Esophageal Adenocarcinoma Methods and Protocols

195

Alfred K. Lam (ed.), Esophageal Adenocarcinoma: Methods and Protocols, Methods in Molecular Biology, vol. 1756,
https://doi.org/10.1007/978-1-4939-7734-5_18, © Springer Science+Business Media, LLC 2018

Chapter 18

Somatic DNA Copy-Number Alterations Detection

for Esophageal Adenocarcinoma Using Digital

Polymerase Chain Reaction

Katherine T. W. Lee, Vinod Gopalan, and Alfred K. Lam

Abstract

Somatic copy-number alterations are commonly found in cancer and play key roles in activating oncogenes
and deactivating tumor suppressor genes. Digital polymerase chain reaction is an effective way to detect
the changes in copy number. In esophageal adenocarcinoma, detection of somatic copy-number altera-
tions could predict the prognosis of patients as well as the response to therapy. This chapter will review the
methods involved in digital polymerase chain reaction for the research or potential clinical applications in
esophageal adenocarcinoma.

Key words Digital PCR, Esophageal adenocarcinoma, DNA, Copy-number alterations, Gene

therapy

1 Introduction

Reports have indicated that genomic mutations are frequent in

esophageal adenocarcinoma [ 1 ]. Among these mutations, somatic

copy-number alterations involve a greater fragment of the genome in

cancer compared to any other mutations [ 2 ]. Somatic copy-number

alterations are changes in the copy number of a genome fragment

within the somatic tissue. Somatic copy-number alterations are

exceptionally common in cancer [ 3 ] and play imperative roles in acti-

vating oncogenes [ 4 , 5 ] and deactivating tumor suppressor genes

[ 5 – 8 ]. Unraveling how somatic copy-number alterations affect the

biological phenotype has enabled further progresses in cancer diag-

nostics and therapeutics [ 9 , 10 ]. Table 1 summarizes the changes in

copy number noted in patients with esophageal adenocarcinoma.

In patients with esophageal adenocarcinoma that received neo-

adjuvant chemotherapy, those that showed a reduction in DNA

copy-number entropy were found to have improved survival despite

the lack of clear morphological evidence in response to the therapy

[ 42 ]. This indicates that copy-number changes might function as a