1
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Ogbonnaya CN, Alsaedi BSO, Alhussaini AJ, Hislop R, Pratt N, Steele JD, Kernohan N, Nabi G. Radiogenomics Map-Based Molecular and Imaging Phenotypical Characterization in Localised Prostate Cancer Using Pre-Biopsy Biparametric MR Imaging. Int J Mol Sci 2024; 25:5379. [PMID: 38791417 PMCID: PMC11121591 DOI: 10.3390/ijms25105379] [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] [Received: 04/13/2024] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
To create a radiogenomics map and evaluate the correlation between molecular and imaging phenotypes in localized prostate cancer (PCa), using radical prostatectomy histopathology as a reference standard. Radiomic features were extracted from T2-weighted (T2WI) and Apparent Diffusion Coefficient (ADC) images of clinically localized PCa patients (n = 15) across different Gleason score-based risk categories. DNA extraction was performed on formalin-fixed, paraffin-embedded (FFPE) samples. Gene expression analysis of androgen receptor expression, apoptosis, and hypoxia was conducted using the Chromosome Analysis Suite (ChAS) application and OSCHIP files. The relationship between gene expression alterations and textural features was assessed using Pearson's correlation analysis. Receiver operating characteristic (ROC) analysis was utilized to evaluate the predictive accuracy of the model. A significant correlation was observed between radiomic texture features and copy number variation (CNV) of genes associated with apoptosis, hypoxia, and androgen receptor (p-value ≤ 0.05). The identified radiomic features, including Sum Entropy ADC, Inverse Difference ADC, Sum Variance T2WI, Entropy T2WI, Difference Variance T2WI, and Angular Secondary Moment T2WI, exhibited potential for predicting cancer grade and biological processes such as apoptosis and hypoxia. Incorporating radiomics and genomics into a prediction model significantly improved the prediction of prostate cancer grade (clinically significant prostate cancer), yielding an AUC of 0.95. Radiomic texture features significantly correlate with genotypes for apoptosis, hypoxia, and androgen receptor expression in localised prostate cancer. Integration of these into the prediction model improved prediction accuracy of clinically significant prostate cancer.
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Affiliation(s)
- Chidozie N. Ogbonnaya
- Division of Imaging Science and Technology, School of Medicine, University of Dundee, Dundee DD1 4HN, UK; (C.N.O.); (A.J.A.); (J.D.S.)
| | | | - Abeer J. Alhussaini
- Division of Imaging Science and Technology, School of Medicine, University of Dundee, Dundee DD1 4HN, UK; (C.N.O.); (A.J.A.); (J.D.S.)
| | - Robert Hislop
- Cytogenetic, Human Genetics Unit, NHS Tayside, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK; (R.H.); (N.P.)
| | - Norman Pratt
- Cytogenetic, Human Genetics Unit, NHS Tayside, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK; (R.H.); (N.P.)
| | - J. Douglas Steele
- Division of Imaging Science and Technology, School of Medicine, University of Dundee, Dundee DD1 4HN, UK; (C.N.O.); (A.J.A.); (J.D.S.)
| | - Neil Kernohan
- Department of Pathology, NHS Tayside, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK;
| | - Ghulam Nabi
- Division of Imaging Science and Technology, School of Medicine, University of Dundee, Dundee DD1 4HN, UK; (C.N.O.); (A.J.A.); (J.D.S.)
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2
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Samlali K, Thornbury M, Venter A. Community-led risk analysis of direct-to-consumer whole-genome sequencing. Biochem Cell Biol 2022; 100:499-509. [PMID: 35939839 DOI: 10.1139/bcb-2021-0506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Direct-to-consumer (DTC) genetic testing is cheaper and more accessible than ever before; however, the intention to combine, reuse, and resell this genetic information as powerful data sets is generally hidden from the consumer. This financial gain is creating a competitive DTC market, reducing the price of whole-genome sequencing (WGS) to under 300 USD. Entering this transition from single-nucleotide polymorphism-based DTC testing to WGS DTC testing, individuals looking for access to their whole-genomic information face new privacy and security risks. Differences between WGS and other methods of consumer genetic tests are left unexplored by regulation, leading to the application of legal data anonymization methods on whole-genome data, and questionable consent methods. Large representative genomic data sets are important for research and improve the standard of medicine and personalized care. However, these data can also be used by market players, law enforcement, and governments for surveillance, population analyses, marketing purposes, and discrimination. Here, we present a summary of the state of WGS DTC genetic testing and its current regulation, through a community-based lens to expose dual-use risks in consumer-facing biotechnologies.
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Affiliation(s)
- Kenza Samlali
- BricoBio Community Biology Lab, Montréal, QC, Canada.,Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, Canada.,Department of Electrical and Computer Engineering, Concordia University, Montréal, QC, Canada
| | - Mackenzie Thornbury
- BricoBio Community Biology Lab, Montréal, QC, Canada.,Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, Canada.,Department of Biology, Concordia University, Montréal, QC, Canada
| | - Andrei Venter
- BricoBio Community Biology Lab, Montréal, QC, Canada
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3
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Hanbazazh M, Morlote D, Mackinnon AC, Harada S. Utility of Single-Gene Testing in Cancer Specimens. Clin Lab Med 2022; 42:385-394. [DOI: 10.1016/j.cll.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Hussen BM, Abdullah ST, Salihi A, Sabir DK, Sidiq KR, Rasul MF, Hidayat HJ, Ghafouri-Fard S, Taheri M, Jamali E. The emerging roles of NGS in clinical oncology and personalized medicine. Pathol Res Pract 2022; 230:153760. [PMID: 35033746 DOI: 10.1016/j.prp.2022.153760] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/29/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has been increasingly popular in genomics studies over the last decade, as new sequencing technology has been created and improved. Recently, NGS started to be used in clinical oncology to improve cancer therapy through diverse modalities ranging from finding novel and rare cancer mutations, discovering cancer mutation carriers to reaching specific therapeutic approaches known as personalized medicine (PM). PM has the potential to minimize medical expenses by shifting the current traditional medical approach of treating cancer and other diseases to an individualized preventive and predictive approach. Currently, NGS can speed up in the early diagnosis of diseases and discover pharmacogenetic markers that help in personalizing therapies. Despite the tremendous growth in our understanding of genetics, NGS holds the added advantage of providing more comprehensive picture of cancer landscape and uncovering cancer development pathways. In this review, we provided a complete overview of potential NGS applications in scientific and clinical oncology, with a particular emphasis on pharmacogenomics in the direction of precision medicine treatment options.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq; Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Sara Tharwat Abdullah
- Department of Pharmacology and Toxicology, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Abbas Salihi
- Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq; Department of Biology, College of Science, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Dana Khdr Sabir
- Department of Medical Laboratory Sciences, Charmo University, Kurdistan Region, Iraq
| | - Karzan R Sidiq
- Department of Biology, College of Education, University of Sulaimani, Sulaimani 334, Kurdistan, Iraq
| | - Mohammed Fatih Rasul
- Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Kurdistan Region, Erbil, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Elena Jamali
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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5
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Khan MA, Vikramdeo KS, Sudan SK, Singh S, Wilhite A, Dasgupta S, Rocconi RP, Singh AP. Platinum-resistant ovarian cancer: From drug resistance mechanisms to liquid biopsy-based biomarkers for disease management. Semin Cancer Biol 2021; 77:99-109. [PMID: 34418576 PMCID: PMC8665066 DOI: 10.1016/j.semcancer.2021.08.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 07/09/2021] [Accepted: 08/12/2021] [Indexed: 12/24/2022]
Abstract
Resistance to platinum-based chemotherapy is a major clinical challenge in ovarian cancer, contributing to the high mortality-to-incidence ratio. Management of the platinum-resistant disease has been difficult due to diverse underlying molecular mechanisms. Over the past several years, research has revealed several novel molecular targets that are being explored as biomarkers for treatment planning and monitoring of response. The therapeutic landscape of ovarian cancer is also rapidly evolving, and alternative therapies are becoming available for the recurrent platinum-resistant disease. This review provides a snapshot of platinum resistance mechanisms and discusses liquid-based biomarkers and their potential utility in effective management of platinum-resistant ovarian cancer.
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Affiliation(s)
- Mohammad Aslam Khan
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL, 36617, United States; Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, United States
| | - Kunwar Somesh Vikramdeo
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL, 36617, United States; Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, United States
| | - Sarabjeet Kour Sudan
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL, 36617, United States; Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, United States
| | - Seema Singh
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL, 36617, United States; Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, United States; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, 36688, United States
| | - Annelise Wilhite
- Department of Gynecologic Oncology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, United States
| | - Santanu Dasgupta
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL, 36617, United States; Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, United States; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, 36688, United States
| | - Rodney Paul Rocconi
- Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, United States
| | - Ajay Pratap Singh
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL, 36617, United States; Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, United States; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, 36688, United States.
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Torres GF, Bonilla CE, Buitrago G, Arrieta O, Malapelle U, Rolfo C, Cardona AF. How clinically useful is comprehensive genomic profiling for patients with non-small cell lung cancer? A systematic review. Crit Rev Oncol Hematol 2021; 166:103459. [PMID: 34461270 DOI: 10.1016/j.critrevonc.2021.103459] [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: 06/14/2021] [Revised: 08/02/2021] [Accepted: 08/22/2021] [Indexed: 12/18/2022] Open
Abstract
Given the lack of a gold standard, the clinical usefulness of Comprehensive Genomic Profiling (CGP) has not been established. This systematic review aimed to evaluate evidence about the clinical benefit of CGP for patients with Non-small cell lung carcinoma (NSCLC). All controlled studies that evaluated the ability of CGP to detect actionable targets (ATs) reported increases in the number of samples with ATs. The frequency of ATs detected in uncontrolled case series ranged from 0.7 % for RET mutations to 45 % for EGFR mutations. The studies that evaluated therapies targeted to EGFR, ALK, ROS-1, MET, and RET mutations documented significant improvement in clinical outcomes. This review suggests that CGP tests may be clinically helpful for treating patients with NSCLC. Although current evidence is associated with a high risk of bias, the significant impact of NSCLC on individuals and society may justify the routine use of CGP testing for this disease.
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Affiliation(s)
| | - Carlos Eduardo Bonilla
- Clinical Oncology Department, Instituto Nacional de Cancerología - INC, Bogotá, Colombia
| | - Giancarlo Buitrago
- Instituto de Investigaciones Clínicas, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Oscar Arrieta
- Thoracic Oncology Unit, National Cancer Institute (INCan), México City, Mexico
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Center, Mount Sinai Hospital System & Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Andrés F Cardona
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogotá, Colombia; Molecular Oncology and Biology Systems Research Group (Fox-G/ONCOLGroup), Universidad el Bosque, Bogotá, Colombia; Clinical and Traslational Oncology Group, Clínica del Country, Bogotá, Colombia
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7
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Zhu L, Xie S, Yang C, Hua N, Wu Y, Wang L, Ni W, Tong X, Fei M, Wang S. Current Progress in Investigating Mature T- and NK-Cell Lymphoma Gene Aberrations by Next-Generation Sequencing (NGS). Cancer Manag Res 2021; 13:5275-5286. [PMID: 34239326 PMCID: PMC8259727 DOI: 10.2147/cmar.s299505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/14/2021] [Indexed: 11/23/2022] Open
Abstract
Despite efforts to abrogate the severe threat to life posed by the profound malignancy of mature natural killer/T-cell lymphoma (NKTCL), therapeutic advances still require further investigation of its inherent regulatory biochemical processes. Next-generation sequencing (NGS) is an increasingly developing gene detection technique, which has been widely used in lymphoma genetic research in recent years. Targeted therapy based on the above studies has also generated a series of advances, making genetic mutation a new research hotspot in lymphoma. Advances in NKTCL-related gene mutations are reviewed in this paper.
