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Honoré N, Galot R, van Marcke C, Limaye N, Machiels JP. Liquid Biopsy to Detect Minimal Residual Disease: Methodology and Impact. Cancers (Basel) 2021; 13:5364. [PMID: 34771526 PMCID: PMC8582541 DOI: 10.3390/cancers13215364] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/15/2022] Open
Abstract
One reason why some patients experience recurrent disease after a curative-intent treatment might be the persistence of residual tumor cells, called minimal residual disease (MRD). MRD cannot be identified by standard radiological exams or clinical evaluation. Tumor-specific alterations found in the blood indirectly diagnose the presence of MRD. Liquid biopsies thus have the potential to detect MRD, allowing, among other things, the detection of circulating tumor DNA (ctDNA), circulating tumor cells (CTC), or tumor-specific microRNA. Although liquid biopsy is increasingly studied, several technical issues still limit its clinical applicability: low sensitivity, poor standardization or reproducibility, and lack of randomized trials demonstrating its clinical benefit. Being able to detect MRD could give clinicians a more comprehensive view of the risk of relapse of their patients and could select patients requiring treatment escalation with the goal of improving cancer survival. In this review, we are discussing the different methodologies used and investigated to detect MRD in solid cancers, their respective potentials and issues, and the clinical impacts that MRD detection will have on the management of cancer patients.
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Affiliation(s)
- Natasha Honoré
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
| | - Rachel Galot
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
- Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Cédric van Marcke
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
- Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Nisha Limaye
- Genetics of Autoimmune Diseases and Cancer, de Duve Institute, Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium;
| | - Jean-Pascal Machiels
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
- Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
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Kim YS, Shin S, Jung SH, Park YM, Park GS, Lee SH, Chung YJ. Genomic progression of precancerous actinic keratosis to squamous cell carcinoma. J Invest Dermatol 2021; 142:528-538.e8. [PMID: 34480890 DOI: 10.1016/j.jid.2021.07.172] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 12/17/2022]
Abstract
The mechanism underlying the progression of actinic keratosis (AK) and cutaneous squamous cell carcinoma in situ (SCCIS) to squamous cell carcinoma (SCC) remains unclear. To investigate this, we performed regional microdissection and targeted deep sequencing in SCC (N=10) and paired adjacent SE (sun-damaged epidermis)/AK/SCCIS (N=13) samples to detect mutations and copy number alterations (CNAs). Most (11/13) SE/AK/SCCIS tissues harbored ≥ 1 driver alterations, indicating their precancerous nature. All pairs except one showed genome architectures representing genomic progression of SE/AK/SCCIS to SCC with common trunks and unique branches (7 parallel and 5 linear progression cases). SE/AK/SCCIS tissues tended to harbor lower mutation/CNA burdens than SCC tissues, but most of them had driver mutations, including NOTCH1 and TP53 mutations. SCC-specific genomic alterations included TP53, PIK3CA, FBXW7, and CDKN2A mutations and a MYC copy-number gain, but they were heterogeneous among cases, suggesting that a single gene or pathway does not explain the progression of AK to SCC. In multiregion analyses of AK lesions, only some AK samples were related to SCC. In conclusion, the SE/AK/SCCIS genomes may have previously acquired truncal driver alterations, such as NOTCH1 and TP53 mutations, which promote parallel or linear progression to SCC upon acquisition of additional genomic alterations.
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Affiliation(s)
- Yoon-Seob Kim
- Department of Microbiology, Seoul, Republic of Korea; Precision Medicine Research Center, Seoul, Republic of Korea; Integrated Research Center for Genome Polymorphism, Seoul, Republic of Korea
| | - Sun Shin
- Department of Microbiology, Seoul, Republic of Korea; Precision Medicine Research Center, Seoul, Republic of Korea; Integrated Research Center for Genome Polymorphism, Seoul, Republic of Korea
| | | | - Young Min Park
- Department of Dermatology, Seoul St. Mary's Hospital, Seoul, Republic of Korea
| | - Gyeong Sin Park
- Department of Hospital Pathology, Seoul St. Mary's Hospital, Seoul, Republic of Korea
| | - Sug Hyung Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, Seoul, Republic of Korea; Department of Pathology, Seoul, Republic of Korea
| | - Yeun-Jun Chung
- Department of Microbiology, Seoul, Republic of Korea; Precision Medicine Research Center, Seoul, Republic of Korea; Integrated Research Center for Genome Polymorphism, Seoul, Republic of Korea.
