Dr. Andrew J. Mungall: So, I'd like to take care of the sentiments
and thank the organizers for selecting this abstract. And it's my great privilege to present
the work of BC Cancer Agency in an exciting project, I hope you'll agree, in precision
medicine, or personalized oncogenomics. Just a little background about the BC Cancer Agency.
The population of British Columbia is 4.5 million, but live in an area about twice the
size of California. The -- we're in quite a unique setting in that we can offer a provincial,
population-wide cancer control program, and this reaches from prevention, screening, diagnosis,
through treatment. The scope of the POG, this personalized oncogenomics, is to bridge the
gap really between genomics research and clinical practice at the Center. We aim to identify
tumor-specific therapeutic targets in cancer patients, and in this POG Phase I project
with late-stage metastatic disease.
And so, the process is outlined in the flow diagram at the bottom. It begins with, of
course, a patient consult and consent process. We typically collect tumor biopsies. We'll
also request an archival FFPE block and match peripheral blood for that patient. And then
we construct PCR-free, whole-genome libraries of the tumor and of peripheral blood normal.
We'll also perform transcriptome sequencing as strand-specific RNAseq. We sequence on
the Illumina HiSeq instruments. And then, once a week, we meet with the referring clinicians,
discuss the relevant finding, and of course, submit a report for their attention with recommendations.
And this is a very busy slide, and I don't intend you to take a lot from it other than
the fact that this is a -- it is complex, but it is also structured, and the color-coding
indicate the sub-departments within our Bioinformatics Department that are analyzing this data. And
I've highlighted just a few of the areas in which TCGA data is actively contributing towards
this project. So these include the comparison to expression database -- and I'll show you
a few examples of that in case studies -- the variant calling, algorithms both from a transcriptome
and from the genome to help filter our calls for somatic mutations. And of course, all
of this feed from samples feed through this process to a final report.
This study has, thus far, enrolled 83 patients. Eight of these are pediatric cases. We've
performed 69 biopsies to date representing 28 tumor types, and the tumor types -- and
the frequency of those tumor types is shown in the bar plot. You can see there's a bias
towards a collection of breast cancer samples, primarily down to the very active participation
of breast cancer clinicians within the BCCA. We generate over 90x coverage of the tumor
genomes, and almost 50x coverage of the archival and matched normal genomes, and over 300 million
reads, on average, for a transcriptome library. Importantly, we've reported 50 cases and counting,
and the average time thus far is 38 days from biopsy to the report.
So here is some of just -- four of the areas in which POG has guided treatment decision-making.
I won't have time to go over all, but we'll give case studies for the top two: so providing
directed cytotoxic chemotherapy, and of course, the targeted therapeutic options, where available.
And the second one on the list is the complementing or even correcting FDA-approved clinical tests.
We also can identify cases of changed diagnosis, or provide a diagnosis where previously the
primary tumor was unknown.
And so, jumping to our first case study is what we call POG 003, is a Squamous cell carcinoma
of the skin. This gentleman arrived in 2007, having had a red rash on his upper chest.
He'd actually been living with this rash for well over a year -- maybe even two years -- and
when he presented was -- had bleeding ulcerations. It was diagnosed as Squamous cell carcinoma,
and he began multiple lines of chemotherapy and radiotherapy; began in 2007 and persisted
through to about 2012 when a new node near his right ear appeared, the pre-auricular
node. Both this node and his chest mass were growing throughout the course of 2012 to a
degree where the ear node was really preventing his hearing and causing extreme pain. So,
in September 2012, both the node and the chest lesion were biopsied for this study. The somatic
mutation status of the tumors is illustrated in the Venn diagrams here, and strikingly,
not only are there many somatic variants, as one might expect from cancers that have
been developing and subjected to a number of rounds of therapies -- so they're in the
high thousands -- but there was very little overlap between these two lesions. They looked
really very different cancers indeed, and no overlap when we looked at the small INDELs.
Likewise, when we look at the copy number profiles for these two tumors, the chest is
shown in the Circos plot in the outer ring, and the pre-auricular node on the inner ring;
and you can see that there's really relatively little commonality between these two tumors
at the copy number level. If we just highlight Chromosome 16 and take a look at the copy
number plots, again, the breakpoint regions are few and far between. There are areas of
gain at 16q that are not apparently gained in the chest lesion; a loss, including a homozygous
loss on Chromosome 16. And so, we can put this data together in the form of Pathway
analyses, and so this is integrating now the genome and the transcriptome data. And this
is looking at the chest tumor again, and you can see that there are many rearrangements
consistent with DNA repair defects that were detected, but importantly -- and I highlight
here -- both loss of PTEN, both in copy number and decreased expression, and [unintelligible]
an increase in AKT expression, and a gain of copy number. And so, this was suggestive
of treatment options.
Contrast that with the pre-auricular tumor, you can see now that we have very elevated
EGFR amplicon; so amplified both in expression and, again, copy number amplifications, just
to name a few. But these ones suggest -- and I apologize for the squeamish in the audience.
These two suggested treatment options, of course, and so in pre-auricular tumor the
over-expression of EGFR suggested erlotinib; and the PTEN homozygous loss and AKT gain
for the chest lesion suggest a treatment with everolimus. The patient was treated initially
with both agents, but exhibited quite a lot of toxic effects, and so was taken off everolimus
initially. The ear tumor responded incredibly well to erlotinib, and decreased from just
after biopsy -- very angry and red, inflamed area -- and the clinicians tell me that this
is really dramatic progress. The involution of the tumor was really recovering after three
short weeks; and also, his hearing recovered in that right ear. The pre-auricular tumor
did progress, sadly, and a second biopsy was performed and, in this biopsy, the analysis
showed even further extreme amplification of EGFR -- so now to 55 copies of the gene
-- and extreme gene expression level, as indicated by the red line. This is now compared to all
of the TCGA data, and was the most extreme express of it that we've identified across
the whole of those TCGA, you know, 8,000 plus samples.