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Affiliation(s)
- Lifen Zhu
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Shufang Xie
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of China
| | - Chen Yang
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
- Department of Clinical Medicine, Qingdao University, Qingdao, Shandong, People’s Republic of China
| | - Nanni Hua
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of China
| | - Yi Wu
- Phase I clinical research center, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Lei Wang
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Wanmao Ni
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Xiangmin Tong
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Min Fei
- Center of Health Management, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Shibing Wang
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
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Circulating tumor DNA in lung cancer: real-time monitoring of disease evolution and treatment response. Chin Med J (Engl) 2021; 133:2476-2485. [PMID: 32960843 PMCID: PMC7575184 DOI: 10.1097/cm9.0000000000001097] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lung cancer is one of the leading causes of all cancer-related deaths. Circulating tumor DNA (ctDNA) is released from apoptotic and necrotic tumor cells. Several sensitive techniques have been invented and adapted to quantify ctDNA genomic alterations. Applications of ctDNA in lung cancer include early diagnosis and detection, prognosis prediction, detecting mutations and structural alterations, minimal residual disease, tumor mutational burden, and tumor evolution tracking. Compared to surgical biopsy and radiographic imaging, the advantages of ctDNA are that it is a non-invasive procedure, allows real-time monitoring, and has relatively high sensitivity and specificity. Given the massive research on non-small cell lung cancer, attention should be paid to small cell lung cancer.
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Wang J, Yu P, Luo J, Sun Z, Yu J, Wang J. Transcriptomic and microRNA Expression Profiles Identify Biomarkers for Predicting Neo-Chemoradiotherapy Response in Esophageal Squamous Cell Carcinomas (ESCC). Front Pharmacol 2021; 12:626972. [PMID: 33935718 PMCID: PMC8082678 DOI: 10.3389/fphar.2021.626972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/10/2021] [Indexed: 01/01/2023] Open
Abstract
Neo-chemoradiotherapy (nCRT) before surgery is a standard treatment for locally advanced esophageal cancers. However, the treatment outcome of nCRT varied with different patients. This study aimed to identify potential biomarkers for prediction of nCRT-response in patients with esophageal squamous cell carcinoma (ESCC). Microarray datasets of nCRT responder and non-responder samples (access number GSE45670 and GSE59974) of patients with ESCC were downloaded from Gene Expression Omnibus (GEO) database. The mRNA expression profiles of cancer biopsies from four ESCC patients were analyzed before and after nCRT. Differentially expressed genes (DEGs) and miRNAs were screened between nCRT responder and non-responder ESCC samples. Functional enrichment analysis was conducted for these DEGs followed by construction of protein-protein interaction (PPI) network and miRNA-mRNA regulatory network. Finally, univariate survival analysis was performed to identify candidate biomarkers with prognostic values in ESCC. We identified numerous DEGs and differentially expressed miRNAs from nCRT responder group. GO and KEGG analysis showed that the dysregulated genes were mainly involved in biological processes and pathways, including "response to stimulus", "cellular response to organic substance", "regulation of signal transduction", "AGE-RAGE signaling pathway in diabetic complications", and "steroid hormone biosynthesis". After integration of PPI network and miRNA-mRNA network analysis, we found eight genes, TNF, AKR1C1, AKR1C2, ICAM1, GPR68, GNB4, SERPINE1 and MMP12, could be candidate genes associated with disease progression. Univariate cox regression analysis showed that there was no significant correlation between dysregulated miRNAs (such as hsa-miR-34b-3p, hsa-miR-127-5p, hsa-miR-144-3p, and hsa-miR-486-5p, et al.) and overall survival of ESCC patients. Moreover, abnormal expression of MMP12 was significantly correlated with pathological degree, TNM stage, lymph nodes metastasis, and overall survival of ESCC patients (p < 0.05). Taken together, our study identified that MMP12 might be a useful tumor biomarker and therapeutic target for ESCC.
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Affiliation(s)
- Jian Wang
- Department of Radiotherapy, Jiangyin People's Hospital, Jiangyin, China
| | - Pengyi Yu
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, Jiangsu, China
| | - Judong Luo
- Department of Radiotherapy, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Jiangsu, China
| | - Zhiqiang Sun
- Department of Radiotherapy, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Jiangsu, China
| | - Jingping Yu
- Department of Radiotherapy, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Jiangsu, China
| | - Jianlin Wang
- Department of Radiotherapy, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Jiangsu, China
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Chen P, Yu X, Huang H, Zeng W, He X, Liu M, Huang B. Evaluation of Ion Torrent next-generation sequencing for thalassemia diagnosis. J Int Med Res 2020; 48:300060520967778. [PMID: 33342339 PMCID: PMC7754798 DOI: 10.1177/0300060520967778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
INTRODUCTION To evaluate a next-generation sequencing (NGS) workflow in the screening and diagnosis of thalassemia. METHODS In this prospective study, blood samples were obtained from people undergoing genetic screening for thalassemia at our centre in Guangzhou, China. Genomic DNA was polymerase chain reaction (PCR)-amplified and sequenced using the Ion Torrent system and results compared with traditional genetic analyses. RESULTS Of the 359 subjects, 148 (41%) were confirmed to have thalassemia. Variant detection identified 35 different types including the most common. Identification of the mutational sites by NGS were consistent with those identified by Sanger sequencing and Gap-PCR. The sensitivity and specificities of the Ion Torrent NGS were 100%. In a separate test of 16 samples, results were consistent when repeated ten times. CONCLUSION Our NGS workflow based on the Ion Torrent sequencer was successful in the detection of large deletions and non-deletional defects in thalassemia with high accuracy and repeatability.
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Affiliation(s)
- Peisong Chen
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xuegao Yu
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hao Huang
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wentao Zeng
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaohong He
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Min Liu
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Bin Huang
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Majewska A, Budny B, Ziemnicka K, Ruchała M, Wierzbicka M. Head and Neck Paragangliomas-A Genetic Overview. Int J Mol Sci 2020; 21:ijms21207669. [PMID: 33081307 PMCID: PMC7589036 DOI: 10.3390/ijms21207669] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/17/2022] Open
Abstract
Pheochromocytomas (PCC) and paragangliomas (PGL) are rare neuroendocrine tumors. Head and neck paragangliomas (HNPGL) can be categorized into carotid body tumors, which are the most common, as well as jugular, tympanic, and vagal paraganglioma. A review of the current literature was conducted to consolidate knowledge concerning PGL mutations, familial occurrence, and the practical application of this information. Available scientific databases were searched using the keywords head and neck paraganglioma and genetics, and 274 articles in PubMed and 1183 in ScienceDirect were found. From these articles, those concerning genetic changes in HNPGLs were selected. The aim of this review is to describe the known genetic changes and their practical applications. We found that the etiology of the tumors in question is based on genetic changes in the form of either germinal or somatic mutations. 40% of PCC and PGL have a predisposing germline mutation (including VHL, SDHB, SDHD, RET, NF1, THEM127, MAX, SDHC, SDHA, SDHAF2, HIF2A, HRAS, KIF1B, PHD2, and FH). Approximately 25–30% of cases are due to somatic mutations, such as RET, VHL, NF1, MAX, and HIF2A. The tumors were divided into three main clusters by the Cancer Genome Atlas (TCGA); namely, the pseudohypoxia group, the Wnt signaling group, and the kinase signaling group. The review also discusses genetic syndromes, epigenetic changes, and new testing technologies such as next-generation sequencing (NGS).
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Affiliation(s)
- Anna Majewska
- Department of Otolaryngology, Head and Neck Surgery, Poznan University of Medical Sciences, 60-355 Poznań, Poland;
- Correspondence:
| | - Bartłomiej Budny
- Department of Endocrinology, Metabolism and Internal Diseases, Poznan University of Medical Sciences, 60-355 Poznań, Poland; (B.B.); (K.Z.); (M.R.)
| | - Katarzyna Ziemnicka
- Department of Endocrinology, Metabolism and Internal Diseases, Poznan University of Medical Sciences, 60-355 Poznań, Poland; (B.B.); (K.Z.); (M.R.)
| | - Marek Ruchała
- Department of Endocrinology, Metabolism and Internal Diseases, Poznan University of Medical Sciences, 60-355 Poznań, Poland; (B.B.); (K.Z.); (M.R.)
| | - Małgorzata Wierzbicka
- Department of Otolaryngology, Head and Neck Surgery, Poznan University of Medical Sciences, 60-355 Poznań, Poland;
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12
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Asthana V, Stern BS, Tang Y, Bugga P, Li A, Ferguson A, Asthana A, Bao G, Drezek RA. Development of a Novel Class of Self-Assembling dsRNA Cancer Therapeutics: A Proof-of-Concept Investigation. MOLECULAR THERAPY-ONCOLYTICS 2020; 18:419-431. [PMID: 32913891 PMCID: PMC7452102 DOI: 10.1016/j.omto.2020.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 07/28/2020] [Indexed: 10/26/2022]
Abstract
Cancer has proven to be an extremely difficult challenge to treat. Several fundamental issues currently underlie cancer treatment, including differentiating self from nonself, functional coupling of the recognition and therapeutic components of various therapies, and the propensity of cancerous cells to develop resistance to common treatment modalities via evolutionary pressure. Given these limitations, there is an increasing need to develop an all-encompassing therapeutic that can uniquely target malignant cells, decouple recognition from treatment, and overcome evolutionarily driven cancer resistance. We describe herein a new class of programmable self-assembling double-stranded RNA (dsRNA)-based cancer therapeutics that uniquely targets aberrant genetic sequences and in a functionally decoupled manner, undergoes oncogenic RNA-activated displacement (ORAD), initiating a therapeutic cascade that induces apoptosis and immune activation. As a proof of concept, we show that RNA strands targeting the EWS/Fli1 fusion gene in Ewing sarcoma cells that are end blocked with phosphorothioate bonds and additionally sealed with a 2'-deoxyuridine (2'-U)-modified DNA protector can be used to induce specific and potent killing of cells containing the target oncogenic sequence but not wild type.
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Affiliation(s)
| | - Brett S Stern
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Yuqi Tang
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Pallavi Bugga
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Ang Li
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Adam Ferguson
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Anantratn Asthana
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Rebekah A Drezek
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
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Yao H, Wu C, Chen Y, Guo L, Chen W, Pan Y, Fu X, Wang G, Ding Y. Spectrum of gene mutations identified by targeted next-generation sequencing in Chinese leukemia patients. Mol Genet Genomic Med 2020; 8:e1369. [PMID: 32638549 PMCID: PMC7507579 DOI: 10.1002/mgg3.1369] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Despite targeted sequencing have identified several mutations for leukemia, there is still a limit of mutation screening for Chinese leukemia. Here, we used targeted next-generation sequencing for testing the mutation patterns of Chinese leukemia patients. METHODS We performed targeted sequencing of 504 tumor-related genes in 109 leukemia samples to identify single-nucleotide variants (SNVs) and insertions and deletions (INDELs). Pathogenic variants were assessed based on the American College of Medical Genetics and Genomics (ACMG) guidelines. The functional impact of pathogenic genes was explored through gene ontology (GO), pathway analysis, and protein-protein interaction network in silico. RESULTS We identified a total of 4,655 SNVs and 614 INDELs in 419 genes, in which PDE4DIP, NOTCH2, FANCA, BCR, and ROS1 emerged as the highly mutated genes. Of note, we were the first to demonstrate an association of PDE4DIP mutation and leukemia. Based on ACMG guidelines, 39 pathogenic and likely pathogenic mutations in 27 genes were found. GO annotation showed that the biological process including gland development, leukocyte differentiation, respiratory system development, myeloid leukocyte differentiation, mesenchymal to epithelial transition, and so on were involved. CONCLUSION Our study provided a map of gene mutations in Chinese patients with leukemia and gave insights into the molecular pathogenesis of leukemia.
