Foundationone liquid cdx

Manufactured by Foundation Medicine

Sourced in United States

FoundationOne Liquid CDx is a laboratory equipment product developed by Foundation Medicine. It is a comprehensive liquid biopsy test that analyzes circulating tumor DNA (ctDNA) to detect genomic alterations across hundreds of cancer-related genes. The test is designed to provide genomic information to support cancer diagnosis, treatment selection, and monitoring.

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Lab products found in correlation

Foundationone cdx, by Foundation Medicine (6 mentions) Foundationone liquid, by Foundation Medicine (2 mentions) Oncoguide ncc oncopanel system, by Sysmex (1 mentions) Oncomine comprehensive assay v3, by Thermo Fisher Scientific (1 mentions) 22c3 pharmdx assay, by Agilent Technologies (1 mentions) Ion torrent pgm system, by Thermo Fisher Scientific (1 mentions) Foundationone, by Foundation Medicine (1 mentions) Foundationact, by Foundation Medicine (1 mentions)

8 protocols using foundationone liquid cdx

Comprehensive Genomic Profiling for Cancer

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CGP testing was performed using hybrid capture-based targeted DNA sequencing with FoundationOne CDx (Foundation Medicine), the OncoGuide NCC Oncopanel System (Sysmex Corporation), in-house NGS testing, or in blood-derived cell-free DNA with FoundationOne Liquid CDx (Foundation Medicine) or Guardant360 CDx (Guardant Health).^{4 (link),25 (link),26 (link),27 (link)} All patients were referred to the NCCH following discussion by regional molecular tumor boards (MTB) comprising medical oncologists, pediatric oncologists, pathologists, bioinformaticians, genome researchers, and genetic counselors.^{3 (link),28 (link)} In addition to reports from the inspection companies, the MTBs used reports containing clinical annotation and information regarding genotype-matched clinical trials from the Center for Cancer Genomics and Advanced Therapeutics national database.^{29 (link),30 (link)}

Uehara Y., Koyama T., Katsuya Y., Sato J., Sudo K., Kondo S., Yoshida T., Shoji H., Shimoi T., Yonemori K, & Yamamoto N. (2023). Travel Time and Distance and Participation in Precision Oncology Trials at the National Cancer Center Hospital. JAMA Network Open, 6(9), e2333188.

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Profiling Oncogenic Mutations via NGS

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METex14 skipping mutations were identified through several methods including NGS of tissue using DNA- and RNA-based assays (TruSight Tumor 26 assay, Ilumina, San Diego CA; Oncomine Comprehensive Assay v3, Thermo Fischer, Waltham, MA; or FoundationOne CDx, Foundation Medicine, Cambridge, MA), or plasma-based NGS with commercially available assays (Guardant360 CDx, Redwood City, CA and FoundationOne LiquidCDx, Foundation Medicine, Cambridge, MA). Programmed death-ligand 1 (PD-L1) assessment was performed using the 22C3 pharmDx assay (Agilent Technologies, Dako, Carpinteria, CA) at all centers.

Lau S.C., Perdrizet K., Fung A.S., Mata D.G., Weiss J., Holzapfel N., Liu G., Bradbury P.A., Shepherd F.A., Sacher A.G., Feilotter H., Sheffield B., Hwang D., Tsao M.S., Cheng S., Cheema P, & Leighl N.B. (2023). Programmed Cell Death Protein 1 Inhibitors and MET Targeted Therapies in NSCLC With MET Exon 14 Skipping Mutations: Efficacy and Toxicity as Sequential Therapies. JTO Clinical and Research Reports, 4(10), 100562.

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Comprehensive Liquid Biopsy Analysis

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cfDNA testing was performed during routine standard-of-care treatment using a commercially available panel, Guardant360 (Guardant Health, Inc., Redwood City, CA, USA) [16 (link)] and FoundationOne Liquid CDx (Foundation Medicine, Inc., Cambridge, MA, USA) [17 (link)]. Tumor sequencing was done using FoundationOne CDx (Foundation Medicine, Inc., Cambridge, MA, USA) and Tempus xT (Tempus, Inc., Chicago, IL, USA). All variant types were analyzed, including small mutations, copy number alterations, and gene rearrangements. Variants of unknown significance were excluded.

