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Penkova A, Kuziakova O, Gulaia V, Tiasto V, Goncharov NV, Lanskikh D, Zhmenia V, Baklanov I, Farniev V, Kumeiko V. Comprehensive clinical assays for molecular diagnostics of gliomas: the current state and future prospects. Front Mol Biosci 2023; 10:1216102. [PMID: 37908227 PMCID: PMC10613994 DOI: 10.3389/fmolb.2023.1216102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/04/2023] [Indexed: 11/02/2023] Open
Abstract
Glioma is one of the most intractable types of cancer, due to delayed diagnosis at advanced stages. The clinical symptoms of glioma are unclear and due to a variety of glioma subtypes, available low-invasive testing is not effective enough to be introduced into routine medical laboratory practice. Therefore, recent advances in the clinical diagnosis of glioma have focused on liquid biopsy approaches that utilize a wide range of techniques such as next-generation sequencing (NGS), droplet-digital polymerase chain reaction (ddPCR), and quantitative PCR (qPCR). Among all techniques, NGS is the most advantageous diagnostic method. Despite the rapid cheapening of NGS experiments, the cost of such diagnostics remains high. Moreover, high-throughput diagnostics are not appropriate for molecular profiling of gliomas since patients with gliomas exhibit only a few diagnostic markers. In this review, we highlighted all available assays for glioma diagnosing for main pathogenic glioma DNA sequence alterations. In the present study, we reviewed the possibility of integrating routine molecular methods into the diagnosis of gliomas. We state that the development of an affordable assay covering all glioma genetic aberrations could enable early detection and improve patient outcomes. Moreover, the development of such molecular diagnostic kits could potentially be a good alternative to expensive NGS-based approaches.
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Affiliation(s)
- Alina Penkova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Olga Kuziakova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Gulaia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vladlena Tiasto
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Nikolay V. Goncharov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Daria Lanskikh
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Zhmenia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Ivan Baklanov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Vladislav Farniev
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vadim Kumeiko
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
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Novel Systemic Treatment Modalities Including Immunotherapy and Molecular Targeted Therapy for Recurrent and Metastatic Head and Neck Squamous Cell Carcinoma. Int J Mol Sci 2022; 23:ijms23147889. [PMID: 35887235 PMCID: PMC9320653 DOI: 10.3390/ijms23147889] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/08/2022] [Accepted: 07/14/2022] [Indexed: 12/15/2022] Open
Abstract
Head and neck squamous cell carcinomas (HNSCCs) are the sixth most common cancers worldwide. More than half of patients with HNSCC eventually experience disease recurrence and/or metastasis, which can threaten their long-term survival. HNSCCs located in the oral cavity and larynx are usually associated with tobacco and/or alcohol use, whereas human papillomavirus (HPV) infection, particularly HPV16 infection, is increasingly recognized as a cause of oropharyngeal HNSCC. Despite clinical, histologic, and molecular differences between HPV-positive and HPV-negative HNSCCs, current treatment approaches are the same. For recurrent disease, these strategies include chemotherapy, immunotherapy with PD-1-inhibitors, or a monoclonal antibody, cetuximab, that targets epidermal growth factor; these therapies can be administered either as single agents or in combination. However, these treatment strategies carry a high risk of toxic side effects; therefore, more effective and less toxic treatments are needed. The landscape of HNSCC therapy is changing significantly; numerous clinical trials are underway to test novel therapeutic options like adaptive cellular therapy, antibody-drug conjugates, new targeted therapy agents, novel immunotherapy combinations, and therapeutic vaccines. This review helps in understanding the various developments in HNSCC therapy and sheds light on the path ahead in terms of further research in this field.
