High throughput sequencing technology and its clinical application in circulating tumor DNA detection in patients with tumors.
Tecnología de secuenciación de alto rendimiento y su aplicación clínica en la detección de ADN tumoral circulante en pacientes oncológicos.
Palabras clave:
secuenciación de alto rendimiento, tumores, ADN tumoral circulante, diagnóstico de tumores, tratamiento de tumores, pronóstico de tumores
Resumen
La secuenciación de alto rendimiento (HTS) es una tecnología popular en el campo de la investigación genómica. Una característica distintiva de este método de secuenciación es su capacidad de generación de datos, que puede generar 100 veces más datos que la Plataforma de secuenciación Sanger de primera generación. La tecnología superconductora de alta temperatura es ampliamente utilizada debido a sus ventajas de alto rendimiento, alta sensibilidad, automatización, densidad de información y rentabilidad. No solo ayuda a tratar y diagnosticar múltiples enfermedades, sino que también proporciona nuevas ideas para la investigación de biología molecular tumoral. Además, la detección de ADN tumoral circulante (ctDNA) basada en la tecnología HTS se utiliza cada vez más ampliamente con fines clínicos. En esta revisión, nos centraremos en los principales logros y rendimiento de HTS, y resumiremos y analizaremos datos de primera mano de una amplia experiencia, discutiremos las ventajas y detalles específicos de cada sistema de secuenciación y resumiremos aún más las características de su aplicación clínica.
Descargas
La descarga de datos todavía no está disponible.
Citas
Siddiqui H, Nederbragt AJ, Lagesen K, Jeansson SL, Jakobsen KS. Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons. BMC Microbiol 2011;11:244.
Xiao H, Xiao H, Zhang Y, Guo L, Dou Z, Liu L, Zhu L, Feng W, Liu B, Hu B, Chen T, Liu G, Wen T. High-throughput sequencing unravels the cell heterogeneity of cerebrospinal fluid in the bacterial meningitis of children. Front Immunol 2022;13:872832.
Novakovic S, Tsui V, Semple T, Martelotto L, McCarthy DJ, Crismani W. SS- NIP-seq: A simple and rapid method for isolation of single-sperm nucleic acid for high-throughput sequencing. PLoS One 2022;17(9):e0275168.
Huang H, Yao T, Wu W, Zhai C, Guan T, Song Y, Sun Y, Xiao C, Liang P, Chen L. Specific microbes of saliva and vaginal fluid of Guangdong Han females based on 16S rDNA high-throughput sequencing. Int J Legal Med 2019;133(3):699-710.
Wang P, Wang J, Wang L, Lv J, Shao Y, He D. High throughput sequencing technology reveals alteration of lower respiratory tract microbiome in severe aspiration pneumonia and its association with inflammation. Infect Genet Evol 2023;116:105533.
Jiang C, Hou X, Gao X, Liu P, Guo X, Hu G, Li Q, Huang C, Li G, Fang W, Mai W, Wu C, Xu Z, Liu P. The 16S rDNA high-throughput sequencing correlation analysis of milk and gut microbial communities in mastitis Holstein cows. BMC Microbiol 2023;23(1):180.
Li D, Gao G, Li Z, Sun W, Li X, Chen N, Sun J, Yang Y. Profiling the T-cell receptor repertoire of patient with pleural tuberculosis by high-throughput sequencing. Immunol Lett 2014;162(1 Pt A):170-180.
Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, Hardison M, Person R, Bekheirnia MR, Leduc MS, Kirby A, Pham P, Scull J, Wang M, Ding Y, Plon SE, Lupski JR, Beaudet AL, Gibbs RA, Eng CM. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med 2013;369(16):1502- 1511.
Sun X, Liu X, Zhao Y, Tian G, Wang W. Detection of Circulating Tumor DNA in Plasma Using Targeted Sequencing. Methods Mol Biol 2023;2695:27-46.
Szász I, Kiss T, Mokánszki A, Koroknai V, Deák J, Patel V, Jámbor K, Ádány R, Balázs M. Identification of liquid biopsy- based mutations in colorectal cancer by targeted sequencing assays. Mol Cell Probes 2023;67:101888.
Sanger F, Coulson AR. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 1975;94(3):441-448.
Park SJ, Saito-Adachi M, Komiyama Y, Nakai K. Advances, practice, and clinical perspectives in high-throughput sequencing. Oral Dis 2016 Jul;22(5):353-64.
Levy SE, Boone BE. Next-Generation Sequencing Strategies. Cold Spring Harb Perspect Med 2019;9(7):a025791.
Pareek CS, Smoczynski R, Tretyn A. Sequencing technologies and genome sequencing. J Appl Genet 2011;52(4):413-435.
Reuter JA, Spacek DV, Snyder MP. High- throughput sequencing technologies. Mol Cell 2015;58(4):586-597.
Soon WW, Hariharan M, Snyder MP. High- throughput sequencing for biology and medicine. Mol Syst Biol 2013;9:640.
Slatko BE, Gardner AF, Ausubel FM. Overview of Next-Generation Sequencing Technologies. Curr Protoc Mol Biol 2018;122(1):e59.