McFarland T.R., Mathew Thomas V., Nussenzveig R., Gebrael G., Sayegh N., Tripathi N., Sahu K.K., Goel D., Maughan B.L., Sirohi D., Agarwal N, & Swami U. (2022). Detection of BRCA1, and BRCA2 Alterations in Matched Tumor Tissue and Circulating Cell-Free DNA in Patients with Prostate Cancer in a Real-World Setting. Biomedicines, 10(12), 3170.

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Tumor Sequencing Techniques in Clinical Oncology

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For patients enrolled from April 2014 to July 2017, sequencing was via amplicon-based Ion AmpliSeq Cancer Hotspot v2 (50 genes, Appendix A), performed in our institution on Ion Torrent/PGM System (Life Technologies, Camarillo, CA, USA) as previously described (22 (link)). Patients enrolled after August 2017 to January 31, 2022, underwent tumour sequencing via FoundationOne CDx (FM1) after an institutional change in panel use. Formalin-fixed, paraffin-embedded (FFPE) tissue was processed per institutional practice, and slides were submitted to Foundation Medicine (Cambridge, MA, USA) for testing. If adequate tissue was not available in patients with no plans for further biopsy, two tubes of whole blood were submitted to Foundation Medicine for analysis under the FoundationOne Liquid CDx platform. Variants identified by FoundationOne CDx are represented as pathogenic or likely pathogenic and variants of unknown significance. For the purposes of this analysis, the variants of uncertain significance were excluded. FoundationOne CDx specimens were also simultaneously profiled for TMB as well as MSI status (23 (link)).

Walsh R.J., Ong R., Cheo S.W., Low P.Q., Jayagopal A., Lee M., Ngoi N., Ow S.G., Wong A.L., Lim S.E., Lim Y.W., Heong V., Sundar R., Soo R.A., Chee C.E., Yong W.P., Goh B.C., Lee S.C., Tan D.S, & Lim J.S. (2024). Molecular profiling of metastatic breast cancer and target-based therapeutic matching in an Asian tertiary phase I oncology unit. Frontiers in Oncology, 14, 1342346.

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Genomic Profiling of Solid Tumors

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We retrospectively recruited 3738 patients with solid tumors, listed in the Keio PleSSision Group Database (Keio University Hospital), based on the following criterion: patients who underwent a 324‐gene somatic genomic profiling test (FoundationOne CDx; Foundation Medicine, Inc.) (n = 3094) or a 324‐gene cfDNA‐based comprehensive genomic profiling assay (FoundationOne Liquid CDx; Foundation Medicine, Inc.) (n = 644) between August 2020 and June 2023. In total, 1320 patients (35.3%) had canonical BRCA‐associated tumors (breast, ovarian, peritoneal, pancreatic, and prostate cancers), and 2418 patients (64.7%) had noncanonical BRCA‐associated tumors (colorectal and endometrial cancers). Table 1 summarizes the patient characteristics. This study was approved by the Ethics Committee of Keio University Hospital (approval number: 20211159). Due to the retrospective nature of this study, informed consent was not required and was waived. The study procedures involving human participants complied with the Declaration of Helsinki.

Nakamura K., Hayashi H., Kawano R., Ishikawa M., Aimono E., Mizuno T., Kuroda H., Kojima Y., Niikura N., Kawanishi A., Takeshita K., Suzuki S., Ueno S., Okuwaki K., Sasaki J., Yamaguchi M., Masuda K., Chiyoda T., Yamagami W., Okada C., Nohara S., Tanishima S, & Nishihara H. (2023). BRCA1/2 reversion mutations in a pan‐cancer cohort. Cancer Science, 115(2), 635-647.