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Sharifi Alishah M, Darvishzadeh R, Ahmadabadi M, Piri Kashtiban Y, Hasanpur K. Identification of differentially expressed genes in salt-tolerant oilseed sunflower (Helianthus annuus L.) genotype by RNA sequencing. Mol Biol Rep 2022; 49:3583-3596. [PMID: 35119610 DOI: 10.1007/s11033-022-07198-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/26/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Sunflower (Helianthus annuus L.) is widely planted as an oilseed crop worldwide. Salt stress is one of the major abiotic stresses that negatively affect crop growth and productivity. To counter the negative impact of salt stress, plants have developed avoidance and tolerance mechanisms. Developing salt-tolerant genotypes requires understanding the molecular basis of adaptive mechanisms in depth. Although using model plants i.e., Arabidopsis has improved our understanding of salt tolerant mechanisms, the relative impotence and regulation mechanisms vary among plant species due to differences in genetic and metabolic backgrounds. On the other hand, sunflower is a highly polymorphic plant due to its cross-pollinated behavior which provides different salt-tolerant genotypes available for comparative analyses. METHODS AND RESULTS In order to gain a better view of molecular mechanisms involved in salt tolerance in sunflower, RNA sequencing analysis was realized by evaluating a tolerant genotype (AS5305) with two biological replicates under control and salt stress conditions in a controlled environment. Salinity stress was applied from NaCl resource at the 8-leaf stage and samplings were done at 24 h post salt stress application. Sequencing data were analyzed using tuxedo software suite. Blast2GO software and the KEGG database were used to identify the functional tasks of each of the assembled transcripts. Analysis of genes with robust expression (i.e., with FPKM > 1 in at least one sample) revealed a total of 121 significantly expressed genes between the saline-stressed and control samples. The differential expression of 11 genes was confirmed by real-time PCR. In the following, the cDNA of MYB44 as one of the selected candidate genes involved in salt tolerance was isolated, cloned, and sequenced for comparison. CONCLUSIONS Overall, the results of the current study may pave the way for the accurate selection of genes involved in salinity to be used in molecular-genetics-assisted breeding programs. In addition, making use of the identified genes may help relieve the damages arising from the salt stress in sunflowers.
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Affiliation(s)
- Masoumeh Sharifi Alishah
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Reza Darvishzadeh
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran. .,Department of Agricultural Biotechnology, Institute of Biotechnology, Urmia University, Urmia, Iran.
| | - Mohammad Ahmadabadi
- Department Agricultural Biotechnology, Faculty of Agriculture, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Yaser Piri Kashtiban
- Department of Agricultural Biotechnology, National Center of Genetic Engineering, Tehran, Iran
| | - Karim Hasanpur
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
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Farah CS. Molecular landscape of head and neck cancer and implications for therapy. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:915. [PMID: 34164549 PMCID: PMC8184465 DOI: 10.21037/atm-20-6264] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Head and neck squamous cell carcinomas (HNSCC) arising from the oral cavity, pharynx, and larynx constitute the 6th most common human cancer. Human papillomavirus (HPV)-positive tumours are distinct from HPV-negative counterparts, with HPV status affording clear clinical utility, prognostic benefit and better treatment outcomes. In contrast to their HPV-positive counterparts, HPV-negative tumours are characterized by high mutational load and chromosomal aberrations, with varying copy number alteration (CNA) profiles. HNSCC are distinct tumours at the chromosomal, gene and expression levels, with additional insight gained from immune profiling. Based on mutational analyses, HNSCC are categorized as HPV-positive, HPV-negative CNA-silent, and HPV-negative CNA-high tumours. Furthermore, gene expression profiling segregates these tumours into atypical, classical, basal, and mesenchymal, with clear differences observed between tumours of the oral cavity, oropharynx, hypopharynx and larynx. Additional immune profiling further classifies tumours as either immune-active or immune-exhausted. The clinical utility and impact of these tumour molecular subtypes however remains to be determined. HNSCC harbor high levels of somatic mutations. They display loss at 3p and 18q and gain at 3q and 8q, with mutations in CDKN2A, TP53, CCND1, EGFR, PIK3CA, PTEN, NOTCH1, NSD1, FAT1, AJUBA and KMT2D. Important pathways include the p53 and RB pathways which are involved in cell cycle control and are frequently lost in HPV-negative tumours, the WNT-β-catenin pathway related to the mesenchymal subtype and smoking etiology, and the PI3K pathway which includes the most common genetic alteration in HPV-positive HNSCC. Understanding the mutational, genomic and transcriptomic landscape of HNSCC has leveraged better therapeutic approaches to manage this group of diseases, and it is hoped that additional insight into the molecular subtypes of HNSCC and its specific subsites will further drive improved strategies to stratify and treat patients with this debilitating disease.
