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Mucignat G, Montanucci L, Elgendy R, Giantin M, Laganga P, Pauletto M, Mutinelli F, Vascellari M, Leone VF, Dacasto M, Granato A. A Whole-Transcriptomic Analysis of Canine Oral Melanoma: A Chance to Disclose the Radiotherapy Effect and Outcome-Associated Gene Signature. Genes (Basel) 2024; 15:1065. [PMID: 39202425 PMCID: PMC11353338 DOI: 10.3390/genes15081065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/07/2024] [Accepted: 08/09/2024] [Indexed: 09/03/2024] Open
Abstract
Oral melanoma (OM) is the most common malignant oral tumour among dogs and shares similarities with human mucosal melanoma (HMM), validating the role of canine species as an immunocompetent model for cancer research. In both humans and dogs, the prognosis is poor and radiotherapy (RT) represents a cornerstone in the management of this tumour, either as an adjuvant or a palliative treatment. In this study, by means of RNA-seq, the effect of RT weekly fractionated in 9 Gray (Gy), up to a total dose of 36 Gy (4 weeks), was evaluated in eight dogs affected by OM. Furthermore, possible transcriptomic differences in blood and biopsies that might be associated with a longer overall survival (OS) were investigated. The immune response, glycosylation, cell adhesion, and cell cycle were the most affected pathways by RT, while tumour microenvironment (TME) composition and canonical and non-canonical WNT pathways appeared to be modulated in association with OS. Taking these results as a whole, this study improved our understanding of the local and systemic effect of RT, reinforcing the pivotal role of anti-tumour immunity in the control of canine oral melanoma (COM).
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Affiliation(s)
- Greta Mucignat
- Department of Comparative Biomedicine and Food Science, University of Padua, Agripolis Legnaro, 35020 Padua, Italy; (G.M.); (M.G.); (M.P.)
| | - Ludovica Montanucci
- McGovern Medical School and Center for Neurogenomics, UTHealth, University of Texas Houston, Houston, TX 77030, USA;
| | - Ramy Elgendy
- Discovery Sciences, Centre for Genomics Research, AstraZeneca, 411 10 Gothenburg, Sweden;
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padua, Agripolis Legnaro, 35020 Padua, Italy; (G.M.); (M.G.); (M.P.)
| | - Paola Laganga
- Anicura—Centro Oncologico Veterinario, Sasso Marconi, 40037 Bologna, Italy; (P.L.); (V.F.L.)
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padua, Agripolis Legnaro, 35020 Padua, Italy; (G.M.); (M.G.); (M.P.)
| | - Franco Mutinelli
- Veterinary and Public Health Institute, Legnaro, 35020 Padua, Italy; (F.M.); (M.V.)
| | - Marta Vascellari
- Veterinary and Public Health Institute, Legnaro, 35020 Padua, Italy; (F.M.); (M.V.)
| | - Vito Ferdinando Leone
- Anicura—Centro Oncologico Veterinario, Sasso Marconi, 40037 Bologna, Italy; (P.L.); (V.F.L.)
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padua, Agripolis Legnaro, 35020 Padua, Italy; (G.M.); (M.G.); (M.P.)
| | - Anna Granato
- Veterinary and Public Health Institute, Legnaro, 35020 Padua, Italy; (F.M.); (M.V.)