Ronaghi M, Karamohamed S, Pettersson B, Uhlén M, Nyrén P. Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 1996;242(1):84-89.
Churko JM, Mantalas GL, Snyder MP, Wu JC. Overview of high throughput sequencing technologies to elucidate molecular pathways in cardiovascular diseases. Circ Res 2013;112(12):1613-1623.
Komarova N, Barkova D, Kuznetsov A. Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology. Int J Mol Sci 2020;21(22):8774.
Fedurco M, Romieu A, Williams S, Lawrence I, Turcatti G. BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res 2006;34(3):e22.
Pereira R, Oliveira J, Sousa M. Bioinformatics and computational tools for Next-generation sequencing analysis in clinical genetics. J Clin Med 2020;9(1):132.
Goldfeder RL, Wall DP, Khoury MJ, Ioannidis JPA, Ashley EA. Human genome sequencing at the population scale: a primer on high-throughput DNA sequencing and analysis. Am J Epidemiol 2017;186(8):1000-1009.
Wu H, Irizarry RA, Bravo HC. Intensity normalization improves color calling in SOLiD sequencing. Nat Methods 2010;7(5):336-337.
Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008;9:387-402.
Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet 2008;24(3):133-141.
Ambardar S, Gupta R, Trakroo D, Lal R, Vakhlu J. High Throughput Sequencing: an overview of sequencing chemistry. Indian J Microbiol 2016 ;56(4):394-404.
Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008; 26(10):1135-1145.
Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011;475(7356):348-352.
Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012;13:341.
McCarthy A. Third generation DNA sequencing: pacific biosciences’ single molecule real time technology. Chem Biol 2010;17(7):675-676.
Athanasopoulou K, Boti MA, Adamopoulos PG, Skourou PC, Scorilas A. Third-generation sequencing: the spearhead towards the radical transformation of modern genomics. Life (Basel). 2021;12(1):30.
Wang Y, Zhao Y, Bollas A, Wang Y, Au KF. Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 2021;39(11):1348-1365.
Akaçin İ, Ersoy Ş, Doluca O, Güngörmüşler M. Comparing the significance of the utilization of next generation and third generation sequencing technologies in microbial metagenomics. Microbiol Res 2022;264:127154.
Petersen LM, Martin IW, Moschetti WE, Kershaw CM, Tsongalis GJ. Third-generation sequencing in the clinical laboratory: exploring the advantages and challenges of Nanopore Sequencing. J Clin Microbiol 2019;58(1):e01315-1319.
Ozsolak F. Third-generation sequencing techniques and applications to drug discovery. Expert Opin Drug Discov 2012;7(3):231-243.
Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M. Comparison of next-generation sequencing systems. J Biomed Bio-technol 2012;2012:251364.
Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N, Bartlett BR, Wang H, Luber B, Alani RM, Antonarakis ES, Azad NS, Bardelli A, Brem H, Cameron JL, Lee CC, Fecher LA, Gallia GL, Gibbs P, Le D, Giuntoli RL, Goggins M, Hogarty MD, Holdhoff M, Hong SM, Jiao Y, Juhl HH, Kim JJ, Siravegna G, Laheru DA, Lauricella C, Lim M, Lipson EJ, Marie SK, Netto GJ, Oliner KS, Olivi A, Olsson L, Riggins GJ, Sartore-Bianchi A, Schmidt K, Shih lM, Oba-Shinjo SM, Siena S, Theodorescu D, Tie J, Harkins TT, Veronese S, Wang TL, Weingart JD, Wolf-gang CL, Wood LD, Xing D, Hruban RH, Wu J, Allen PJ, Schmidt CM, Choti MA, Velculescu VE, Kinzler KW, Vogelstein B, Papadopoulos N, Diaz LA Jr. Detection of circulating tumor DNA in early and late stage human malignancies. Sci Transl Med 2014;6(224):224ra24.
Taylor C, Chacko S, Davey M, Lacroix J, MacPherson A, Finn N, Wajnberg G, Ghosh A, Crapoulet N, Lewis SM, Ouellette RJ. Peptide-affinity precipitation of extracellular vesicles and cell-free DNA improves sequencing performance for the detection of pathogenic mutations in lung cancer patient plasma. Int J Mol Sci 2020;21(23):9083.
Govind KB, Koppaka D, Dasappa L, Jacob LA, C Babu SM, Lokesh NK, Haleshappa RA, Rajeev LK, Saldanha SC, Abhishek A, Asati V, Chethan R, Ramprasad VL. Detection of clinically relevant epidermal growth factor receptor pathway mutations in circulating cell-free tumor DNA using next generation sequencing in squamous cell carcinoma lung. South Asian J Cancer 2019;8(4):247-249.
Yamamoto G, Kikuchi M, Kobayashi S, Arai Y, Fujiyoshi K, Wakatsuki T, Kakuta M, Yamane Y, Iijima Y, Mizutani H, Nakajima Y, Sudo J, Kinoshita H, Kurimoto F, Akiyama H, Uramoto H, Sakai H, Akagi Y, Akagi K. Routine genetic testing of lung cancer specimens derived from surgery, bronchoscopy and fluid aspiration by next generation sequencing. Int J Oncol 2017;50(5):1579-1589.
