Largest Data Set of Cancer-Related Genetic Variations Generated for Researchers
|
By LabMedica International staff writers Posted on 29 Jul 2013 |
|
US scientists have generated a data set of cancer-specific genetic variations and are making these data available to the research community.
The investigators, from the US National Cancer Institute (NCI; Bethesda, MD, USA), published their study’s findings July 15, 2013, online in Cancer Research, a journal of the American Association for Cancer Research.
This new technology will help cancer researchers better illuminate drug response and resistance to cancer treatments. “To date, this is the largest database worldwide, containing six billion data points that connect drugs with genomic variants for the whole human genome across cell lines from nine tissues of origin, including breast, ovary, prostate, colon, lung, kidney, brain, blood, and skin,” said Yves Pommier, MD, PhD, chief of the laboratory of molecular pharmacology at the NCI in an interview. “We are making this data set public for the greater community to use and analyze. Opening this extensive data set to researchers will expand our knowledge and understanding of tumorigenesis, as more and more cancer-related gene aberrations are discovered. This comes at a great time, because genomic medicine is becoming a reality, and I am very hopeful this valuable information will change the way we use drugs for precision medicine.”
Dr. Pommier and colleagues conducted whole-exome sequencing of the NCI-60 human cancer cell-line panel, which is an assortment of 60 human cancer cell lines, and generated a comprehensive list of cancer-specific genetic variations. Early research conducted by the researchers show that the extensive data set has the potential to greatly enhance understanding of the links between specific cancer-related genetic variations and drug response, which will hasten the drug development process.
The NCI-60 human cancer cell-line panel is used extensively by cancer researchers to discover novel anticancer drugs. To conduct whole-exome sequencing, Dr. Pommier and his NCI team extracted DNA from the 60 different cell lines from tumors of the lung, colon, brain, ovary, prostate, breast, and kidney, as well as melanoma and leukemia, and cataloged the genetic coding variants for the complete human genome. The genetic variations identified were of two types: type I variants corresponding to variants found in the normal population, and type II variants, which are cancer-specific.
The scientists then employed the Super Learner algorithm to predict the sensitivity of cells harboring type II variants to 103 anticancer drugs approved by the US Food and Drug Administration (FDA) and an additional 207 investigational new pharmaceutical agents. They were able to assess the correlations between key cancer-related genes and clinically pertinent anticancer drugs, and predict the outcome.
The data generated in this project provide a way to identify new determinants of response and processes of drug resistance, and offer opportunities to target genomic defects and overcome acquired resistance, according to Dr. Pommier. To accomplish this, the researchers are making these data available to all researchers by way of two database portals, called the CellMiner database and the Ingenuity systems database.
Related Links:
US National Cancer Institute
The investigators, from the US National Cancer Institute (NCI; Bethesda, MD, USA), published their study’s findings July 15, 2013, online in Cancer Research, a journal of the American Association for Cancer Research.
This new technology will help cancer researchers better illuminate drug response and resistance to cancer treatments. “To date, this is the largest database worldwide, containing six billion data points that connect drugs with genomic variants for the whole human genome across cell lines from nine tissues of origin, including breast, ovary, prostate, colon, lung, kidney, brain, blood, and skin,” said Yves Pommier, MD, PhD, chief of the laboratory of molecular pharmacology at the NCI in an interview. “We are making this data set public for the greater community to use and analyze. Opening this extensive data set to researchers will expand our knowledge and understanding of tumorigenesis, as more and more cancer-related gene aberrations are discovered. This comes at a great time, because genomic medicine is becoming a reality, and I am very hopeful this valuable information will change the way we use drugs for precision medicine.”
Dr. Pommier and colleagues conducted whole-exome sequencing of the NCI-60 human cancer cell-line panel, which is an assortment of 60 human cancer cell lines, and generated a comprehensive list of cancer-specific genetic variations. Early research conducted by the researchers show that the extensive data set has the potential to greatly enhance understanding of the links between specific cancer-related genetic variations and drug response, which will hasten the drug development process.
The NCI-60 human cancer cell-line panel is used extensively by cancer researchers to discover novel anticancer drugs. To conduct whole-exome sequencing, Dr. Pommier and his NCI team extracted DNA from the 60 different cell lines from tumors of the lung, colon, brain, ovary, prostate, breast, and kidney, as well as melanoma and leukemia, and cataloged the genetic coding variants for the complete human genome. The genetic variations identified were of two types: type I variants corresponding to variants found in the normal population, and type II variants, which are cancer-specific.
The scientists then employed the Super Learner algorithm to predict the sensitivity of cells harboring type II variants to 103 anticancer drugs approved by the US Food and Drug Administration (FDA) and an additional 207 investigational new pharmaceutical agents. They were able to assess the correlations between key cancer-related genes and clinically pertinent anticancer drugs, and predict the outcome.
The data generated in this project provide a way to identify new determinants of response and processes of drug resistance, and offer opportunities to target genomic defects and overcome acquired resistance, according to Dr. Pommier. To accomplish this, the researchers are making these data available to all researchers by way of two database portals, called the CellMiner database and the Ingenuity systems database.