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Affiliation(s)
- Camile S Farah
- Australian Centre for Oral Oncology Research & Education, Nedlands, WA, Australia.,Oral, Maxillofacial and Dental Surgery, Fiona Stanley Hospital, Murdoch WA, Australia.,Head and Neck Pathology, Australian Clinical Labs, Subiaco WA, Australia.,Genomics for Life, Brisbane, QLD, Australia
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Exome sequencing of oral leukoplakia and oral squamous cell carcinoma implicates DNA damage repair gene defects in malignant transformation. Oral Oncol 2019; 96:42-50. [PMID: 31422212 DOI: 10.1016/j.oraloncology.2019.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/28/2019] [Accepted: 07/05/2019] [Indexed: 12/19/2022]
Abstract
OBJECTIVES To map the genomic pathways of patients with oral leukoplakia (OLK) which transformed to cancer (progressive) and those which did not (non-progressive), and to compare their exomic profiles. MATERIALS AND METHODS Whole exome sequencing was performed on 42 sequential samples from five progressive and eight non-progressive patients. Association of genomic variant frequencies with progression or lesion severity were analysed by non-parametric tests (Kruskal-Wallis and Mann-Whitney-Wilcoxon) and multivariate sparse partial least squares discriminant analysis (sPLS-DA). Enrichment analysis was used to characterise the effect of mutations upon biological pathways. Confirmatory studies used qPCR and immunohistochemistry. RESULTS Using sPLS-DA, the variant frequency of a small number of genes could be used to classify the samples based on lesion severity or progressive status. Enrichment analysis showed that DNA damage repair gene related pathways were highly impacted in lesions which progressed to cancer. Multivariate analysis of a set of 148 DNA damage repair genes could be used to classify progressive lesions using mutation frequency. BRCA1, BRCA2 and other double strand break (DSB) repair Fanconi anaemia (FA)/BRCA pathway genes were prominent contributors to this classification. CONCLUSION Patients with progressive and non-progressive OLK can be differentiated using the frequency of exomic variants, particularly in DNA damage repair pathway genes. To our knowledge, this is the first report of FA/BRCA (DSB) pathway involvement in malignant transformation of OLK to oral squamous cell carcinoma (OSCC).
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Iliescu FS, Poenar DP, Yu F, Ni M, Chan KH, Cima I, Taylor HK, Cima I, Iliescu C. Recent advances in microfluidic methods in cancer liquid biopsy. BIOMICROFLUIDICS 2019; 13:041503. [PMID: 31431816 PMCID: PMC6697033 DOI: 10.1063/1.5087690] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 06/24/2019] [Indexed: 05/04/2023]
Abstract
Early cancer detection, its monitoring, and therapeutical prediction are highly valuable, though extremely challenging targets in oncology. Significant progress has been made recently, resulting in a group of devices and techniques that are now capable of successfully detecting, interpreting, and monitoring cancer biomarkers in body fluids. Precise information about malignancies can be obtained from liquid biopsies by isolating and analyzing circulating tumor cells (CTCs) or nucleic acids, tumor-derived vesicles or proteins, and metabolites. The current work provides a general overview of the latest on-chip technological developments for cancer liquid biopsy. Current challenges for their translation and their application in various clinical settings are discussed. Microfluidic solutions for each set of biomarkers are compared, and a global overview of the major trends and ongoing research challenges is given. A detailed analysis of the microfluidic isolation of CTCs with recent efforts that aimed at increasing purity and capture efficiency is provided as well. Although CTCs have been the focus of a vast microfluidic research effort as the key element for obtaining relevant information, important clinical insights can also be achieved from alternative biomarkers, such as classical protein biomarkers, exosomes, or circulating-free nucleic acids. Finally, while most work has been devoted to the analysis of blood-based biomarkers, we highlight the less explored potential of urine as an ideal source of molecular cancer biomarkers for point-of-care lab-on-chip devices.
