A novel data-driven method to personalize cancer treatment

June 1, 2018, The National Centre for Cancer Research
PanDrugs is a new computational methodology that prioritizes drug treatments based on patient genomic data. Credit: Spanish National Cancer Research Centre (CNIO)

Identifying and prioritizing treatment options based on a patient's profile of genetic alterations is a major challenge in personalized cancer medicine. A new data-driven approach called PanDrugs can help to this end. This new computational resource has been developed by researchers from the Bioinformatics Unit at the Spanish National Cancer Research Centre (CNIO) and is described in a paper published in Genome Medicine.

A large majority of cancers have many whose biological and clinical relevance are unclear. Several tools have been developed to identify clinically actionable genomic alterations and to suggest targeted therapies, but they have limitations, and there's still a gap between raw genomic data and clinical usefulness.

To address this, researchers led by Fátima Al-Shahrour, head of the Bioinformatics Unit at the CNIO, developed PanDrugs. "The main novelty introduced in this methodology compared with current tools is the broadening of the search space to provide therapeutic options," explains Al-Shahrour.

In other words, PanDrugs suggests treatments for direct targets (e.g. genes that contribute to disease phenotype and can be directly targeted by a drug) and biomarkers (e.g. genes that have a genetic status associated with drug response but the protein product is not the drug target itself). PanDrugs also integrates a knowledge-based systems biology layer that automatically inspects biological circuits, expanding cancer candidate therapies from beyond limited cancer-related gene lists to the whole druggable pathway.

"This novel strategy (called 'pathway member') extends the treatment opportunities of cancer patients by enriching the therapeutic arsenal against tumours and opens new avenues for personalized medicine," says Al-Shahrour. Thanks to pathway member strategy, the paper describes how PanDrugs is able to identify treatments used in clinical practice that might benefit prostate, breast and colorectal cancer patients without druggable driver altered genes.

The PanDrugs database represents a remarkable contribution. "This database is the largest public repository of drug-target associations available from well-known targeted therapies to preclinical drugs. Current version of PanDrugs integrates data from 24 primary sources and supports >56000 drug-target associations."

PanDrugs can be fully integrated with custom pipelines through its programmatic API and its docker image facilitates in-house installation, enhancing reproducibility and improving performance. PanDrugs and PanDrugsdb are open-source and fully available at http://www.pandrugs.org.

Explore further: New precision cancer model opens doors to personalized cancer treatment

More information: Elena Piñeiro-Yáñez et al, PanDrugs: a novel method to prioritize anticancer drug treatments according to individual genomic data, Genome Medicine (2018). DOI: 10.1186/s13073-018-0546-1

Related Stories

New precision cancer model opens doors to personalized cancer treatment

April 13, 2018
Researchers at the Spanish National Cancer Research Centre (CNIO) have developed an extremely powerful and versatile mouse model that will improve cancer research and accelerate pre-clinical testing of novel targeted therapies. ...

Genomic analysis unravels complexities of the most common form of lymphoma and enables personalized treatment

April 30, 2018
The majority of patients with diffuse large B cell lymphoma (DLBCL) can be treated effectively. However, people whose disease recurs face a shortage of good options, especially because the disease is driven by a complicated ...

Even smokers may benefit from targeted lung cancer treatments

December 13, 2017
Smokers are less likely than non-smokers to have lung cancers caused by targetable genetic changes. But a study published this week in the journal Clinical Cancer Research shows that when they do, smokers benefit just as ...

Routine genomic testing is feasible, but only a subset of patients benefit

June 5, 2017
Genomic testing of tumor samples can enable personalized treatment selection, where targeted treatments are matched to genetic changes in the tumor. Although a growing number of patients with advanced cancers receive some ...

New models of kidney cancer may drive immunotherapy research

June 9, 2017
University of North Carolina Lineberger Comprehensive Cancer Center scientists have developed preclinical laboratory models of the two most common types of kidney cancer, an advancement that may aid in the evaluation of novel ...

New precision medicine tool helps optimize cancer treatment

December 22, 2016
Columbia University Medical Center (CUMC) researchers have created a computational tool that can rapidly predict which genes are implicated in an individual's cancer and recommend treatments. It is among the most comprehensive ...

Recommended for you

New kind of compound shows early promise against prostate cancer

October 23, 2018
A new type of molecule blocks the action of genes that drive the growth of therapy-resistant prostate cancer, a new study finds.

RNA thought to spread cancer shows ability to suppress breast cancer metastasis

October 22, 2018
Researchers at The University of Texas MD Anderson Cancer Center have discovered that a form of RNA called metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) appears to suppress breast cancer metastasis in mice, ...

Revealing the molecular mystery of human liver cells

October 22, 2018
A map of the cells in the human liver has been created by University Health Network Transplant Program and University of Toronto researchers, revealing for the first time differences between individual cells at the molecular ...

Targeting a hunger hormone to treat obesity

October 22, 2018
About 64 per cent of Canadian adults are overweight or obese, according to Health Canada. That's a problem, because obesity promotes the emergence of chronic diseases such as type 2 diabetes, heart disease and some cancers.

New tool gives deeper understanding of glioblastoma

October 22, 2018
Researchers in the lab of Charles Danko at the Baker Institute for Animal Health have developed a new tool to study genetic "switches" active in glioblastoma tumors that drive growth of the cancer. In a new paper in Nature ...

Pancreatic cancer genetic marker may predict outcomes with radiation therapy

October 22, 2018
Pancreatic cancer is one of the most difficult cancers to treat and is a leading cause of cancer-related deaths. Now, Sidney Kimmel Cancer Center—Jefferson Health and Lankenau Institute for Medical Research scientists find ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.