How to query Patents Public Search for the Cancer Moonshot initiative

By Dr. Jesse P. Frumkin, PhD, Bioinformatics Patent Examiner and Data Scientist

In 2016, USPTO Chief Economist Office and the USPTO Enterprise Advanced Analytics Branch crowdsourced insights from the public regarding hundreds of thousands of cancer-related patent documents, as documented in Frumkin, Jesse and Myers, Amanda F., Cancer Moonshot Patent Data (August, 2016). Here, I address the need to continuously monitor and analyze cancer-related patent documents using the tool of your choice, such as the USPTO’s new Patents Public Search, the global patent documents in World Intellectual Property Organization’s Patentscope, or the chemogenomic linkages in the U.S. National Library of Medicine’s PubChem Classification Browser.

Each initiative that is championed by the Cancer Moonshot’s Blue Ribbon Panel Report maps to various patent topics derived from the work of patent classifiers. Specifically, each topic maps to classification symbols from the Cooperative Patent Classification scheme that is used by patent offices to categorize the technological topics in patent documents.Note that some of the symbols below retrieve cancer-specific documents, while others reflect broad bioinformatics inventions applicable to both cancer research and other biomedical fields. In general, there is a trend toward more diversity and quantity of biological and computational inventions that drive modern research in cancer biology.

The views and comments expressed herein are solely the opinion of the author and are not endorsed by, nor should be construed as, any viewpoint official or unofficial of the United States Patent and Trademark Office. The author confirms to the best of his knowledge that no information contained herein is privileged, confidential, or classified.

A. Network for Direct Patient Engagement

Excerpts from the

Blue Ribbon Panel Report

Pertinent topics, abbreviated from the

Cooperative Patent Classification

Symbols for
Patents Public Search to combine with keywords

“Develop a federated, large-scale patient participation network through which patients will be offered comprehensive tumor profiling.”

Mining of medical data, e.g. analyzing previous cases of other patients

G16H50/70

Computer-aided diagnosis, e.g. based on medical expert systems

G16H50/20

Therapies or health-improving plans relating to drugs or medications, e.g. for ensuring correct administration to patients

G16H20/10

“Molecular characterization, including detailed genomic profiling, of tumors has demonstrated the heterogeneity of cancer and has identified genetic alterations that may allow selection of targeted therapeutic interventions based on the unique profile of a patient’s tumor.”

Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism

C12Q2600/106

Nucleic acid products used in the analysis of nucleic acids for cancer

C12Q1/6886

Oligonucleotides for prognosis of disease development

C12Q2600/118

Oligonucleotides that are polymorphic or mutational markers

C12Q2600/156

Oligonucleotides for disease subtyping, staging or classification

C12Q2600/112

Proteomics, glycomics, lipidomics, omics, etc.

G01N2570/00

“The vast majority of Americans do not have easy access to precision cancer testing since oncology clinical trials are offered mainly at large academic cancer centers and not at community cancer centers where most cancer patients receive their treatments.”

Electronic clinical trials or questionnaires

G16H10/20

“Although comprehensive genomic profiling is technically feasible, its current application in clinical practice has been fragmented and inefficient, limited by cost, lack of standardization of genomic profiling panels and tumor collection, insufficient evidence of broad-based clinical utility, and barriers to data sharing among the research community.”

Facilitating communication between medical practitioners or patients, e.g. for collaborative diagnosis, therapy or health monitoring

G16H80/00

Data warehousing and computing architectures in bioinformatics

G16B50/30

Functional genomics or proteomics, e.g. genotype-phenotype associations

G16B20/00

“When patients pre-register and provide their cancer tissue, it would be necessary to safeguard their privacy and ensure the genetic and clinical information provided to the network is secure and protected.”

