Evaluating the role of next-generation sequencing and radiological techniques in rare disease diagnosis
Challenges and opportunities
Keywords:
Next-generation sequencing, rare diseases, genomics, diagnostics, omics integration, radiological imagingAbstract
Aim: This article evaluates the utility of next-generation sequencing (NGS) and radiological techniques in the diagnosis of rare diseases, emphasizing the challenges and opportunities presented by these technologies. Methods: A comprehensive review of existing literature on NGS technologies, including first, second, and third-generation sequencing methods, as well as their applications in genomics, transcriptomics, and epigenomics, was conducted alongside radiological imaging techniques such as MRI and CT scans. Results: NGS has revolutionized rare disease diagnosis by enabling high-throughput, cost-effective sequencing, facilitating the identification of pathogenic mutations, and advancing personalized medicine. Radiological techniques provide complementary insights into anatomical abnormalities and disease progression. Despite significant advantages, challenges such as data interpretation, cost, and ethical considerations persist. Conclusion: NGS and radiological imaging offer transformative potential in rare disease diagnosis, enhancing our understanding of genetic and anatomical aspects of disorders and enabling targeted therapeutic approaches. Continued technological advancements and integrative analyses with other omics data and imaging findings will further enhance their diagnostic utility.
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Goodwin, S.; McPherson, J.D.; McCombie, W.R. Coming of age: Ten years of next-generation sequencing technologies. Nat. Rev. Genet. 2016, 17, 333–351.
Levy, S.E.; Myers, R.M. Advancements in Next-Generation Sequencing. Annu. Rev. Genom. Hum. Genet. 2016, 17, 95–115.
Rhoads, A.; Au, K.F. PacBio Sequencing and Its Applications. Genom. Proteom. Bioinform. 2015, 13, 278–289.
Vaser, R.; Sović, I.; Nagarajan, N.; Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 2017, 27, 737–746.
Amarasinghe, S.L.; Su, S.; Dong, X.; Zappia, L.; Ritchie, M.E.; Gouil, Q. Opportunities and challenges in long-read sequencing data analysis. Genome Biol. 2020, 21, 30.
Metzker, M.L. Emerging technologies in DNA sequencing. Genome Res. 2005, 15, 1767–1776.
Kumar, K.R.; Cowley, M.J.; Davis, R.L. Next-Generation Sequencing and Emerging Technologies. Semin. Thromb. Hemost. 2019, 45, 661–673.
Sakamoto, Y.; Sereewattanawoot, S.; Suzuki, A. A new era of long-read sequencing for cancer genomics. J. Hum. Genet. 2020, 65, 3–10.
Goto, Y.; Akahori, R.; Yanagi, I.; Takeda, K.-I. Solid-state nanopores towards single-molecule DNA sequencing. J. Hum. Genet. 2020, 65, 69–77
Salk, J.J.; Schmitt, M.W.; Loeb, L.A. Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations. Nat. Rev. Genet. 2018, 19, 269–285.
Holley, R.W.; Apgar, J.; Everett, G.A.; Madison, J.T.; Marquisee, M.; Merrill, S.H.; Penswick, J.R.; Zamir, A. Structure of a Ribonucleic Acid. Science 1965, 147, 1462–1465.
Heather, J.M.; Chain, B. The sequence of sequencers: The history of sequencing DNA. Genomics 2016, 107, 1–8.
Sanger, F.; Nicklen, S.; Coulson, A.R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 1977, 74, 5463–5467
Barba, M.; Czosnek, H.; Hadidi, A. Historical Perspective, Development and Applications of Next-Generation Sequencing in Plant Virology. Viruses 2013, 6, 106–136.
Schuster, S.C. Next-generation sequencing transforms today’s biology. Nat. Methods 2008, 5, 16–18
Hutchison, C.A. DNA sequencing: Bench to bedside and beyond. Nucleic Acids Res. 2007, 35, 6227–6237.
Pervez, M.T.; Hasnain, M.J.U.; Abbas, S.H.; Moustafa, M.F.; Aslam, N.; Shah, S.S.M. A Comprehensive Review of Performance of Next-Generation Sequencing Platforms. BioMed Res. Int. 2022.
