The U.S. Food and Drug Administration (FDA) has approved Foundation Medical‘s FoundationOne®Liquid CDx for three new companion diagnostic in indications to help match patients who may benefit from treatment with specific FDA-approved targeted therapies.

The test is a qualitative next generation sequencing (NGS-) based in vitro diagnostic test for prescription use only that uses targeted high throughput hybridization-based capture technology to analyze 324 genes utilizing circulating cell-free DNA (cfDNA) isolated from plasma derived from anti-coagulated peripheral whole blood of advanced cancer patients.

Short variants
The test is FDA-approved to report short variants in over 300 genes and is a companion diagnostic to identify patients who may benefit from treatment with specific therapies in accordance with the approved therapeutic product labeling.

According to the company, additional genomic findings may be reported. However, these additional findings are not prescriptive or conclusive for labeled use of any specific therapeutic product. Furthermore, the company states that the use of the test does not guarantee that a patient will be matched to a treatment. A negative result does not rule out the presence of an alteration. Patients who are negative for companion diagnostic mutations should be reflexed to tumor tissue testing and mutation status confirmed using an FDA-approved tumor tissue test, if feasible.

The new indications are for:

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  • Alpelisib (Piqray®; Novartis), a kinase inhibitor indicated for use in combination with fulvestrant for the treatment of postmenopausal women, and men, with hormone receptor (HR)-positive, human epidermal growth factor receptor 2 (HER2)-negative, PIK3CA mutated, advanced or metastatic breast cancer following progression on or after an endocrine-based regimen. PIK3CA is the most commonly mutated gene in HR+/HER2- breast cancer; approximately 40% of patients living with HR+/HER2- breast cancer have this mutation. [1]
  • Rucaparib (Rubraca®; Clovis Oncology), a poly (ADP-ribose) polymerase (PARP) inhibitor for the treatment of adult patients with a deleterious BRCA mutation (germline and/or somatic)-associated epithelial ovarian, fallopian tube, or primary peritoneal cancer who have been treated with two or more chemotherapies. Select patients for therapy based on an FDA-approved companion diagnostic for Rubraca. An estimated one in four women with epithelial ovarian cancer have a mutation of the BRCA1 or BRCA2 gene.[2]
  • Alectinib (Alecensa®; Chugai Pharmaceutical), a tyrosine kinase inhibitor (TKI) from Genentech/Roche, indicated for the treatment of patients with anaplastic lymphoma kinase (ALK)-positive mNSCLC, as detected by an FDA-approved test.ALK rearrangements are identified in approximately 5% of NSCLC patients.[3]

The FDA also approved a label expansion for FoundationOne Liquid CDx to report additional select copy number alterations and genomic rearrangements.

The FoundationOne Liquid CDx is designed to analyzes the largest genomic region of any FDA-approved comprehensive liquid biopsy test and was approved in August to provide tumor mutation profiling in accordance with professional guidelines for patients with any solid tumor.

PARP inhibitor
Concurrently, it was approved as a companion diagnostic for a poly (ADP-ribose) polymerase (PARP) inhibitor approved by the FDA for the treatment of metastatic castration-resistant prostate cancer patients with qualifying BRCA1/2 alterations, and for three first-line EGFR tyrosine kinase inhibitors (TKIs) for the treatment of non-small cell lung cancer patients.

“FoundationOne Liquid CDx offers oncologists an important and minimally invasive tool to consider when making treatment decisions for their patients, regardless of the type of cancer they have,” said Brian Alexander, M.D., M.P.H., chief medical officer at Foundation Medicine.

“These three additional companion diagnostic claims expand the test’s clinical utility into breast and ovarian cancer, demonstrating our commitment to bringing precision medicine to more patients, and we plan to continue working with our biopharma partners to increase that reach,” Alexander added.

Using a blood sample, FoundationOne Liquid CDx analyzes over 300 cancer-related genes for genomic alterations. FoundationOne Liquid CDx results are delivered in an integrated report that identifies alterations matched to FDA-approved therapies. It also enables accelerated companion diagnostic development for biopharma companies developing precision therapeutics.

As a laboratory professional service which has not been reviewed or approved by the FDA, the FoundationOne Liquid CDx report delivers information about the genomic signatures microsatellite instability (MSI) and blood tumor mutational burden (bTMB), as well as single gene alterations, including NTRK fusions, to help inform the use of other therapies including immunotherapies. Furthermore, as a laboratory professional service, the report provides relevant clinical trial information and includes interpretive content developed in accordance with professional guidelines in oncology for patients with any solid tumor.

Highlights of prescribing information
Alpelisib (Piqray®; Novartis) [Prescribing Information]
Rucaparib (Rubraca®; Clovis Oncology) [Prtescribing Informarion]
Alectinib (Alecensa®; Chugai Pharmaceutical) [Prescribing Information]
FoundationOne®Liquid CDx; Foundation Medical [Technical Information]

References
[1] The Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490(7418):61-70.
[2] Pennington KP, Walsh T, Harrell MI, Lee MK, Pennil CC, Rendi MH, Thornton A, Norquist BM, Casadei S, Nord AS, Agnew KJ, Pritchard CC, Scroggins S, Garcia RL, King MC, Swisher EM. Germline and somatic mutations in homologous recombination genes predict platinum response and survival in ovarian, fallopian tube, and peritoneal carcinomas. Clin Cancer Res. 2014 Feb 1;20(3):764-75. doi: 10.1158/1078-0432.CCR-13-2287. Epub 2013 Nov 15. PMID: 24240112; PMCID: PMC3944197.
[3] Dearden S, Stevens J, Wu YL, Blowers D. Mutation incidence and coincidence in non small-cell lung cancer: meta-analyses by ethnicity and histology (mutMap). Ann Oncol. 2013 Sep;24(9):2371-6. doi: 10.1093/annonc/mdt205. Epub 2013 May 30. PMID: 23723294; PMCID: PMC3755331.

Featured Image: Despair patient after diagnosis. Photo courtesy: © 2016 – 2020 Fotolia/Adobe. Used with permission.

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