Mohan S, Foy V, Ayub M, Leong HS, Schofield P, Sahoo S, Descamps T, Kilerci B, Smith NK, Carter M, Priest L, Zhou C, Carr TH, Miller C, Faivre-Finn C, Black-hall F, Rothwell DG, Dive C, Brady G. Profiling of circulating free DNA using targeted and genome-wide sequencing in patients with SCLC. J Thorac Oncol 2020;15(2):216-230.
Peng M, Xie Y, Li X, Qian Y, Tu X, Yao X, Cheng F, Xu F, Kong D, He B, Liu C, Cao F, Yang H, Yu F, Xu C, Tian G. Resectable lung lesions malignancy assessment and cancer detection by ultra-deep sequencing of targeted gene mutations in plasma cell- free DNA. J Med Genet 2019;56(10):647- 653.
Beltran H, Romanel A, Conteduca V, Casiraghi N, Sigouros M, Franceschini GM, Orlando F, Fedrizzi T, Ku SY, Dann E, Alonso A, Mosquera JM, Sboner A, Xiang J, Elemento O, Nanus DM, Tagawa ST, Benelli M, Demichelis F. Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer. J Clin Invest 2020;130(4):1653- 1668.
Cai J, Chen L, Zhang Z, Zhang X, Lu X, Liu W, Shi G, Ge Y, Gao P, Yang Y, Ke A, Xiao L, Dong R, Zhu Y, Yang X, Wang J, Zhu T, Yang D, Huang X, Sui C, Qiu S, Shen F, Sun H, Zhou W, Zhou J, Nie J, Zeng C, Stroup EK, Zhang X, Chiu BC, Lau WY, He C, Wang H, Zhang W, Fan J. Genome-wide mapping of 5-hydroxymethylcytosines in circulating cell-free DNA as a non-invasive approach for early detection of hepatocellular carcinoma. Gut 2019;68(12):2195-2205.
Kotoh Y, Suehiro Y, Saeki I, Hoshida T, Maeda M, Iwamoto T, Matsumoto T, Hidaka I, Ishikawa T, Takami T, Higaki S, Fujii I, Suzuki C, Shindo Y, Tokumitsu Y, Nagano H, Sakaida I, Yamasaki T. Novel liquid biopsy test based on a sensitive methylated SEPT9 assay for diagnosing hepatocellular carcinoma. Hepatol Commun 2020;4(3):461-470.
Kopetz S, Guthrie KA, Morris VK, Lenz HJ, Magliocco AM, Maru D, Yan Y, Lanman R, Manyam G, Hong DS, Sorokin A, Atreya CE, Diaz LA, Allegra C, Raghav KP, Wang SE, Lieu CH, McDonough SL, Philip PA, Hochster HS. Randomized trial of irinotecan and cetuximab with or without vemurafenib in BRAF-Mutant metastatic colorectal cancer (SWOG S1406). J Clin Oncol 2021;39(4):285-294.
Zhou Y, Zhang X, Wu X, Zhou Y, Zhang B, Liu X, Wu X, Li Y, Shen L, Li J. A prospective multicenter phase II study on the efficacy and safety of dasatinib in the treatment of metastatic gastrointestinal stromal tumors failed by imatinib and sunitinib and analysis of NGS in peripheral blood. Cancer Med 2020;9(17):6225-6233.
Grommes C, Tang SS, Wolfe J, Kaley TJ, Daras M, Pentsova EI, Piotrowski AF, Stone J, Lin A, Nolan CP, Manne M, Codega P, Campos C, Viale A, Thomas AA, Berger MF, Hatzoglou V, Reiner AS, Panageas KS, DeAngelis LM, Mellinghoff IK. Phase 1b trial of an ibrutinib-based combination therapy in recurrent/refractory CNS lymphoma. Blood 2019 ;133(5):436-445.
Hayashi H, Takiguchi Y, Minami H, Akiyoshi K, Segawa Y, Ueda H, Iwamoto Y, Kondoh C, Matsumoto K, Takahashi S, Yasui H, Sawa T, Onozawa Y, Chiba Y, Togashi Y, Fujita Y, Sakai K, Tomida S, Nishio K, Nakagawa K. Site-specific and targeted therapy based on molecular profiling by Next-Generation Sequencing for cancer of unknown primary site: a nonrandomized Phase 2 Clinical Trial. JAMA Oncol 2020;6(12):1931-1938.
Radovich M, Jiang G, Hancock BA, Chitambar C, Nanda R, Falkson C, Lynce FC, Gallagher C, Isaacs C, Blaya M, Paplomata E, Walling R, Daily K, Mahtani R, Thompson MA, Graham R, Cooper ME, Pavlick DC, Albacker LA, Gregg J, Solzak JP, Chen YH, Bales CL, Cantor E, Shen F, Storniolo AMV, Badve S, Ballinger TJ, Chang CL, Zhong Y, Savran C, Miller KD, Schneider BP. Association of Circulating Tumor DNA and Circulating Tumor Cells after neoadjuvant chemotherapy with disease recurrence in patients with Triple-Negative Breast Cancer: pre-planned secondary analysis of the BRE12- 158 randomized clinical trial. JAMA Oncol 2020;6(9):1410-1415.
