Customer case study
Field of study: Oncology
With a Focus on Patient
Care, UC Davis Scientists
Track Cancer Mutations
in NGS Data
At an NCI-designated comprehensive cancer
center, Cliff Tepper uses Ingenuity® Variant
Analysis™ to analyze tumor samples and
circulating DNA for clinically relevant mutations. Whether the data is from gene panels
or whole exomes, the QIAGEN application
delivers useful results that are easy to share
with oncologists.
Sample to Insight
“
It’s actually phenomenal — it takes the data
we have analyzed and
helps us prioritize the variants based on their functional impact and whether
they’ve been found to be
associated with cancers.
As technical director of the Genomics Shared
investigators there. Run through the Department
Resource at the University of California, Davis,
of Pathology and Laboratory Medicine, the
Comprehensive Cancer Center, Cliff Tepper
core lab has a real need to churn out high-qual-
routinely faces a series of challenges: closely
ity results that can be understood by scientists
monitoring new technologies; adapting plat-
and physicians alike.
forms for translational use; interrogating a
broad array of cancers; and tailoring results
“We try to provide a comprehensive genomic
reports for investigators with diverse expertise
solution to all of the investigators that want
ranging from molecular biology to clinical
to use our core, whether it’s a physician who
oncology.
doesn’t have a lab or a highly skilled molecular biologist,” Tepper says. His team can help
To meet these challenges, Tepper works closely
clients with everything from sample acquisition
with scientists and physicians — both at the
to data analysis, relying on a host of cutting-
cancer center and at other institutions — and
edge genomic technologies in between. “We
keeps an eye on peer-reviewed research for
do a lot of bioinformatics analysis, and provide
the latest information about technologies and
support for results interpretation as well as
cancer studies. He also invests in leading
manuscript and grant preparations,” he adds.
informatics solutions to get the best results for
his clients. Recently, he began using Ingenuity
As an NCI-designated cancer center, there’s a
Variant Analysis from QIAGEN, an application
big emphasis on demonstrating that results of
that he calls “phenomenal.”
these studies could make a difference in medicine down the road. “The NCI wants to see
Two recent projects highlight the utility of
that what we’re doing can be translated into
Ingenuity Variant Analysis. In one, Tepper was
the clinic and have an impact on some aspect
able to home in on important variants detected
of patient care,” Tepper says.
in circulating tumor DNA — variants seen at
such low levels they were missed by other
One approach that has proven very promising
analytical solutions. In the other, the applica-
is using targeted sequencing panels that cover
tion helped Tepper quickly analyze mutations
a host of genes implicated in different types
from exome data derived from bladder cancer
of cancer. Tepper uses QIAGEN’s GeneRead
samples.
DNAseq Targeted Panel for human cancer,
which looks across 160 commonly mutated
Translating Results
cancer-relevant genes in more than 740 kb
of sequence. This helps put the focus on key
mutations in each tumor, rather than the site
2
The UC Davis Comprehensive Cancer Center
of origin or genes associated with just one
got its prestigious designation from the National
form of cancer. “Many aberrations apply to all
Cancer Institute in 2001, and Tepper’s core
cancers,” he says, “so we’re going to a more
facility was one of the first shared resources for
pan-cancer approach for our studies.” That
With a Focus on Patient Care, UC Davis Scientists Track Cancer Mutations in NGS Data
universal view of cancer is one way he and his
cancer in samples from a cohort of nearly
team are ensuring that the work they do will
30 patients. To figure out whether KRAS
ultimately make a difference for patients.
mutations found in circulating DNA — associated with a poor patient prognosis —were
Once the targeted panel is used to enrich
truly representative of the tumor, they also
for relevant cancer genes, Tepper and his
sequenced tumor samples from three of the
colleagues sequence the samples and submit
patients.
“
We just upload raw
data, and in the morning
it’s com­pletely analyzed
for variants. It’s a very
nice analysis solution.
the results to the GeneRead DNAseq Variant
Calling Pipeline for sequence alignment, anno-
“In general what we found was that if we
tation, and variant classification. “We just
manually looked through the data, the assay
upload raw data, and in the morning it’s com-
does pick up the KRAS mutations in all of the
pletely analyzed for variants,” Tepper says.
samples,” Tepper says. The challenge is that
“It’s a very nice analysis solution.”
with some analysis tools, standard threshold
settings are too high to detect variants at the
Diving into Variants
low levels seen in the data. “Sometimes these
mutants weren’t being called even though the
reads were there,” he adds. “Much of the
Once Tepper gets initial results from the por-
sequencing is expended on the background
tal, he turns them over to Ingenuity Variant
normal DNA, and this decreases the sensitivi-
Analysis, a tool he recently brought into the
ty for detecting the tumor-derived mutations.”