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Affiliation(s)
- Hongxia Yao
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Congming Wu
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Yueqing Chen
- Hainan General Hospital, University of South China, Haikou, Hainan, China
| | - Li Guo
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Wenting Chen
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Yanping Pan
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Xiangjun Fu
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Guyun Wang
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Yipeng Ding
- Department of General Practice, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
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14
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Abstract
Abstract
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. This can be achieved by leveraging omics information for accurate molecular characterization of tumors. Tumor tissue biopsies are currently the main source of information for molecular profiling. However, biopsies are invasive and limited in resolving spatiotemporal heterogeneity in tumor tissues. Alternative non-invasive liquid biopsies can exploit patient’s body fluids to access multiple layers of tumor-specific biological information (genomes, epigenomes, transcriptomes, proteomes, metabolomes, circulating tumor cells, and exosomes). Analysis and integration of these large and diverse datasets using statistical and machine learning approaches can yield important insights into tumor biology and lead to discovery of new diagnostic, predictive, and prognostic biomarkers. Translation of these new diagnostic tools into standard clinical practice could transform oncology, as demonstrated by a number of liquid biopsy assays already entering clinical use. In this review, we highlight successes and challenges facing the rapidly evolving field of cancer biomarker research.
Lay Summary
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. The discovery of biomarkers for precision oncology has been accelerated by high-throughput experimental and computational methods, which can inform fine-grained characterization of tumors for clinical decision-making. Moreover, advances in the liquid biopsy field allow non-invasive sampling of patient’s body fluids with the aim of analyzing circulating biomarkers, obviating the need for invasive tumor tissue biopsies. In this review, we highlight successes and challenges facing the rapidly evolving field of liquid biopsy cancer biomarker research.
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15
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Khan K, Valeri N, Dearman C, Rao S, Watkins D, Starling N, Chau I, Cunningham D. Targeting EGFR pathway in metastatic colorectal cancer- tumour heterogeniety and convergent evolution. Crit Rev Oncol Hematol 2019; 143:153-163. [PMID: 31678702 DOI: 10.1016/j.critrevonc.2019.09.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 08/28/2019] [Accepted: 09/03/2019] [Indexed: 12/30/2022] Open
Abstract
Despite significant progress in management of metastatic colorectal cancer (mCRC) pertaining to better screening procedures and amelioration of the therapeutic armamentarium with targeted therapies, prognosis remains poor. Targeting epidermal growth factor receptor (EGFR) has been of particular interest owing to favourable efficacy benefits demonstrated by monoclonal antibodies (cetuximab and panitumumab) in various clinical settings and development of predictive biomarkers informing treatment decisions respectively. In spite of optimal patient selection based on RAS mutation status, primary and secondary resistance to monoclonal antibodies is higher than desired. Further research into predictive biomarkers is therefore essential, but has, to date, been conducted with considerable limitations. Whilst molecular heterogeneity has been demonstrated by several studies in mCRC, for incomprehensible reasons, multiple resistant genetic alterations that emerge under the selective pressure of EGFR-targeted therapies are somehow able to influence the biological and clinical behaviour of cancer cells, despite being detectable at extremely low frequencies. Intriguingly, these subclonal events largely seem to converge on RAS/RAF/MAPK pathway in patients treated with EGFR-targeted monoclonal antibodies. This review describes the clinical and biological evolution and development of EGFR targeted therapies in mCRC, the challenges in the presence of molecular complexities, the role of cell free (cf)-DNA and future strategies that could lead to further optimal discovery of clinically meaningful biomarkers and application of precision medicine.
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Affiliation(s)
- Khurum Khan
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK; Gastrointestinal Unit, University College London Hospitals, 250 Euston Road London, NW1 2AF, UK
| | - Nicola Valeri
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK
| | - Charles Dearman
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK
| | - Sheela Rao
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK
| | - David Watkins
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK
| | - Naureen Starling
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK
| | - Ian Chau
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK
| | - David Cunningham
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK.
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Yu J, Hu Y, Xu Y, Wang J, Kuang J, Zhang W, Shao J, Guo D, Wang Y. LUADpp: an effective prediction model on prognosis of lung adenocarcinomas based on somatic mutational features. BMC Cancer 2019; 19:263. [PMID: 30902072 PMCID: PMC6431052 DOI: 10.1186/s12885-019-5433-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/03/2019] [Indexed: 02/08/2023] Open
Abstract
Background Lung adenocarcinoma is the most common type of lung cancers. Whole-genome sequencing studies disclosed the genomic landscape of lung adenocarcinomas. however, it remains unclear if the genetic alternations could guide prognosis prediction. Effective genetic markers and their based prediction models are also at a lack for prognosis evaluation. Methods We obtained the somatic mutation data and clinical data for 371 lung adenocarcinoma cases from The Cancer Genome Atlas. The cases were classified into two prognostic groups (3-year survival), and a comparison was performed between the groups for the somatic mutation frequencies of genes, followed by development of computational models to discrete the different prognosis. Results Genes were found with higher mutation rates in good (≥ 3-year survival) than in poor (< 3-year survival) prognosis group of lung adenocarcinoma patients. Genes participating in cell-cell adhesion and motility were significantly enriched in the top gene list with mutation rate difference between the good and poor prognosis group. Support Vector Machine models with the gene somatic mutation features could well predict prognosis, and the performance improved as feature size increased. An 85-gene model reached an average cross-validated accuracy of 81% and an Area Under the Curve (AUC) of 0.896 for the Receiver Operating Characteristic (ROC) curves. The model also exhibited good inter-stage prognosis prediction performance, with an average AUC of 0.846 for the ROC curves. Conclusion The prognosis of lung adenocarcinomas is related with somatic gene mutations. The genetic markers could be used for prognosis prediction and furthermore provide guidance for personal medicine. Electronic supplementary material The online version of this article (10.1186/s12885-019-5433-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiaxian Yu
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Yueming Hu
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Yafei Xu
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Jue Wang
- State Key Laboratory of Agrobiotechnology and School of Life Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Jiajie Kuang
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Wei Zhang
- Sehnzhen GenRead Technology Co., Ltd., Shenzhen, 518000, China
| | - Jianlin Shao
- Zhejiang Hospital, 12 Lingyin Rd, Hangzhou, 310003, China
| | - Dianjing Guo
- State Key Laboratory of Agrobiotechnology and School of Life Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Yejun Wang
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Shenzhen, 518060, China.
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17
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Zhang L, Luo M, Yang H, Zhu S, Cheng X, Qing C. Next-generation sequencing-based genomic profiling analysis reveals novel mutations for clinical diagnosis in Chinese primary epithelial ovarian cancer patients. J Ovarian Res 2019; 12:19. [PMID: 30786925 PMCID: PMC6381667 DOI: 10.1186/s13048-019-0494-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/07/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Ovarian cancer (OC) is one of the most malignant gynecological tumors, associated with excess death rate (50-60%) in ovarian cancer patients. Particularly, among newly occurred ovarian cancer patients, 70% of clinical cases are diagnosed at the advanced stage, which definitely delay the timely treatment and lead to high mortality rate within 5 years post diagnosis. Therefore, identification of sensitive gene markers, as well as development of reliable genetic diagnosis, are important for the early detection and precise therapy for OC patients. This study aims to identify novel genetic mutations and develop a feasible clinical approach for early OC diagnosis. METHODS The OC tissue-derived DNA sample was acquired from 31 OC patients, and the somatic gene mutations will be identified after comparison with normal samples, using Genome-wide analysis and next-generation sequencing. RESULTS A total of 463 somatic mutations, which were considered as potential pathogenic sites, were assigned to 473 genes. Among them, 15 genes (TP53, TTN, MUC16, OR4N2, BRCA1, CAD, CCDC129, INSR, NAV3, NELL2, NRAS, OBSCN, PGLYRP4, RBM15B and TRPC7) were mutated on at least two sites. These genes were mapped to RNA sequencing (RNAseq) data, and a total of 117 genes had an absolute fold- change ≥ 2 and p ≤ 0.01. Five genes were mutated in at least two OC patients. Gene ontology (GO) classification indicated that a majority of genes participated in biological processes. Kyoto Enrichment of Genes and Genomes (KEGG) enrichment pathway analysis revealed that the genes were mainly involved in the regulation of metabolic signaling pathways. CONCLUSIONS Taken together, this study identified several novel genetic alterations pathway for early clinical diagnosis and provided abundant information for understanding molecular mechanisms of the OC occurrence and development.
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Affiliation(s)
- Lei Zhang
- School of Pharmaceutical Sciences & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Cheng Gong District, Kunming, Yunnan, 650500, People's Republic of China.,Department of Gynecology, Yunnan Tumor Hospital & The Third Affiliated Hospital of Kunming Medical University, 519 Kunzhou Road, Xishan District, Kunming, Yunnan, 650118, People's Republic of China
| | - Min Luo
- School of Pharmaceutical Sciences & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Cheng Gong District, Kunming, Yunnan, 650500, People's Republic of China
| | - Hongying Yang
- Department of Gynecology, Yunnan Tumor Hospital & The Third Affiliated Hospital of Kunming Medical University, 519 Kunzhou Road, Xishan District, Kunming, Yunnan, 650118, People's Republic of China
| | - Shaoyan Zhu
- School of Pharmaceutical Sciences & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Cheng Gong District, Kunming, Yunnan, 650500, People's Republic of China
| | - Xianliang Cheng
- School of Pharmaceutical Sciences & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Cheng Gong District, Kunming, Yunnan, 650500, People's Republic of China
| | - Chen Qing
- School of Pharmaceutical Sciences & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Cheng Gong District, Kunming, Yunnan, 650500, People's Republic of China.
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18
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Schröder J, Kumar A, Wong SQ. Overview of Fusion Detection Strategies Using Next-Generation Sequencing. Methods Mol Biol 2019; 1908:125-138. [PMID: 30649725 DOI: 10.1007/978-1-4939-9004-7_9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Structural gene fusion rearrangements leading to aberrant signaling are frequently detected in many cancer types. Gene fusions have significant prognostic and predictive value and are screened as part of molecular pathology testing for patient management. Many bioinformatic approaches have been developed to detect fusion mutations including whole-genome sequencing, targeted-based hybridization capture, and transcriptome-based approaches. Here we describe the most commonly used experimental methods to sequence and identify gene fusions using either DNA or RNA. We contrast experimental approaches both in the research and diagnostic setting and describe typical bioinformatic pipelines and software packages used to identify fusions.
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Affiliation(s)
- Jan Schröder
- Peter MacCallum Cancer Center, Melbourne, VIC, Australia
| | - Amit Kumar
- Peter MacCallum Cancer Center, Melbourne, VIC, Australia
| | - Stephen Q Wong
- Peter MacCallum Cancer Center, Melbourne, VIC, Australia.