Related Links:
US National Cancer Institute
New
Platinum Member
Flu SARS-CoV-2 Combo Test
OSOM® Flu SARS-CoV-2 Combo Test
POCT Fluorescent Immunoassay Analyzer
FIA Go
New
Gold Member
Automatic Nucleic Acid Extractor
GeneRotex 24
Latest BioResearch News
- Genome Analysis Predicts Likelihood of Neurodisability in Oxygen-Deprived Newborns
- Gene Panel Predicts Disease Progession for Patients with B-cell Lymphoma
- New Method Simplifies Preparation of Tumor Genomic DNA Libraries
- New Tool Developed for Diagnosis of Chronic HBV Infection
- Panel of Genetic Loci Accurately Predicts Risk of Developing Gout
- Disrupted TGFB Signaling Linked to Increased Cancer-Related Bacteria
- Gene Fusion Protein Proposed as Prostate Cancer Biomarker
- NIV Test to Diagnose and Monitor Vascular Complications in Diabetes
- Semen Exosome MicroRNA Proves Biomarker for Prostate Cancer
- Genetic Loci Link Plasma Lipid Levels to CVD Risk
- Newly Identified Gene Network Aids in Early Diagnosis of Autism Spectrum Disorder
- Link Confirmed between Living in Poverty and Developing Diseases
- Genomic Study Identifies Kidney Disease Loci in Type I Diabetes Patients
- Liquid Biopsy More Effective for Analyzing Tumor Drug Resistance Mutations
- New Liquid Biopsy Assay Reveals Host-Pathogen Interactions
- Method Developed for Enriching Trophoblast Population in Samples
Channels
Clinical Chemistry
view channel
New ADLM Guidance Provides Expert Recommendations on Clinical Testing For Respiratory Viral Infections
Respiratory tract infections, predominantly caused by viral pathogens, are a common reason for healthcare visits. Accurate and swift diagnosis of these infections is essential for optimal patient management.... Read more
3D Printed Point-Of-Care Mass Spectrometer Outperforms State-Of-The-Art Models
Mass spectrometry is a precise technique for identifying the chemical components of a sample and has significant potential for monitoring chronic illness health states, such as measuring hormone levels... Read more.jpg "Image: Reaching speeds up to 6,000 RPM, this centrifuge forms the basis for a new type of inexpensive, POC biomedical test (Photo courtesy of Duke University)")
POC Biomedical Test Spins Water Droplet Using Sound Waves for Cancer Detection
Exosomes, tiny cellular bioparticles carrying a specific set of proteins, lipids, and genetic materials, play a crucial role in cell communication and hold promise for non-invasive diagnostics.... Read more
Highly Reliable Cell-Based Assay Enables Accurate Diagnosis of Endocrine Diseases
The conventional methods for measuring free cortisol, the body's stress hormone, from blood or saliva are quite demanding and require sample processing. The most common method, therefore, involves collecting... Read moreMolecular Diagnostics
view channel
Blood-Based Test Outperforms Ultrasound in Early Liver Cancer Detection
Patients with liver cirrhosis and chronic hepatitis B are at a higher risk for developing hepatocellular carcinoma (HCC), the most prevalent type of liver cancer. The American Association for the Study... Read more
Four-In-One Molecular Test Detects and Differentiates Among Most Prevalent Respiratory Viruses in 20 Minutes
The U.S. Centers for Disease Control and Prevention (CDC) has reported that respiratory diseases in the United States reached high levels during the recent autumn and winter seasons, with SARS-CoV-2 leading... Read more.jpeg "Image: Screening for prostate cancer with first-line MRI is less cost-effective than first-line PSA testing (Photo courtesy of Adobe Stock)")
First-Line PSA Testing More Cost-Effective Than First-Line MRI for Prostate Cancer Screening
Current prostate cancer (PCa) screening protocols typically begin with prostate-specific antigen (PSA) testing, which, if elevated, may lead to further assessment using multiparametric magnetic resonance... Read more
Proteomics Platform Identifies Proteins in Blood to Give Cancer Warning 7 Years before Diagnosis
To improve cancer survival rates, it's crucial to understand the disease during its initial stages. Research involving data from thousands of cancer patients has uncovered exciting findings about how blood... Read moreHematology
view channel
Next Generation Instrument Screens for Hemoglobin Disorders in Newborns
Hemoglobinopathies, the most widespread inherited conditions globally, affect about 7% of the population as carriers, with 2.7% of newborns being born with these conditions. The spectrum of clinical manifestations... Read more
First 4-in-1 Nucleic Acid Test for Arbovirus Screening to Reduce Risk of Transfusion-Transmitted Infections
Arboviruses represent an emerging global health threat, exacerbated by climate change and increased international travel that is facilitating their spread across new regions. Chikungunya, dengue, West... Read more
POC Finger-Prick Blood Test Determines Risk of Neutropenic Sepsis in Patients Undergoing Chemotherapy
Neutropenia, a decrease in neutrophils (a type of white blood cell crucial for fighting infections), is a frequent side effect of certain cancer treatments. This condition elevates the risk of infections,... Read more