Ronaghi, M.; Karamohamed, S.; Pettersson, B.; Uhlén, M.; Nyrén, P. Real-Time DNA Sequencing Using Detection of Pyrophosphate Release. Anal. Biochem. 1996, 242, 84–89.
Slatko, B.E.; Gardner, A.F.; Ausubel, F.M. Overview of Next-Generation Sequencing Technologies. Curr. Protoc. Mol. Biol. 2018, 122, e59.
Henson, J.; Tischler, G.; Ning, Z. Next-generation sequencing and large genome assemblies. Pharmacogenomics 2012, 13, 901–915.
Rothberg, J.M.; Hinz, W.; Rearick, T.M.; Schultz, J.; Mileski, W.; Davey, M.; Leamon, J.H.; Johnson, K.; Milgrew, M.J.; Edwards, M.; et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011, 475, 348–352.
Buermans, H.P.J.; Den Dunnen, J.T. Next generation sequencing technology: Advances and applications. Biochim. Biophys. Acta (BBA)—Mol. Basis Dis. 2014, 1842, 1932–1941.
Shendure, J.; Porreca, G.J.; Reppas, N.B.; Lin, X.; McCutcheon, J.P.; Rosenbaum, A.M.; Wang, M.D.; Zhang, K.; Mitra, R.D.; Church, G.M. Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome. Science 2005, 309, 1728–1732.
Drmanac, R.; Sparks, A.B.; Callow, M.J.; Halpern, A.L.; Burns, N.L.; Kermani, B.G.; Carnevali, P.; Nazarenko, I.; Nilsen, G.B.; Yeung, G.; et al. Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays. Science 2010, 327, 78–81.
Xu, Y.; Lin, Z.; Tang, C.; Tang, Y.; Cai, Y.; Zhong, H.; Wang, X.; Zhang, W.; Xu, C.; Wang, J.; et al. A new massively parallel nanoball sequencing platform for whole exome research. BMC Bioinform. 2019, 20, 153.
Hart, C.; Lipson, D.; Ozsolak, F.; Raz, T.; Steinmann, K.; Thompson, J.; Milos, P.M. Single-Molecule Sequencing. Methods Enzymol. 2010, 472, 407–430.
Thompson, J.F.; Steinmann, K.E. Single Molecule Sequencing with a HeliScope Genetic Analysis System. Curr. Protoc. Mol. Biol. 2010, 92, 7.10.1–7.10.14
Eid, J.; Fehr, A.; Gray, J.; Luong, K.; Lyle, J.; Otto, G.; Peluso, P.; Rank, D.; Baybayan, P.; Bettman, B.; et al. Real-Time DNA Sequencing from Single Polymerase Molecules. Science 2009, 323, 133–138.
Roberts, R.J.; Carneiro, M.O.; Schatz, M.C. The advantages of SMRT sequencing. Genome Biol. 2013, 14, 405.
Jain, M.; Olsen, H.E.; Paten, B.; Akeson, M. The Oxford Nanopore MinION: Delivery of nanopore sequencing to the genomics community. Genome Biol. 2016, 17, 239.
Mantere, T.; Kersten, S.; Hoischen, A. Long-Read Sequencing Emerging in Medical Genetics. Front. Genet. 2019, 10, 426.
Costain, G.; Cohn, R.D.; Scherer, S.W.; Marshall, C.R. Genome sequencing as a diagnostic test. Can. Med. Assoc. J. 2021, 193, E1626–E1629.
Logsdon, G.A.; Vollger, M.R.; Eichler, E.E. Long-read human genome sequencing and its applications. Nat. Rev. Genet. 2020, 21, 597–614.
Rabbani, B.; Tekin, M.; Mahdieh, N. The promise of whole-exome sequencing in medical genetics. J. Hum. Genet. 2014, 59, 5–15.
Iglesias, A.; Anyane-Yeboa, K.; Wynn, J.; Wilson, A.; Cho, M.T.; Guzman, E.; Sisson, R.; Egan, C.; Chung, W.K. The usefulness of whole-exome sequencing in routine clinical practice. Anesth. Analg. 2014, 16, 922–931.
Van Dijk, E.L.; Auger, H.; Jaszczyszyn, Y.; Thermes, C. Ten years of next-generation sequencing technology. Trends Genet. 2014, 30, 418–426.