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19
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Sapna G, Gokul S. Next generation sequencing in oral disease diagnostics. World J Stomatol 2018; 6:6-10. [DOI: 10.5321/wjs.v6.i2.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 08/31/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023] Open
Abstract
DNA sequencing is the method of identifying the precise order of DNA nucleotides within a molecule. The information of DNA sequencing is of prime requisite for basic biological research as well as in various clinical specialties. They can be used to determine the individual genetic sequence, larger genetic regions, chromosomes as well as to sequence RNA and proteins. Since the first DNA sequencing in 1970s, there has been tremendous advancements in the technologies aimed to determine the entire human genome. The need for rapid and accurate sequencing of human genome has resulted in the introduction of next generation sequencing (NGS) technology. NGS refers to the second-generation DNA sequencing technologies where millions of DNA can be sequenced simultaneously. Some of the next gen sequencing methods employed are Roche/454 life science, Illumina/Solexa, SOLiD system and HeliScope. Application of NGS in decoding the genomic database of various oral diseases may possess therapeutic and prognostic value. This presentation provides an overview of the basics of NGS and their potential applications in oral disease diagnostics.
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Affiliation(s)
- Gokul Sapna
- Department of periodontics, Nair Hospital Dental College, Mumbai 400008, India
| | - Sridharan Gokul
- Oral Pathology and Microbiology, YMT Dental College and Hospital, Mumbai 410210, India
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20
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Tack V, Spans L, Schuuring E, Keppens C, Zwaenepoel K, Pauwels P, Van Houdt J, Dequeker EMC. Describing the Reportable Range Is Important for Reliable Treatment Decisions: A Multiple Laboratory Study for Molecular Tumor Profiling Using Next-Generation Sequencing. J Mol Diagn 2018; 20:743-753. [PMID: 30055348 DOI: 10.1016/j.jmoldx.2018.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/14/2018] [Accepted: 06/05/2018] [Indexed: 01/04/2023] Open
Abstract
Because interpretation of next-generation sequencing (NGS) data remains challenging, optimization of the NGS process is needed to obtain correct sequencing results. Therefore, extensive validation and continuous monitoring of the quality is essential. NGS performance was compared with traditional detection methods and technical quality of nine NGS technologies was assessed. First, nine formalin-fixed, paraffin-embedded patient samples were analyzed by 114 laboratories by using different detection methods. No significant differences in performance were observed between analyses with NGS and traditional techniques. Second, two DNA control samples were analyzed for a selected number of variants by 26 participants with the use of nine different NGS technologies. Quality control metrics were analyzed from raw data files and a survey about routine procedures. Results showed large differences in coverages, but observed variant allele frequencies in raw data files were in line with predefined variant allele frequencies. Many false negative results were found because of low-quality regions, which were not reported as such. It is recommended to disclose the reportable range, the fraction of targeted genomic regions for which calls of acceptable quality can be generated, to avoid any errors in therapy decisions. NGS can be a reliable technique, only if essential quality control during analysis is applied and reported.
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Affiliation(s)
- Véronique Tack
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | - Lien Spans
- Center for Human Genetics, University of Leuven, Leuven, Belgium
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cleo Keppens
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | - Karen Zwaenepoel
- Department of Pathology, University Hospital Antwerp, Edegem, Belgium
| | - Patrick Pauwels
- Center for Oncologic Research (CORE), University of Antwerp, Antwerp, Belgium
| | | | - Elisabeth M C Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium; Department of Medical Diagnostics, University Hospital Leuven, Leuven, Belgium.
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21
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Luo Z, Fan X, Su Y, Huang YS. Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants. Bioinformatics 2018; 34:2004-2011. [PMID: 29385401 PMCID: PMC9881684 DOI: 10.1093/bioinformatics/bty043] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/26/2018] [Indexed: 02/02/2023] Open
Abstract
Motivation Tumor purity and ploidy have a substantial impact on next-gen sequence analyses of tumor samples and may alter the biological and clinical interpretation of results. Despite the existence of several computational methods that are dedicated to estimate tumor purity and/or ploidy from The Cancer Genome Atlas (TCGA) tumor-normal whole-genome-sequencing (WGS) data, an accurate, fast and fully-automated method that works in a wide range of sequencing coverage, level of tumor purity and level of intra-tumor heterogeneity, is still missing. Results We describe a computational method called Accurity that infers tumor purity, tumor cell ploidy and absolute allelic copy numbers for somatic copy number alterations (SCNAs) from tumor-normal WGS data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs). Results from both in silico and real sequencing data demonstrated that Accurity is highly accurate and robust, even in low-purity, high-ploidy and low-coverage settings in which several existing methods perform poorly. Accounting for tumor purity and ploidy, Accurity significantly increased signal/noise gaps between different copy numbers. We are hopeful that Accurity is of clinical use for identifying cancer diagnostic biomarkers. Availability and implementation Accurity is implemented in C++/Rust, available at http://www.yfish.org/software/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Yao Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yu S Huang
- To whom correspondence should be addressed.
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22
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Liang C, Wu Z, Gan X, Liu Y, You Y, Liu C, Zhou C, Liang Y, Mo H, Chen AM, Zhang J. Detection of Rare Mutations in EGFR-ARMS-PCR-Negative Lung Adenocarcinoma by Sanger Sequencing. Yonsei Med J 2018; 59:13-19. [PMID: 29214771 PMCID: PMC5725350 DOI: 10.3349/ymj.2018.59.1.13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 09/02/2017] [Accepted: 09/07/2017] [Indexed: 11/27/2022] Open
Abstract
PURPOSE This study aimed to identify potential epidermal growth factor receptor (EGFR) gene mutations in non-small cell lung cancer that went undetected by amplification refractory mutation system-Scorpion real-time PCR (ARMS-PCR). MATERIALS AND METHODS A total of 200 specimens were obtained from the First Affiliated Hospital of Guangzhou Medical University from August 2014 to August 2015. In total, 100 ARMS-negative and 100 ARMS-positive specimens were evaluated for EGFR gene mutations by Sanger sequencing. The methodology and sensitivity of each method and the outcomes of EGFR-tyrosine kinase inhibitor (TKI) therapy were analyzed. RESULTS Among the 100 ARMS-PCR-positive samples, 90 were positive by Sanger sequencing, while 10 cases were considered negative, because the mutation abundance was less than 10%. Among the 100 negative cases, three were positive for a rare EGFR mutation by Sanger sequencing. In the curative effect analysis of EGFR-TKIs, the progression-free survival (PFS) analysis based on ARMS and Sanger sequencing results showed no difference. However, the PFS of patients with a high abundance of EGFR mutation was 12.4 months [95% confidence interval (CI), 11.6-12.4 months], which was significantly higher than that of patients with a low abundance of mutations detected by Sanger sequencing (95% CI, 10.7-11.3 months) (p<0.001). CONCLUSION The ARMS method demonstrated higher sensitivity than Sanger sequencing, but was prone to missing mutations due to primer design. Sanger sequencing was able to detect rare EGFR mutations and deemed applicable for confirming EGFR status. A clinical trial evaluating the efficacy of EGFR-TKIs in patients with rare EGFR mutations is needed.
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Affiliation(s)
- Chaoyue Liang
- Department of Pulmonary Medicine, The Brain Hospital of Guangxi Zhuang Autonomous Region, Liuzhou, China
| | - Zhuolin Wu
- Department of Biomedical Engineering, University of Minnesota, Twin Cities, Minneapolis, USA
| | - Xiaohong Gan
- Guangzhou Life Technologies Daan Diagnostics Co., Ltd., Guangzhou, China
| | - Yuanbin Liu
- Guangzhou Institute of Respiratory Disease, Guangzhou, China
- Department of Internal Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - You You
- Guangzhou Institute of Respiratory Disease, Guangzhou, China
- Department of Internal Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chenxian Liu
- Department of Pulmonary Medicine, The Brain Hospital of Guangxi Zhuang Autonomous Region, Liuzhou, China
| | - Chengzhi Zhou
- Guangzhou Institute of Respiratory Disease, Guangzhou, China
- Department of Internal Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ying Liang
- Guangzhou Institute of Respiratory Disease, Guangzhou, China
| | - Haiyun Mo
- Department of Health Care, Maternal and Child Health Hospital of Haizhu District, Guangzhou, China
| | - Allen M Chen
- Guangzhou Life Technologies Daan Diagnostics Co., Ltd., Guangzhou, China
- Mendel Genes, Inc., Manhattan Beach, CA, USA.
| | - Jiexia Zhang
- Guangzhou Institute of Respiratory Disease, Guangzhou, China
- Department of Internal Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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Abstract
The majority of cancer-related deaths result from metastasis, the process by which cancer cells escape the primary tumor site and enter into the blood circulation in order to disseminate to secondary locations throughout the body. Tumor cells found within the circulation are referred to as circulating tumor cells (CTCs), and their detection and enumeration correlate with poor prognosis. The epithelial-to-mesenchymal transition (EMT) is a dynamic process that imparts epithelial cells with mesenchymal-like properties, thus facilitating tumor cell dissemination and contributing to metastasis. However, EMT also results in the downregulation of various epithelial proteins typically utilized by CTC technologies for enrichment and detection of these rare cells, resulting in reduced detection of some CTCs, potentially those with a more metastatic phenotype. In addition to the current clinical role of CTCs as a prognostic biomarker, they also have potential as a predictive biomarker via CTC characterization. However, CTC characterization is complicated by the unknown biological significance of CTCs possessing an EMT-like phenotype, and the ability to capture and understand this CTC subpopulation is an essential step in the utilization of CTCs for patient management. This chapter will review the process of EMT and its contribution to metastasis; discusses current and future clinical applications of CTCs; and describes both traditional and novel methods for CTC enrichment, detection, and characterization with a specific focus on CTCs with an EMT phenotype.
