preferential amplification using coamplification at lower denaturation temperature-PCR (COLD-PCR) of the mutant sequence and subsequent HybProbe melting curve detection or pyrosequencing were performed in comparison to normal processing. RESULTS COLD-PCR-based amplification allowed the detection of 0.125% T790M mutant DNA in a background of wild-type DNA in comparison to 5% while normal processing. These results were reproducible. CONCLUSIONS COLD-PCR is a powerful and cost-effective tool for routine diagnostic to detect underrepresented tumor clones in clinical samples. A diagnostic tool for unambiguous identification of T790M-mutated minor tumor clones is now available enabling optimized therapy.
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Affiliation(s)
- Fabian D Mairinger
- *Institute of Pathology and Neuropathology, University Hospital Essen, University of Duisburg-Essen ∥Department of Interventional Pneumology, Ruhrlandklinik-University Hospital, Essen †Institute of Pathology, University Hospital Cologne, Cologne Departments of ‡Pathology ¶Pneumology, Helios Klinikum Emil von Behring §TIB MOLBIOL Syntheselabor GmbH, Berlin, Germany
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Kvist T, Sondt-Marcussen L, Mikkelsen MJ. Partition enrichment of nucleotide sequences (PINS)--a generally applicable, sequence based method for enrichment of complex DNA samples. PLoS One 2014; 9:e106817. [PMID: 25203653 PMCID: PMC4159240 DOI: 10.1371/journal.pone.0106817] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 08/11/2014] [Indexed: 12/20/2022] Open
Abstract
The dwindling cost of DNA sequencing is driving transformative changes in various biological disciplines including medicine, thus resulting in an increased need for routine sequencing. Preparation of samples suitable for sequencing is the starting point of any practical application, but enrichment of the target sequence over background DNA is often laborious and of limited sensitivity thereby limiting the usefulness of sequencing. The present paper describes a new method, Probability directed Isolation of Nucleic acid Sequences (PINS), for enrichment of DNA, enabling the sequencing of a large DNA region surrounding a small known sequence. A 275,000 fold enrichment of a target DNA sample containing integrated human papilloma virus is demonstrated. Specifically, a sample containing 0.0028 copies of target sequence per ng of total DNA was enriched to 786 copies per ng. The starting concentration of 0.0028 target copies per ng corresponds to one copy of target in a background of 100,000 complete human genomes. The enriched sample was subsequently amplified using rapid genome walking and the resulting DNA sequence revealed not only the sequence of a the truncated virus, but also 1026 base pairs 5' and 50 base pairs 3' to the integration site in chromosome 8. The demonstrated enrichment method is extremely sensitive and selective and requires only minimal knowledge of the sequence to be enriched and will therefore enable sequencing where the target concentration relative to background is too low to allow the use of other sample preparation methods or where significant parts of the target sequence is unknown.
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Luke JJ, Oxnard GR, Paweletz CP, Camidge DR, Heymach JV, Solit DB, Johnson BE. Realizing the potential of plasma genotyping in an age of genotype-directed therapies. J Natl Cancer Inst 2014; 106:dju214. [PMID: 25106647 DOI: 10.1093/jnci/dju214] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The identification of oncogenic driver mutations in cancer has led to the rapid rise of genotype-directed treatments such as EGFR and BRAF kinase inhibitors. Standard tumor biopsy remains a cumbersome and morbid procedure for patients, leading to a growing interest in noninvasive plasma genotyping approaches. Circulating tumor cells are of interest; however, the processing of specimens is complicated and time consuming. By comparison, cell-free DNA (cfDNA) genotyping has the potential to be convenient and relatively simple to process in a short time period. Several technologies are under development for cfDNA analysis, such as allele-specific polymerase chain reaction (PCR), coamplification at Lower Denaturation temperatures (COLD) PCR, emulsion PCR, and massively parallel sequencing. Broad clinical validity will need to be established for different assays, and clinical utility will need to be evaluated within prospective trials to determine which assays will best predict the efficacy of therapy and patient outcomes. In addition, assay standardization will be critical prior to widespread use in routine clinical practice. The Cell Free DNA Working Group, under the sponsorship of Transgenomic, was convened to evaluate the molecular assays in development and provide recommendations for application and interpretation of these tests in the context of future clinical research. The consensus commentary of the Cell Free DNA Working Group for the use of cfDNA plasma genotyping assays is presented here, including future steps in the development of these technologies.
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Affiliation(s)
- Jason J Luke
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA (JJL, GRO, CPP, BEJ), Memorial Sloan-Kettering Cancer Center, New York, NY (DBS), University of Colorado Cancer Center, Denver, CO (DRC); The University of Texas MD Anderson Cancer Center, Houston, TX (JVH)
| | - Geoffrey R Oxnard
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA (JJL, GRO, CPP, BEJ), Memorial Sloan-Kettering Cancer Center, New York, NY (DBS), University of Colorado Cancer Center, Denver, CO (DRC); The University of Texas MD Anderson Cancer Center, Houston, TX (JVH)
| | - Cloud P Paweletz
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA (JJL, GRO, CPP, BEJ), Memorial Sloan-Kettering Cancer Center, New York, NY (DBS), University of Colorado Cancer Center, Denver, CO (DRC); The University of Texas MD Anderson Cancer Center, Houston, TX (JVH)
| | - D Ross Camidge
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA (JJL, GRO, CPP, BEJ), Memorial Sloan-Kettering Cancer Center, New York, NY (DBS), University of Colorado Cancer Center, Denver, CO (DRC); The University of Texas MD Anderson Cancer Center, Houston, TX (JVH)
| | - John V Heymach
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA (JJL, GRO, CPP, BEJ), Memorial Sloan-Kettering Cancer Center, New York, NY (DBS), University of Colorado Cancer Center, Denver, CO (DRC); The University of Texas MD Anderson Cancer Center, Houston, TX (JVH)
| | - David B Solit
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA (JJL, GRO, CPP, BEJ), Memorial Sloan-Kettering Cancer Center, New York, NY (DBS), University of Colorado Cancer Center, Denver, CO (DRC); The University of Texas MD Anderson Cancer Center, Houston, TX (JVH)
| | - Bruce E Johnson
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA (JJL, GRO, CPP, BEJ), Memorial Sloan-Kettering Cancer Center, New York, NY (DBS), University of Colorado Cancer Center, Denver, CO (DRC); The University of Texas MD Anderson Cancer Center, Houston, TX (JVH).
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