INTERPRETING GENETIC
MUTATIONAL DATA FOR
CLINICAL ONCOLOGY
Ben Ho Park, M.D., Ph.D.
Associate Professor of Oncology
Johns Hopkins University
May 2014
DNA, Genes and Cancer
 DNA is a cellular “blueprint” using four different
bases: Adenine, Cytosine, Guanine, Thymine
(A,C,G,T)
 DNA  RNA  Protein
 Two copies (generally) of DNA in each cell
Why look for mutated genes?
 Because most human cancers arise from somatic
mutations, this makes a physical change in the
cancer cell that is different from normal cells, i.e.
good target for therapy
 Also because mutations leading to cancer are
somatic, it can in theory be a marker of cancer
and used for detection and possible prognosis
 Sequencing involves amplifying via polymerase
chain reaction (PCR) a “coding” region of DNA,
and then determining the base pairs that are
present, e.g. A, C, G, T using a sequencing
machine
How is sequencing done?
EXONs
Primers
Sequencing “trace”
The problem
Fig. 1. The genomic landscapes of colorectal and breast cancers. The genomes of human cancers contain mutations in many different genes at low
frequency (hills) and only a few genes that are mutated at high frequency (mountains). From Wood et al. Science 2007.
Next Generation Sequencing
 Next generation sequencing involves cutting
DNA into small fragments and sequencing
these in parallel. With enough “coverage” the
entire genome can be sequenced quickly
Next generation sequencing
Workflow (future)
 Biopsy of lesion
 NGS of tumor to find “actionable” mutations
 Mutations with FDA approved drugs
 Mutations with FDA approved drugs for other cancer types
 Mutations that might match to a clinical trial
 Convene tumor board to discuss results
 Enter report with list of
recommendations/suggestions prioritized by level of
evidence
 All within 28 days
9
Challenges to overcome
 Need for fresh biopsy or not
 May be able to use blood as liquid biopsy
 Ability to sequence with acceptable time and
costs
 Commercial vs. in house
 Levels of evidence for mutations, drugs,
clinical trials…need for expert curation
 Tumor board with broad expertise: oncology,
genetics, molecular pathology, NGS, ethics,
legal, patient advocate
 Genetic Alterations In Tumors With Actionable
Yields (GAITWAY) tumor board
Current Challenge with Metastatic
Disease: Intratumoral Mutational
Heterogeneity
Gerlinger et al, NEJM 366:883, 2012
Exon Sequencing of ptDNA to test
Heterogeneity of Metastatic Breast Cancer
 Whole exome sequencing of ptDNA in metastatic disease is
possible (Nature 2013)
 Can sequencing of ptDNA yield additional mutations than
sequencing of a single metastatic site?
In collaboration with
Foundation Medicine,
we will obtain matched
metastatic biopsies and
plasma samples and
compare mutational
spectra of one metastasis
to ptDNA.
Not randomized
12
Exon Sequencing of ptDNA to test Heterogeneity
of Metastatic Breast Cancer
 J12129 protocol for 40 patients, IMAGE
Study: Individualized Molecular Analyses
Guide Efforts in Breast Cancer
 Triple negative metastatic breast cancer
patients eligible.
 Biopsy of one lesion performed and sent for
targeted gene sequencing (FoundationOne).
 Blood collected and ptDNA sequenced for
same Foundation One panel; results
compared
13
Conclusions
 Molecular genetics and genomic approaches
have increased our understanding of breast
cancer and our ability to make clinical
decisions regarding risk, therapies and
prognosis
 The use of both germline and tumor DNA in
particular has revealed new insights into the
complexities of breast cancer that will pave
the way for future studies towards
individualizing treatment plans for each
patient