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Chudnovsky Y, Kumar RD, Schrock AB, Connelly C, Gowen K, Frampton GM, Erlich RL, Stephens PJ, Miller VA, Ross JS, Ali SM, Bose R. Response of a Metastatic Breast Carcinoma With a Previously Uncharacterized ERBB2 G776V Mutation to Human Epidermal Growth Factor Receptor 2–Targeted Therapy. JCO Precis Oncol 2017; 1:1-9. [DOI: 10.1200/po.16.00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Yakov Chudnovsky
- Yakov Chudnovsky, Alexa B. Schrock, Caitlin Connelly, Kyle Gowen, Garrett M. Frampton, Rachel L. Erlich, Philip J. Stephens, Vincent A. Miller, Jeffery S. Ross, and Siraj M. Ali, Foundation Medicine, Cambridge, MA; Runjun D. Kumar and Ron Bose, Washington University School of Medicine, St Louis, MO
| | - Runjun D. Kumar
- Yakov Chudnovsky, Alexa B. Schrock, Caitlin Connelly, Kyle Gowen, Garrett M. Frampton, Rachel L. Erlich, Philip J. Stephens, Vincent A. Miller, Jeffery S. Ross, and Siraj M. Ali, Foundation Medicine, Cambridge, MA; Runjun D. Kumar and Ron Bose, Washington University School of Medicine, St Louis, MO
| | - Alexa B. Schrock
- Yakov Chudnovsky, Alexa B. Schrock, Caitlin Connelly, Kyle Gowen, Garrett M. Frampton, Rachel L. Erlich, Philip J. Stephens, Vincent A. Miller, Jeffery S. Ross, and Siraj M. Ali, Foundation Medicine, Cambridge, MA; Runjun D. Kumar and Ron Bose, Washington University School of Medicine, St Louis, MO
| | - Caitlin Connelly
- Yakov Chudnovsky, Alexa B. Schrock, Caitlin Connelly, Kyle Gowen, Garrett M. Frampton, Rachel L. Erlich, Philip J. Stephens, Vincent A. Miller, Jeffery S. Ross, and Siraj M. Ali, Foundation Medicine, Cambridge, MA; Runjun D. Kumar and Ron Bose, Washington University School of Medicine, St Louis, MO
| | - Kyle Gowen
- Yakov Chudnovsky, Alexa B. Schrock, Caitlin Connelly, Kyle Gowen, Garrett M. Frampton, Rachel L. Erlich, Philip J. Stephens, Vincent A. Miller, Jeffery S. Ross, and Siraj M. Ali, Foundation Medicine, Cambridge, MA; Runjun D. Kumar and Ron Bose, Washington University School of Medicine, St Louis, MO
| | - Garrett M. Frampton
- Yakov Chudnovsky, Alexa B. Schrock, Caitlin Connelly, Kyle Gowen, Garrett M. Frampton, Rachel L. Erlich, Philip J. Stephens, Vincent A. Miller, Jeffery S. Ross, and Siraj M. Ali, Foundation Medicine, Cambridge, MA; Runjun D. Kumar and Ron Bose, Washington University School of Medicine, St Louis, MO
| | - Rachel L. Erlich
- Yakov Chudnovsky, Alexa B. Schrock, Caitlin Connelly, Kyle Gowen, Garrett M. Frampton, Rachel L. Erlich, Philip J. Stephens, Vincent A. Miller, Jeffery S. Ross, and Siraj M. Ali, Foundation Medicine, Cambridge, MA; Runjun D. Kumar and Ron Bose, Washington University School of Medicine, St Louis, MO
| | - Philip J. Stephens
- Yakov Chudnovsky, Alexa B. Schrock, Caitlin Connelly, Kyle Gowen, Garrett M. Frampton, Rachel L. Erlich, Philip J. Stephens, Vincent A. Miller, Jeffery S. Ross, and Siraj M. Ali, Foundation Medicine, Cambridge, MA; Runjun D. Kumar and Ron Bose, Washington University School of Medicine, St Louis, MO
| | - Vincent A. Miller
- Yakov Chudnovsky, Alexa B. Schrock, Caitlin Connelly, Kyle Gowen, Garrett M. Frampton, Rachel L. Erlich, Philip J. Stephens, Vincent A. Miller, Jeffery S. Ross, and Siraj M. Ali, Foundation Medicine, Cambridge, MA; Runjun D. Kumar and Ron Bose, Washington University School of Medicine, St Louis, MO
| | - Jeffrey S. Ross
- Yakov Chudnovsky, Alexa B. Schrock, Caitlin Connelly, Kyle Gowen, Garrett M. Frampton, Rachel L. Erlich, Philip J. Stephens, Vincent A. Miller, Jeffery S. Ross, and Siraj M. Ali, Foundation Medicine, Cambridge, MA; Runjun D. Kumar and Ron Bose, Washington University School of Medicine, St Louis, MO
| | - Siraj M. Ali
- Yakov Chudnovsky, Alexa B. Schrock, Caitlin Connelly, Kyle Gowen, Garrett M. Frampton, Rachel L. Erlich, Philip J. Stephens, Vincent A. Miller, Jeffery S. Ross, and Siraj M. Ali, Foundation Medicine, Cambridge, MA; Runjun D. Kumar and Ron Bose, Washington University School of Medicine, St Louis, MO
| | - Ron Bose
- Yakov Chudnovsky, Alexa B. Schrock, Caitlin Connelly, Kyle Gowen, Garrett M. Frampton, Rachel L. Erlich, Philip J. Stephens, Vincent A. Miller, Jeffery S. Ross, and Siraj M. Ali, Foundation Medicine, Cambridge, MA; Runjun D. Kumar and Ron Bose, Washington University School of Medicine, St Louis, MO
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Song Y, Tian T, Shi Y, Liu W, Zou Y, Khajvand T, Wang S, Zhu Z, Yang C. Enrichment and single-cell analysis of circulating tumor cells. Chem Sci 2017; 8:1736-1751. [PMID: 28451298 PMCID: PMC5396552 DOI: 10.1039/c6sc04671a] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 12/07/2016] [Indexed: 12/28/2022] Open
Abstract
Up to 90% of cancer-related deaths are caused by metastatic cancer. Circulating tumor cells (CTCs), a type of cancer cell that spreads through the blood after detaching from a solid tumor, are essential for the establishment of distant metastasis for a given cancer. As a new type of liquid biopsy, analysis of CTCs offers the possibility to avoid invasive tissue biopsy procedures with practical implications for diagnostics. The fundamental challenges of analyzing and profiling CTCs are the extremely low abundances of CTCs in the blood and the intrinsic heterogeneity of CTCs. Various technologies have been proposed for the enrichment and single-cell analysis of CTCs. This review aims to provide in-depth insights into CTC analysis, including various techniques for isolation of CTCs with capture methods based on physical and biochemical principles, and single-cell analysis of CTCs at the genomic, proteomic and phenotypic level, as well as current developmental trends and promising research directions.
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Affiliation(s)
- Yanling Song
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation , The Key Laboratory of Chemical Biology of Fujian Province , State Key Laboratory of Physical Chemistry of Solid Surfaces , Collaborative Innovation Center of Chemistry for Energy Materials , Department of Chemical Engineering , Department of Chemical Biology , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China .
- College of Biological Science and Engineering , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Tian Tian
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation , The Key Laboratory of Chemical Biology of Fujian Province , State Key Laboratory of Physical Chemistry of Solid Surfaces , Collaborative Innovation Center of Chemistry for Energy Materials , Department of Chemical Engineering , Department of Chemical Biology , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China .
| | - Yuanzhi Shi
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation , The Key Laboratory of Chemical Biology of Fujian Province , State Key Laboratory of Physical Chemistry of Solid Surfaces , Collaborative Innovation Center of Chemistry for Energy Materials , Department of Chemical Engineering , Department of Chemical Biology , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China .
| | - Wenli Liu
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation , The Key Laboratory of Chemical Biology of Fujian Province , State Key Laboratory of Physical Chemistry of Solid Surfaces , Collaborative Innovation Center of Chemistry for Energy Materials , Department of Chemical Engineering , Department of Chemical Biology , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China .
| | - Yuan Zou
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation , The Key Laboratory of Chemical Biology of Fujian Province , State Key Laboratory of Physical Chemistry of Solid Surfaces , Collaborative Innovation Center of Chemistry for Energy Materials , Department of Chemical Engineering , Department of Chemical Biology , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China .
| | - Tahereh Khajvand
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation , The Key Laboratory of Chemical Biology of Fujian Province , State Key Laboratory of Physical Chemistry of Solid Surfaces , Collaborative Innovation Center of Chemistry for Energy Materials , Department of Chemical Engineering , Department of Chemical Biology , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China .
| | - Sili Wang
- Department of Hematology , The First Affiliated Hospital of Xiamen University , Xiamen 361005 , China
| | - Zhi Zhu
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation , The Key Laboratory of Chemical Biology of Fujian Province , State Key Laboratory of Physical Chemistry of Solid Surfaces , Collaborative Innovation Center of Chemistry for Energy Materials , Department of Chemical Engineering , Department of Chemical Biology , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China .
| | - Chaoyong Yang
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation , The Key Laboratory of Chemical Biology of Fujian Province , State Key Laboratory of Physical Chemistry of Solid Surfaces , Collaborative Innovation Center of Chemistry for Energy Materials , Department of Chemical Engineering , Department of Chemical Biology , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China .
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de Abreu FB, Peterson JD, Amos CI, Wells WA, Tsongalis GJ. Effective quality management practices in routine clinical next-generation sequencing. Clin Chem Lab Med 2017; 54:761-71. [PMID: 26872315 DOI: 10.1515/cclm-2015-1190] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/14/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Molecular technologies have allowed laboratories to detect and establish the profiles of human cancers by identifying a variety of somatic variants. In order to improve personalized patient care, we have established a next-generation sequencing (NGS) test to screen for somatic variants in primary or advanced cancers. In this study, we describe the laboratory quality management program for NGS testing, and also provide an overview of the somatic variants identified in over 1000 patient samples as well as their implications in clinical practice. METHODS Over the past one-and-a-half years, our laboratory received a total of 1028 formalin-fixed, paraffin-embedded (FFPE) tumor tissues, which consisted of non-small-cell lung carcinomas (NSCLCs), colon adenocarcinomas, glioma/glioblastomas, melanomas, breast carcinomas, and other tumor types. During this time period, we implemented a series of quality control (QC) checks that included (1) pre-DNA extraction, (2) DNA quantification, (3) DNA quality, (4) library quantification, (5) post-emulsification PCR, and (6) post-sequencing metrics. At least 10 ng of genomic DNA (gDNA) were used to prepare barcoded libraries using the AmpliSeq CHPv2. Samples were multiplexed and sequenced on Ion Torrent 318 chips using the Ion PGM System. Variants were identified using the Variant Caller Plugin, and annotation and functional predictions were performed using the Golden Helix SVS. RESULTS A total of 1005 samples passed QC1-3, and following additional library preparation QC checkpoints, 877 samples were sequenced. Samples were classified into two categories: wild-type (127) and positive for somatic variants (750). Somatic variants were classified into clinically actionable (60%) and non-actionable (40%). CONCLUSIONS The use of NGS in routine clinical laboratory practice allowed for the detection of tumor profiles that are essential for the selection of targeted therapies and identification of applicable clinical trials, contributing to the improvement of personalized patient care in oncology.
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Ross JS, Gay LM. Comprehensive genomic sequencing and the molecular profiles of clinically advanced breast cancer. Pathology 2017; 49:120-132. [DOI: 10.1016/j.pathol.2016.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/09/2016] [Accepted: 11/09/2016] [Indexed: 02/06/2023]
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Next-Generation Sequencing Reveals Pathway Activations and New Routes to Targeted Therapies in Cutaneous Metastatic Melanoma. Am J Dermatopathol 2017; 39:1-13. [PMID: 28045747 DOI: 10.1097/dad.0000000000000729] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Comprehensive genomic profiling of clinical samples by next-generation sequencing (NGS) can identify one or more therapy targets for the treatment of metastatic melanoma (MM) with a single diagnostic test. METHODS NGS was performed on hybridization-captured, adaptor ligation-based libraries using DNA extracted from 4 formalin-fixed paraffin-embedded sections cut at 10 microns from 30 MM cases. The exons of 182 cancer-related genes were fully sequenced using the Illumina HiSeq 2000 at an average sequencing depth of 1098X and evaluated for genomic alterations (GAs) including point mutations, insertions, deletions, copy number alterations, and select gene fusions/rearrangements. Clinically relevant GAs (CRGAs) were defined as those identifying commercially available targeted therapeutics or therapies in registered clinical trials. RESULTS The 30 American Joint Committee on Cancer Stage IV MM included 17 (57%) male and 13 (43%) female patients with a mean age of 59.5 years (range 41-83 years). All MM samples had at least 1 GA, and an average of 2.7 GA/sample (range 1-7) was identified. The mean number of GA did not differ based on age or sex; however, on average, significantly more GAs were identified in amelanotic and poorly differentiated MM. GAs were most commonly identified in BRAF (12 cases, 40%), CDKN2A (6 cases, 20%), NF1 (8 cases, 26.7%), and NRAS (6 cases, 20%). CRGAs were identified in all patients, and represented 77% of the GA (64/83) detected. The median and mean CRGAs per tumor were 2 and 2.1, respectively (range 1-7). CONCLUSION Comprehensive genomic profiling of MM, using a single diagnostic test, uncovers an unexpectedly high number of CRGA that would not be identified by standard of care testing. Moreover, NGS has the potential to influence therapy selection and can direct patients to enter relevant clinical trials evaluating promising targeted therapies.
