Computational Systems Biology Methods and Protocols.7z

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EGFR have been shown to be hyperresponsive to the EGFR tyro-
sine kinase inhibitor (TKI) gefitinib (IRESSA).
The clinical utility of liquid biopsy-based techniques for treat-
ment decision-making is well exemplified by the determination of
EGFR mutations in blood ctDNA to guide the use of EGFR TKIs
for advanced-stage NSCLC patients. Several studies have compared
the status of EGFR mutations in blood ctDNA and matched tissue
samples of lung cancer patients [27, 44, 45]. The first attempt to
detect EGFR mutations in blood sample was reported in 2006
[46]. Since then, numerous studies, including NCT01788163
and NCT01785888 (two large, multinational, diagnostic, non-
comparative intervention trials), as well as two meta-analyses
[47, 48], have confirmed that EGFR mutations are detectable in
ctDNA with high specificity (>93%), but improvable sensitivity
(<70%), indicating the diagnostic value of ctDNA.
EURTAC and FASTACT-2 are two randomized clinical trials
of first-generation EGFR TKIs, which have addressed the clinical
utility of liquid biopsy and ctDNA analysis for EGFR genotyping
[25, 49]. EURTAC was the first trial to assess the feasibility of
cfDNA from blood samples as a surrogate of tumor biopsy for
determining EGFR mutation status and to correlate EGFR muta-
tions in cfDNA with outcome. The trial assigned advanced NSCLC
patients to receive erlotinib or a platinum-based chemotherapy
doublet. These patients could offer baseline serum or plasma sam-
ples harboring oncogenicEGFRmutations in the tumor. EGFR
exon 19 deletions and L858R mutation were examined in cfDNA
by a multiplex RT-PCR assay. The result revealed that blood and
tissue biomarkers had comparable predictive power. It was found
that EGFR L858R mutation, no matter detected in tissue DNA or
ctDNA, negatively affected median PFS and overall survival in
erlotinib-treated patients compared with those whose tumors har-
bor exon 19 deletions [25].
In the FASTACT-2 trial, cobas EGFR blood test was used to
evaluate predictive biomarkers of induction chemotherapy plus
either erlotinib or placebo, followed by erlotinib or placebo main-
tenance treatment [49]. This retrospective analysis also revealed
that baseline EGFR mutation-positive patients who became
EGFR-negative in plasma ctDNA at the end of the induction
period would have better PFS and overall survival than those who
remained EGFR mutation-positive. This trial enabled the detection
of G719A/C/S, L858R, L861Q, S768I, and T790M mutations,
19 deletions, and 5 insertions in exon 20 afterward in another
clinical trial (NCT00815971). The trial result also came to the
conclusion that the EGFR gene in plasma samples is feasible and
represents a noninvasive supplement to tissue biopsy analysis [50].
EGFR T790M mutation occurs in half of NSCLC patients with
acquired EGFR TKI (TKI) resistance, which could be dynamically

The Introduction and Clinical Application of Cell-Free Tumor DNA 53

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