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Pervez MT, Hasnain MJU, Abbas SH, Moustafa MF, Aslam N, Shah SSM. A Comprehensive Review of Performance of Next-Generation Sequencing Platforms. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3457806. [PMID: 36212714 PMCID: PMC9537002 DOI: 10.1155/2022/3457806] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022]
Abstract
Background Next-generation sequencing methods have been developed and proposed to investigate any query in genomics or clinical activity involving DNA. Technical advancement in these sequencing methods has enhanced sequencing volume to several billion nucleotides within a very short time and low cost. During the last few years, the usage of the latest DNA sequencing platforms in a large number of research projects helped to improve the sequencing methods and technologies, thus enabling a wide variety of research/review publications and applications of sequencing technologies. Objective The proposed study is aimed at highlighting the most fast and accurate NGS instruments developed by various companies by comparing output per hour, quality of the reads, maximum read length, reads per run, and their applications in various domains. This will help research institutions and biological/clinical laboratories to choose the sequencing instrument best suited to their environment. The end users will have a general overview about the history of the sequencing technologies, latest developments, and improvements made in the sequencing technologies till now. Results The proposed study, based on previous studies and manufacturers' descriptions, highlighted that in terms of output per hour, Nanopore PromethION outperformed all sequencers. BGI was on the second position, and Illumina was on the third position. Conclusion The proposed study investigated various sequencing instruments and highlighted that, overall, Nanopore PromethION is the fastest sequencing approach. BGI and Nanopore can beat Illumina, which is currently the most popular sequencing company. With respect to quality, Ion Torrent NGS instruments are on the top of the list, Illumina is on the second position, and BGI DNB is on the third position. Secondly, memory- and time-saving algorithms and databases need to be developed to analyze data produced by the 3rd- and 4th-generation sequencing methods. This study will help people to adopt the best suited sequencing platform for their research work, clinical or diagnostic activities.
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Affiliation(s)
- Muhammad Tariq Pervez
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Pakistan
| | - Mirza Jawad ul Hasnain
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Pakistan
| | - Syed Hassan Abbas
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Pakistan
| | - Mahmoud F. Moustafa
- Department of Biology, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena, Egypt
| | - Naeem Aslam
- Department of Computer Science, NFCIET, Khanewal Road, Multan, Pakistan
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Stenzinger A, Alber M, Allgäuer M, Jurmeister P, Bockmayr M, Budczies J, Lennerz J, Eschrich J, Kazdal D, Schirmacher P, Wagner AH, Tacke F, Capper D, Müller KR, Klauschen F. Artificial intelligence and pathology: From principles to practice and future applications in histomorphology and molecular profiling. Semin Cancer Biol 2021; 84:129-143. [PMID: 33631297 DOI: 10.1016/j.semcancer.2021.02.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/29/2021] [Accepted: 02/16/2021] [Indexed: 02/07/2023]
Abstract
The complexity of diagnostic (surgical) pathology has increased substantially over the last decades with respect to histomorphological and molecular profiling. Pathology has steadily expanded its role in tumor diagnostics and beyond from disease entity identification via prognosis estimation to precision therapy prediction. It is therefore not surprising that pathology is among the disciplines in medicine with high expectations in the application of artificial intelligence (AI) or machine learning approaches given their capabilities to analyze complex data in a quantitative and standardized manner to further enhance scope and precision of diagnostics. While an obvious application is the analysis of histological images, recent applications for the analysis of molecular profiling data from different sources and clinical data support the notion that AI will enhance both histopathology and molecular pathology in the future. At the same time, current literature should not be misunderstood in a way that pathologists will likely be replaced by AI applications in the foreseeable future. Although AI will transform pathology in the coming years, recent studies reporting AI algorithms to diagnose cancer or predict certain molecular properties deal with relatively simple diagnostic problems that fall short of the diagnostic complexity pathologists face in clinical routine. Here, we review the pertinent literature of AI methods and their applications to pathology, and put the current achievements and what can be expected in the future in the context of the requirements for research and routine diagnostics.
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Affiliation(s)
- Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, Heidelberg, 69120, Germany; German Cancer Consortium (DKTK), Partner Site Heidelberg, and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Center for Lung Research (DZL), Partner Site Heidelberg, Heidelberg, Germany.
