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    Companion Diagnostics | November 2019 Newsletter

    Companion-Diagnostics-November-2019-Newsletter

    Using patent filings and FDA approvals related to in vitro diagnostic devices, we elaborate on the role of companion diagnostics in the advancement of personalized medicine. 

    Companion Diagnostics (CDx): FDA Approvals and Patent Filings On the Rise

    Companion diagnostics (CDx), sometimes called in vitro diagnostic devices (IVD), are diagnostic tests "coupled" with a therapeutic drug to evaluate its applicability to a specific group of patients based on one or more biomarkers. While most companion diagnostic devices and nucleic acid tests are used with a specific therapy, there are others which can help choose the appropriate therapy. Companion diagnostic devices may include kits, assays, and specific software to analyze results, aid in discerning results and make decisions regarding treatment.

    Companion diagnostics are particularly relevant in the current era of personalized medicine. Personalized medicine refers to the practice that uses specific patient characteristics to determine the appropriate treatment. Our current practice in personalized pharmaceuticals uses the understanding of the patient’s demographics, history, and environment combined with cutting edge procedures, such as neuroimaging, pharmacogenomics, cellular and molecular phenotyping, and database mining.

    Patent filings for companion diagnostics indicate a steady increase in filing activity (illustrated in Figure 1) with US being the top filer contributing 52% of all patent families. China is a distant second with 15% of the first filings. Europe has a little over 1,000 families originating from the European Patent Office, whereas PCT applications claim filing priority for about 200 patent families.

    image6-51image4-53

     

    Figure 1: Charts Illustrating the Patent Filing Trend and Map Indicating Geographical Origins of First Filing. EP and PCT Filings Account for about 1000 and 200 Patent Families Respectively

    Selected FDA approvals related to nucleic acid based devices since 2015 have been listed below (Table 1). Among these approvals, eighteen (18) of them were Class III devices that required a PMA pathway, whereas nine (9) approvals required de novo pathway for novel medical devices. About 21% of approvals were under the 510(k) premarket notification. 23andMe had the highest approvals (5) relating to nucleic acid based in vitro devices. The not-for-profit, ARUP Laboratories, developed two devices that received approvals under the Humanitarian Device Exemption pathway.

    Table 1: FDA Approvals Related to Nucleic acid Based In Vitro Devices Since January 2015

    Condition

    Kits / Assays/ Systems/ Software

    Approval Pathway

    Company

    Decision Date

    Tumor Profiling

    FoundationOne CDx

    PMA

    Foundation Medicine, Inc.

    6-Nov-2019

    Tumor Profiling

    Myriad myChoice CDx

    PMA

    Myriad Genetic Laboratories, Inc.

    23-Oct-2019

    Chronic Myeloid Leukemia

    Xpert BCR-ABL Ultra, GeneXpert Dx System, GeneXpert Infinity-48s And GeneXpert Infinity-80 Systems

    510(k)

    Cepheid

    27-Sep-2019

    Breast Cancer

    Therascreen PIK3CA RGQ PCR Kit

    PMA

    Qiagen GMBH

    28-May-2019

    Breast Cancer

    INFORM HER2 Dual ISH DNA Probe Cocktail

    PMA

    Ventana Medical Systems, Inc.

    3-May-2019

    Urothelial Cancer

    Therascreen FGFR RGQ RT-PCR Kit

    PMA

    Qiagen GmbH

    26-April-2019

    Prostate Cancer

    Progensa PCA3 Assay

    PMA

    Gen-Probe, Inc.

    15-Mar-2019

    Ovarian Cancer

    BRACAnalysis CDx

    PMA

    Myriad Genetic Laboratories, Inc.

    6-Mar-2019

    Chronic Myeloid Leukemia

    QXDx BCR-ABL %IS Kit for use On The QXDx AutoDG DdPCR System

    510(k)

    Bio-Rad Laboratories, Inc.

    13-Feb-2019

    Colorectal Cancer Predisposition

    MUTYH-Associated Polyposis (MAP)

    510(k)

    23andMe

    18-Jan-2019

    Hematologic Malignancies

    MLL (KMT2A) Breakapart FISH Probe Kit; AML1 (RUNX1) Breakapart FISH Probe Kit, P53 (TP53) Deletion FISH Probe Kit; EVI1 (MECOM) Breakapart FISH Probe Kit, DEL(20Q) Deletion FISH Probe Kit; AML1/ETO (RUNX1/RUNXIT1)) Translocation, Dual FUSI, CBFB (CBFB) /MYH11 Translocation, Dual Fusion FISH Probe Kit,DEL(5Q) Deletion FISH Probe Kit; DEL(7Q) Deletion FISH Probe Kit

    De Novo

    Cytocell Ltd.