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Shahsiah R, DeKoning J, Samie S, Latifzadeh SZ, Kashi ZM. Validation of a next generation sequencing panel for detection of hotspot cancer mutations in a clinical laboratory. Pathol Res Pract 2016; 213:98-105. [PMID: 28049581 DOI: 10.1016/j.prp.2016.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/24/2016] [Accepted: 11/29/2016] [Indexed: 11/27/2022]
Abstract
Recent advances in sequencing technologies have enabled us to scrutinize the versatile underlying mechanisms of cancer more precisely. However, adopting these new sophisticated technologies is challenging for clinical labs as it involves complex workflows, and requires validation for diagnostic purposes. The aim of this work is towards the analytical validation of a next generation sequencing (NGS) panel for cancer hotspot mutation analysis. Characterized formalin-fixed paraffin-embedded (FFPE) samples including biopsy specimens and cell-lines were examined by NGS methods utilizing the Ion Torrent™ Oncomine™ Focus DNA Assay and the PGM™ platform. Important parameters for somatic mutations including the threshold for differentiation of a positive and a negative result, coverage, sensitivity, specificity, and limit of detection (LoD) were analyzed. Variant calls with coverage of <100x were found to be inaccurate. The limit of detection for identifying hotspot mutations was determined to be 4.3%. The sensitivity and specificity of the method were 96.1% and 97.8% respectively. No statistically significant difference was found between different gene targets in terms of performance of hotspot frequency measurement for the subset tested. In every validation study, the number of samples, the manner of sample selection, and the number and type of variants play a role in the outcome. Therefore, these parameters should be assessed according to the clinical needs of each laboratory undertaking the validation.
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Affiliation(s)
- Reza Shahsiah
- Cancer Research Center, Tehran University of Medical Sciences, Iran.
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Basic Molecular Pathology and Cytogenetics for Practicing Pathologists: Correlation With Morphology and With a Focus on Aspects of Diagnostic or Therapeutic Utility. Adv Anat Pathol 2016; 23:368-380. [PMID: 27740961 DOI: 10.1097/pap.0000000000000124] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Morphology, as confronted in the everyday practice, often correlates with specific molecular features, which have important implications not only in pathogenesis and in diagnosis but also in prognosis and therapy. Thus, it is important that the classical pathology includes a sound knowledge of molecular aspects of disease. These molecular concepts are complex and not easily understood by all engaged in the routine practice of histopathology. Thus, the aim of this review is to present a summary of most of the necessary concepts for pathologists involving molecular pathology and genetics, beginning from basic definitions and mechanisms to major abnormalities and the methodology to detect them, correlating at the same time, the specific morphologic features associated with every abnormality.
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Jang JS, Wang X, Vedell PT, Wen J, Zhang J, Ellison DW, Evans JM, Johnson SH, Yang P, Sukov WR, Oliveira AM, Vasmatzis G, Sun Z, Jen J, Yi ES. Custom Gene Capture and Next-Generation Sequencing to Resolve Discordant ALK Status by FISH and IHC in Lung Adenocarcinoma. J Thorac Oncol 2016; 11:1891-1900. [PMID: 27343444 PMCID: PMC5731243 DOI: 10.1016/j.jtho.2016.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/05/2016] [Accepted: 06/11/2016] [Indexed: 10/21/2022]
Abstract
INTRODUCTION We performed a genomic study in lung adenocarcinoma cases with discordant anaplastic lymphoma receptor tyrosine kinase gene (ALK) status by fluorescent in situ hybridization (FISH) and immunohistochemical (IHC) analysis. METHODS DNA from formalin-fixed paraffin-embedded tissues of 16 discordant (four FISH-positive/IHC-negative and 12 FISH-negative/IHC-positive) cases by Vysis ALK Break Apart FISH and ALK IHC testing (ALK1 clone) were subjected to whole gene capture and next-generation sequencing (NGS) of nine genes, including ALK, echinoderm microtubule associated protein like 4 gene (EML4), kinesin family member 5B gene (KIF5B), staphylococcal nuclease and tudor domain containing 1 gene (SND1), BRAF, ret proto-oncogene (RET), ezrin gene (EZR), ROS1, and telomerase reverse transcriptase (TERT). All discordant cases (except one FISH-negative/IHC-positive case without sufficient tissue) were analyzed by IHC with D5F3 antibody. In one case with fresh frozen tissue, whole transcriptome sequencing was also performed. Twenty-six concordant (16 FISH-positive/IHC-positive and 10 FISH-negative/IHC-negative) cases were included as controls. RESULTS In four ALK FISH-positive/IHC-negative cases, no EML4-ALK fusion gene was observed by NGS, but in one case using fresh frozen tissue, we identified EML4-baculoviral AIP repeat containing 6 gene (BIRC6) and AP2 associated kinase 1 gene (AAK1)-ALK fusion genes. Whole transcriptome sequencing revealed a highly expressed EML4-BIRC6 fusion transcript and a minimally expressed AAK1 transcript. Among the 12 FISH-negative/IHC-positive cases, no evidence of ALK gene rearrangement was detected by NGS. Eleven of 12 FISH-negative/IHC-positive cases detected by ALK1 clone were concordant by repeat ALK IHC with D5F3 antibody (i.e., FISH-negative/IHC-negative by D5F3 clone). Among the 16 ALK FISH-positive/IHC-positive positive controls, whole gene capture identified ALK gene fusion in 15 cases, including in one case with Huntington interacting protein 1 gene (HIP1)-ALK. No ALK fusion gene was observed in any of the 10 FISH-negative/IHC-negative cases. Other fusion genes involving ROS1, EZR, BRAF, and SND1 were also found. CONCLUSIONS ALK FISH results appeared to be false-positive in three of four FISH-positive/IHC-negative cases, whereas no false-negative ALK FISH case was identified among 12 ALK FISH-negative/IHC-positive cases by ALK1 clone, which was in keeping with the concordant FISH-negative/IHC-negative status by D5F3 clone. Our targeted whole gene capture approach using formalin-fixed paraffin embedded samples was effective for detecting rearrangements involving ALK and other actionable oncogenes.
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Affiliation(s)
- Jin Sung Jang
- Genome Analysis Core, Medical Genome Facility, Mayo Clinic, Rochester, Minnesota; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Xiaoke Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Peter T Vedell
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Ji Wen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jared M Evans
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Sarah H Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Ping Yang
- Division of Epidemiology, Mayo Clinic, Rochester, Minnesota
| | - William R Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Andre M Oliveira
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - George Vasmatzis
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Zhifu Sun
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Jin Jen
- Genome Analysis Core, Medical Genome Facility, Mayo Clinic, Rochester, Minnesota; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Eunhee S Yi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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Calabria I, Pedrola L, Berlanga P, Aparisi MJ, Sánchez-Izquierdo D, Cañete A, Cervera J, Millán JM, Castel V. El nuevo reto en oncología: la secuenciación NGS y su aplicación a la medicina de precisión. An Pediatr (Barc) 2016; 85:273.e1-273.e7. [DOI: 10.1016/j.anpedi.2016.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 05/12/2016] [Indexed: 11/29/2022] Open
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The new challenge in oncology: Next-generation sequencing and its application in precision medicine. An Pediatr (Barc) 2016. [DOI: 10.1016/j.anpede.2016.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Proctor A, Zigoneanu IG, Wang Q, Sims CE, Lawrence DS, Allbritton NL. Development of a protease-resistant reporter to quantify BCR-ABL activity in intact cells. Analyst 2016; 141:6008-6017. [PMID: 27704073 PMCID: PMC5111365 DOI: 10.1039/c6an01378c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A peptidase-resistant ABL kinase substrate was developed by identifying protease-susceptible bonds on an ABL substrate peptide and replacing flanking amino acids with non-native amino acids. After an iterative design process, the lead, or designed, peptide X-A possesses a six-fold longer life in a cytosolic lysate than that of the starting peptide. The catalytic efficiency (kcat/KM) of purified ABL kinase for the lead peptide (125 s-1 μM-1) is similar to that of the starting peptide (103 s-1 μM-1) demonstrating preservation of the peptide's ability to serve as a kinase substrate. When incubated in cytosolic lysates, the lead peptide is slowly degraded into 4 fragments over time. In contrast, when loaded into intact cells, the peptide is metabolized into 5 fragments, with only 2 of the fragments corresponding to those in the lysate. Thus the two environments possess differing peptidase activities, which must be accounted for when designing peptidase-resistant peptides. In both settings, the substrate is phosphorylated by BCR-ABL providing a readout of BCR-ABL activity. A small panel of tyrosine kinase inhibitors verified the substrate's specificity for BCR-ABL/ABL kinase activity in both lysates and cells in spite of the multitude of other kinases present. The designed peptide X-A acts as a long-lived BCR-ABL kinase reporter in the leukemic cells possessing the BCR-ABL mutation.
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Affiliation(s)
- Angela Proctor
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Imola G Zigoneanu
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599, USA, and North Carolina State University, Raleigh, NC, 27695, USA
| | - Qunzhao Wang
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Christopher E Sims
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - David S Lawrence
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Chemical Biology and Medicinal Chemistry, School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Nancy L Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599, USA, and North Carolina State University, Raleigh, NC, 27695, USA
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Clinical Applications of Next-Generation Sequencing in Cancer Diagnosis. Pathol Oncol Res 2016; 23:225-234. [PMID: 27722982 DOI: 10.1007/s12253-016-0124-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 10/04/2016] [Indexed: 12/22/2022]
Abstract
With the advancement and improvement of new sequencing technology, next-generation sequencing (NGS) has been applied increasingly in cancer genomics research fields. More recently, NGS has been adopted in clinical oncology to advance personalized treatment of cancer. NGS is utilized to novel diagnostic and rare cancer mutations, detection of translocations, inversions, insertions and deletions, detection of copy number variants, detect familial cancer mutation carriers, provide the molecular rationale for appropriate targeted, therapeutic and prognostic. NGS holds many advantages, such as the ability to fully sequence all types of mutations for a large number of genes (hundreds to thousands) and the sensitivity, speed in a single test at a relatively low cost compared to be other sequencing modalities. Here we described the technology, methods and applications that can be immediately considered and some of the challenges that lie ahead.
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Microfluidic Devices for Forensic DNA Analysis: A Review. BIOSENSORS-BASEL 2016; 6:bios6030041. [PMID: 27527231 PMCID: PMC5039660 DOI: 10.3390/bios6030041] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/07/2016] [Accepted: 07/25/2016] [Indexed: 12/16/2022]
Abstract
Microfluidic devices may offer various advantages for forensic DNA analysis, such as reduced risk of contamination, shorter analysis time and direct application at the crime scene. Microfluidic chip technology has already proven to be functional and effective within medical applications, such as for point-of-care use. In the forensic field, one may expect microfluidic technology to become particularly relevant for the analysis of biological traces containing human DNA. This would require a number of consecutive steps, including sample work up, DNA amplification and detection, as well as secure storage of the sample. This article provides an extensive overview of microfluidic devices for cell lysis, DNA extraction and purification, DNA amplification and detection and analysis techniques for DNA. Topics to be discussed are polymerase chain reaction (PCR) on-chip, digital PCR (dPCR), isothermal amplification on-chip, chip materials, integrated devices and commercially available techniques. A critical overview of the opportunities and challenges of the use of chips is discussed, and developments made in forensic DNA analysis over the past 10–20 years with microfluidic systems are described. Areas in which further research is needed are indicated in a future outlook.