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Multimodal Profiling of Metastatic NSCLC

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Patients were identified who underwent liquid biopsy profiling at the time of enrollment in the Prospective Clinicogenomic Program clinical trial (ClinicalTrials.gov identifier NCT04180176).²⁰ In this ongoing multicenter study, up to 1000 adult patients with metastatic NSCLC or SCLC enroll before initiating SOC systemic anticancer therapy. All patients sign consent to participate in the study, which must be approved by the institutional review board at the participating site. In the study, each patient has peripheral blood submitted for CGP of ctDNA with FoundationOne Liquid (Foundation Medicine, Cambridge, Massachusetts) or FoundationOne Liquid CDx (Foundation Medicine, Cambridge, Massachusetts). In addition, tumor tissue specimens available at enrollment may be optionally submitted for CGP with FoundationOne CDx. Liquid biopsy is then repeated on treatment and at progression or end of treatment. Longitudinal EHR-derived data are linked to CGP results. As follow-up is ongoing, for this initial analysis, we only studied pretreatment data including clinical features and molecular testing results, leveraging a data cut with recency of June 30, 2021. Patients were included in this analysis if they had a chart abstraction-confirmed diagnosis of metastatic nonsquamous NSCLC.

Schwartzberg L.S., Li G., Tolba K., Bourla A.B., Schulze K., Gadgil R., Fine A., Lofgren K.T., Graf R.P., Oxnard G.R, & Daniel D. (2022). Complementary Roles for Tissue- and Blood-Based Comprehensive Genomic Profiling for Detection of Actionable Driver Alterations in Advanced NSCLC. JTO Clinical and Research Reports, 3(9), 100386.

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Comprehensive RET Fusion Analysis

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For this study, we included all RET fusions as detected by the FoundationOne®CDx/FoundationOne® and FoundationOne Liquid CDx assays (Foundation Medicine, Inc., Cambridge, MA). All rearrangements without a fusion partner were excluded from the analysis and only cases where the kinase domain of RET was preserved were included in this study.

Parimi V., Tolba K., Danziger N., Kuang Z., Sun D., Lin D.I., Hiemenz M.C., Schrock A.B., Ross J.S., Oxnard G.R, & Huang R.S. (2023). Genomic landscape of 891 RET fusions detected across diverse solid tumor types. NPJ Precision Oncology, 7, 10.

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Comprehensive Genomic Profiling of Cancers

Cited 1 time

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The majority of molecularly characterized patients were sequenced using biopsy tissue at initial diagnosis, prior to the start of any therapy. A hybrid capture-based next-generation sequencing assay was utilized for patient samples in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory. Mutations were characterized using either solid tumor tissue or circulating cell-free DNA (cfDNA) to screen for single nucleotide variants, insertions/deletions, copy number gains, and gene fusions. Tissue-based testing assessed up to 324 genes and associated biomarkers, with FoundationOne CDx (Foundation Medicine, Cambridge, MA, USA) serving as the most recently utilized assay [20 ]. Liquid biopsies were performed by obtaining peripheral blood, isolating plasma, and extracting DNA after which genomic profiling was performed. Most commonly, liquid biopsy genomic profiling was obtained using the FoundationACT, FoundationOne Liquid, or FoundationOne Liquid CDx (Foundation Medicine, Cambridge, MA, USA) assays [21 (link),22 ]. Additionally, immunohistochemistry was used for DNA mismatch repair enzymes (MLH1, MSH2, MSH6, PMS2), and further testing was ordered at the discretion of the treating medical oncologist.

De B., Abu-Gheida I., Patel A., Ng S.S., Zaid M., Thunshelle C.P., Elganainy D., Corrigan K.L., Rooney M.K., Javle M., Raghav K., Lee S.S., Vauthey J.N., Tzeng C.W., Tran Cao H.S., Ludmir E.B., Minsky B.D., Smith G.L., Holliday E.B., Taniguchi C.M., Koong A.C., Das P, & Koay E.J. (2021). Benchmarking Outcomes after Ablative Radiotherapy for Molecularly Characterized Intrahepatic Cholangiocarcinoma. Journal of Personalized Medicine, 11(12), 1270.

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