Personalized Health Care (PHC) in Cancer - Genomic Biomarkers for Pharmaceutical Development - page 31

active ALK) and NSCLC (fusion between ALK and EML4 leads to constitutively active
ALK). The EML4-ALK fusion causes ligand-independent dimerization of the ALK kinase
domain, leading to constitutive proliferation and inhibition of apoptosis [57] . The EML4-
ALK fusion is found in 2-7% of unselected NSCLC patients, but this number can increase
to approximately 13% in patients who are female, Asian, never / light smoker, and have an
adenocarcinoma histology to their tumor [58] . Although there is a relatively low percent-
age of NSCLC patients with this genetic alteration, a 57% overall response rate to treat-
ment with crizotinib was observed in a cohort of 82 patients with ALK rearrangements,
as detected by FISH, with virtually no responses in the absence of ALK abnormalities [54-
56,58-60] . Additionally, in individuals matched for clinical characteristics, ALK-positive
patients receiving crizotinib had an improved two-year overall survival (57% compared to
36%) compared to ALK-positive patients who did not receive crizotinib [55] . FDA approval
of crizotinib occurred in 2011, with accelerated approval due to the existence of a prospec-
tive genomic biomarker and parallel companion diagnostic development [61] . Required for
this approval was that ALK testing be performed using a FDA approved test; therefore, the
Vysis ALK break-apart FISH probe kit (Abbott Molecular) was approved for the detection of
ALK translocation-positive NSCLC in parallel with the approval of crizotinib.
Acute promyelocytic leukemia (APL) accounts for 10% of all acute myeloid leukemias
and more than 99% of cases have a fusion between the retinoic acid receptor and the PML
gene (PML-RARa fusion) [62-65] . The detection of a PML-RARa t(15,17) translocation is
a diagnostic biomarker for APL and this genetic change functions to repress retinoic acid
responsive target genes. Its presence correlates with response to ATRA therapy (all trans
retinoic acid) followed by arsenic trioxide, which targets the fusion protein for degradation
[62,64,65] .
BRAF MUTATION FOR VEMURAFENIB
BRAF is a serine-threonine kinase that activates the MAP / ERK kinase signaling pathway
[66] . In 2002, an important advance in the understanding of v-raf murine sarcoma viral onco-
gene homolog B1 (BRAF) function came from the discovery that the BRAF gene is mutated
in many different cancers [67] . Most mutations occur at codon 600, replacing valine most
typically with glutamic acid (V600E mutation) and leading to significant increases in kinase
activity that drive cancer cell proliferation [67] . This mutation occurs in about half of all mela-
nomas [68] and has varying prevalence in other cancers [67] . Vemurafenib is a BRAF inhibi-
tor synthesized in early 2002 possessing mild selectivity for BRAF V600E over the wild type
enzyme in biochemical assays, but a pronounced selectivity for mutant BRAF compared to
wild type in inhibiting proliferation of melanoma cell lines [67] . Before initiating clinical stud-
ies, work was initiated to develop a companion diagnostic to identify melanoma patients with
a BRAF mutation. Roche Diagnostics developed a real-time PCR assay to detect the BRAF
V600E mutation in FFPE tissue samples that had exceptional analytical performance (125ng
genomic DNA containing 5% mutant alleles produced >96% hit rate) providing greater sen-
sitivity and specificity over conventional sequencing [69] . In Phase I studies of vemurafenib,
32 patients with metastatic melanoma treated with 960 mg of vemurafenib twice daily had an
incredible 81% response rate in patients with V600E mutation [66,67] . In Phase II and Phase
III trials, the BRAF V600E diagnostic assay was used as an enrollment criterion [69] . Results