Li Y, Guo D, Zhang Y, Wang L, Sun T, Li Z, Zhang X, Wang S, Chen Y, Wu A. Rapid screening for individualized chemotherapy optimization of colorectal cancer: A novel conditional reprogramming technology-based functional diagnostic assay. Transl Oncol 2021;14(1):100935.
Zhang W, Qi L, Liu Z, He S, Wang CZ, Wu Y, Han L, Liu Z, Fu Z, Tu C, Li Z. Integrated multiomic analysis and high-through put screening reveal potential gene targets and synergetic drug combinations for osteosarcoma therapy. MedComm (2020) 2023;4(4):e317.
Cazet AS, Hui MN, Elsworth BL, Wu SZ, Roden D, Chan CL, Skhinas JN, Collot R, Yang J, Harvey K, Johan MZ, Cooper C, Nair R, Herrmann D, McFarland A, Deng N, Ruiz-Borrego M, Rojo F, Trigo JM, Bezares S, Caballero R, Lim E, Timpson P, O’Toole S, Watkins DN, Cox TR, Samuel MS, Martín M, Swarbrick A. Targeting stromal remodeling and cancer stem cell plasticity overcomes chemoresistance in triple negative breast cancer. Nat Commun 2018;9(1):2897.
Roesel R, Epistolio S, Molinari F, Saletti P, De Dosso S, Valli M, Franzetti-Pellanda A, Deantonio L, Biggiogero M, Spina P, Popeskou SG, Cristaudi A, Mongelli F, Mazzucchelli L, Stefanini FM, Frattini M, Christoforidis D. A pilot, prospective, observational study to investigate the value of NGS in liquid biopsies to predict tumor response after neoadjuvant chemo-radio-therapy in patients with locally advanced rectal cancer: The LiBReCa Study. Front Oncol 2022;12:900945.
Luo BH, Huang JQ, Huang CY, Tian P, Chen AZ, Wu WH, Ma XM, Yuan YX, Yu L. Screening of lymphoma radiotherapy-resistant genes with CRISPR Activation Library. Pharmgenomics Pers Med 2023;16:67-80.
Kim JS, Yang S, Jeong K, Kim DY, Kim K, Kang HC. Plasma cell-free DNA in uterine cervical cancer: therapeutic monitoring and prognostic values after radical radiotherapy. Cancer Res Treat 2023;55(2):659-670.
Cargnin S, Barizzone N, Basagni C, Pisani C, Ferrara E, Masini L, D’Alfonso S, Krengli M, Terrazzino S. Targeted Next-Generation Sequencing for the identification of genetic predictors of radiation- induced late skin toxicity in breast cancer patients: a preliminary study. J Pers Med 2021;11(10):967.
Tie J, Cohen JD, Wang Y, Christie M, Simons K, Lee M, Wong R, Kosmider S, Ananda S, McKendrick J, Lee B, Cho JH, Faragher I, Jones IT, Ptak J, Schaeffer MJ, Silliman N, Dobbyn L, Li L, Tomasetti C, Papadopoulos N, Kinzler KW, Vogelstein B, Gibbs P. Circulating Tumor DNA analyses as markers of recurrence risk and benefit of Adjuvant Therapy for Stage III Colon Cancer. JAMA Oncol 2019;5(12):1710- 1717.
Ma F, Guan Y, Yi Z, Chang L, Li Q, Chen S, Zhu W, Guan X, Li C, Qian H, Xia X, Yang L, Zhang J, Husain H, Liao Z, Futreal A, Huang J, Yi X, Xu B. Assessing tumor heterogeneity using ctDNA to predict and monitor therapeutic response in metastatic breast cancer. Int J Cancer 2020;146(5):1359-1368.
Elez E, Chianese C, Sanz-García E, Martinelli E, Noguerido A, Mancuso FM, Caratù G, Matito J, Grasselli J, Car
done C, Esposito Abate R, Martini G, Santos C, Macarulla T, Argilés G, Capdevila J, Garcia A, Mulet N, Maiello E, Normanno N, Jones F, Tabernero J, Ciardello F, Salazar R, Vivancos A. Impact of circulating tumor DNA mutant allele fraction on prognosis in RAS-mutant metastatic colorectal cancer. Mol Oncol 2019;13(9):1827-1835.
Zhao W, Qiu L, Liu H, Xu Y, Zhan M, Zhang W, Xin Y, He X, Yang X, Bai J, Xiao J, Guan Y, Li Q, Chang L, Yi X, Li Y, Chen X, Lu L. Circulating tumor DNA as a potential prognostic and predictive bio- marker during interventional therapy of unresectable primary liver cancer. J Gastrointest Oncol 2020;11(5):1065-1077.
Anagnostou V, Forde PM, White JR, Niknafs N, Hruban C, Naidoo J, Marrone K, Sivakumar IKA, Bruhm DC, Rosner S, Phallen J, Leal A, Adleff V, Smith KN, Cottrell TR, Rhymee L, Palsgrove DN, Hann CL, Levy B, Feliciano J, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Isbell JM, Sauter JL, Taube J, Scharpf RB, Karchin R, Pardoll DM, Chaft JE, Hellmann MD, Brahmer JR, Velculescu VE. Dynamics of tumor and immune responses during immune checkpoint blockade in Non-Small Cell Lung Cancer. Cancer Res 2019;79(6):1214-1225.
