231Alfred K. Lam (ed.), Esophageal Adenocarcinoma: Methods and Protocols, Methods in Molecular Biology, vol. 1756,
https://doi.org/10.1007/978-1-4939-7734-5_20, © Springer Science+Business Media, LLC 2018
Chapter 20
DNA Genome Sequencing in Esophageal Adenocarcinoma
Suja Pillai, Vinod Gopalan, and Alfred K. Lam
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 pow-
erful tool to identify inherited and acquired genetic alterations associated with the development of esopha-
geal 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 detect-
ing 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.
Key words Esophageal adenocarcinoma, Next-generation sequencing, Whole-genome sequencing,
Whole-exome sequencing, DNA1 Introduction
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
[ 1 ]. Simultaneous testing of multiple genes for mutation is afford-
able and time-efficient compared to conventional Sanger sequenc-
ing which is expensive and single gene testing is impractical in
clinical use [ 2 , 3 ].
Next-generation sequencing technologies have helped in
unveiling the genomic landscape of esophageal adenocarcinoma by
identifying several critical genes and pathways important in the
tumorigenesis of esophageal adenocarcinoma [ 4 ]. Depending on
the purpose, next-generation sequencing is applied in esophageal
adenocarcinoma research in the form of whole-genome, whole-
exome, targeted gene sequencing, RNA sequencing, and ChIP-
sequencing [ 4 ]. These technologies initiate opportunities to
translate the analysis of DNA into tools that can help in the devel-
opment of more effective personalized therapies in esophageal
adenocarcinoma [ 3 ].