Foundation Medicine and Memorial Sloan Kettering Publish Validation Data for FoundationOne® Heme in the Journal Blood

CAMBRIDGE, Mass. & NEW YORK–(BUSINESS WIRE)– Foundation
Medicine, Inc. (NASDAQ:FMI) and Memorial
Sloan Kettering Cancer Center (MSK) today announced the publication
of new, seminal data validating FoundationOne® Heme – the fully
informative comprehensive genomic profiling assay for hematologic
malignancies developed as part of their collaboration – further
supporting its integration into oncology clinical practice. The data,
available online as a first edition and soon to be published in an
upcoming issue of the journal Blood, demonstrate that
FoundationOne Heme has proven highly accurate in detecting the types of
genomic alterations known to impact diagnosis, therapy selection and
prognosis in hematologic cancers. Importantly, the publication
demonstrates the molecular information gleaned from comprehensive
genomic profiling can be utilized to accurately match patients with an
appropriate therapeutic approach.

“Foundation Medicine has an established track record of developing
genomic profiling assays with the highest standards of analytical and
clinical validation,” said Vincent Miller, M.D., chief medical officer,
Foundation Medicine. “Publication of our validation data in this highly
regarded, peer-reviewed journal supports the clinical significance of
the FoundationOne Heme assay, in particular, for its ability to identify
specific therapeutic targets, to help refine underlying diagnosis, and
to improve prognostic and risk stratification of hematologic cancers.”

“The development of FoundationOne Heme represents a state-of-the-art
genomics assay which can be used to profile patients with hematologic
malignancies worldwide, which is a critical step in improving outcomes
for all patients,” stated Ross Levine, M.D., a physician-scientist and
the Laurence Joseph Dineen chair in leukemia research at MSK. “Our
team’s expertise in hematologic malignancies and in translating genomics
to the clinic has allowed us to partner with Foundation Medicine to
bring this innovative genomic test to the patients we treat.”

Conventional diagnostic assays, including FISH and real-time PCR, are
designed to identify a sub-set of genomic alterations, and in some
cases, there are no assays that can reliably identify specific
rearrangements. FoundationOne Heme, an integrated DNA/RNA platform using
targeted hybrid-capture next-generation sequencing, is a proven and
effective comprehensive genomic profile developed to detect all types of
genomic alterations with therapeutic relevance, including
single-nucleotide substitutions, insertions and deletions, copy number
alterations and rearrangements, which are not fully evaluated using
conventional diagnostic assays.

MSK and Foundation Medicine collaborated to develop FoundationOne Heme,
which was commercially launched in 2013. The assay is performed using
archived FFPE, blood or bone marrow samples with high accuracy in a
clinically relevant timeframe in Foundation Medicine’s laboratory, which
is certified by New York State and CLIA and is CAP accredited.
FoundationOne Heme simultaneously detects all classes of genomic
alterations in the DNA of 405 cancer-related genes and employs RNA
sequencing across 265 genes to capture a broad range of gene fusions, a
type of alteration that is a common driver of hematologic cancers. It is
designed to provide physicians with clinically actionable information to
guide treatment options for patients based on the genomic profile of
their cancer.

Key Study Findings

• Established analytic accuracy of detecting substitutions, insertions
  and deletions (indels) and copy number alterations (CNAs) by comparing
  the performance of the new assay with Foundation Medicine’s DNA-only
  assay that has previously undergone comprehensive validation across a
  large number of clinical samples. Compared to FoundationOne,
  FoundationOne Heme contains an additional 90 genes relevant to
  hematologic malignancies.
  • Samples that were previously profiled with a validated test in
    which 169 alterations were identified in 55 genes common to both
    assays. The concordance between the two sets of results was 99.4%.
• Blinded comparisons were performed with CLIA-certified diagnostic
  assays, including Sequenom, RT-PCR, FISH and PCR fragment analysis,
  for 76 clinical specimens previously tested for 214 clinical relevant
  alterations in 11 genes that are known and routinely tested in
  clinical practice in AML, ALL and MDS.
  • Overall concordance was 99% (211/214).
  • In addition to the concordance analysis, genomic profiling of the
    76 test samples identified 126 additional somatic alterations
    which are not covered by available hot spot assays in the given
    disease type, including clinically relevant genomic alterations in KRAS,
    TET2, EZH2, and DNMT3A.
  • In independent low frequency variants (<10% mutant allele
    frequency), 20 of 21 variants were confirmed from AmpliSeq assay
    and another hotspot clinical assay.

