A preliminary study comparing two commercially
available, next-generation genetic sequencing tests
in the same cancer patients shows results can differ
widely. The findings are reported Dec. 15 in JAMA
Oncology, a scientific journal of the American
Medical Association.
Genetic testing is used in thousands of cancer
patients each year.
Clinical testing for cancer-associated genetic
alterations is growing because of the need to better
match cancer patients with effective therapies, the
authors note. They explained that tests are done to
target drug selection to tumor characteristics.
Test reports also sometimes pull up research trials
in which the patient might consider participating.
However, according to the researchers, little
information is available about how closely the
output of various sequencing assays match up for an
individual’s case.
The research was led by Dr. Tony Blau, a faculty
member in the Department of Medicine at the
University of Washington School of Medicine, and
investigators at the UW Medicine Center for Cancer
Innovation. Blau is also with the UW Medicine
Institute for Stem Cell and Regenerative Medicine
Research.
In their study, nine patients from a community
cancer-care practice received reports from two
testing platforms: FoundationOne, from
FoundationMedicine, and The Guardant360, from
Guardant Health.
FoundationOne tests tumor samples to characterize
315 cancer-associated genes and 28 other genes prone
to rearrangement.
The Guardant360 takes blood samples to examine the
cell-free DNA that dying tumor cells release into
the bloodstream of cancer patients. It sequences 70
genes.
In one patient, neither test found any genetic
alterations.
The remaining patients as a group had 45
alterations, just 10 of which (22 percent) were
discovered by both platforms.
For two patients, no results matched between the two
reports.
The test reports of 8 patients with identified
alterations mentioned a total of 36 possible
treatment drugs.
Only 9 drugs were called out by both tests for the
same patients.
For 5 patients, there was no overlap between the
suggested drugs.
“Our findings indicate that the output from genetic
testing can differ markedly depending on which test
is applied,” the researchers noted. Because both
types of test are performed in thousands of patients
every year, they added, the findings are clinically
relevant.
The FoundationOne test may be detecting a broader
range of aberrations than the Guardant360, but the
researchers think the discordance between the two
tests stems from other causes.
The researchers pointed to at least two other
studies with similar observations, including one
based only on tumor tissue-sampling and another that
compared blood and tumor testing.
To improve the clinical usefulness of
next-generation sequencing tests for cancer
treatment, the researchers point to a need for more
in-depth comparisons of test results across larger
numbers of patients.
SouthSound CARE and the Chan Soon-Shiong Family
Foundation funded this study. Other institutions
participating included Northwest Medical Specialties
in Puyallup, Wash., and the Fred Hutchinson
Institute for Cancer Outcomes Research.
For more information
JAMA Oncology
Comparison of 2 Commercially Available
Next-Generation Sequencing Platforms in Oncology
Link...
University of Washington
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