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Cheng D, Liu F, Xie K, Zeng C, Li X, Ni X, Ge J, Shu L, Zhou Y, Shi H, Liu H, Chen J. Donor-derived cell-free DNA: An independent biomarker in kidney transplant patients with antibody-mediated rejection. Transpl Immunol 2021; 69:101404. [PMID: 33971294 DOI: 10.1016/j.trim.2021.101404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/23/2021] [Accepted: 05/06/2021] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Antibody-mediated rejection (ABMR) is a major cause of kidney transplant failure which requires donor-specific antibodies (DSA) for a definitive diagnosis. Donor-derived cell-free DNA (ddcfDNA) is an emerging biomarker used to assess kidney allograft injury. However, current data is limited to predict the accuracy of ddcfDNA in ABMR diagnosis. This study was conducted to compare the performance of DSA with plasma ddcfDNA for the diagnosis of ABMR. METHODS In this retrospective single-center observational study, we enrolled 50 kidney transplant recipients who were diagnosed with the suspicion of rejection between June 2018 and May 2019 at the Jinling Hospital. Plasma ddcfDNA was measured by using a novel target region capture sequencing methodology. A total of 37 patients who were tested with DSA and biopsy were divided into four subgroups (ABMR+/DSA+, ABMR+/DSA-, ABMR-/DSA+, ABMR-/DSA-) for the distribution of ddcfDNA (%) by ABMR and DSA. RESULTS The median level of ddcfDNA in biopsy showed that the ABMR group (1.66%, IQR 1.34-3.76%) was significantly higher than the median level (0.63%, IQR 0.43-0.74%) in non-ABMR (p < 0.001). With a ddcfDNA cutoff of 0.96%, the AUC was 0.90 (95%CI, 0.86-0.95), which was associated with a sensitivity of 90.5% (95%CI, 69.6-98.8%) and specificity of 96.6% (95%CI, 82.2-100%), a PPV of 95% (95%CI, 73.4-99.2%) and NPV of 93.3% (95%CI, 78.9-98.1%) were also observed. Among the four subgroups, ddcfDNA had no significant difference in both DSA+ group and DSA-group (p > 0.05). In the diagnosis of ABMR, the specificity, sensitivity, PPV and NPV of DSA were 50%, 74.1%, 41.7%, 80%, respectively. CONCLUSIONS ddcfDNA levels in the blood could highly distinguish (biopsy-supported) ABMR occurrence, irrespective of whether this method is accompanied by DSA or not.
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Affiliation(s)
- Dongrui Cheng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Feng Liu
- AlloDx Biotech Co, Ltd, Shanghai, 201100, China
| | - Kenan Xie
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Caihong Zeng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Xue Li
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Xuefeng Ni
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Jun Ge
- AlloDx Biotech Co, Ltd, Shanghai, 201100, China
| | - Lipin Shu
- AlloDx Biotech Co, Ltd, Shanghai, 201100, China
| | - Yang Zhou
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Haifeng Shi
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Haitao Liu
- AlloDx Biotech Co, Ltd, Shanghai, 201100, China
| | - Jinsong Chen
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China.
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Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables. Comput Struct Biotechnol J 2019; 17:561-569. [PMID: 31049166 PMCID: PMC6482431 DOI: 10.1016/j.csbj.2019.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/12/2019] [Accepted: 04/03/2019] [Indexed: 01/10/2023] Open
Abstract
Deep sequencing genomic analysis is becoming increasingly common in clinical research and practice, enabling accurate identification of diagnostic, prognostic, and predictive determinants. Variant calling, distinguishing between true mutations and experimental errors, is a central task of genomic analysis and often requires sophisticated statistical, computational, and/or heuristic techniques. Although variant callers seek to overcome noise inherent in biological experiments, variant calling can be significantly affected by outside factors including those used to prepare, store, and analyze samples. The goal of this review is to discuss known experimental features, such as sample preparation, library preparation, and sequencing, alongside diverse biological and clinical variables, and evaluate their effect on variant caller selection and optimization.
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