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Endrullat C, Glökler J, Franke P, Frohme M. Standardization and quality management in next-generation sequencing. Appl Transl Genom 2016; 10:2-9. [PMID: 27668169 PMCID: PMC5025460 DOI: 10.1016/j.atg.2016.06.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/13/2016] [Accepted: 06/29/2016] [Indexed: 11/30/2022]
Abstract
DNA sequencing continues to evolve quickly even after > 30 years. Many new platforms suddenly appeared and former established systems have vanished in almost the same manner. Since establishment of next-generation sequencing devices, this progress gains momentum due to the continually growing demand for higher throughput, lower costs and better quality of data. In consequence of this rapid development, standardized procedures and data formats as well as comprehensive quality management considerations are still scarce. Here, we listed and summarized current standardization efforts and quality management initiatives from companies, organizations and societies in form of published studies and ongoing projects. These comprise on the one hand quality documentation issues like technical notes, accreditation checklists and guidelines for validation of sequencing workflows. On the other hand, general standard proposals and quality metrics are developed and applied to the sequencing workflow steps with the main focus on upstream processes. Finally, certain standard developments for downstream pipeline data handling, processing and storage are discussed in brief. These standardization approaches represent a first basis for continuing work in order to prospectively implement next-generation sequencing in important areas such as clinical diagnostics, where reliable results and fast processing is crucial. Additionally, these efforts will exert a decisive influence on traceability and reproducibility of sequence data.
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Key Words
- ABRF, Association of Biomolecular Resource Facilities
- BAM, binary alignment/map
- CAP, College of American Pathologist's
- CEN, European Committee for Standardization
- CLIA, Clinical Laboratory Improvement Amendments
- Data quality
- ERCC, External RNA Controls Consortium
- FDA, Food and Drug Administration
- FFPE, formalin-fixed, paraffin-embedded
- FMEA, failure mode and effects analysis
- GATK, genome analysis toolkit
- GSC, Genomic Standards Consortium
- Guideline
- HGP, Human Genome Project
- Indel, insertion or deletion
- MAQC, MicroArray Quality Control Project
- MIGS, minimum information about a genome sequence
- MOL, molecular pathology checklist
- NGS, next-generation sequencing
- NIST, National Institute of Standards and Technology
- NTC, no-template control
- Nex-StoCT, next generation sequencing — standardization of clinical testing
- Next-generation sequencing
- PT, proficiency testing
- QA, quality assurance
- QC, quality control
- QM, quality management
- QMS, quality management system
- Quality management
- RIN, RNA integrity number
- SAM, sequence alignment/map
- SEQC, sequencing quality control
- SNP, single nucleotide polymorphism
- SOP, standard operating procedure
- Standardization
- TN, technical note
- VCF, variant call format
- Validation
- ddPCR, digital droplet PCR
- mtDNA, mitochondrial DNA
- qPCR, quantitative PCR
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Affiliation(s)
- Christoph Endrullat
- Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Jörn Glökler
- Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Philipp Franke
- Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Marcus Frohme
- Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
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Marino-Enriquez A. Advances in the Molecular Analysis of Soft Tissue Tumors and Clinical Implications. Surg Pathol Clin 2016; 8:525-37. [PMID: 26297069 DOI: 10.1016/j.path.2015.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The emergence of high-throughput molecular technologies has accelerated the discovery of novel diagnostic, prognostic and predictive molecular markers. Clinical implementation of these technologies is expected to transform the practice of surgical pathology. In soft tissue tumor pathology, accurate interpretation of comprehensive genomic data provides useful diagnostic and prognostic information, and informs therapeutic decisions. This article reviews recently developed molecular technologies, focusing on their application to the study of soft tissue tumors. Emphasis is made on practical issues relevant to the surgical pathologist. The concept of genomically-informed therapies is presented as an essential motivation to identify targetable molecular alterations in sarcoma.
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Affiliation(s)
- Adrian Marino-Enriquez
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
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Ross JS, Wang K, Gay L, Otto GA, White E, Iwanik K, Palmer G, Yelensky R, Lipson DM, Chmielecki J, Erlich RL, Rankin AN, Ali SM, Elvin JA, Morosini D, Miller VA, Stephens PJ. Comprehensive Genomic Profiling of Carcinoma of Unknown Primary Site: New Routes to Targeted Therapies. JAMA Oncol 2016; 1:40-49. [PMID: 26182302 DOI: 10.1001/jamaoncol.2014.216] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
IMPORTANCE For carcinoma of unknown primary site (CUP), determining the primary tumor site may be uninformative and often does not improve outcome. OBJECTIVE To discover opportunities for targeted therapies in patients with CUP not currently searched for in routine practice. DESIGN, SETTING, AND PARTICIPANTS Comprehensive genomic profiling on 200 CUP formalin-fixed paraffin-embedded specimens (mean, 756× coverage) using the hybrid-capture-based FoundationOne assay at academic and community oncology clinics. MAIN OUTCOMES AND MEASURES Presence of targetable genomic alterations (GAs) in CUP and responses to targeted therapies. RESULTS There were 125 adenocarcinomas of unknown primary site (ACUPs) and 75 carcinomas of unknown primary site without features of adenocarcinoma (non-ACUPs). At least 1 GA was found in 192 (96%) of CUP specimens, with a mean (SD) of 4.2 (2.8) GAs per tumor. The most frequent GAs were in TP53 (110 [55%]), KRAS (40 [20%]), CDKN2A (37 [19%]), MYC (23 [12%]), ARID1A (21 [11%]), MCL1 (19 [10%]), PIK3CA (17 [9%]), ERBB2 (16 [8%]), PTEN (14 [7%]), EGFR (12 [6%]), SMAD4 (13 [7%]), STK11 (13 [7%]), SMARCA4 (12 [6%]), RB1 (12 [6%]), RICTOR (12 [6%]), MLL2 (12 [6%]), BRAF (11 [6%]), and BRCA2 (11 [6%]). One or more potentially targetable GAs were identified in 169 of 200 (85%) CUP specimens. Mutations or amplifications of ERBB2 were more frequent in ACUPs (13 [10%]) than in non-ACUPs (3 [4%]). Alterations of EGFR (10 [8%] vs 2 [3%]) and BRAF (8 [6%] vs 3 [4%]) were more common in ACUPs than in non-ACUPs. Strikingly, clinically relevant alterations in the receptor tyrosine kinase (RTK)/Ras signaling pathway including alterations in ALK, ARAF, BRAF, EGFR, FGFR1, FGFR2, KIT, KRAS, MAP2K1, MET, NF1, NF2, NRAS, RAF1, RET, and ROS1 were found in 90 (72%) ACUPs but in only 29 (39%) non-ACUPs (P < .001). CONCLUSIONS AND RELEVANCE Almost all CUP samples harbored at least 1 clinically relevant GA with potential to influence and personalize therapy. The ACUP tumors were more frequently driven by GAs in the highly druggable RTK/Ras/mitogen-activated protein kinase (MAPK) signaling pathway than the non-ACUP tumors. Comprehensive genomic profiling can identify novel treatment paradigms to address the limited options and poor prognoses of patients with CUP.
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Affiliation(s)
- Jeffrey S Ross
- Foundation Medicine Inc, Cambridge, Massachusetts.,Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York
| | - Kai Wang
- Foundation Medicine Inc, Cambridge, Massachusetts
| | - Laurie Gay
- Foundation Medicine Inc, Cambridge, Massachusetts
| | - Geoff A Otto
- Foundation Medicine Inc, Cambridge, Massachusetts
| | - Emily White
- Foundation Medicine Inc, Cambridge, Massachusetts
| | - Kiel Iwanik
- Foundation Medicine Inc, Cambridge, Massachusetts
| | - Gary Palmer
- Foundation Medicine Inc, Cambridge, Massachusetts
| | | | | | | | | | | | - Siraj M Ali
- Foundation Medicine Inc, Cambridge, Massachusetts
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Sasaki Y, Tamura M, Koyama R, Nakagaki T, Adachi Y, Tokino T. Genomic characterization of esophageal squamous cell carcinoma: Insights from next-generation sequencing. World J Gastroenterol 2016; 22:2284-2293. [PMID: 26900290 PMCID: PMC4735002 DOI: 10.3748/wjg.v22.i7.2284] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/29/2015] [Accepted: 12/21/2015] [Indexed: 02/06/2023] Open
Abstract
Two major types of cancer occur in the esophagus: squamous cell carcinoma, which is associated with chronic smoking and alcohol consumption, and adenocarcinoma, which typically arises in gastric reflux-associated Barrett’s esophagus. Although there is increasing incidence of esophageal adenocarcinoma in Western counties, esophageal squamous cell carcinoma (ESCC) accounts for most esophageal malignancies in East Asia, including China and Japan. Technological advances allowing for massively parallel, high-throughput next-generation sequencing (NGS) of DNA have enabled comprehensive characterization of somatic mutations in large numbers of tumor samples. Recently, several studies were published in which whole exome or whole genome sequencing was performed in ESCC tumors and compared with matched normal DNA. Mutations were validated in several genes, including in TP53, CDKN2A, FAT1, NOTCH1, PIK3CA, KMT2D and NFE2L2, which had been previously implicated in ESCC. Several new recurrent alterations have also been identified in ESCC. Combining the clinicopathological characteristics of patients with information obtained from NGS studies may lead to the development of effective diagnostic and therapeutic approaches for ESCC. As this research becomes more prominent, it is important that gastroenterologist become familiar with the various NGS technologies and the results generated using these methods. In the present study, we describe recent research approaches using NGS in ESCC.
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Abstract
Experts increasingly recognize the hypothesis of "over-diagnosis" as the main factor of the raising incidence of thyroid cancers (TC). The detection of multiple microtumors, mainly of a papillary type, at a sub-clinical stage, with the use of sensitive detection methods supports this hypothesis. However, the intensive management and monitoring of these cancers failed to reduce mortality. Environmental and other risk factors cannot provide a sufficient explanation, as previously thought. In this context, the use of improved tools is needed, and the most promising perspective lies in molecular biology applied to thyroid cancer for diagnosis, evaluation of prognosis and treatment. The next generation sequencing (NGS) has demonstrated its diagnostic performances in recent clinical trials. Its interest in cases with indeterminate cytology is demonstrated and should help better targeting surgical indications. Its promising prognostic and therapeutic applications must be confirmed by additional studies. The integration of NGS in current practice should have a real medical, economic and scientific impact. Indeed, the exponential increase in our knowledge of molecular mechanisms of thyroid tumorigenesis strengthens the will to "reclassify" these cancers into molecular rather than histological subtypes, in order to offer patients more specific and targeted treatment.
