Abstract
Next-generation sequencing refers to the high-throughput DNA sequencing technologies, which are capable of sequencing large numbers of different DNA sequences in a single/parallel reaction. It is a powerful tool to identify inherited and acquired genetic alterations associated with the development of esophageal adenocarcinoma. Whole-genome sequencing is the most comprehensive but expensive, whereas whole-exome sequencing is cost-effective but it only works for the known genes. Thus, second-generation sequencing methods can provide a complete picture of the esophageal adenocarcinoma genome by detecting and discovering different type of alterations in the cancer. This would help in diagnostics and will further help in developing personalized medicine in esophageal adenocarcinoma.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Mardis ER (2013) Next-generation sequencing platforms. Annu Rev Anal Chem 6:287–303
Pillai S, Gopalan V, Lo CY et al (2016) Silent genetic alterations identified by targeted next-generation sequencing in pheochromocytoma/paraganglioma: a clinicopathological correlations. Exp Mol Pathol 102:41–46
Zheng H, Wang Y, Tang C et al (2016) TP53, PIK3CA, FBXW7 and KRAS mutations in esophageal cancer identified by targeted sequencing. Cancer Genomics Proteomics 13:231–238
Weaver JM, Ross-Innes CS, Fitzgerald RC (2014) The ‘-omics’ revolution and esophageal adenocarcinoma. Nat Rev Gastroenterol Hepatol 11:19–27
van El CG, Cornel MC, Borry P et al (2013) Whole-genome sequencing in health care: recommendations of the European Society of Human Genetics. Eur J Hum Genet 21:1–5
Ding L, Wendl MC, Koboldt DC et al (2010) Analysis of next-generation genomic data in cancer: accomplishments and challenges. Hum Mol Genet 19:188–196
Ross-Innes CS, Becq J, Warren A et al (2015) Whole-genome sequencing provides new insights into the clonal architecture of Barrett’s esophagus and esophageal adenocarcinoma. Nat Genet 47:1038–1046
Dulak AM, Stojanov P, Peng S et al (2013) Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Nat Genet 45:478–486
Streppel MM, Lata S, DelaBastide M et al (2014) Next-generation sequencing of endoscopic biopsies identifies ARID1A as a tumor-suppressor gene in Barrett’s esophagus. Oncogene 33:347–357
Bainbridge MN, Wang M, Burgess DL et al (2010) Whole exome capture in solution with 3 Gbp of data. Genome Biol 11:R62
Meyerson M, Gabriel S, Getz G (2010) Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 11:685–696
Rabbani B, Tekin M, Mahdieh N (2014) The promise of whole-exome sequencing in medical genetics. J Hum Genet 59:5–15
Agrawal N, Jiao Y, Bettegowda C, Hutfless SM et al (2012) Comparative genomic analysis of esophageal adenocarcinoma and squamous cell carcinoma. Cancer Discov 2:899–905
Wang X, Li X, Cheng Y et al (2015) Copy number alterations detected by whole-exome and whole-genome sequencing of esophageal adenocarcinoma. Hum Genomics 9:22
Findlay JM, Castro-Giner F, Makino S et al (2016) Differential clonal evolution in esophageal cancers in response to neo-adjuvant chemotherapy. Nat Commun 7:11111
Parla JS, Iossifov I, Grabill I et al (2011) A comparative analysis of exome capture. Genome Biol 12:97
Welander J, Andreasson A, Juhlin CC et al (2014) Rare germline mutations identified by targeted next-generation sequencing of susceptibility genes in pheochromocytoma and paraganglioma. J Clin Endocrinol Metab 99:1352–1360
Quail MA, Smith M, Coupland P et al (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13:341
Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 43:376–380
Moorthie S, Mattocks CJ, Wright CF (2011) Review of massively parallel DNA sequencing technologies. HUGO J 5:1–12
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Pillai, S., Gopalan, V., Lam, A.K. (2018). DNA Genome Sequencing in Esophageal Adenocarcinoma. In: Lam, A. (eds) Esophageal Adenocarcinoma. Methods in Molecular Biology, vol 1756. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7734-5_20
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7734-5_20
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7733-8
Online ISBN: 978-1-4939-7734-5
eBook Packages: Springer Protocols