core facility. “That’s been working very well,”
he says. “It’s actually phenomenal — it takes
But loading the data into Variant Analysis
the data we have analyzed and helps us pri-
revealed the whole picture. “We can see
oritize the variants based on their functional
the mutations there,” Tepper says. “We got
impact and whether they’ve been found to
a good idea of what somatic mutations
be associated with cancers.” The application
were present in the tumor just based on the
also gives the team critical information about
circulating DNA.” The ability to easily adjust
how commonly those variants are seen in the
thresholds and change filters in the applica-
general population to allow for quick exclusion
tion is a big advantage for the genomics
based on normal human genetic diversity.
core team. They can set up a filter cascade
for various traits they’re interested in, such as
In a recent study that Tepper presented in a
depth of coverage, sequencing quality, com-
poster at this year’s annual meeting of the
mon variants, as well as more specialized
American Association for Cancer Research,
filters for variants implicated in cancer, muta-
his team used Variant Analysis to filter variants
tions associated with cancer therapeutics,
found in circulating tumor DNA from patients
and expression levels. Essential information,
with pancreatic cancer. The project aimed to
such as gene location and base change, is
generate proof-of-principle data to understand
shown clearly. And the tool’s inclusion of the
the utility of circulating DNA for this type of
COSMIC database makes it a cinch to pick
With a Focus on Patient Care, UC Davis Scientists Track Cancer Mutations in NGS Data
3
out known somatic mutations. In a separate
all right there for you,” he says. “The interface
who have been on diagnostic
odysseys.
Variant
is one
tooltothey’ve
is much
easier
go through than the standard
study, Tepper
and RGI
his teamIngenuity
generated
wholeAnalysis
enables patients to obtain
genome
or exome
used
for RGI
patients, Excel
and file.”
Haraksingh says
exome
data from
patients with
bladder
cancer.
sequencing, often supported
byVariant
crowdfunditsusease
of use makes the application a
“We used
Analysis tothat
help
determine
ing. But there’s still a lottheof somatic
data interpretation
natural
for volunteers
who his
come
from other focus, though, the real
With
translational
mutations in the
tumorfit and
filter
required to get usefulaway
information
to
backgrounds.
“It allows
people
aren’t
payoff
for who
Tepper
is generating results that
potentialback
germline
variants,”
he says.
patients. Often, the standard
analysisforperin genomics
quickly
ask questions
be easily
understood by all of his clients.
“It was helpful
quicklyexperts
consolidating
all tocan
formed by sequencing that
centers
is not sufficient
about
without A
having
to worry
about who looked over the
clinical
pathologist
information
and applying
it tothe
ourdata
sample
for understanding theseset.”
rareInand
putting
all the components
together
to make
the “liked the presentation
Variant
Analysis
results
that particularly
study, he imported
RNA-seq
data
challenging cases.
informatics
says. it“Variant
a lotshe
because
is easy to examine the data,
from the same samples into best
Variant
Analysis pipelines,”
to
Analysis
is sotointuitive
and it’s
easy
to clear
use that
and
very
what it means as well,”
determine whether mutations
were likely
be
“As the director of RGI’s
Science
2.0
initiathey’re
able
to
pick
it
up
quickly.”
Tepper says. “The interface is very user-friendly
expressed.
tive, I lead a team of 12 researchers with the
and you can organize the columns based on
mission of analyzing the
genomic
Ultimately,
hopes
the most
deepinterested in seeing. That
the
thingsthat
you’re
Tepper
also and
finds medithat Variant
AnalysisHaraksingh
saves
cal data from our patients
to figure
analysis samples
she can at
provide
to patients
helps
us sharewill
thisyield
data with oncologists.”
time tobytryletting
him out
see numerous
what’s going on,” Haraksingh
says. Ultimately,
progress, ifdata
not the
once, organizing
and summarizing
forexact answer, for each case
the volunteers write an in-depth
research
report
— bebe
it acompared
new genetic lead or connecting the
all of them.
Variants
can easily
for each patient that is across
used to
refer the
case with
patient
to a impact
specialist who can provide more
multiple
samples,
functional
to outside specialists orinformation
garner knowledge
for
insight.
“It’s“Itbeen
gratifying to apply
readily accessible
as well.
has extremely
it
future research from RGI’s global network of
my expertise in the nonprofit sector,” she says.
scientists.
QIAGEN Silicon Valley
V
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Tel. +1 650 381 5100
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ty, CA 94063
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genuityy.com
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genuityy.com
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Impact of Human Variation on Disease
4
With a Focus on Patient Care, UC Davis Scientists Track Cancer Mutations in NGS Data