Zhang Q, Luo J, Wu S, Si H, Gao C, Xu W, Abdullah SE, Higgs BW, Dennis PA, van der Heijden MS, Segal NH, Chaft JE, Hembrough T, Barrett JC, Hellmann MD. Prognostic and predictive impact of Circulating Tumor DNA in patients with advanced cancers treated with immune checkpoint blockade. Cancer Discov 2020;10(12):1842-1853.
Xiao H, Xiao H, Zhang Y, Guo L, Dou Z, Liu L, Zhu L, Feng W, Liu B, Hu B, Chen T, Liu G, Wen T. High-throughput sequencing unravels the cell heterogeneity of cerebrospinal fluid in the bacterial meningitis of children. Front Immunol 2022;13:872832.
Novakovic S, Tsui V, Semple T, Martelotto L, McCarthy DJ, Crismani W. SS- NIP-seq: A simple and rapid method for isolation of single-sperm nucleic acid for high-throughput sequencing. PLoS One 2022;17(9):e0275168.
Huang H, Yao T, Wu W, Zhai C, Guan T, Song Y, Sun Y, Xiao C, Liang P, Chen L. Specific microbes of saliva and vaginal fluid of Guangdong Han females based on 16S rDNA high-throughput sequencing. Int J Legal Med 2019;133(3):699-710.
Wang P, Wang J, Wang L, Lv J, Shao Y, He D. High throughput sequencing technology reveals alteration of lower respiratory tract microbiome in severe aspiration pneumonia and its association with inflammation. Infect Genet Evol 2023;116:105533.
Jiang C, Hou X, Gao X, Liu P, Guo X, Hu G, Li Q, Huang C, Li G, Fang W, Mai W, Wu C, Xu Z, Liu P. The 16S rDNA high-throughput sequencing correlation analysis of milk and gut microbial communities in mastitis Holstein cows. BMC Microbiol 2023;23(1):180.
Li D, Gao G, Li Z, Sun W, Li X, Chen N, Sun J, Yang Y. Profiling the T-cell receptor repertoire of patient with pleural tuberculosis by high-throughput sequencing. Immunol Lett 2014;162(1 Pt A):170-180.
Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, Hardison M, Person R, Bekheirnia MR, Leduc MS, Kirby A, Pham P, Scull J, Wang M, Ding Y, Plon SE, Lupski JR, Beaudet AL, Gibbs RA, Eng CM. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med 2013;369(16):1502- 1511.
Sun X, Liu X, Zhao Y, Tian G, Wang W. Detection of Circulating Tumor DNA in Plasma Using Targeted Sequencing. Methods Mol Biol 2023;2695:27-46.
Szász I, Kiss T, Mokánszki A, Koroknai V, Deák J, Patel V, Jámbor K, Ádány R, Balázs M. Identification of liquid biopsy- based mutations in colorectal cancer by targeted sequencing assays. Mol Cell Probes 2023;67:101888.
Sanger F, Coulson AR. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 1975;94(3):441-448.
Park SJ, Saito-Adachi M, Komiyama Y, Nakai K. Advances, practice, and clinical perspectives in high-throughput sequencing. Oral Dis 2016 Jul;22(5):353-64.
Levy SE, Boone BE. Next-Generation Sequencing Strategies. Cold Spring Harb Perspect Med 2019;9(7):a025791.
Pareek CS, Smoczynski R, Tretyn A. Sequencing technologies and genome sequencing. J Appl Genet 2011;52(4):413-435.
Reuter JA, Spacek DV, Snyder MP. High- throughput sequencing technologies. Mol Cell 2015;58(4):586-597.
Soon WW, Hariharan M, Snyder MP. High- throughput sequencing for biology and medicine. Mol Syst Biol 2013;9:640.
Slatko BE, Gardner AF, Ausubel FM. Overview of Next-Generation Sequencing Technologies. Curr Protoc Mol Biol 2018;122(1):e59.
Ronaghi M, Karamohamed S, Pettersson B, Uhlén M, Nyrén P. Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 1996;242(1):84-89.
Churko JM, Mantalas GL, Snyder MP, Wu JC. Overview of high throughput sequencing technologies to elucidate molecular pathways in cardiovascular diseases. Circ Res 2013;112(12):1613-1623.
Komarova N, Barkova D, Kuznetsov A. Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology. Int J Mol Sci 2020;21(22):8774.
Fedurco M, Romieu A, Williams S, Lawrence I, Turcatti G. BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res 2006;34(3):e22.
Pereira R, Oliveira J, Sousa M. Bioinformatics and computational tools for Next-generation sequencing analysis in clinical genetics. J Clin Med 2020;9(1):132.
Goldfeder RL, Wall DP, Khoury MJ, Ioannidis JPA, Ashley EA. Human genome sequencing at the population scale: a primer on high-throughput DNA sequencing and analysis. Am J Epidemiol 2017;186(8):1000-1009.
Wu H, Irizarry RA, Bravo HC. Intensity normalization improves color calling in SOLiD sequencing. Nat Methods 2010;7(5):336-337.
Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008;9:387-402.
Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet 2008;24(3):133-141.
Ambardar S, Gupta R, Trakroo D, Lal R, Vakhlu J. High Throughput Sequencing: an overview of sequencing chemistry. Indian J Microbiol 2016 ;56(4):394-404.
Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008; 26(10):1135-1145.
Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011;475(7356):348-352.
Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012;13:341.
McCarthy A. Third generation DNA sequencing: pacific biosciences’ single molecule real time technology. Chem Biol 2010;17(7):675-676.
Athanasopoulou K, Boti MA, Adamopoulos PG, Skourou PC, Scorilas A. Third-generation sequencing: the spearhead towards the radical transformation of modern genomics. Life (Basel). 2021;12(1):30.
Wang Y, Zhao Y, Bollas A, Wang Y, Au KF. Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 2021;39(11):1348-1365.
Akaçin İ, Ersoy Ş, Doluca O, Güngörmüşler M. Comparing the significance of the utilization of next generation and third generation sequencing technologies in microbial metagenomics. Microbiol Res 2022;264:127154.
Petersen LM, Martin IW, Moschetti WE, Kershaw CM, Tsongalis GJ. Third-generation sequencing in the clinical laboratory: exploring the advantages and challenges of Nanopore Sequencing. J Clin Microbiol 2019;58(1):e01315-1319.
Ozsolak F. Third-generation sequencing techniques and applications to drug discovery. Expert Opin Drug Discov 2012;7(3):231-243.
Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M. Comparison of next-generation sequencing systems. J Biomed Bio-technol 2012;2012:251364.
Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N, Bartlett BR, Wang H, Luber B, Alani RM, Antonarakis ES, Azad NS, Bardelli A, Brem H, Cameron JL, Lee CC, Fecher LA, Gallia GL, Gibbs P, Le D, Giuntoli RL, Goggins M, Hogarty MD, Holdhoff M, Hong SM, Jiao Y, Juhl HH, Kim JJ, Siravegna G, Laheru DA, Lauricella C, Lim M, Lipson EJ, Marie SK, Netto GJ, Oliner KS, Olivi A, Olsson L, Riggins GJ, Sartore-Bianchi A, Schmidt K, Shih lM, Oba-Shinjo SM, Siena S, Theodorescu D, Tie J, Harkins TT, Veronese S, Wang TL, Weingart JD, Wolf-gang CL, Wood LD, Xing D, Hruban RH, Wu J, Allen PJ, Schmidt CM, Choti MA, Velculescu VE, Kinzler KW, Vogelstein B, Papadopoulos N, Diaz LA Jr. Detection of circulating tumor DNA in early and late stage human malignancies. Sci Transl Med 2014;6(224):224ra24.
Taylor C, Chacko S, Davey M, Lacroix J, MacPherson A, Finn N, Wajnberg G, Ghosh A, Crapoulet N, Lewis SM, Ouellette RJ. Peptide-affinity precipitation of extracellular vesicles and cell-free DNA improves sequencing performance for the detection of pathogenic mutations in lung cancer patient plasma. Int J Mol Sci 2020;21(23):9083.
Govind KB, Koppaka D, Dasappa L, Jacob LA, C Babu SM, Lokesh NK, Haleshappa RA, Rajeev LK, Saldanha SC, Abhishek A, Asati V, Chethan R, Ramprasad VL. Detection of clinically relevant epidermal growth factor receptor pathway mutations in circulating cell-free tumor DNA using next generation sequencing in squamous cell carcinoma lung. South Asian J Cancer 2019;8(4):247-249.
Yamamoto G, Kikuchi M, Kobayashi S, Arai Y, Fujiyoshi K, Wakatsuki T, Kakuta M, Yamane Y, Iijima Y, Mizutani H, Nakajima Y, Sudo J, Kinoshita H, Kurimoto F, Akiyama H, Uramoto H, Sakai H, Akagi Y, Akagi K. Routine genetic testing of lung cancer specimens derived from surgery, bronchoscopy and fluid aspiration by next generation sequencing. Int J Oncol 2017;50(5):1579-1589.
Mohan S, Foy V, Ayub M, Leong HS, Schofield P, Sahoo S, Descamps T, Kilerci B, Smith NK, Carter M, Priest L, Zhou C, Carr TH, Miller C, Faivre-Finn C, Black-hall F, Rothwell DG, Dive C, Brady G. Profiling of circulating free DNA using targeted and genome-wide sequencing in patients with SCLC. J Thorac Oncol 2020;15(2):216-230.
Peng M, Xie Y, Li X, Qian Y, Tu X, Yao X, Cheng F, Xu F, Kong D, He B, Liu C, Cao F, Yang H, Yu F, Xu C, Tian G. Resectable lung lesions malignancy assessment and cancer detection by ultra-deep sequencing of targeted gene mutations in plasma cell- free DNA. J Med Genet 2019;56(10):647- 653.
Beltran H, Romanel A, Conteduca V, Casiraghi N, Sigouros M, Franceschini GM, Orlando F, Fedrizzi T, Ku SY, Dann E, Alonso A, Mosquera JM, Sboner A, Xiang J, Elemento O, Nanus DM, Tagawa ST, Benelli M, Demichelis F. Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer. J Clin Invest 2020;130(4):1653- 1668.