• Combined DNA and RNA sequencing approach accurately detects a wide
  variety of genomic rearrangements and gene fusions with immediate
  clinical value in hematologic malignancies.
  • Sensitivity for fusion detection at 20% or greater tumor fraction
    was 100% (161/161) and 98% (84/86) at 10% tumor fraction.
• Clinical experiences from 3,696 hematologic malignancies are
  summarized, with a high fraction of clinically relevant genomic
  alteration detected.
  • At least one driver alteration was identified in 95% tumor
    specimens, and 77% cases harbored at least one alteration linked
    to a commercially available targeted therapy or one that is in
    clinical development. In addition, 61% of cases harbored at least
    one alteration with known prognostic relevance in that tumor type.
  • Genomic rearrangements were detected from 37% of clinical
    hematologic malignancies; known and novel fusions in kinase drug
    targets are highlighted.
  • In 16 cases of high-risk, BCR-ABL-negative B-ALL malignancies,
    known and novel clinical relevant genomic alterations were
    detected by FoundationOne Heme, and gene fusions involving JAK2,
    CRLF2 and EPOR were detected in 9 of 16 cases.

About Foundation Medicine

Foundation Medicine (NASDAQ: FMI) is a molecular information company
dedicated to a transformation in cancer care in which treatment is
informed by a deep understanding of the genomic changes that contribute
to each patient’s unique cancer. The company’s clinical assays,
FoundationOne for solid tumors and FoundationOne Heme for hematologic
malignancies, sarcomas and pediatric cancers, provide a fully
informative genomic profile to identify the molecular alterations in a
patient’s cancer and match them with relevant targeted therapies and
clinical trials. Foundation Medicine’s molecular information platform
aims to improve day-to-day care for patients by serving the needs of
clinicians, academic researchers and drug developers to help advance the
science of molecular medicine in cancer. For more information, please
visit http://www.FoundationMedicine.com
or follow Foundation Medicine on Twitter (@FoundationATCG).

About Memorial Sloan Kettering

We are the world’s oldest and largest private cancer center, home to
more than 14,000 physicians, scientists, nurses, and staff united by a
relentless dedication to conquering cancer. As an independent
institution, we combine 130 years of research and clinical leadership
with the freedom to provide highly individualized, exceptional care to
each patient. And our always-evolving educational programs continue to
train new leaders in the field, here and around the world. For more
information, go to www.mskcc.org.

Foundation Medicine^®, FoundationOne^®
and FoundationOne^® Heme are registered
trademarks of Foundation Medicine, Inc.

Cautionary Note Regarding Forward-Looking Statements for Foundation
Medicine

This press release contains « forward-looking statements » within the
meaning of the Private Securities Litigation Reform Act of 1995,
including, but not limited to, statements regarding the performance of
FoundationOne Heme; the ability of comprehensive genomic profiling,
including FoundationOne Heme, to match patients with therapeutic
treatments; and the integration of FoundationOne Heme into clinical
practice. All such forward-looking statements are based on
management’s current expectations of future events and are subject to a
number of risks and uncertainties that could cause actual results to
differ materially and adversely from those set forth in or implied by
such forward-looking statements. These risks and uncertainties
include the risks that FoundationOne Heme does not perform in the same
manner as the published data and the risks described under the caption
« Risk Factors » in Foundation Medicine’s Annual Report on Form 10-K for
the year ended December 31, 2015, which is on file with the Securities
and Exchange Commission, as well as other risks detailed in Foundation
Medicine’s subsequent filings with the Securities and Exchange
Commission. All information in this press release is as of the
date of the release, and Foundation Medicine undertakes no duty to
update this information unless required by law.

View source version on businesswire.com: http://www.businesswire.com/news/home/20160323006579/en/