218
disease-causing genetic variant identification [ 28 ], and examina-
tion of targeted genomic regions with large sample sizes [ 29 – 31 ].2 Materials
Prepare all reagents using ultrapure water and molecular grade
chemicals. Ensure all plastic ware and reagents are DNase-free and
sterile. Store all reagents at room temperature unless indicated. Try
to reduce the amount of freeze–thaw cycles for each reagent by
dividing them in aliquots and storing them. Wear appropriate per-
sonal protective equipment during experiments to safeguard oneself
against laboratory dangers and minimize potential contamination.
In addition, follow the rules and regulations for waste disposal.Refer to Chapter 18 , Subheading 2.1.- DNase-free water.
- Micropipettes (10, 20, 200, and 1000 μL).
2.1 Tissue Collection
and DNA Extraction
2.2 PCR Run and
Cleanup
Table 2
Clusters of genes implicated in esophageal adenocarcinoma
Gene clusters Implications in esophageal adenocarcinoma Ref.ELMO1, DOCK2 Dimerization partners and intracellular mediators of Rho
family GTPase, RAC1 a gene previously implicated with
other cancers[ 3 ]SMAD4, KRAS Amplification of the oncogene KRAS and deletion of the
SMAD4 tumor suppressor gene may facilitate esophageal
adenocarcinoma progression[ 1 ]TP53, CDKN2A, APC Loss of CDKN2A followed by TP53 inactivation and
aneuploidy led to esophageal adenocarcinoma C
progression from Barrett esophagus[ 10 ]TP53, CDKN2A, and APC combined mutations may be
useful for dysplasia and cancer surveillance in patients with
Barrett esophagus[ 15 ]Combination of LOH and DNA abnormalities in 17p and 9p
provides better risk protection than any single TP53,
CDKN2A, or DNA abnormality alone in esophageal
adenocarcinoma[ 16 ]SKI, PRKZ Deleted in esophageal adenocarcinoma and could possibly
function as a novel biomarker for esophageal
adenocarcinoma[ 39 ]Katherine T. W. Lee et al.