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Lund HL, Hughesman CB, McNeil K, Clemens S, Hocken K, Pettersson R, Karsan A, Foster LJ, Haynes C. Initial diagnosis of chronic myelogenous leukemia based on quantification of M-BCR status using droplet digital PCR. Anal Bioanal Chem 2015; 408:1079-94. [DOI: 10.1007/s00216-015-9204-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 11/11/2015] [Accepted: 11/18/2015] [Indexed: 01/25/2023]
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Tam AL, Lim HJ, Wistuba II, Tamrazi A, Kuo MD, Ziv E, Wong S, Shih AJ, Webster RJ, Fischer GS, Nagrath S, Davis SE, White SB, Ahrar K. Image-Guided Biopsy in the Era of Personalized Cancer Care: Proceedings from the Society of Interventional Radiology Research Consensus Panel. J Vasc Interv Radiol 2015; 27:8-19. [PMID: 26626860 DOI: 10.1016/j.jvir.2015.10.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 10/23/2015] [Accepted: 10/23/2015] [Indexed: 02/07/2023] Open
Affiliation(s)
- Alda L Tam
- Departments of Interventional Radiology, Houston, Texas.
| | - Howard J Lim
- Division of Medical Oncology, University of British Columbia, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Anobel Tamrazi
- Division of Vascular and Interventional Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michael D Kuo
- Department of Radiological Sciences, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Etay Ziv
- Departments of Interventional Radiology and Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Stephen Wong
- Department of Systems Medicine & Bioengineering, Houston Methodist Research Institute, Houston, Texas
| | - Albert J Shih
- Departments of Mechanical and Biomechanical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Robert J Webster
- Department of Mechanical Engineering, Vanderbilt University, Nashville, Tennessee
| | - Gregory S Fischer
- Automation and Interventional Medicine Robotics Lab, Department of Mechanical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts
| | - Sunitha Nagrath
- Chemical and Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Suzanne E Davis
- Division of Cancer Medicine, Research Planning and Development, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Sarah B White
- Department of Systems Medicine & Bioengineering, Houston Methodist Research Institute, Houston, Texas; Departments of Radiology, Neuroscience, Pathology & Laboratory Medicine, Weill Cornell Medical College of Cornell University, New York, New York; Division of Vascular and Interventional Radiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Kamran Ahrar
- Departments of Interventional Radiology, Houston, Texas
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44
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Next generation sequencing in cardiomyopathy: towards personalized genomics and medicine. Mol Biol Rep 2015; 41:4881-8. [PMID: 24908287 DOI: 10.1007/s11033-014-3418-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Next generation sequencing (NGS) is perhaps one of the most exciting advances in the field of life sciences and biomedical research in the last decade. With the availability of massive parallel sequencing, human DNA blueprint can be decoded to explore the hidden information with reduced time and cost. This technology has been used to understand the genetic aspects of various diseases including cardiomyopathies. Mutations for different cardiomyopathies have been identified and cataloging mutations on phenotypic basis are underway and are expected to lead to new discoveries that may translate to novel diagnostic, prognostic and therapeutic targets. With ease in handling NGS, cost effectiveness and fast data output, NGS is now considered as a diagnostic tool for cardiomyopathy by providing targeted gene sequencing. In addition to the number of genetic variants that are identified in cardiomyopathies, there is a need of quicker and easy way to screen multiple genes associated with the disease. In this review, an attempt has been made to explain the NGS technology, methods and applications in cardiomyopathies and their perspective in clinical practice and challenges which are to be addressed.
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45
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Weyant GW, Wisotzkey JD, Benko FA, Donaldson KJ. BRAF mutation testing in solid tumors: a methodological comparison. J Mol Diagn 2015; 16:481-5. [PMID: 25132480 DOI: 10.1016/j.jmoldx.2014.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 05/05/2014] [Accepted: 05/12/2014] [Indexed: 02/07/2023] Open
Abstract
Solid tumor genotyping has become standard of care for the characterization of proto-oncogene mutational status, which has traditionally been accomplished with Sanger sequencing. However, companion diagnostic assays and comparable laboratory-developed tests are becoming increasingly popular, such as the cobas 4800 BRAF V600 Mutation Test and the INFINITI KRAS-BRAF assay, respectively. This study evaluates and validates the analytical performance of the INFINITI KRAS-BRAF assay and compares concordance of BRAF status with two reference assays, the cobas test and Sanger sequencing. DNA extraction from FFPE tissue specimens was performed followed by multiplex PCR amplification and fluorescent label incorporation using allele-specific primer extension. Hybridization to a microarray, signal detection, and analysis were then performed. The limits of detection were determined by testing dilutions of mutant BRAF alleles within wild-type background DNA, and accuracy was calculated based on these results. The INFINITI KRAS-BRAF assay produced 100% concordance with the cobas test and Sanger sequencing and had sensitivity equivalent to the cobas assay. The INFINITI assay is repeatable with at least 95% accuracy in the detection of mutant and wild-type BRAF alleles. These results confirm that the INFINITI KRAS-BRAF assay is comparable to traditional sequencing and the Food and Drug Administration-approved companion diagnostic assay for the detection of BRAF mutations.
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Affiliation(s)
- Grace W Weyant
- Department of Pathology, Penn State College of Medicine-Hershey Medical Center, Hershey, Pennsylvania.
| | | | - Floyd A Benko
- Department of Pathology, Penn State College of Medicine-Hershey Medical Center, Hershey, Pennsylvania
| | - Keri J Donaldson
- Department of Pathology, Penn State College of Medicine-Hershey Medical Center, Hershey, Pennsylvania
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Gemoll T, Meyer R, Habermann JK. Applying Genomics and Proteomics in Translational Surgical Oncology Research. Eur Surg Res 2015; 55:184-97. [PMID: 26339997 DOI: 10.1159/000438860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/20/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND Translational surgical research can range from investigating clinically oriented basic pathophysiological research via the correlation of molecular findings with a patient's clinical outcome to conducting treatment response studies. Herein, the specialist's opinion as a 'surgeon scientist' plays a pivotal role, e.g. in planning experimental setups focusing on the clinically most relevant needs. SUMMARY AND KEY MESSAGES: This review provides a survey of genomic and proteomic technologies and gives an up-to-date overview of those studies applying these technologies exemplarily in colorectal cancer-based biomarker research. Although current results are promising, future validation studies within multicenter networks are required to promote the translation of 'omics' from bench to bedside. In this endeavor, departments of surgery and institutes of experimental surgery together should play a fundamental role. The program for 'clinician scientists' recently launched by the German Research Society (DFG) could be one tool to promote interdisciplinary networks and surgeons' impact on translational research.
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Affiliation(s)
- Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lx00FC;beck and University Medical Center Schleswig-Holstein (UKSH), Lx00FC;beck, Germany
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47
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Laissue P. Aetiological coding sequence variants in non-syndromic premature ovarian failure: From genetic linkage analysis to next generation sequencing. Mol Cell Endocrinol 2015; 411:243-57. [PMID: 25960166 DOI: 10.1016/j.mce.2015.05.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 04/14/2015] [Accepted: 05/04/2015] [Indexed: 01/19/2023]
Abstract
Premature ovarian failure (POF) is a frequent pathology affecting 1-1.5% of women under 40 years old. Despite advances in diagnosing and treating human infertility, POF is still classified as being idiopathic in 50-80% of cases, strongly suggesting a genetic origin for the disease. Different types of autosomal and X-linked genetic anomalies can originate the phenotype in syndromic and non-syndromic POF cases. Particular interest has been focused on research into non-syndromic POF causative coding variants during the past two decades. This has been based on the assumption that amino acid substitutions might modify the intrinsic physicochemical properties of functional proteins, thereby inducing pathological phenotypes. In this case, a restricted number of mutations might originate the disease. However, like other complex pathologies, POF might result from synergistic/compensatory effects caused by several low-to-mildly drastic mutations which have frequently been classified as non-functional SNPs. Indeed, reproductive phenotypes can be considered as quantitative traits resulting from the subtle interaction of many genes. Although numerous sequencing projects have involved candidate genes, only a few coding mutations explaining a low percentage of cases have been described. Such apparent failure to identify aetiological coding sequence variations might have been due to the inherent molecular complexity of mammalian reproduction and to the difficulty of simultaneously analysing large genomic regions by Sanger sequencing. The purpose of this review is to present the molecular and cellular effects caused by non-synonymous mutations which have been formally associated, by functional tests, with the aetiology of hypergonadotropic non-syndromic POF. Considerations have also been included regarding the polygenic nature of reproduction and POF, as well as future approaches for identifying novel aetiological genes based on next generation sequencing (NGS).
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Affiliation(s)
- Paul Laissue
- Unidad de Genética, Grupo GENIUROS, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia.
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48
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Fong KM, Daniels M, Goh F, Yang IA, Bowman RV. The current and future roles of genomics. Lung Cancer 2015. [DOI: 10.1183/2312508x.10009614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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49
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Gurzadyan VG, Yan H, Vlahovic G, Kashin A, Killela P, Reitman Z, Sargsyan S, Yegorian G, Milledge G, Vlahovic B. Detecting somatic mutations in genomic sequences by means of Kolmogorov-Arnold analysis. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150143. [PMID: 26361546 PMCID: PMC4555851 DOI: 10.1098/rsos.150143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/27/2015] [Indexed: 06/05/2023]
Abstract
The Kolmogorov-Arnold stochasticity parameter technique is applied for the first time to the study of cancer genome sequencing, to reveal mutations. Using data generated by next-generation sequencing technologies, we have analysed the exome sequences of brain tumour patients with matched tumour and normal blood. We show that mutations contained in sequencing data can be revealed using this technique, thus providing a new methodology for determining subsequences of given length containing mutations, i.e. its value differs from those of subsequences without mutations. A potential application for this technique involves simplifying the procedure of finding segments with mutations, speeding up genomic research and accelerating its implementation in clinical diagnostics. Moreover, the prediction of a mutation associated with a family of frequent mutations in numerous types of cancers based purely on the value of the Kolmogorov function indicates that this applied marker may recognize genomic sequences that are in extremely low abundance and can be used in revealing new types of mutations.
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Affiliation(s)
- V. G. Gurzadyan
- NSF Computational Center of Research Excellence and NASA University Research Center for Aerospace Device, NCCU, Durham, NC, USA
- Yerevan Physics Institute and Yerevan State University, Yerevan, Armenia
| | - H. Yan
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center at Duke, and Pediatric Brain Tumor Foundation Institute at Duke, Durham, NC, USA
| | - G. Vlahovic
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center at Duke, and Pediatric Brain Tumor Foundation Institute at Duke, Durham, NC, USA
| | - A. Kashin
- Yerevan Physics Institute and Yerevan State University, Yerevan, Armenia
| | - P. Killela
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center at Duke, and Pediatric Brain Tumor Foundation Institute at Duke, Durham, NC, USA
| | - Z. Reitman
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center at Duke, and Pediatric Brain Tumor Foundation Institute at Duke, Durham, NC, USA
| | - S. Sargsyan
- Yerevan Physics Institute and Yerevan State University, Yerevan, Armenia
| | - G. Yegorian
- Yerevan Physics Institute and Yerevan State University, Yerevan, Armenia
| | - G. Milledge
- NSF Computational Center of Research Excellence and NASA University Research Center for Aerospace Device, NCCU, Durham, NC, USA
| | - B. Vlahovic
- NSF Computational Center of Research Excellence and NASA University Research Center for Aerospace Device, NCCU, Durham, NC, USA
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Abstract
PURPOSE AND DESIGN In recent years, there have been dramatic improvements in the diagnosis and treatment of patients with melanoma. The development of molecular markers and associated targeted therapies have given new hope to subsets of patients with advanced disease. Here we discuss the most important advances in molecular targeted therapy and how these developments are likely to affect the practice of the clinical surgeon. RESULTS AND CONCLUSIONS Germ-line and somatic mutations are common in melanoma and provide prognostic information that can now be harnessed to provide a more personalized approach to cancer treatment. BRAF mutation at the V600 position is the most commonly identified mutation in patients with melanoma. Treatment with targeted inhibitors in patients with BRAF-mutant melanoma has afforded dramatic responses in about half of selected patients. Unfortunately, disease control is not durable and recurrences are common. We predict an increasing role for the surgeon in the multidisciplinary treatment of patients with metastatic disease, as well as a role for molecular profiling in patients with high-risk early stage disease. Further, we are only beginning to understand the prognostic significance of various gene mutations in patients with melanoma.
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Affiliation(s)
- Danielle K DePeralta
- Division of Surgical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Genevieve M Boland
- Division of Surgical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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