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Affiliation(s)
- Florina S. Iliescu
- School of Applied Science, Republic Polytechnic, Singapore 738964, Singapore
| | - Daniel P. Poenar
- VALENS-Centre for Bio Devices and Signal Analysis, School of EEE, Nanyang Technological University, Singapore 639798, Singapore
| | - Fang Yu
- Singapore Institute of Manufacturing Technology, A*STAR, Singapore 138634, Singapore
| | - Ming Ni
- School of Biological Sciences and Engineering, Yachay Technological University, San Miguel de Urcuquí 100105, Ecuador
| | - Kiat Hwa Chan
- Division of Science, Yale-NUS College, Singapore 138527, Singapore
| | | | - Hayden K. Taylor
- Department of Mechanical Engineering, University of California, Berkeley, California 94720, USA
| | - Igor Cima
- DKFZ-Division of Translational Oncology/Neurooncology, German Cancer Consortium (DKTK), Heidelberg and University Hospital Essen, Essen 45147, Germany
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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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Ianov L, De Both M, Chawla MK, Rani A, Kennedy AJ, Piras I, Day JJ, Siniard A, Kumar A, Sweatt JD, Barnes CA, Huentelman MJ, Foster TC. Hippocampal Transcriptomic Profiles: Subfield Vulnerability to Age and Cognitive Impairment. Front Aging Neurosci 2017; 9:383. [PMID: 29276487 PMCID: PMC5727020 DOI: 10.3389/fnagi.2017.00383] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/07/2017] [Indexed: 01/11/2023] Open
Abstract
The current study employed next-generation RNA sequencing to examine gene expression differences related to brain aging, cognitive decline, and hippocampal subfields. Young and aged rats were trained on a spatial episodic memory task. Hippocampal regions CA1, CA3, and the dentate gyrus were isolated. Poly-A mRNA was examined using two different sequencing platforms, Illumina, and Ion Proton. The Illumina platform was used to generate seed lists of genes that were statistically differentially expressed across regions, ages, or in association with cognitive function. The gene lists were then retested using the data from the Ion Proton platform. The results indicate hippocampal subfield differences in gene expression and point to regional differences in vulnerability to aging. Aging was associated with increased expression of immune response-related genes, particularly in the dentate gyrus. For the memory task, impaired performance of aged animals was linked to the regulation of Ca2+ and synaptic function in region CA1. Finally, we provide a transcriptomic characterization of the three subfields regardless of age or cognitive status, highlighting and confirming a correspondence between cytoarchitectural boundaries and molecular profiling.
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Affiliation(s)
- Lara Ianov
- Departments of Neuroscience and Genetics and Genomics Program, Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, United States.,Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Matt De Both
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Monica K Chawla
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, United States
| | - Asha Rani
- Departments of Neuroscience and Genetics and Genomics Program, Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, United States
| | - Andrew J Kennedy
- Evelyn F. McKnight Brain Institute, University of Alabama, Birmingham, AL, United States
| | - Ignazio Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Jeremy J Day
- Evelyn F. McKnight Brain Institute, University of Alabama, Birmingham, AL, United States
| | - Ashley Siniard
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Ashok Kumar
- Departments of Neuroscience and Genetics and Genomics Program, Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, United States
| | - J David Sweatt
- Evelyn F. McKnight Brain Institute, University of Alabama, Birmingham, AL, United States.,Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
| | - Carol A Barnes
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, United States.,Departments of Psychology, Neurology and Neuroscience, University of Arizona, Tucson, AZ, United States
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States.,Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, United States
| | - Thomas C Foster
- Departments of Neuroscience and Genetics and Genomics Program, Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, United States
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Next-Generation Sequencing in Cancer Diagnostics. J Mol Diagn 2016; 18:813-816. [PMID: 27664753 DOI: 10.1016/j.jmoldx.2016.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 08/23/2016] [Indexed: 12/14/2022] Open
Abstract
This commentary highlights the article by Misyura et al that underscores the use of next-generation sequencing platforms for detection and verification of somatic variants.
