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EN Cancer Prediction
Overview
Cancer prediction is ubiquitous across the spectrum of cancer care from screening to hospice. Many of the early stage cancers cause no symptoms, and treatment is recommended because of a prediction that tumor progression would ultimately threaten a patient's quality of life and survival. There are two cancer disease prediction models. The first one is Artificial intelligence (AI) cancer risk prediction model and the second is Cancer Gene expression prediction model.1) Artificial intelligence (AI) cancer risk prediction model
2) Cancer gene testing with gene expression prediction model
3) Cancer gene testing with chromosomes prediction model
Genetic testing looks for changes, sometimes called mutations or variants, in your DNA. Genetic testing is useful in many areas of medicine and can change the medical care you or your family member receives. Reasons for cancer genetic testing are:
1) To learn whether you have a genetic condition that runs in your family before you have symptoms 2) To learn about the chance a current or future pregnancy will have a genetic condition
3) To diagnose a genetic condition if you or your child has symptoms
4) To understand and guide your cancer prevention, prediction or treatment plan
Cancer Genetic testing takes NGS next-generation gene sequencing as the mainstream, and the basic principle of the platform operation process can be divided into four major steps:
1) Fragmentation: Sample library preparation nucleic acid fragmentation
2) Library Construction
3) Sequencing Reaction: High-throughput Sequencing Reaction
4) Data analysis
The basic concept of NGS is to perform large-scale sequencing analysis at the same time after fragmentation of nucleic acid. The purpose of the experiment is to find known or unknown sequence information. The premise of finding the known is that the species of the experimental sample must have a reference sequence ( Reference Sequence, based on its similarity to perform Mapping and Counting analysis. If there is no reference sequence for this species today, it must be assembled through further prediction and verification to obtain sequence information.
I).Artificial intelligence (AI) cancer risk prediction model
Recent years have seen attempts to formalize risk prediction in cancer care such as cancer stage the Artificial intelligence (AI) prediction tools that provide a quantitative estimate of the probability of a specific event for an individual patient. AI Prediction models generally have greater accuracy than reliance on stage or risk groupings. It can incorporate novel predictors such as genomic data, and can be used more rationally to make treatment decisions.Several Artificial intelligence (AI) prediction models are now widely used in clinical practice. Even the burgeoning complexity of diagnostic and prognostic information, there is simply to incorporating multiple variables into a single prediction
particularly with respect to their effects on clinical outcomes. Artificial intelligence (AI) approaches have emerged aspromisingmodel. Key issues will be integration of models into the electronic health record and more careful evaluation of models, tools to address important unmet needs across different specialties in medicine, including oncology, radiology, and pathology.
Artificial Intelligence (AI) is really changing the world, especially in the field of healthcare and medical treatments
where it can easily detect several deadly diseases like cancer and tumors at the initial stage of development with more accuracy compare to doctors. AI-enabled such screening machines are now used at hospitals to diagnosis the different types of cancers.Actually, AI-enabled models are developed with the help of a huge amount of healthcare training data in the form of medical imaging like X-Rays, CT Scan, MRI or other kinds of annotated reports. All these images showing the symptoms of cancer are feed into a machine learning algorithm to learn the patterns showing the early sign of cancer development and predict the chances of having this deadly disease in the future.
AI Machine Learning(ML) risk prediction
Artificial intelligence (AI) and machine learning (ML) are two of the latest trends in the industry. The typical workflow AI and machine learning for network data training comes from raw data collection, data feature extraction, machine learning model construction, model verification, and deployment of predictive inference.AI machine learning algorithms include Convolutional Neural Network (CNN), Generative Adversarial Network (GAN), Recurrent Neural Network (RNN), 3D UNet model, ResNet model, Yolo V5 model structure, etc. AI artificial intelligence and machine learning have been successfully applied The key is not mathematics, but having
domain expertise, access to correct data and practical experience to verify the solution. CNN convolutional neural network is a deep artificial neural network architecture layer:1) Image data (input layer Input: training data Dataset)-Labeling training dataset
2) Image features extraction(convolutional layer: CONV, function layer: ReLU, pooling layer :POOLING)
3) Image classification (Output layer: Flatten, Fully Connection-FC, Regression: SoftMax)
4) Image recognition Inference (Accuracy rate ACC = 0~1)
The detail of CNN block diagrm and feature extraction with inference test can be check the related diagram from CNN1 and CNN2. CNN1: 3-layer CNN architecture composed by layers of convolutional and pooling layers, a full-connected layer and a logistic regression classifier to predict if an image patch belongs to a IDC tissues or not. CNN2: Tumor decision probability map. Based on the AI Machine Learning(ML) risk prediction, the prdiction vale can be up to 0.99 if the labeling data is well trained.