Protecting personal data, e.g. for financial or medical purposes

G06F21/6245

Encryption of genetic data

G16B50/40

“A Network for direct patient engagement would provide comprehensive tumor profiling for a large-scale cohort of cancer patients by linking and leveraging a number of existing pilot programs across the nation that use next generation genomic sequencing”

Heterogeneous data integration in bioinformatics

G16B50/20

“In addition, if patients are willing and able to provide serial biopsies at clinical inflection points (pre treatment, during treatment, at time of clinical recurrence or progression) throughout their care, this profiling could help us gain a better understanding of how resistance to targeted therapies develops and can be overcome.”

Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalized medicine

G01N2800/52

Mechanisms involved with cancer identification

G01N2800/7028

Medical reports, e.g. generation or transmission thereof

G16H15/00

B. Cancer Immunotherapy Translational Science Network

Excerpts from the

2016 Blue Ribbon Panel Report

Pertinent topics, abbreviated from the

Cooperative Patent Classification

Symbols for
Patents Public Search to combine with keywords

“Organize a Cancer Immunotherapy Translational Science Network that will develop and implement a national strategy to discover and evaluate novel immune-based approaches to treat and prevent both adult and pediatric cancers.”

Antibodies against tumor tissues, cells, antigens

A61K39/39558

Cancer antigens

A61K39/0011

Tumor specific antigens; Tumor rejection antigen precursors

C07K14/4748

“Our immune system has the intrinsic potential to recognize cancer cells as foreign and kill them.”

Medicinal preparations containing lymphocytes; B-cells; T-cells; natural killer cells; interferon-activated or cytokine-activated lymphocytes

A61K35/17

Medicinal preparations containing cells of the myeloid line, e.g. granulocytes, basophils, eosinophils, neutrophils, leucocytes, monocytes, macrophages or mast cells; myeloid precursor cells; antigen-presenting cells, e.g. dendritic cells

A61K35/15

“Another barrier to effective T cell immunotherapy is that tumors generate a disabling immunosuppressive tumor microenvironment that limits the ability of the immune system to act against the cancer.”

Chemical compounds or medicinal preparations that are immunostimulants

A61P37/04

Chemical compounds or medicinal preparations that are immunomodulators

A61P37/02

“…an important goal is getting activated effector T cells that recognize unique cancer neoantigens, which occur on adult cancer cells, into the tumor to maximize anticancer T cell activity.”

Antigen-pulsed cells, e.g. T-cells

A61K2039/5158

“… we will need to identify antigens that arise from the earliest genetic changes that initiate cancers…”

Cancer antigen: receptors, cell surface antigens or cell surface determinants

A61K39/001102

Growth factor receptor

- Epidermal growth factor

- Her-2, Her-3, Her 4

- Fibroblast growth factor

- Platelet-derived growth factor

- Vascular endothelial growth factor

- Hepatocyte growth factor

A61K39/001103

A61K39/001104

A61K39/001106

A61K39/001107

A61K39/001108

A61K39/001109

A61K39/00111

Immunoglobulin

- CD19

- CD22

- CD74, MHC class II

A61K39/001111

A61K39/001112

A61K39/001113

A61K39/001114

Receptors for cytokines

- Tumor necrosis factor receptors

- Colony stimulating factor receptors

- Interleukins receptors

- Interferon receptors

- Chemokine receptors

A61K39/001116

A61K39/001117

A61K39/001118

A61K39/001119

A61K39/00112

A61K39/001121

Ephrin receptor

A61K39/001122

CD20

A61K39/001124

CD38, not IgG

A61K39/001126

CD44, not IgG

A61K39/001128

Misc. "CD" designations

A61K39/001129

Growth factors

- Epidermal growth factor

- Fibroblast growth factors

- Platelet-derived growth factor

- Transforming growth factor

- Vascular endothelial growth factor

A61K39/00113

A61K39/001131

A61K39/001132

A61K39/001133

A61K39/001134

A61K39/001135

Cytokines

- Tumor necrosis factors

- Colony stimulating factors

- Interleukins

- Interferons

- Chemokines

A61K39/001136

A61K39/001138

A61K39/001139

A61K39/00114

A61K39/001141

A61K39/001142

Hormones

A61K39/001144

Development regulators

- Cell cycle regulated proteins

- Apoptosis related proteins

- p53

A61K39/001148

A61K39/001149

A61K39/00115

A61K39/001151

Transcription factors

- Wilms tumor 1

A61K39/001152

A61K39/001153

Enzymes

- Tyrosinase and related proteinases

- Telomerase, TERT

- Proteinases:

- Matrix metalloproteinases

- Serine proteases

- Caspases

- Kinases

- Phosphatases

- GTPases

A61K39/001154

A61K39/001156

A61K39/001157

A61K39/001158

A61K39/001159

A61K39/00116

A61K39/001161

A61K39/001162

A61K39/001163

A61K39/001164

Adhesion molecules

- Mesothelin

A61K39/001166

A61K39/001168

Tumor associated carbohydrate

- Mucins

- Gangliosides

- sialyl Thomson-nouvelle antigen

- Globo-H

A61K39/001169

A61K39/00117

A61K39/001171

A61K39/001172

A61K39/001173

Proteoglycans

A61K39/001174

Heat shock proteins

A61K39/001176

Tumor rejection antigen precursors

A61K39/001178

Antigens from embryonic or fetal origin

- Alpha-feto protein

- Carcinoembryonic antigen

A61K39/00118

A61K39/001181

A61K39/001182

Cancer testis antigens

- MAGE

- NY-ESO

- PRAME

A61K39/001184

A61K39/001186

A61K39/001188

A61K39/001189

Melanoma antigens

- Melan-A/MART

- Glycoprotein 100

A61K39/00119

A61K39/001191

A61K39/001192

Prostate associated antigens

- Prostate specific antigen

- Prostate specific membrane antigen

A61K39/001193

A61K39/001194

A61K39/001195

Fusion protein due to translocation

- BCR-ABL

- Pml-RARalpha

A61K39/001196

A61K39/001197

A61K39/001198

“identifying cancer-specific antigens that can serve as the basis for both antibody- and cell-based immunotherapies”

Antibodies against tumor tissues, cells, antigens

A61K39/39558

Antibodies against tumor antigens

- Carcino-embryonic antigens

- Breast

- Lung

- Liver or pancreas

- Kidney, bladder

- Stomach, intestines

- Skin, nerves, brain

- Blood cells

- Reproductive system

- Tumor-associated Moieties

- Gangliosides

- Mucins

- Translation products of oncogenes

C07K16/30

C07K16/3007

C07K16/3015

C07K16/3023

C07K16/303

C07K16/3038

C07K16/3046

C07K16/3053

C07K16/3061

C07K16/3069

C07K16/3076

C07K16/3084

C07K16/3092

C07K16/32

Antibody-drug conjugate (anti-tumor)

- Carcino-embryonic antigens

- Breast

- Lung

- Liver or pancreatic

- Kidney or bladder

- Stomach or intestinal

- Skin, nerves, or brain

- Blood cancer

- Reproductive system

A61K47/6851

A61K47/6853

A61K47/6855

A61K47/6857

A61K47/6859

A61K47/6861

A61K47/6863

A61K47/6865

A61K47/6867

A61K47/6869

Radioactive antibody (therapy/testing)

- Carcino-embryonic antigen

- Breast cancer

- Lung

- Liver or pancreas

- Kidney or bladder

- Stomach or intestines

- Skin

- Blood cancers

- Reproductive system

A61K51/1045

A61K51/1048

A61K51/1051

A61K51/1054

A61K51/1057

A61K 51/106

A61K51/1063

A61K51/1066

A61K51/1069

A61K51/1072

“… develop novel vaccine approaches that can produce effector T cells that recognize these antigens.”