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10
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Wiley GB, Kelly JA, Gaffney PM. Use of next-generation DNA sequencing to analyze genetic variants in rheumatic disease. Arthritis Res Ther 2015; 16:490. [PMID: 25789374 PMCID: PMC4396863 DOI: 10.1186/s13075-014-0490-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Next-generation DNA sequencing has revolutionized the field of genetics and genomics, providing researchers with the tools to efficiently identify novel rare and low frequency risk variants, which was not practical with previously available methodologies. These methods allow for the sequence capture of a specific locus or small genetic region all the way up to the entire six billion base pairs of the diploid human genome. Rheumatic diseases are a huge burden on the US population, affecting more than 46 million Americans. Those afflicted suffer from one or more of the more than 100 diseases characterized by inflammation and loss of function, mainly of the joints, tendons, ligaments, bones, and muscles. While genetics studies of many of these diseases (for example, systemic lupus erythematosus, rheumatoid arthritis, and inflammatory bowel disease) have had major successes in defining their genetic architecture, causal alleles and rare variants have still been elusive. This review describes the current high-throughput DNA sequencing methodologies commercially available and their application to rheumatic diseases in both case–control as well as family-based studies.
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11
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Farah CS, Dalley AJ, Nguyen P, Batstone M, Kordbacheh F, Perry-Keene J, Fielding D. Improved surgical margin definition by narrow band imaging for resection of oral squamous cell carcinoma: A prospective gene expression profiling study. Head Neck 2015; 38:832-9. [DOI: 10.1002/hed.23989] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2014] [Indexed: 12/26/2022] Open
Affiliation(s)
- Camile S. Farah
- University of Queensland Centre for Clinical Research, The University of Queensland; Brisbane Queensland Australia
- Australian Centre for Oral Oncology Research and Education; Brisbane Queensland Australia
| | - Andrew J. Dalley
- University of Queensland Centre for Clinical Research, The University of Queensland; Brisbane Queensland Australia
| | - Phan Nguyen
- Department of Thoracic Medicine; Royal Adelaide Hospital; Adelaide Australia
| | - Martin Batstone
- University of Queensland Centre for Clinical Research, The University of Queensland; Brisbane Queensland Australia
- Maxillofacial Unit; Royal Brisbane and Women's Hospital; Brisbane Queensland Australia
| | - Farzaneh Kordbacheh
- University of Queensland Centre for Clinical Research, The University of Queensland; Brisbane Queensland Australia
| | - Joanna Perry-Keene
- Department of Pathology; Royal Brisbane and Women's Hospital; Brisbane Queensland Australia
| | - David Fielding
- Department of Thoracic Medicine; Royal Brisbane and Women's Hospital; Brisbane Queensland Australia
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12
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Recent advances and current issues in single-cell sequencing of tumors. Cancer Lett 2015; 365:1-10. [PMID: 26003306 DOI: 10.1016/j.canlet.2015.04.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 04/19/2015] [Accepted: 04/20/2015] [Indexed: 12/28/2022]
Abstract
Intratumoral heterogeneity is a recently recognized but important feature of cancer that underlies the various biocharacteristics of cancer tissues. The advent of next-generation sequencing technologies has facilitated large scale capture of genomic data, while the recent development of single-cell sequencing has allowed for more in-depth studies into the complex molecular mechanisms of intratumoral heterogeneity. In this review, the recent advances and current challenges in single-cell sequencing methodologies are discussed, highlighting the potential power of these data to provide insights into oncological processes, from tumorigenesis through progression to metastasis and therapy resistance.