II).Cancer gene testing with gene expression prediction model
Cancer is badly affecting a large set of population. If it is not diagnosed on time, it becomes difficult for the doctor to save the patient’s life. There are many methods available to predict cancer. However, presently, gene expression data is attracting people towards it. As there is big data, various AI deep learning methods are used to predict the cancerous and noncancerous genes. it was found that the gene expression data provides some added details that help to enhance the classification, prediction and diagnosis of cancer. Therefore, it means one can work with the gene expression data for better results.Altered Gene Expression in Cancer
Cancer, a disease of altered gene expression, is the result of gene mutations or dramatic changes in gene regulation. Cancer can be described as a disease of altered gene expression. There are many proteins that are turned on or off (gene activation or gene silencing) that dramatically alter the overall activity of the cell. A gene that is not normally expressed in that cell can be switched on and expressed at high levels. This can be the result of gene mutation or changes in gene regulation ( epigenetic, transcription, post-transcription, translation, or post-translation).
Researchers are working to understand the common changes that give rise to certain types of cancer or how a modification
might be exploited to destroy a tumor cell. Between that, scientists are using knowledge of the regulation of gene expression in individual cancers to develop new ways to treat target diseased cells and prevent the disease from occurring and target therapies exploit the overexpression of a specific protein or gene mutation to develop new medications to against the specific cancer.
Epigenetic Alterations in Cancer
Common in cancer cells, silencing genes, which occur through epigenetic mechanisms, include modifications to histone proteins and DNA. In cancer cells, silencing genes through epigenetic mechanisms is a common occurrence. Mechanisms can include modifications to histone proteins and DNA associated with these silencing genes.Cancer and Transcriptional/Post-Transcriptional Control
Increased transcriptional activation of genes result in alterations of cell growth leading to abnormal gene expression, as seen in cancer. Transcription factors, especially some that are proto-oncogenes or tumor suppressors, help regulate the cell cycle; however, when regulation gives rise to cancer cells, then transcriptional control of gene expression is affected.
Modifications, such as the overexpression of miRNAs, in the post-transcriptional control of a gene can result in cancer. Overexpression of miRNAs could be detrimental to normal cellular activity because miRNAs bind to the 3′ UTR of RNA molecules to degrade them. Specific types of miRNAs are only found in cancer cells.
Cancer and Translational/Post-translational Control
There are many examples of translational or post-translational modifications of proteins that arise in cancer. Modifications are found in cancer cells from the increased translation of a protein to changes in protein phosphorylation to alternative splice variants of a protein.Targeted Therapy : New Drugs to Combat Cancer
Researchers are using what is known about the regulation of gene expression in cancer states, including , to develop new ways to treat and prevent disease development. They are designing drugs on the basis of the gene expression patterns within individual tumors. This idea, that therapy and medicines can be tailored to an individual, has given rise to the field of personalized medicine.With an increased understanding of gene regulation and gene function, medicines can be designed to specifically target diseased cells without harming healthy cells. Some new medicines, called targeted therapies, have exploited the overexpression of a specific protein or the mutation of a gene to develop a new medication to treat disease. One example is the useof anti-EGF receptor medications to treat the subset of breast cancer tumors that have very high levels of the EGF protein. Of course, more targeted therapies will be developed as researchers learn more about how gene expression changes can cause cancer.