| | - Maximilian Alber
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; Aignostics GmbH, Schumannstr. 17, Berlin, 10117, Germany
| | - Michael Allgäuer
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, Heidelberg, 69120, Germany
| | - Philipp Jurmeister
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Bockmayr
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Research Institute, Children's Cancer Center Hamburg, Hamburg, Germany
| | - Jan Budczies
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, Heidelberg, 69120, Germany; German Cancer Consortium (DKTK), Partner Site Heidelberg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jochen Lennerz
- Department of Pathology, Center for Integrated Diagnostics, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Johannes Eschrich
- Department of Hepatology & Gastroenterology, Charité University Medical Center, Berlin, Germany
| | - Daniel Kazdal
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, Heidelberg, 69120, Germany; German Center for Lung Research (DZL), Partner Site Heidelberg, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, Heidelberg, 69120, Germany; German Cancer Consortium (DKTK), Partner Site Heidelberg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alex H Wagner
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, 43210, USA
| | - Frank Tacke
- Department of Hepatology & Gastroenterology, Charité University Medical Center, Berlin, Germany
| | - David Capper
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Klaus-Robert Müller
- Machine Learning Group, Technische Universität Berlin, Berlin, 10587, Germany; Department of Artificial Intelligence, Korea University, Seoul, 136-713, South Korea; Max-Planck-Institute for Informatics, Saarland Informatics Campus E1 4, Saarbrücken, 66123, Germany; Google Research, Brain Team, Berlin, Germany.
| | - Frederick Klauschen
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute of Pathology, Ludwig-Maximilians-Universität München, Thalkirchner Strasse 36, München, 80337, Germany.
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Asavei T, Bobeica M, Nastasa V, Manda G, Naftanaila F, Bratu O, Mischianu D, Cernaianu MO, Ghenuche P, Savu D, Stutman D, Tanaka KA, Radu M, Doria D, Vasos PR. Laser-driven radiation: Biomarkers for molecular imaging of high dose-rate effects. Med Phys 2019; 46:e726-e734. [PMID: 31357243 PMCID: PMC6899889 DOI: 10.1002/mp.13741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 04/11/2019] [Accepted: 07/03/2019] [Indexed: 12/15/2022] Open
Abstract
Recently developed short‐pulsed laser sources garner high dose‐rate beams such as energetic ions and electrons, x rays, and gamma rays. The biological effects of laser‐generated ion beams observed in recent studies are different from those triggered by radiation generated using classical accelerators or sources, and this difference can be used to develop new strategies for cancer radiotherapy. High‐power lasers can now deliver particles in doses of up to several Gy within nanoseconds. The fast interaction of laser‐generated particles with cells alters cell viability via distinct molecular pathways compared to traditional, prolonged radiation exposure. The emerging consensus of recent literature is that the differences are due to the timescales on which reactive molecules are generated and persist, in various forms. Suitable molecular markers have to be adopted to monitor radiation effects, addressing relevant endogenous molecules that are accessible for investigation by noninvasive procedures and enable translation to clinical imaging. High sensitivity has to be attained for imaging molecular biomarkers in cells and in vivo to follow radiation‐induced functional changes. Signal‐enhanced MRI biomarkers enriched with stable magnetic nuclear isotopes can be used to monitor radiation effects, as demonstrated recently by the use of dynamic nuclear polarization (DNP) for biomolecular observations in vivo. In this context, nanoparticles can also be used as radiation enhancers or biomarker carriers. The radiobiology‐relevant features of high dose‐rate secondary radiation generated using high‐power lasers and the importance of noninvasive biomarkers for real‐time monitoring the biological effects of radiation early on during radiation pulse sequences are discussed.