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13
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The practice of oral medicine in the United States in the twenty-first century: an update. Oral Surg Oral Med Oral Pathol Oral Radiol 2015; 119:408-15. [DOI: 10.1016/j.oooo.2014.12.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 12/05/2014] [Accepted: 12/19/2014] [Indexed: 11/15/2022]
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14
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Bennett NC, Farah CS. Next-generation sequencing in clinical oncology: next steps towards clinical validation. Cancers (Basel) 2014; 6:2296-312. [PMID: 25412366 PMCID: PMC4276967 DOI: 10.3390/cancers6042296] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 11/07/2014] [Accepted: 11/10/2014] [Indexed: 02/05/2023] Open
Abstract
Compelling evidence supports the transition of next generation sequencing (NGS) technology from a research environment into clinical practice. Before NGS technologies are fully adopted in the clinic, they should be thoroughly scrutinised for their potential as powerful diagnostic and prognostic tools. The importance placed on generating accurate NGS data, and consequently appropriate clinical interpretation, has stimulated much international discussion regarding the creation and implementation of strict guidelines and regulations for NGS clinical use. In the context of clinical oncology, NGS technologies are currently transitioning from a clinical research background into a setting where they will contribute significantly to individual patient cancer management. This paper explores the steps that have been taken, and those still required, for the transition of NGS into the clinical area, with particular emphasis placed on validation in the setting of clinical oncology.
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Affiliation(s)
- Nigel C Bennett
- The University of Queensland, UQ Centre for Clinical Research, Herston Qld 4029, Australia.
| | - Camile S Farah
- The University of Queensland, UQ Centre for Clinical Research, Herston Qld 4029, Australia.
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15
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Farah CS. Response to: 'the many generations of sequencing technology'. Oral Oncol 2014; 50:e62. [PMID: 25218001 DOI: 10.1016/j.oraloncology.2014.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Camile S Farah
- University of Queensland, UQ Centre for Clinical Research, Building 71/918 Royal Brisbane, Women's Hospital Campus, Herston, 4029 Brisbane, QLD, Australia.
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16
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Luo G, Angelidaki I. Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing. WATER RESEARCH 2014; 60:156-163. [PMID: 24852413 DOI: 10.1016/j.watres.2014.04.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/22/2014] [Accepted: 04/27/2014] [Indexed: 05/13/2023]
Abstract
The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors.
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Affiliation(s)
- Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 200433 Shanghai, China; Department of Environmental Engineering, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark.
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Oral cancer and oral potentially malignant disorders. Int J Dent 2014; 2014:853479. [PMID: 24891850 PMCID: PMC4033498 DOI: 10.1155/2014/853479] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 03/17/2014] [Indexed: 12/20/2022] Open
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Jessri M, Farah CS. Harnessing massively parallel sequencing in personalized head and neck oncology. J Dent Res 2014; 93:437-44. [PMID: 24557572 DOI: 10.1177/0022034514524783] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Advances in the management of patients with head and neck squamous cell carcinoma (HNSCC) have not significantly changed the prognosis of this tumor over the past five decades. Molecular heterogeneity of HNSCC and its association with HPV, in addition to the increase in the number of cancers arising in traditionally low-risk patients, are among some of the obstacles to the successful management of this group of tumors. Massively parallel sequencing, otherwise known as next-generation sequencing (NGS), is rapidly changing conventional patient management by providing detailed information about each patient's genome and transcriptome. Despite major advances in technology and a significant reduction in the cost of sequencing, NGS remains mainly limited to research facilities. In addition, there are only a few published studies that have utilized this technology in HNSCC. This paper aims to report briefly on current commercially available NGS platforms and discuss their clinical applications, ethical considerations, and utilization in personalized patient care, particularly as this relates to head and neck cancer.
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Affiliation(s)
- M Jessri
- The University of Queensland, UQ Centre for Clinical Research, Herston, Qld 4029, Australia
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Bragazzi NL, Pechkova E, Nicolini C. Proteomics and Proteogenomics Approaches for Oral Diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:125-62. [DOI: 10.1016/b978-0-12-800453-1.00004-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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