III).Cancer gene testing with chromosomes prediction model
DNA is packaged into structures called chromosomes. Some tests look for changes in chromosomes rather than gene changes. Examples of these tests are karyotype and chromosomal microarrays.A karyotype is an individual's collection of chromosomes. The term also refers to a laboratory technique that produces an image of an individual's chromosomes. The karyotype is used to look for abnormal numbers or structures of chromosomes.
Chromosomal microarray(CMA) analysis is a high-resolution, whole-genome technique used to identify chromosomal abnormalities, including those detected by conventional cytogenetic techniques, as well as small submicroscopic deletions and duplications referred to as copy number variants.Because chromosomal microarray analysis has a greater resolution than conventional karyotyping, it can detect deletions and duplications down to a 50- to 100-kb level.
There are 2 major microarray platforms used in prenatal diagnosis: single-nucleotide polymorphism (SNP) arrays and comparative genomic hybridization (CGH) arrays. With SNP and CGH arrays, DNA from a fetal sample, such as CVS or amniocentesis, is hybridized to an array platform consisting of DNA probes on a solid surface, such as a microscope slide or a silicon chip. Chromosomal microarray (CMA) testing looks for extra (duplicated) or missing (deleted) chromosomal segments, sometimes called copy number variants (CNVs). CMA is clearly useful for individuals who don’t fit a specific known syndrome such as cancer.
IV).Cancer gene testing items:
The main purpose of genetic testing is to indicate the risk factors and risks in genes that may cause diseases. After the subjects understand their genes, they can discuss and plan future health management life with their doctors, so that they can prevent diseases early. There are approximately 30,000 genes in the human genome. Among them, proto-oncogenes can cause uncontrolled cell division. Tumor suppressors are a class of genes that inhibit cell overgrowth and proliferation, thereby suppressing tumor formation.Proto-oncogenes are genes that control cell proliferation and differentiation. Normal proto-oncogenes can be mutated into oncogenes. Tumor suppressor genes are genes that inhibit the abnormal growth and malignant transformation of cells.
According to studies such as genetic epidemiology and chromosome analysis, it has been confirmed that the occurrence of tumors has an obvious genetic basis. Some tumors are inherited by a single gene (retinoblastoma, Wilms tumor, neuroblastoma, skin squamous cell carcinoma, pheochromocytoma) Cell tumors and multiple neurofibromatosis, etc.), some tumors are genetically inherited (breast cancer, cervical cancer, colon cancer, lung cancer, gastric cancer, prostate cancer, etc.), and some are related to chromosomal abnormalities (chronic myelogenous leukemia, etc.) In addition, certain genetic defects or diseases tend to be prone to certain tumors (patients with Edwards syndrome are prone to Wilms tumor, and patients with ataxia telangiectasia are prone to lymphoma or leukemia )
Basically, the probability of cancer occurrence is as follows:
Probability of cancer occurrence (p) = number of cell divisions (a) * number of mutations produced per division (b) * probability of failure of the immune system to clear cancer cells * probability of a mutated gene as an oncogene (d)
Contents of cancer genetic testing items:
(1) Accuracy (2) Precision/Reproducibility (3) Reportable Range (4) Cut-off Value (5) Traceability (6) Sensitivity (7) Specificity (8) Interference Study (9) Stability (10) Flow chart of the detection process and its Description (11) Test result (Prediction Result)
Gene testing item table:
| System | Cancer Item | Gene |
| Lymphatic immune system | Lymphatic cancer | CDKN2A |
| Digestive system | Stomach Cancer, Liver Cancer, Oropharyngeal Cancer, Gastric Carcinoid | STK11,MLH1,APC,CDH1,FGFR!,HNF1, KITKRAS,MET,PDGFRA,PIK3CA,SMAD4,SRC,TP53 |
| Endocrine System | Parathyroid Cancer, Pancreatic Cancer, Liver Cancer | VHL,FGFR2,KRAS,RET,STK11 |
| Cranial nervous system | Brain Cancer,Head Neck Cancer | VHL,ALK,IDH1,IDH2,PIK3CA,PTEN,RB1,SMARCB1,TP53 |
| Reproductive system | Prostate Cancer, Cervical Cancer, Ovarian Cancer, Breast Cancer | BRINP2,ATM,CDH1,ERBB2,ERBB4,EZH2,FGRR1,FGRR2,KIT,PIK3CA,PTEN,SRC,STK11,TP53 |