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Affiliation(s)
- Theodor Asavei
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Mariana Bobeica
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Viorel Nastasa
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania.,National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor Street, RO-077125, Bucharest-Magurele, Romania
| | - Gina Manda
- Cellular and Molecular Medicine Department, "Victor Babes" National Institute of Pathology, 99-101 Splaiul Independentei, Bucharest, 050096, Romania
| | - Florin Naftanaila
- Carol Davila University of Medicine and Pharmacy Bucharest, Dr Carol Davila Central Mil University Emergency Hospital, 88th Mircea Vulcanescu Str, Bucharest, Romania.,Amethyst Radiotherapy Clinic, Dr Odaii 42, Otopeni, Romania
| | - Ovidiu Bratu
- Carol Davila University of Medicine and Pharmacy Bucharest, Dr Carol Davila Central Mil University Emergency Hospital, 88th Mircea Vulcanescu Str, Bucharest, Romania
| | - Dan Mischianu
- Carol Davila University of Medicine and Pharmacy Bucharest, Dr Carol Davila Central Mil University Emergency Hospital, 88th Mircea Vulcanescu Str, Bucharest, Romania
| | - Mihail O Cernaianu
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Petru Ghenuche
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Diana Savu
- Department of Life and Environmental Physics, Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Dan Stutman
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania.,National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor Street, RO-077125, Bucharest-Magurele, Romania.,Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland, 21218, USA
| | - Kazuo A Tanaka
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Mihai Radu
- Department of Life and Environmental Physics, Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Domenico Doria
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania.,Centre for Plasma Physics, School of Mathematics and Physics, Queen's University Belfast, Belfast, BT7 1NN, United Kingdom
| | - Paul R Vasos
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania.,Research Institute of the University of Bucharest (ICUB), 36-46 B-dul M. Kogalniceanu, RO-050107, Bucharest, Romania
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Personalising Prostate Radiotherapy in the Era of Precision Medicine: A Review. J Med Imaging Radiat Sci 2018; 49:376-382. [PMID: 30514554 DOI: 10.1016/j.jmir.2018.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/27/2017] [Accepted: 01/18/2018] [Indexed: 12/14/2022]
Abstract
Prostate cancer continues to be the most commonly diagnosed cancer among Canadian men. The introduction of routine screening and advanced treatment options have allowed for a decrease in prostate cancer-related mortality, but outcomes following treatment continue to vary widely. In addition, the overtreatment of indolent prostate cancers causes unnecessary treatment toxicities and burdens health care systems. Accurate identification of patients who should undergo aggressive treatment, and those which should be managed more conservatively, needs to be implemented. More tumour and patient information is needed to stratify patients into low-, intermediate-, and high-risk groups to guide treatment options. This paper reviews the current literature on personalised prostate cancer management, including targeting tumour hypoxia, genomic and radiomic prognosticators, and radiobiological tumour targeting. A review of the current applications and future directions for the use of big data in radiation therapy is also presented. Prostate cancer management has a lot to gain from the implementation of personalised medicine into practice. Using specific tumour and patient characteristics to personalise prostate radiotherapy in the era of precision medicine will improve survival, decrease unnecessary toxicities, and minimise the heterogeneity of outcomes following treatment.
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Abstract
Cellular chromosomal DNA is the principal target through which ionising radiation exerts it diverse biological effects. This chapter summarises the relevant DNA damage signalling and repair pathways used by normal and tumour cells in response to irradiation. Strategies for tumour radiosensitisation are reviewed which exploit tumour-specific DNA repair deficiencies or signalling pathway addictions, with a special focus on growth factor signalling, PARP, cancer stem cells, cell cycle checkpoints and DNA replication. This chapter concludes with a discussion of DNA repair-related candidate biomarkers of tumour response which are of crucial importance for implementing precision medicine in radiation oncology.
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Cheung KY. Systems medicine for the delivery of better healthcare Services- International Union for Physical and Engineering Sciences (IUPESM) perspective. HEALTH AND TECHNOLOGY 2017. [DOI: 10.1007/s12553-016-0164-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kamran N, Calinescu A, Candolfi M, Chandran M, Mineharu Y, Asad AS, Koschmann C, Nunez FJ, Lowenstein PR, Castro MG. Recent advances and future of immunotherapy for glioblastoma. Expert Opin Biol Ther 2016; 16:1245-64. [PMID: 27411023 PMCID: PMC5014608 DOI: 10.1080/14712598.2016.1212012] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/08/2016] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Outcome for glioma (GBM) remains dismal despite advances in therapeutic interventions including chemotherapy, radiotherapy and surgical resection. The overall survival benefit observed with immunotherapies in cancers such as melanoma and prostate cancer has fuelled research into evaluating immunotherapies for GBM. AREAS COVERED Preclinical studies have brought a wealth of information for improving the prognosis of GBM and multiple clinical studies are evaluating a wide array of immunotherapies for GBM patients. This review highlights advances in the development of immunotherapeutic approaches. We discuss the strategies and outcomes of active and passive immunotherapies for GBM including vaccination strategies, gene therapy, check point blockade and adoptive T cell therapies. We also focus on immunoediting and tumor neoantigens that can impact the efficacy of immunotherapies. EXPERT OPINION Encouraging results have been observed with immunotherapeutic strategies; some clinical trials are reaching phase III. Significant progress has been made in unraveling the molecular and genetic heterogeneity of GBM and its implications to disease prognosis. There is now consensus related to the critical need to incorporate tumor heterogeneity into the design of therapeutic approaches. Recent data also indicates that an efficacious treatment strategy will need to be combinatorial and personalized to the tumor genetic signature.
