Esophageal Adenocarcinoma Methods and Protocols

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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
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