| Respiratory system | Lung Cancer, Oral Cavity Cancer, Nasopharyngeal Carcinoma | ALK,EGFR,KRAS,NOTCH1,PIK3CA,STK11 |
| Skin system | Skin Cancer | ATK1,BRAF,CTNNB1,GNA11,GNAQ,NRAS,PTEN,SMO,STK11 |
| Cardiovascular circulatory system | Kidney Cancer, Urethral Cancer | ABL1,EZH2,FBXW7,FGFR1,FGFR3,FTL3,LDH1,LDH3,JAK2,KDR,NPM1,PDGFRA,PTPN11 |
| Skeletal system | Rhabdomyosarcoma | CFS1R,TP53 | Urinary system | Bladder Cancer, Upper Urinary Tract Epithelial Cancer | VHL,FGFR3,HNF1A,HRAS,MET,PB1,SMARCB1,TP53 |
| Visual system | Retinoblastoma | RB1 |
Related gene testing application technologies:
The developments in genomics sequencing testing technologies have the potential to transform the prediction, diagnosis and treatment of many diseases, specifically inherited and cancers. Medicines based on clinical genomics companies are making progess in the fields of cancer oncology, infection, pharmacology Moreover, the genetic variants in the human genome, both at the whole genome and at the exome level, provide a rational approach to prediction, diagnosis, therapy, and personalized medicine.
Here are major clinical genomics testing companies reference information:
Eurofins Scientific SE (Luxembourg) was founded in 1987 and is headquartered in Luxembourg, Europe. The company offers a portfolio over 130,000 analytical methods and more than 150 million assays performed each year to establish the safety, identity, composition, authenticity, origin, traceability, and purity of biological substances and products, as well as carry out the human diagnostic system. The company has its geographic presence across 39 countries in Europe, North and South America, and Asia-Pacific. Read More...
Myriad Genetics Inc.(Salt Lake City) was founded in 1992 and is headquartered in Salt Lake City, Utah; Myriad Genetics, Inc., a molecular diagnostic company, focuses on developing and marketing novel predictive medicine, personalized medicine, and prognostic medicine tests worldwide. It through three reportable segments, namely Research, Molecular Diagnostics, and Clinical Services. The company offers various molecular diagnostics tests to assess the risk of developing breast and ovarian cancer. The company has its geographic presence in the U.S., Canada, Europe, and Australiaand, China, Japan, Brazil. Read More...
OPKO Health Inc.(Miami) was incorporated in 1991 and is headquartered in Miami, Florida; U.S. The Company has two reportable segments, namely Diagnostics and Pharmaceuticals. The Diagnostics segment primarily consists of the clinical laboratory operations through the acquisitions of Bio-Reference Laboratories, Inc. The company has its geographic presence in the U.S., Ireland, Chile, Spain, Israel, Mexico, and other countries. Read More...
Foundation Medicine Inc.(Massachusetts) was founded in 2009 and is headquartered in Cambridge, Massachusetts, the U.S.; Foundation Medicine, Inc. has one operating segment, which delivers molecular information about cancer products in the U.S. The company’s molecular information platform is mainly used by biopharmaceutical companies, physicians, and patients. The company offers its products and services in the U.S. and generates majority of their revenue from this country.
Read More...
Exact Sciences Inc.(Massachusetts) was founded in 1995 in Marlborough, Massachusetts. Exact Sciences Corp. is a molecular diagnostics company specialising in the detection of early stage cancers. The company's initial focus was on the early detection and prevention of colorectal cancer. Exact Sciences is changing the way we think about detecting and treating cancer. As a leader in cancer testing, we are committed to providing earlier answers and life-changing treatment guidance. Read More...
Natera Inc.(San Carlos) Headquartered in San Carlos, California, the U.S. Natera, Inc. is rapidly growing diagnostic company, providing molecular and bioinformatics technology for the management of genetic disease worldwide. The company offers various products, such as NIPT tests, carrier screening, pre-implantation genetic screening& pre-implantation genetic diagnosis, and products of conception test. The company offers products through its direct sales force, as well as through a network of approximately 70 laboratory and distribution partners in the US, Europe, Middle East & Africa, and India. Read More...