Cai J, Chen L, Zhang Z, Zhang X, Lu X, Liu W, Shi G, Ge Y, Gao P, Yang Y, Ke A, Xiao L, Dong R, Zhu Y, Yang X, Wang J, Zhu T, Yang D, Huang X, Sui C, Qiu S, Shen F, Sun H, Zhou W, Zhou J, Nie J, Zeng C, Stroup EK, Zhang X, Chiu BC, Lau WY, He C, Wang H, Zhang W, Fan J. Genome-wide mapping of 5-hydroxymethylcytosines in circulating cell-free DNA as a non-invasive approach for early detection of hepatocellular carcinoma. Gut 2019;68(12):2195-2205.
Kotoh Y, Suehiro Y, Saeki I, Hoshida T, Maeda M, Iwamoto T, Matsumoto T, Hidaka I, Ishikawa T, Takami T, Higaki S, Fujii I, Suzuki C, Shindo Y, Tokumitsu Y, Nagano H, Sakaida I, Yamasaki T. Novel liquid biopsy test based on a sensitive methylated SEPT9 assay for diagnosing hepatocellular carcinoma. Hepatol Commun 2020;4(3):461-470.
Kopetz S, Guthrie KA, Morris VK, Lenz HJ, Magliocco AM, Maru D, Yan Y, Lanman R, Manyam G, Hong DS, Sorokin A, Atreya CE, Diaz LA, Allegra C, Raghav KP, Wang SE, Lieu CH, McDonough SL, Philip PA, Hochster HS. Randomized trial of irinotecan and cetuximab with or without vemurafenib in BRAF-Mutant metastatic colorectal cancer (SWOG S1406). J Clin Oncol 2021;39(4):285-294.
Zhou Y, Zhang X, Wu X, Zhou Y, Zhang B, Liu X, Wu X, Li Y, Shen L, Li J. A prospective multicenter phase II study on the efficacy and safety of dasatinib in the treatment of metastatic gastrointestinal stromal tumors failed by imatinib and sunitinib and analysis of NGS in peripheral blood. Cancer Med 2020;9(17):6225-6233.
Grommes C, Tang SS, Wolfe J, Kaley TJ, Daras M, Pentsova EI, Piotrowski AF, Stone J, Lin A, Nolan CP, Manne M, Codega P, Campos C, Viale A, Thomas AA, Berger MF, Hatzoglou V, Reiner AS, Panageas KS, DeAngelis LM, Mellinghoff IK. Phase 1b trial of an ibrutinib-based combination therapy in recurrent/refractory CNS lymphoma. Blood 2019 ;133(5):436-445.
Hayashi H, Takiguchi Y, Minami H, Akiyoshi K, Segawa Y, Ueda H, Iwamoto Y, Kondoh C, Matsumoto K, Takahashi S, Yasui H, Sawa T, Onozawa Y, Chiba Y, Togashi Y, Fujita Y, Sakai K, Tomida S, Nishio K, Nakagawa K. Site-specific and targeted therapy based on molecular profiling by Next-Generation Sequencing for cancer of unknown primary site: a nonrandomized Phase 2 Clinical Trial. JAMA Oncol 2020;6(12):1931-1938.
Radovich M, Jiang G, Hancock BA, Chitambar C, Nanda R, Falkson C, Lynce FC, Gallagher C, Isaacs C, Blaya M, Paplomata E, Walling R, Daily K, Mahtani R, Thompson MA, Graham R, Cooper ME, Pavlick DC, Albacker LA, Gregg J, Solzak JP, Chen YH, Bales CL, Cantor E, Shen F, Storniolo AMV, Badve S, Ballinger TJ, Chang CL, Zhong Y, Savran C, Miller KD, Schneider BP. Association of Circulating Tumor DNA and Circulating Tumor Cells after neoadjuvant chemotherapy with disease recurrence in patients with Triple-Negative Breast Cancer: pre-planned secondary analysis of the BRE12- 158 randomized clinical trial. JAMA Oncol 2020;6(9):1410-1415.
Li Y, Guo D, Zhang Y, Wang L, Sun T, Li Z, Zhang X, Wang S, Chen Y, Wu A. Rapid screening for individualized chemotherapy optimization of colorectal cancer: A novel conditional reprogramming technology-based functional diagnostic assay. Transl Oncol 2021;14(1):100935.
Zhang W, Qi L, Liu Z, He S, Wang CZ, Wu Y, Han L, Liu Z, Fu Z, Tu C, Li Z. Integrated multiomic analysis and high-through put screening reveal potential gene targets and synergetic drug combinations for osteosarcoma therapy. MedComm (2020) 2023;4(4):e317.
Cazet AS, Hui MN, Elsworth BL, Wu SZ, Roden D, Chan CL, Skhinas JN, Collot R, Yang J, Harvey K, Johan MZ, Cooper C, Nair R, Herrmann D, McFarland A, Deng N, Ruiz-Borrego M, Rojo F, Trigo JM, Bezares S, Caballero R, Lim E, Timpson P, O’Toole S, Watkins DN, Cox TR, Samuel MS, Martín M, Swarbrick A. Targeting stromal remodeling and cancer stem cell plasticity overcomes chemoresistance in triple negative breast cancer. Nat Commun 2018;9(1):2897.
