Esophageal Adenocarcinoma Methods and Protocols

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genes in this cancer [ 8 ]. In addition, it comes with considerably

less price than whole-genome sequencing [ 10 ].

Agrawal et al. published the first whole-exome sequencing on

twenty-three esophageal cancers (11 adenocarcinomas, 12 squa-

mous cell carcinomas) reporting significant differences in the spec-

trum of mutations between the two histological subtypes [ 13 ].

Copy number alterations are frequently assessed using array-

based technology. Recently, Wang and colleagues analyzed whole-

exome sequencing and whole-genome sequencing data for

detecting copy number alterations in esophageal adenocarcinoma

from a published large-scale genomic study of esophageal adeno-

carcinoma. They concluded that next-generation sequencing can

replace microarrays to detect copy number alterations in esopha-

geal adenocarcinoma. The study also reported whole-exome

sequencing as more cost-effective compared to whole-genome

sequencing [ 14 ].

Findlay et al. utilizing whole-exome sequencing of 30 paired

esophageal adenocarcinoma pre- and post-neoadjuvant chemo-

therapy noted that the mutational spectrum of genes in esophageal

adenocarcinoma, specifically TP53, may change during treatment.

They also noted that mutations in other genes may appear, indicat-

ing the dynamic nature of these cancers [ 15 ].

Even though whole-exome sequencing eliminates the high

redundancy of whole-genome sequencing, there are some limitations

to this approach, particularly in relation to the study of cancer

genomes. Whole-exome sequencing misses regions adjoining the

exons such as promoters, enhancers, and transcription factor binding

sites, unless the probe set is expanded to cover them [ 16 ]. In addi-

tion, whole-exome sequencing typically requires a sample containing

several fold more DNA than whole-genome sequencing as a result of

inefficiencies in multiple steps of the sequencing process [ 15 ].

Overall, whole-exome sequencing represents an immense

reduction in time, resources, and cost as well as allowing for more

effective detection of rare mutations through the improved cover-

age. It is a trustworthy and economical way to identify variations in

the genome of esophageal adenocarcinoma. The technique could

also observe molecular changes during treatment which could be

clinically useful in esophageal adenocarcinoma. Furthermore, the

limitations of the use of whole-exome sequencing will be signifi-

cantly diminished as technologies improve.

Targeted sequencing is a variation of re-sequencing when we need

to sequence only a small subset of the genome. In this method of

sequencing, known genes/exons are tested by designing custom-

made primers to target genes of interest [ 17 ]. Even though this

approach will not detect structural variants, targeted gene sequenc-

ing represents an economic way of identifying somatic mutations

1.3 Targeted
Next-Generation
Sequencing

Next Generation Sequencing and Esophageal Adenocarcinoma