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Affiliation(s)
- Neha Kamran
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell and Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
| | - Alexandra Calinescu
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell and Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
| | - Marianela Candolfi
- c Instituto de Investigaciones Biomédicas (CONICET-UBA), Facultad de Medicina , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - Mayuri Chandran
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell and Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
| | - Yohei Mineharu
- d Department of Neurosurgery , Kyoto University Graduate School of Medicine , Kyoto , Japan
| | - Antonela S Asad
- c Instituto de Investigaciones Biomédicas (CONICET-UBA), Facultad de Medicina , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - Carl Koschmann
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell and Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
| | - Felipe J Nunez
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell and Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
| | - Pedro R Lowenstein
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell and Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
| | - Maria G Castro
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell and Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
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Ashktorab H, Azimi H, Nickerson ML, Bass S, Varma S, Brim H. Targeted Exome Sequencing Outcome Variations of Colorectal Tumors within and across Two Sequencing Platforms. ACTA ACUST UNITED AC 2016; 3. [PMID: 27547838 DOI: 10.4172/2469-9853.1000123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND AND AIM Next generation sequencing (NGS) has quickly the tool of choice for genome and exome data generation. The multitude of sequencing platforms as well as the variabilities within each platform need to be assessed. In this paper we used two platforms (ION TORRENT AND ILLUMINA) to assess single nucleotides variants in colorectal cancer (CRC) specimens. METHODS CRC specimens (n = 13) collected from 6 CRC (cancer and matched normal) patients were used to establish the mutational profile using ION TORRENT AND ILLUMINA sequencing platforms. We analyzed a set of samples from Formalin Fixed Paraffin Embedded and FF (FF) samples on both platforms to assess the effect of sample nature (FFPE vs. FF) on sequencing outcome and to evaluate the similarity/differences of SNVs across the two platforms. In addition, duplicates of FF samples were sequenced on each platform to assess variability within platform. RESULTS The comparison of FF replicates to each other gave a concordance of 77% (± 15.3%) in Ion Torrent and 70% (± 3.7%) in Illumina. FFPE vs. FF replicates gave a concordance of 40% (± 32%) in Ion Torrent and 49% (± 19%) in Illumina. For the cross platform concordance were FFPE compared to FF (Average of 75% (± 9.8%) for FFPE samples and 67% (± 32%) for FF and 70% (± 26.8%) overall average). CONCLUSION Our data show a significant variability within and across platforms. Also the number of detected variants depend on the nature of the specimen; FF vs. FFPE. Validation of NGS discovered mutations is a must to rule-out false positive mutants. This validation might either be performed through a second NGS platform or through Sanger sequencing.
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Affiliation(s)
- Hassan Ashktorab
- Department of Medicine and Cancer Center, Howard University College of Medicine, Washington DC
| | - Hamed Azimi
- Department of Medicine and Cancer Center, Howard University College of Medicine, Washington DC
| | | | - Sara Bass
- Center for Cancer Research, National Cancer Institute, Frederick, USA
| | - Sudhir Varma
- Hithru LLC, Silver Spring, Center for Cancer Research, National Cancer Institute, Frederick, USA
| | - Hassan Brim
- Department of Pathology, Howard University College of Medicine, Washington DC
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