CENTRAL NERVOUS SYSTEM TUMORS
2009 Clinical Science Symposium
Longitudinal tumor-wide sampling of glioblastoma reveals diverse genomic drivers
of the earliest clonal expansion at diagnosis and recurrence.
Benjamin Joshua Lerman, Chibo Hong, Lee Chen, Ivan V Smirnov, Joanna J. Phillips, Anny Shai, Janine Lupo, Joseph Costello; University of California, San Francisco, San
Francisco, CA
Background: Despite decades of clinical trials, glioblastoma (GBM) remains a rapidly fatal
disease. Much of therapy resistance in GBM is attributed to intratumoral heterogeneity in which
subclones rapidly evolve and treatment-resistant cell populations emerge. Understanding
heterogeneity at diagnosis and its relationship to the origins of recurrence are critical to
selecting therapies that are efficacious across the entire tumor. However, few genomic studies
go beyond analyzing single tumor samples per patient. Methods: A spatially oriented, whole
tumor sampling approach was used to obtain 43 biopsies from 3 GBMs at diagnosis and
recurrence. Pyclone and ClonEvol were applied to whole exome sequencing to reconstruct
clonal evolution, FACETs identified copy number variations and HATCHet estimated tumor
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purity. Candidate driver mutations were evaluated in relation to the Catalogue of Somatic
Mutations In Cancer. Results: A single founding clone and multiple subclones were identified
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for each diagnosis-recurrence pair. Tumor-wide clonal alterations representing initial clonal
expansions of these GBMs included both canonical changes (Chr 7 gain, Chr 10 loss, CDKN2A
deletion, EGFR amplification) and a diverse set of large-scale copy number variations (Chr 19,
20 gain), driver mutations (PTEN, KDR, CDH11, CNTNAP2), and fusions (LIMCH1::UCHL1,
KANK::DOCK8). A second subset of alterations (Chr 8 gain, ATRX mutation), appeared to be
tumor wide at diagnosis but were not identified at recurrence. Cancer drivers were also present
subclonally, including CDKN2A deletion, MDM2 amplification, and mutations in NF1, and
GRM3. Evolutionary trees consisted of 5 generations of clones in Patient 323 (P323), 3 in
P454, and 4 in P534. Divergence of the recurrent tumors from their matched primary occurred
in the second generation in P454 and P534 and in the third in P323. As a result, an average of
37% of potential drivers of oncogenesis and clonal expansion across the cohort appear after
divergence. Furthermore, each recurrent tumor contained at least one tumor wide driver
alteration that was subclonal or undetected at diagnosis. Conclusions: Whole-tumor sampling
of three GBM patients at both diagnosis and recurrence identified a diversity of genomic drivers
and deeper and more complex genetic roots of individual GBM than previously seen in single-
biopsy studies. Tumor recurrences consistently arose from a single subclone that diverged early
in evolution of the primary tumor and contained clonal drivers either not detected or subclonal
in the primary—suggesting a role for these drivers in persistence and expansion. In the age of
personalized medicine, our study highlights the clinical potential of tumor wide sampling in
identifying therapeutic targets that could avoid heterogeneity-related therapeutic failures.
Research Sponsor: U.S. National Institutes of Health; CA 151022-14.
