Published On: December 2nd, 2019Categories: Patent Applications, Patents

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.

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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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