Cancer vaccine

- Blood cancer vaccine

- Breast cancer vaccine

- Colon cancer vaccine

- Stomach cancer vaccine

- Intestinal cancer vaccine

- Liver cancer vaccine

- Pancreatic cancer vaccine

- Lung cancer vaccine

- Kidney cancer vaccine

- Melanoma/skin cancer vaccine

- Prostate cancer vaccine

- Reproductive system cancer vaccine

A61K2039/80

A61K2039/804

A61K2039/812

A61K2039/82

A61K2039/828

A61K2039/836

A61K2039/844

A61K2039/852

A61K2039/86

A61K2039/868

A61K2039/876

A61K2039/884

A61K2039/892

C. Therapeutic Target Identification to Overcome Drug Resistance

Excerpts from the 2016 Blue Ribbon Panel Report	Pertinent topics, abbreviated from the *Cooperative Patent Classification*	Symbols for Patents Public Search to combine with keywords
“…determine points of cancer cell weakness, known as vulnerabilities, that can be used as targets for the development of new therapies that prevent or overcome a tumor’s ability to resist or become non-responsive to cancer therapies”	Detection or diagnosis of multiple drug resistance	G01N2800/44
	Anti-neoplastic agents	A61P35/00
	Anti-neoplastic agents specific for metastases	A61P35/04
	Functional genomics or proteomics involving mutagenesis	G16B20/50
	Radio-sensitizing, i.e. administration of pharmaceutical agents that enhance the effect of radiotherapy	A61K41/0038
	Non-coding nucleic acids modulating the expression of oncogenes and tumor suppressor genes	C12N15/1135
	Differentiation of cancer cell lines, e.g., reversion of tumor cells	C12N2506/30
“Being able to accurately predict when a patient may develop drug resistance, and potentially who is at higher risk, could have profound implications for selecting appropriate cancer therapies for individual patients.”	Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalized medicine; Prognosis	G01N2800/52
	Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism	C12Q2600/106
	Testing for anti-neoplastic activity of chemical or biological drugs involving human or animal cells	G01N33/5011

D. A National Cancer Data Ecosystem for Sharing and Analysis

Excerpts from the 2016 Blue Ribbon Panel Report	Pertinent topics, abbreviated from the *Cooperative Patent Classification*	Symbols for Patents Public Search to combine with keywords
“Create a national infrastructure for sharing and processing cancer data”	Data warehousing and computing architectures in bioinformatics	G16B50/30
	Heterogeneous data integration in bioinformatics	G16B50/20
	Cheminformatics computing architectures, database systems, data warehousing, and programming languages	G16C20/90
“enable researchers to more effectively mine cancer-related data to develop new strategies to prevent, diagnose, and treat cancers as well as to understand the fundamental nature of the disease.”	Mining of medical data, e.g. analyzing previous cases of other patients	G16H50/70
	Facilitating communication between medical practitioners or patients, e.g. for collaborative diagnosis, therapy or health monitoring	G16H80/00

E. Fusion Oncoproteins in Childhood Cancers

Excerpts from the 2016 Blue Ribbon Panel Report	Pertinent topics, abbreviated from the *Cooperative Patent Classification*	Symbols for Patents Public Search to combine with keywords
“Improve our understanding of the molecular and biochemical mechanisms of transformation driven by fusion oncoproteins.”	Cancer antigens from fusion proteins originating from gene translocation in cancer cells	A61K39/001196
	Breakpoint cluster region-abelson tyrosine kinase	A61K39/001197
	Pml-RARalpha	A61K39/001198
	Fusion polypeptides	C07K2319/00
	Anti-neoplastic agents specific for leukemia	A61P35/02

