Features | Partner Sites | Information | LinkXpress
Sign In
JIB
GLOBETECH PUBLISHING
GLOBETECH PUBLISHING

Largest Data Set of Cancer-Related Genetic Variations Generated for Researchers

By BiotechDaily 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



comments powered by Disqus

Channels

Genomics/Proteomics

view channel
Image: A scheme for the generation of induced pluripotent stem cells (IPSC). (1) Isolate and culture donor cells. (2) Transfect stem cell-associated genes into the cells by viral vectors. Red cells indicate the cells expressing the exogenous genes. (3)  Harvest and culture the cells using mitotically inactivated feeder cells. (4) A small subset of the transfected cells forms iPSC cell colonies (Photo courtesy of Wikimedia Commons).

Innovative Technique Produces More Reliable Pluripotent Stem Cells

A recent paper described a more reliable way to induce the formation of pluripotent stem cells (iPSCs) from adult cells in a mouse model. Reliable high-quality iPSCs are needed for the development of... Read more

Drug Discovery

view channel
Image: S-649266 has more robust antibacterial activity than established antibiotics against multidrug-resistant bacteria (Photo courtesy of Shionogi).

Novel Antibiotic Shows Potential for Broad Range of Infections

The emergence of bacterial resistance to known antibacterial agents is becoming a major challenge in treating the infection caused by multi drug resistant (MDR) bacteria. In order to treat bacterial... Read more

Business

view channel

Collaboration of Mayo Clinic and IBM Cognitive Computer Devised to Improve Clinical Trial Research

The Mayo Clinic (Rochester, MN, USA) and IBM (Armonk, NY, USA) recently announced plans to pilot Watson, the IBM cognitive computer, to match patients more rapidly with suitable clinical trials. A proof-of-concept phase is currently ongoing, with the intent to introduce it into clinical use in early 2015.... Read more
 
Copyright © 2000-2014 Globetech Media. All rights reserved.