NeoGenomics Inc.(Fort Myers) was founded in 2001 and is headquartered in Fort Myers, Florida, the U.S.; .NeoGenomics Laboratories, Inc. offers diagnostics and pharma services to pathologist, hospitals, oncologists, researchers and other clinicians. The company mainly provides molecular and genetic testing in the U.S. with facilities in eight different laboratory locations, including Fort Myers, Florida; West Sacramento, California; Aliso Viejo, California; Irvine, California, and Houston, Texas. The company also has three smaller laboratory locations in Fresno, California; Nashville, Tennessee, and Tampa, Florida. Read More...
Illumina, Inc.(San Diego) was founded in 1998 and is headquartered in San Diego, the U.S. Illumina, Inc. serves in markets such as life sciences, translational, and clinical genomics. The company operates with two reportable segments namely Core Illumina and Consolidated VIEs. The core Illumina segment comprised of products and services in the research, clinical and applied markets, and enables the adoption of a variety of genomic solutions. Illumina, Inc. has its geographic presence in North America, Europe, Latin America, Asia-pacific, and others. Read More...
Quest Diagnostics Incorporated (New Jersey) was founded in 1967 and is headquartered in Madison, New Jersey, U.S.; Quest Diagnostics Incorporated has two reportable segments such as Diagnostics Information Services and Diagnostics Solutions. The company’s diagnostic information services business segment develops and delivers diagnostic testing information and services, such as routine clinical testing, gene-based and esoteric testing, as well as anatomic pathology services, and related services. The company has its geographic presence in the U.S., Puerto Rico, India, Ireland, and Mexico. Read More...
PerkinElmer Inc. (Massachusetts) was founded in 1947 and is headquartered in Waltham, Massachusetts, the U.S.; PerkinElmer, Inc. provide products, services and solutions for the diagnostics, life sciences research, and laboratory services markets. The company operates through its two reporting segments, Discovery & Analytical Solutions and Diagnostics. The company has its facilities located in Europe (France, Germany, and Belgium), United States and Asia (China, India, Japan and Taiwan). Read More...
Cancer Treatment Centers of America® CTCA (USA) was founded in 1988. CTCA mission is to never stop searching for and providing powerful and innovative therapies to heal the whole person, CTCA is using leading-edge technologies and advanced cancer treatment options to deliver personalized, whole-person care to improve quality of life and restore hope. Read More...
Spark Therapeutics(Philadelphia) the goal of gene therapy is to treat or possibly prevent disease. Scientists have been investigating and evolving gene therapy for more than 50 years. One goal of gene therapy research is to determine whether a new or functional gene can be used to restore the function of, or inactivate, a mutated gene. Read More...
BioNTech SE(Germany) aims to discover and develop the next generation of small molecule immunomodulatory compounds to improve the standard of care. Read More...
Novartis(Swiss) works closely with healthcare professionals around the work to support their treatment of patients and collaborate on unmet needs Read More...
APAC Biotech(India) is a biotechnology company focused on the research and development of dendritic cell based personalised immunotherapies for cancer treatment With more than a decade of research, our versatile team of scientists and doctors are going deeper into creating unmatched customised cancer therapeutics to enhance the immune system further, enabling it to fight cancer better. Read More...
BeiGene Ltd(China) innovation team consists of dedicated scientists in biology, chemistry, pharmacology, translational medicine, and clinical science who are challenged with the mission of innovating tomorrow’s medicines. Their responsibility, their passion, is the opportunity to help the world’s cancer patients. Read More...
Sanofi(France) is investing in the next generation of cancer medicines. With clear focus, deep internal expertise, and industry-leading partners, its scientists are designing new and potentially life-transforming medicines for cancer patients worldwide. Read More...
Cellectis(France) Cellectis is designing next generation immunotherapies based on gene-edited allogeneic CAR T-cells. Allogeneic product candidates are a future-defining shift in simplicity, availability, and cost effectiveness. Read More...