    21-Dec-2018

    Pharmacogenetic Reports

    23AandMe Personal Genome Service (PGS) Pharmacogenetic Reports

    De Novo

    23andMe

    31-Oct-2018

    Multiple Myeloma / Acute Lymphoblastic Leukemia (MRD)

    Adaptive Biotechnologies  CLONOSEQ ASSAY

    De Novo

    Adaptive Biotechnologies Corp

    28-Sep-2018

    Acute Myeloid Leukemia

    Abbott RealTime IDH1

    PMA

    Abbott Molecular Inc.

    20-Jul-2018

    Coagulation, late-onset Alzheimer's, Parkinson's, Celiac, Alpha-1 antitrypsin deficiency, Early-onset primary dystonia, Factor IX deficiency, Gaucher Type 1, Glucose-6-phosphate dehydrogenase deficiency, Hereditary hemochromatosis, Hereditary thrombophilia

    Personal Genome Service (PGS) Genetic Health Risk Test for Hereditary Thrombophilia

    De Novo

    23andME

    6-Apr-2018

    Tissue of Origin

    Tissue of Origin Test Kit - FFPE

    510(k)

    Cancer Genetics, Inc.

    15-Mar-2018

    Breast Cancer

    23andMe PGS Genetic Health Risk Report for BRCA1/BRCA2 (Selected Variants)

    De Novo

    23andMe

    6-Mar-2018

    Myeloproliferative disease/ Polycythemia Vera

    Ipsogen JAK2 RGQ PCR Kit

    510(k)

    Qiagen INC

    12-Jan-2018

    Chronic Myeloid Leukemia

    MRDx BCR-ABL Test, MRDx BCR-ABL Test Software

    510(k)

    MolecularMD Corporation

    22-Dec-2017

    Tumor Profiling

    MSK-IMPACT (Integrated Mutation Profiling of Actionable Cancer Targets):A Hybridization-Capture based Next Generation Sequencing Assay

    De Novo

    Memorial Sloan-Kettering Cancer Center

    15-Nov-2017

    Colorectal Cancer

    Ventana ANTI-MLH-1(M1) Mouse Monoclonal Primary Antibody, Ventana ANTI-PMS2 (A16-4) Mouse Monoclonal Primary Antibody, Ventana ANTI-MSH2 (G219-1129) Mouse Monoclonal Primary Antibody, Ventana ANTI-MSH6 (SP 93) Mouse Monoclonal Primary Antibody, Ventana ANTI-BRAF V600E (VE1) Mouse Monoclonal Primary Antibody

    De Novo

    Ventana Medical Systems

    27-Oct-2017

    Chromosome Abnormalities

    GenetiSure Dx Postnatal Assay

    510(k)

    Agilent Technologies, Inc.

    11-Aug-2017

    Colorectal Cancer

    Praxis Extended RAS Panel

    PMA

    Illumina, Inc.

    29-Jun-2017

    Non-Small Cell Lung Cancer

    Oncomine Dx Target Test

    PMA

    Life Technologies Corp

    22-Jun-2017

    Acute Myeloid Leukemia

    LeukoStrat CDx FLT3 Mutation Assay

    PMA

    Invivoscribe Technologies, Inc.

    28-April-2017

    Breast Cancer

    HER2 CISH pharmDxTM Kit

    PMA

    Dako Denmark A/S

    12-April-2017

    Ovarian Cancer

    FoundationFocus CDxBRCA

    PMA

    Foundation Medicine, Inc.

    19-Dec-2016

    Cystic Fibrosis

    xTAG Cystic Fibrosis 60 Kit v2, xTAG Data Analysis Software (TDAS) CFTR

    510(k)

    Luminex Molecular Diagnostics

    15-Dec-2016

    Chronic Myeloid Leukemia

    Quantidex qPCR BCR-ABL IS Kit

    De Novo

    Asuragen, Inc.

    22-Jul-2016

    Non-Small Cell Lung Cancer

    Cobas EGFR Mutation Test v2

    PMA

    Roche Molecular Systems, Inc.

    6-Jun-2016

    Colorectal Cancer

    Epi ProColon®

    PMA

    Epigenomics AG

    12-April-2016

    B-cell chronic lymphocytic leukemia

    VYSIS CLL FISH Probe Kit

    PMA

    Abbott Molecular Inc.