F. Symptom Management Research

Excerpts from the 2016 Blue Ribbon Panel Report	Pertinent topics, abbreviated from the *Cooperative Patent Classification*	Symbols for Patents Public Search to combine with keywords
“Accelerate research that can identify approaches to monitor and manage patient reported symptoms, and integrate the information to revise and update national guidelines for symptom control and support.”	Anti-neoplastic agents specific for metastases	A61P35/04
“Both disease and treatment cause deleterious symptoms and side effects that occur during the course of treatment or appear long after treatment is completed.”	General protective or anti-noxious agents	A61P39/00
	Drugs for nausea, cinetosis or vertigo; Antiemetics	A61P1/08
	Non-central analgesic, antipyretic or anti-inflammatory agents	A61P29/00
	Immunostimulants	A61P37/04
	Immunomodulators	A61P37/02
	Anti-infectives	A61P31/00
	Drugs for ulcers, gastritis or reflux esophagitis	A61P1/04
	Drugs for peripheral neuropathies	A61P25/02
“Treatment delays and nonadherence to treatment due to symptoms are particularly concerning because they decrease treatment effectiveness and increase the risk for recurrence and death.”	Healthcare informatics for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance	G16H20/00

G. Prevention and Early Detection: Implementation of Evidence-Based Approaches

Excerpts from the 2016 Blue Ribbon Panel Report	Pertinent topics, abbreviated from the *Cooperative Patent Classification*	Symbols for Patents Public Search to combine with keywords
“Sponsor initiatives to improve the current state of early detection, genetic testing, genetic counseling, and knowledge landscape of the mechanisms and biomarkers associated with cancer development and conduct implementation science research to accelerate development, testing, and broader adoption of proven strategies to significantly reduce cancer risk and address cancer health disparities in these areas.”	Mammography	G06T2207/30068
	Evaluating skin marks, e.g. mole, nevi, tumor, scar	A61B5/444
	Biomedical imaging of tumors and lesions	G06T2207/30096
	Detecting organic movements or changes, e.g. tumors, cysts, swellings	A61B8/08
	Healthcare informatics for the handling or processing of medical images	G16H30/20
“There are a number of cancers that are preventable, but evidence-based strategies to prevent them are not currently accessible to all individuals or are being adopted by too few people, leaving millions of Americans at high risk for preventable, yet deadly cancers.”	Healthcare informatics for facilitating communication between medical practitioners or patients, e.g. for collaborative diagnosis, therapy or health monitoring	G16H80/00
	Topical preparations for affording protection against sunlight or other radiation	A61Q17/04
	Foods, ingredients or supplements having a functional effect on cancer prevention	A23V2200/308
“Hereditary cancer testing in appropriate populations is a cancer prevention strategy that is currently underused, leading to unnecessarily lost lives and diminished quality of life.”	Assays involving translation products from oncogenes	G01N2333/82
	Assays for p53 protein	G01N2333/4748
	Assays for retinoblastoma protein	G01N 2333/4736

H. Retrospective Analysis of Biospecimens from Patients Treated with Standard of Care

Excerpts from the

2016 Blue Ribbon Panel Report

Pertinent topics, abbreviated from the

Cooperative Patent Classification

Symbols for
Patents Public Search to combine with keywords

“Conduct retrospective analyses of archival tumor samples from cancer patients treated with standard of care and whose outcomes are known in order to better understand and target the mechanisms driving individual tumor types.”

Healthcare informatics for handling or processing of patient-related laboratory analysis (e.g., patient specimen analysis)

G16H10/40

Healthcare informatics for mining of medical data

G16H50/70

Healthcare informatics for handling and processing of patient-specific data (e.g., electronic patient records)

G16H10/60

“Constructing human tumor atlases that trace tumor cell populations over time in adult and childhood cancers will require an interdisciplinary effort that involves the collection, annotation, and careful analysis of biopsies taken from paired primary and metastatic cancers or metastases from a single primary cancer to different anatomical sites, and of tissue biopsies taken before, during, and after treatment, with specimens that represent the diversity of the population”

Immunoassays for cancer

Immunoassays & specific cancers:

- Cervix

- Breast

- Colon

- Lung

- Leukemia

- Skin/melanoma

- Prostate

- Liver

- Uterus/endometrial

- Stomach/intestine

- Ovaries

G01N33/574

G01N33/57407

G01N33/57411

G01N33/57415

G01N33/57419

G01N33/57423

G01N33/57426

G01N33/5743

G01N33/57434

G01N33/57438
G01N33/57442

G01N33/57446

G01N33/57449

- Tumor-associated glycolinkage

- Carcino-embryonic antigen

- Oncofetal proteins

- Oncogenic proteins

G01N33/57469

G01N33/57473

G01N33/57476

G01N33/5748

Immunoassay: compound/marker

- In body fluids

- Localized on membranes

- Intracellular compounds

G01N33/57484

G01N33/57488

G01N33/57492

G01N33/57496

I. Generation of Human Tumor Atlases

Excerpts from the 2016 Blue Ribbon Panel Report	Pertinent topics, abbreviated from the *Cooperative Patent Classification*	Symbols for Patents Public Search to combine with keywords
“Develop human tumor atlases for adult and pediatric cancers that map the evolution of human tumors by documenting the genetic lesions, molecular pathways, and cellular interactions that guide tumor development from pre-malignant tissue to primary cancer, progression to metastasis, response to therapy and acquisition of resistance.”	Functional genomics or proteomics involving mutagenesis	G16B20/50
	Ploidy or copy number detection	G16B20/10
	Modeling or simulations in systems biology	G16B5/00
“…studies of cancer processes typically focus on relationships among a limited set of variables, at a single point in time, and are at best an oversimplification of the true dynamics occurring within a tumor.”	Systems biology involving dynamic time models	G16B5/30
	Determining trends in physiological measurement data	A61B5/7275
	Intracellular tumor markers	G01N33/57496

J. Development of New Enabling Cancer Technologies

Excerpts from the 2016 Blue Ribbon Panel Report	Pertinent topics, abbreviated from the *Cooperative Patent Classification*	Symbols for Patents Public Search to combine with keywords
“Develop innovative new technologies in the areas of imaging…”	Biomedical image analysis or image enhancement of a tumor or lesion	G06T2207/30096
	Biomedical image inspection	G06T7/0012
	Recognition of patterns in medical or anatomical images	G06V2201/03
“Develop innovative new technologies in the areas of… instrumentation (e.g., multidimensional single cell imaging and molecular analysis technologies devices…)”	Biomedical image processing of in vitro cell structures and in vitro tissue sections	G06T2207/30024
	Image or video recognition or understanding involving microscopic objects (e.g., biological cells or cellular parts)	G06V20/69
	Intracellular compounds serving as markers for tumor, cancer, neoplasia	G01N33/57496
	Involving compounds localized on the membrane of tumor or cancer cells	G01N33/57492
“…intra-tumoral microdosing…”	Biologically active materials in bandages, wound dressings, absorbent pads, or medical devices containing anti-neoplastic, anti-proliferative, anti-restenosis, or anti-angiogenic agents (e.g., paclitaxel, sirolimus)	A61L2300/416
“Develop innovative new technologies in the areas of… biological models (e.g., patient-derived tissues and 3-dimensional organlike cultures and humanized mouse models)…”	Animal models for proliferative disease	A01K2267/0331
	Genetically modified animal models for proliferative disease	C12N2015/8572
	Cancer cell lines	C12N5/0693
	Cancer cell lines of blood cancers	C12N5/0694
	Cancer cell lines that are stem cells, progenitor cells, and precursor cells	C12N5/0695
	Coculturing with tumor cells and conditioned media produced by tumor cells	C12N2502/30
	General methods for 3D culture	C12N5/0062
“Develop innovative new technologies in the areas of… computational platforms (e.g., integrated multiscale data systems) that interconnect molecular, cellular, tissue, and patient-derived information.”	Healthcare informatics for handling medical images	G16H30/20
	Data warehousing and computing architectures in bioinformatics	G16B50/30

Author

Dr. Jesse P. Frumkin, PhD, Bioinformatics Patent Examiner and Data Scientist

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