Pfizer(New York) Find out more about how our pioneering work is unlocking the promise of gene therapy for patients with rare genetic diseases. Read More...
Astrazeneca(Cambridge UK) Astrazeneca has a bold ambition to provide cures for cancer in every form. Astrazeneca is following the science to understand cancer and all its complexities to discover, develop and deliver life-changing treatments and increase the potential to save the lives of people around the world. Read More...
Moderna Inc(Cambridge UK) recognizes the impact of rare diseases on patients and their families, particularly when the disease lacks any effective treatment options. We are advancing mRNA-based therapeutics with the goal of one day bringing treatment options to patients and their families. Read More...
MIT CSAIL(Massachusetts) Robust artificial intelligence tools to predict future cancer Researchers created a risk-assessment algorithm that shows consistent performance across datasets from US, Europe, and Asia. Read More...
Related cancer prediction application APP Tools:
These related cancer prediction application APP tools are based on information from hundreds or even thousands of people with cancer. The tools can be used to predict cancer outcomes or assess risk based on specific characteristics of a patient and of his or her diseases. Here are major clinical genomics testing companies reference information:
Memorial Sloan Kettering Cancer Center (New York) The use of prediction tools known as nomograms to help patients make important treatment decisions please check below items: Bladder Cancer Breast Cancer Clinical Trials Colorectal Cancer Endometrial Cancer Gastric Carcinoma Gastrointestinal Stromal Tumor Liver Cancer Lung Cancer Tool Melanoma Ovarian Cancer Prostate Cancer Renal Cell Carcinoma Sarcoma Uterine Leiomyosarcom for advance.. Read More Tool...
Cleveland Clinic Risk Calculator Library (Ohio) Cleveland Clinic has expertise in all aspects of clinical research. From study design to statistical analysis to preparing applications. Bladder Cancer Benign Prostatic Hyperplasia Clinical Trials Brain Cancer Breast Cancer Colorectal Cancer Gastric Cancer R Lidney Cancer Oral Cancer Ovarian Cancer Pancretic Cancer Penile Cancer Prostate Cancer Thyroid Cancer for advance.. Read More Tool...
NHS (UK) The tool applies to women who have had surgery for early invasive breast cancer. Predict is an online tool that helps patients and clinicians see how different treatments for early invasive breast cancer might improve survival rates after surgery.
Breast Cancer Tool...
ONCOASSIST (Ireland) Users will be presented with an intuitive user interface and easy to read graphics charts that can be used to help inform patients as to why you may or may not be prescribing chemotherapy. The cancer prediction tool included ● Breast Cancer- Prediction algorithm estimating survival rates for breast cancer ● Colon Tool- Prediction algorithm estimating survival rates for colon cancer● GIST Tool- Prediction algorithm estimating relapse rates for GIST. ● Lung Cancer- Prediction algorithm estimating survival rates for lung cance ONCO Cancer Tool...
CDC MFHP Cancer (USA) Millions of people at risk for cardiovascular disease can be identified by family history. Pleasee learn more your risk for breast, ovarian and/or colorectal cancer MFHP Cancer Tool...
Targeted Cancer Therapies (USA) Targeted cancer therapies are drugs or other substances that block the growth and spread of cancer by interfering with specific molecules. Many targeted cancer therapies have been approved by the Food and Drug Administration (FDA) to treat specific types of cancer. Cancer Tool...
Red Ventures (North Carolina)
Visus uses Deep Learning algorithms for the diagnosis of over 7 skin cancers. Red Ventures a global company, driven by purpose, It is not measure by profit but in ability to positively change the trajectory of the people and communities we touch. SKin Cancer Tool... 
MD Anderson Cancer Center(Texas University)
is one of the world’s most respected centers devoted exclusively to cancer patient care, research, education and prevention. From smartphone apps to interactive websites, plenty of tools exist to help you lead a healthier life. Apps included Risk Assessment Tools,Screening Exams Apps,General Health Information Apps,Exercise Apps,Nutrition Apps,Sun-Safety Apps etc. Apps to help prevent cancer tools..