Warr, A.; Robert, C.; Hume, D.; Archibald, A.; Deeb, N.; Watson, M. Exome Sequencing: Current and Future Perspectives. G3 Genes Genom. Genet. 2015, 5, 1543–1550.
Williams, M.J.; Sottoriva, A.; Graham, T.A. Measuring Clonal Evolution in Cancer with Genomics. Annu. Rev. Genom. Hum. Genet. 2019, 20, 309–329.
Kim, M. Targeted Panels or Exome—Which Is the Right NGS Approach for Inherited Disease Research? 2017. Available online: https://admin.acceleratingscience.com/behindthebench/targeted-panels-or-exome-which-is-the-right-ngs-approach-for-inherited-disease-research/
Li, J.; Liu, C. Coding or Noncoding, the Converging Concepts of RNAs. Front. Genet. 2019, 10, 496.
Lucchinetti, E.; Zaugg, M. RNA Sequencing. Anesthesiology 2020, 133, 976–978.
Choi, S.-W.; Kim, H.-W.; Nam, J.-W. The small peptide world in long noncoding RNAs. Brief. Bioinform. 2019, 20, 1853–1864.
Lasda, E.; Parker, R. Circular RNAs: Diversity of form and function. RNA 2014, 20, 1829–1842.
Chen, J.-W.; Shrestha, L.; Green, G.; Leier, A.; Marquez-Lago, T.T. The hitchhikers’ guide to RNA sequencing and functional analysis. Brief. Bioinform. 2023, 24, bbac529.
Stark, R.; Grzelak, M.; Hadfield, J. RNA sequencing: The teenage years. Nat. Rev. Genet. 2019, 20, 631–656.
Ura, H.; Togi, S.; Niida, Y. A comparison of mRNA sequencing (RNA-Seq) library preparation methods for transcriptome analysis. BMC Genom. 2022, 23, 303.
Kolanowska, M.; Kubiak, A.; Jażdżewski, K.; Wójcicka, A. MicroRNA Analysis Using Next-Generation Sequencing. Methods Mol. Biol. 2018, 1823, 87–101.
Grillone, K.; Riillo, C.; Scionti, F.; Rocca, R.; Tradigo, G.; Guzzi, P.H.; Alcaro, S.; Di Martino, M.T.; Tagliaferri, P.; Tassone, P. Non-coding RNAs in cancer: Platforms and strategies for investigating the genomic “dark matter”. J. Exp. Clin. Cancer Res. 2020, 39, 117.
Atkinson, S.R.; Marguerat, S.; Bähler, J. Exploring long non-coding RNAs through sequencing. Semin. Cell Dev. Biol. 2012, 23, 200–205.
Wang, Z.; Gerstein, M.; Snyder, M. RNA-Seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10, 57–63.
Benesova, S.; Kubista, M.; Valihrach, L. Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis. Diagnostics 2021, 11, 964.
Cao, J. The functional role of long non-coding RNAs and epigenetics. Biol. Proced. Online 2014, 16, 42.
Kumar, S.; Gonzalez, E.A.; Rameshwar, P.; Etchegaray, J.-P. Non-Coding RNAs as Mediators of Epigenetic Changes in Malignancies. Cancers 2020, 12, 3657.
Mozdarani, H.; Ezzatizadeh, V.; Parvaneh, R.R. The emerging role of the long non-coding RNA HOTAIR in breast cancer development and treatment. J. Transl. Med. 2020, 18, 152.
Raghavan, V.; Kraft, L.; Mesny, F.; Rigerte, L. A simple guide to de novo transcriptome assembly and annotation. Brief. Bioinform. 2022, 23, bbab563.
Kulkarni, A.; Anderson, A.G.; Merullo, D.P.; Konopka, G. Beyond bulk: A review of single cell transcriptomics methodologies and applications. Curr. Opin. Biotechnol. 2019, 58, 129–136.