Roesel R, Epistolio S, Molinari F, Saletti P, De Dosso S, Valli M, Franzetti-Pellanda A, Deantonio L, Biggiogero M, Spina P, Popeskou SG, Cristaudi A, Mongelli F, Mazzucchelli L, Stefanini FM, Frattini M, Christoforidis D. A pilot, prospective, observational study to investigate the value of NGS in liquid biopsies to predict tumor response after neoadjuvant chemo-radio-therapy in patients with locally advanced rectal cancer: The LiBReCa Study. Front Oncol 2022;12:900945.
Luo BH, Huang JQ, Huang CY, Tian P, Chen AZ, Wu WH, Ma XM, Yuan YX, Yu L. Screening of lymphoma radiotherapy-resistant genes with CRISPR Activation Library. Pharmgenomics Pers Med 2023;16:67-80.
Kim JS, Yang S, Jeong K, Kim DY, Kim K, Kang HC. Plasma cell-free DNA in uterine cervical cancer: therapeutic monitoring and prognostic values after radical radiotherapy. Cancer Res Treat 2023;55(2):659-670.
Cargnin S, Barizzone N, Basagni C, Pisani C, Ferrara E, Masini L, D’Alfonso S, Krengli M, Terrazzino S. Targeted Next-Generation Sequencing for the identification of genetic predictors of radiation- induced late skin toxicity in breast cancer patients: a preliminary study. J Pers Med 2021;11(10):967.
Tie J, Cohen JD, Wang Y, Christie M, Simons K, Lee M, Wong R, Kosmider S, Ananda S, McKendrick J, Lee B, Cho JH, Faragher I, Jones IT, Ptak J, Schaeffer MJ, Silliman N, Dobbyn L, Li L, Tomasetti C, Papadopoulos N, Kinzler KW, Vogelstein B, Gibbs P. Circulating Tumor DNA analyses as markers of recurrence risk and benefit of Adjuvant Therapy for Stage III Colon Cancer. JAMA Oncol 2019;5(12):1710- 1717.
Ma F, Guan Y, Yi Z, Chang L, Li Q, Chen S, Zhu W, Guan X, Li C, Qian H, Xia X, Yang L, Zhang J, Husain H, Liao Z, Futreal A, Huang J, Yi X, Xu B. Assessing tumor heterogeneity using ctDNA to predict and monitor therapeutic response in metastatic breast cancer. Int J Cancer 2020;146(5):1359-1368.
Elez E, Chianese C, Sanz-García E, Martinelli E, Noguerido A, Mancuso FM, Caratù G, Matito J, Grasselli J, Car
done C, Esposito Abate R, Martini G, Santos C, Macarulla T, Argilés G, Capdevila J, Garcia A, Mulet N, Maiello E, Normanno N, Jones F, Tabernero J, Ciardello F, Salazar R, Vivancos A. Impact of circulating tumor DNA mutant allele fraction on prognosis in RAS-mutant metastatic colorectal cancer. Mol Oncol 2019;13(9):1827-1835.
Zhao W, Qiu L, Liu H, Xu Y, Zhan M, Zhang W, Xin Y, He X, Yang X, Bai J, Xiao J, Guan Y, Li Q, Chang L, Yi X, Li Y, Chen X, Lu L. Circulating tumor DNA as a potential prognostic and predictive bio- marker during interventional therapy of unresectable primary liver cancer. J Gastrointest Oncol 2020;11(5):1065-1077.
Anagnostou V, Forde PM, White JR, Niknafs N, Hruban C, Naidoo J, Marrone K, Sivakumar IKA, Bruhm DC, Rosner S, Phallen J, Leal A, Adleff V, Smith KN, Cottrell TR, Rhymee L, Palsgrove DN, Hann CL, Levy B, Feliciano J, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Isbell JM, Sauter JL, Taube J, Scharpf RB, Karchin R, Pardoll DM, Chaft JE, Hellmann MD, Brahmer JR, Velculescu VE. Dynamics of tumor and immune responses during immune checkpoint blockade in Non-Small Cell Lung Cancer. Cancer Res 2019;79(6):1214-1225.
Zhang Q, Luo J, Wu S, Si H, Gao C, Xu W, Abdullah SE, Higgs BW, Dennis PA, van der Heijden MS, Segal NH, Chaft JE, Hembrough T, Barrett JC, Hellmann MD. Prognostic and predictive impact of Circulating Tumor DNA in patients with advanced cancers treated with immune checkpoint blockade. Cancer Discov 2020;10(12):1842-1853.
Publicado
2024-12-02
Cómo citar
Xu, C., Zhou, D., & Zhu, M. (2024). High throughput sequencing technology and its clinical application in circulating tumor DNA detection in patients with tumors.: Tecnología de secuenciación de alto rendimiento y su aplicación clínica en la detección de ADN tumoral circulante en pacientes oncológicos. Investigación Clínica, 65(4), 476-494. https://doi.org/10.54817/IC.v65n4a09
Sección
Revisiones