And, turning to the second case study, to finish, this was a 68-year-old Asian male,
a lifelong never-smoker, who was diagnosed with non-small-cell lung adenocarcinoma in
January of 2013. And he had the approved clinical tests for EGFR and ALK through break-apart
FISH probes, and these were negative in the clinic; subsequently had multiple lines of
radiation and chemotherapeutic therapy between March and July of 2013, but continued to progress
of the disease, and so in August, we took the same node out for biopsy. And almost immediately
the data yelled the transcriptome fusion between EML4 exons 1 to 13, and ALK exons 20 to 29,
a really pretty canonical fusion for non-small-cell lung cancer patients. And yet, I just told
you that the clinical test had been a negative with only 3 percent of the cells exhibiting
break-apart. Closer inspection of the sequence, both at the genomic level and the transcriptome
level, revealed that not only did the inversion that gives rise to this gene fusion exist,
but a much larger inversion of Chromosome 2 and subsequent insertion into the Chromosome
12 locus had prevented one of the Vysis FISH probes from binding adequately, and hence,
the negative result in the clinical assay.
And if we look at the expression level as a consequence of this oncogenetic fusion,
we see that again it's an extreme -- this particular patient is an extreme expresser
for ALK, here on the right, the 99th percentile of all expression compared to the TCGA lung
adenocarcinoma data set. And ROS1, which is a second target for Crizotinib, again, was
at high expression in the 94th percentile. And so, this of course did suggest that Crizotinib
should be administered. Happily, the patient was just well enough to receive Crizotinib
within a day of the report being given to the clinician, and the tumor responded really
dramatically with it. So within less than three months the tumors that you can see highlighted
with the red arrows had really began to shrink away, and in fact, were not visible for this
lower lesion.
And so to summarize the overall POG results for this Phase I study -- Phase I of this
study -- for each patient we've sequenced three or more genomes and a transcriptome.
Eighty-three consented patients now, actually with advanced cancer, have been enrolled.
Seventy-four biopsies attempted. Some of them have failed, giving us 69 biopsy materials;
and we have full data available for those 50 patients. And importantly, they've been
clinically evaluated in 38 cases, and going back to the clinician, the referring clinicians,
and asking, "Can they ascribe actionable or treatable information from this genomic and
transcriptome data?" They report that in 87 percent of those cases, there was actionable
treatment possible, and it was offered in -- to 55 percent of those 33 cases. Of course,
a number of patients, as in a late-stage setting, had died during, or shortly after the analysis.
What's next for personalized oncogenomics? Well, we've just had approval for 5,000 cases,
and we intend to achieve these 5,000 cases within the next five years. This will take
us from about one patient a week on average currently to greater than one patient per
day in the coming years. We'll continue an emphasis on genome and transcriptome sequencing,
but we will include a more elaborate OncoPanel for rapid turnaround time and a first look
at these tumors when they arrive. We will bring forward from late-stage disease to fresh
diagnostic biopsies, and of course, increase -- always aim to increase our speed and accuracy
of the sequence analysis and the report generation. And importantly, we'll be verifying actionable
results, and continue to verify actionable results in a clinical lab prior to the treatment
of the patient.
And finally, just leave me to thank the large multi-disciplinary team at the BC Cancer Agency,
expertly led by, on the clinical side, Janessa Laskin, and on the research side, Marco Marra.
So I'm very, very grateful to all the colleagues, and most in particular, the patients and their
families and the BC Cancer Foundation for funding this project. And I have had to race
through this a little, and so I'll be happy to see you at poster number 10 if you have
specific questions we can't address in the time left here, but I thank you for your attention.
[applause]
Male Speaker: What, if any, are the plans to make these
data public?
Dr. Andrew J. Mungall: So, we -- obviously, we need to be very careful
about the confidentiality of these individuals. We will -- we certainly need to discuss this
more in-depth, so there's no immediate plans to release this data.
Male Speaker: It just is a lost opportunity, and we should
try to figure out -- all this wonderful sequencing helping patients -- we need to then use it
to help all the patients and learn more.
Dr. Andrew J. Mungall: Absolutely. So, I mean, of course there are
publications. There's one publication in press currently. The --
Male Speaker: But I mean, it's the mining --
Dr. Andrew J. Mungall: Yes. Sure.
Male Speaker: Yeah.
Dr. Andrew J. Mungall: Yeah.
Male Speaker: One question, very simple: so do you worry
about tumor heterogeneity when you analyze your data?
Dr. Andrew J. Mungall: Yes, we do, and so one of the aspects I didn't
touch on is that we require tumor content of over 40 percent before we will progress
with all this deep genome and transcriptome sequencing. Heterogeneity certainly plays
a big part, and in the analysis we try and tease apart as much about heterogeneity as
possible, but a lot of it comes down to the sequence depth we're able to achieve with
deep sequencing.
Han Liang: So for the timing interest, let us move to
next speaker. So for TCGA we face the same data, but we use a different type reason to
interpret the data. This particular highlighted by mutation calling. So, recently, the ICGC
and TCGA organized a DREAM Challenge. So let us see the speech from Dr. Paul Boutros from
the OIRC -- OICR, talk about the summary from the first round ICGC-TCGA DREAM Challenge
about mutation calling.
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