First Affordable and Rapid Test for Beta Thalassemia Demonstrates 99% Diagnostic Accuracy
Hemoglobin disorders rank as some of the most prevalent monogenic diseases globally. Among various hemoglobin disorders, beta thalassemia, a hereditary blood disorder, affects about 1.5% of the world's... Read moreImmunology
view channel.jpg "Image: The AI tool predicts whether someone’s cancer will respond to immune checkpoint inhibitors (Photo courtesy of National Cancer Institute)")
AI Tool Predicts Cancer Patients’ Response to Immunotherapy
Immune checkpoint inhibitors are a form of immunotherapy drug that enables immune cells to target and destroy cancer cells. At present, the Food and Drug Administration has approved two predictive biomarkers... Read more
Molecular Profiling Improves Diagnosis for Children with High Risk Cancers
Cancer remains the leading cause of disease-related death among children in most developed nations, and approximately one-fourth of these patients are diagnosed with aggressive, high-risk, or relapsed... Read more
.jpg "Image: The AI predictive model identifies the most potent cancer killing immune cells for use in immunotherapies (Photo courtesy of Shutterstock)")
Microbiology
view channel
POC STI Test Shortens Time from ED Arrival to Test Results
In a 2024 sexually transmitted infections (STIs) surveillance report by the World Health Organization (WHO), over 2.5 million cases were recorded, alongside a rise in the inappropriate use of antibiotics... Read more
Integrated Solution Ushers New Era of Automated Tuberculosis Testing
Tuberculosis (TB) is responsible for 1.3 million deaths every year, positioning it as one of the top killers globally due to a single infectious agent. In 2022, around 10.6 million people were diagnosed... Read more
Automated Sepsis Test System Enables Rapid Diagnosis for Patients with Severe Bloodstream Infections
Sepsis affects up to 50 million people globally each year, with bacteraemia, formerly known as blood poisoning, being a major cause. In the United States alone, approximately two million individuals are... Read more
Enhanced Rapid Syndromic Molecular Diagnostic Solution Detects Broad Range of Infectious Diseases
GenMark Diagnostics (Carlsbad, CA, USA), a member of the Roche Group (Basel, Switzerland), has rebranded its ePlex® system as the cobas eplex system. This rebranding under the globally renowned cobas name... Read morePathology
view channel
New Technique Reveals Earliest Signs of Genetic Mutations
Mutations are alterations in the molecular "letters" that constitute the DNA code, which serves as the blueprint for all living cells. While some of these changes may be inconsequential, others can lead... Read more
New WHO Reporting System for Lung Cytopathology to Enhance Diagnostic Accuracy
Lung cancer continues to be the most common cause of cancer-related deaths worldwide and ranks as the second most frequently diagnosed cancer in both men and women. The role of lung cytopathology, which... Read more
Self-Taught AI Tool Diagnoses and Predicts Severity of Common Lung Cancer
A computer program powered by artificial intelligence (AI) and trained on nearly half a million tissue images can effectively diagnose cases of adenocarcinoma, the most prevalent type of lung cancer.... Read more
Novel AI-Powered Method for Tissue Analysis Improves Understanding of Disease Pathology
Scientists at Brown University (Providence, RI, USA) and the University of Michigan (Ann Arbor, MI, USA) have created a groundbreaking computational technique to examine complex tissue data, potentially... Read moreTechnology
view channel
Microneedle Patch Detects Skin Cancer Early
Wearable bioelectronics has emerged as a significant innovation in healthcare, especially in the field of biosensing, providing a new method to monitor individual health for both diagnostic and therapeutic purposes.... Read more
New Diagnostic System Achieves PCR Testing Accuracy
While PCR tests are the gold standard of accuracy for virology testing, they come with limitations such as complexity, the need for skilled lab operators, and longer result times. They also require complex... Read more
Industry
view channel
Roche and Hitachi High-Tech Extend 46-Year Partnership for Breakthroughs in Diagnostic Testing
Roche (Basel, Switzerland) and Hitachi High-Tech (Tokyo, Japan) have renewed their collaboration agreement, committing to a further 10 years of partnership. This extension brings together their long-standing... Read more
Danaher and Johns Hopkins University Collaborate to Improve Neurological Diagnosis
Unlike severe traumatic brain injury (TBI), mild TBI often does not show clear correlations with abnormalities detected through head computed tomography (CT) scans. Consequently, there is a pressing need... Read more
Beckman Coulter and MeMed Expand Host Immune Response Diagnostics Partnership
Beckman Coulter Diagnostics (Brea, CA, USA) and MeMed BV (Haifa, Israel) have expanded their host immune response diagnostics partnership. Beckman Coulter is now an authorized distributor of the MeMed... Read more_1.jpg "Image: Thermo Fisher will distribute Bio-Techne products across Europe (Photo courtesy of 123RF)")