Adil, A.; Kumar, V.; Jan, A.T.; Asger, M. Single-Cell Transcriptomics: Current Methods and Challenges in Data Acquisition and Analysis. Front. Neurosci. 2021, 15, 591122
Wang, J.; Tian, T.; Li, X.; Zhang, Y. Noncoding RNAs Emerging as Drugs or Drug Targets: Their Chemical Modification, Bio-Conjugation and Intracellular Regulation. Molecules 2022, 27, 6717.
López-Camarillo, C.; Gallardo-Rincón, D.; Álvarez-Sánchez, M.E.; Marchat, L.A. Pharmaco-epigenomics: On the Road of Translation Medicine. In Translational Research and Onco-Omics Applications in the Era of Cancer Personal Genomics; Springer: Berlin/Heidelberg, Germany, 2019; Volume 1168, pp. 31–42
National Human Genoe Research Institute. Epigenomics Fact Sheet. 2020. Available online: https://www.genome.gov/about-genomics/fact-sheets/Epigenomics-Fact-Sheet
Handy, D.E.; Castro, R.; Loscalzo, J. Epigenetic Modifications. Circulation 2011, 123, 2145–2156.
Fuso, A. Aging and Disease. In Epigenetics in Human Disease; Academic Press: Cambridge, MA, USA, 2018; pp. 935–973.
Metere, A.; Graves, C.E. Factors Influencing Epigenetic Mechanisms: Is There a Role for Bariatric Surgery? Biotech 2020, 9, 6.
Heyn, H.; Esteller, M. DNA methylation profiling in the clinic: Applications and challenges. Nat. Rev. Genet. 2012, 13, 679–692
Zhu, H.; Zhu, H.; Tian, M.; Wang, D.; He, J.; Xu, T. DNA Methylation and Hydroxymethylation in Cervical Cancer: Diagnosis, Prognosis and Treatment. Front. Genet. 2020, 11, 347.
Sarda, S.; Hannenhalli, S. Next-Generation Sequencing and Epigenomics Research: A Hammer in Search of Nails. Genom. Inform. 2014, 12, 2–11.
Barros-Silva, D.; Marques, C.J.; Henrique, R.; Jerónimo, C. Profiling DNA Methylation Based on Next-Generation Sequencing Approaches: New Insights and Clinical Applications. Genes 2018, 9, 429
Wreczycka, K.; Gosdschan, A.; Yusuf, D.; Grüning, B.; Assenov, Y.; Akalin, A. Strategies for analyzing bisulfite sequencing data. J. Biotechnol. 2017, 261, 105–115.
Frommer, M.; E McDonald, L.; Millar, D.S.; Collis, C.M.; Watt, F.; Grigg, G.W.; Molloy, P.L.; Paul, C.L. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. USA 1992, 89, 1827–1831.
Lu, R.J.-H.; Liu, Y.-T.; Huang, C.W.; Yen, M.-R.; Lin, C.-Y.; Chen, P.-Y. ATACgraph: Profiling Genome-Wide Chromatin Accessibility from ATAC-seq. Front. Genet. 2021, 11, 618478.
Mansisidor, A.R.; Risca, V.I. Chromatin accessibility: Methods, mechanisms, and biological insights. Nucleus 2022, 13, 238–278.
Liu, E.T.; Pott, S.; Huss, M. Q&A: ChIP-seq technologies and the study of gene regulation. BMC Biol. 2010, 8, 56.
Furey, T.S. ChIP—Seq and beyond: New and improved methodologies to detect and characterize protein—DNA interactions. Nat. Rev. Genet. 2012, 13, 840–852.
O’geen, H.; Echipare, L.; Farnham, P.J. Using ChIP-Seq Technology to Generate High-Resolution Profiles of Histone Modifications. Methods Mol. Biol. 2011, 791, 265–286.
Nakato, R.; Sakata, T. Methods for ChIP-seq analysis: A practical workflow and advanced applications. Methods 2021, 187, 44–53.
Feng, F.; Yao, Y.; Wang, X.Q.D.; Zhang, X.; Liu, J. Connecting high-resolution 3D chromatin organization with epigenomics. Nat. Commun. 2022, 13, 2054.
Tang, B.; Cheng, X.; Xi, Y.; Chen, Z.; Zhou, Y.; Jin, V.X. Advances in Genomic Profiling and Analysis of 3D Chromatin Structure and Interaction. Genes 2017, 8, 223.
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