    11-Apr-2016

    Aggressive Systemic Mastocytosi

    Kit D816V Assay

    HDE

    Arup Laboratories

    18-Dec-2015

    Myelodysplastic syndrome / myeloproliferative disease

    Fluorescence in situ hybridization, platelet-derived growth factor receptor, beta polypeptide (pdgfrb), rearrangement

    HDE

    Arup Laboratories

    18-Dec-2015

    Colorectal Cancer

    Cobas KRAS Mutation Test

    PMA

    Roche Molecular Systems, Inc.

    7-May-2015

    Autosomal Recessive Carrier Screening

    23ANDME Personal Genome Service

    De Novo

    23andMe

    19-Feb-2015

    Breast Cancer

    SPoT-Light HER2 CISH Kit

    PMA

    Invitrogen Corporation

    7-Jan-2015

     

    Despite the recent FDA approvals and policy initiatives, there are various challenges that need to be addressed for personalized medicine to be successfully implemented. The FDA is still working to ensure the accuracy of Next Generation Sequence (NGS) tests, so that patients and clinicians can receive accurate and clinically meaningful test results. The vast amount of data obtained from one’s genetic material makes it difficult to draw meaning from genomic profiling of patients. Several genomic and proteomic related companies are partnering with players in other technologies to overcome these challenges. Partners include technology and information management companies, as well as academic institutions and hospitals. Table 2 presents some of the partnering companies/universities and the purpose of their collaborations from recent times.

    Table 2: Collaborations in Companion Diagnostics

    Collaborating Partners

    Purpose

    Date

    Akoya Biosciences & Precision for Medicine (formerly ApoCell)

    To advance immuno-oncology candidates in clinical trials using both tumor biopsies and liquid biopsies to generate data required for assessing drug efficacy and validation of companion diagnostics (CDx)

    05-Nov-19

    MEDx (Suzhou) Translational Medicine & Lucence

    To pursue a strategic partnership in China to co-develop cancer-care tests that would benefit patients and pharmaceutical companies

    06-Nov-19

    ArcherDX & Ayala Pharmaceuticals

    To develop companion diagnostic (CDx) tests targeting cancers bearing Notch activating mutations and fusions

    08-Jul-19

    Adial Pharmaceuticals & Eurofins Scientific

    To study AD04, a genetically targeted therapeutic agent for the treatment of Alcohol Use Disorder

    07-May-19

    Kiyatec & CarThera

    To advance innovation and improve treatments for patients diagnosed with glioblastoma

    18-Nov-19

    Shriners Hospitals for Children & Genome Medical

    To offer high-quality genomic services and precision medicine for pediatric patients

    30-Oct-19

    NEC Corporation & VAXIMM AG

    To develop novel personalized neoantigen cancer vaccines

    12-Nov-19

    Promega & Merck

    To develop Microsatellite Instability (MSI) companion diagnostic for use with Keytruda

    06-Nov-19

    Caris Life Sciences & Debiopharm

    To develop a companion diagnostic for an oncology drug being developed by Debiopharm

    30-May-19

    Myriad & AstraZeneca & Merck

    To identify germline BRCA mutations in men who have metastatic castrate-resistant prostate (mCRPC) cancer

    04-Apr-19

    Thermo Fisher & Eli Lilly

    To develop a companion diagnostic for LOXO-292, a cancer candidate

    09-Sep-19

    Agilent & SomaLogic

    To drive biomarker discovery efforts as well as novel diagnostics and accelerated pharmaceutical development

    30-Apr-19

    Agilent & NUS & NUH, Singapore

    To develop new methods of transforming clinical research into diagnostics

    19-Aug-19

    Biocartis & Bristol-Myers Squibb

    To use the Idylla™ MSI test in connection with immuno-oncology therapies

    12-Mar-19

    Qiagen & Illumina

    To accelerate the adoption of next-generation sequencing (NGS) in clinical decision-making

    07-Oct-19

     

    Available treatment options for several conditions are ineffective, cause severe side effects, or result in treatment resistance. Medical professionals are optimistic that personalized treatment approaches would improve outcomes in such diseases. In spite of the FDA’s strides in creating draft guidance and other archives that concern a regulatory pathway for personalized medicine, uncertainty remains regarding regulations related to laboratory-developed tests for specific conditions.  Proof of therapeutic outcomes for many conditions as well as, clinical and economic impacts of treatments are still pending.  A set approach for obtaining this information has yet to surface. With international regulations, as well as collaborations and partnerships between companion diagnostic players, we might move closer to making personalized medicine a reality.

     

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