'Wildly heterogeneous genes'

September 15, 2013, University of California - San Diego

Cancer tumors almost never share the exact same genetic mutations, a fact that has confounded scientific efforts to better categorize cancer types and develop more targeted, effective treatments.

In a paper published in the September 15 advanced online edition of Nature Methods, researchers at the University of California, San Diego propose a new approach called network-based stratification (NBS), which identifies cancer subtypes not by the singular mutations of individual patients, but by how those mutations affect shared or systems.

"Subtyping is the most basic step toward the goal of personalized medicine," said principal investigator Trey Ideker, PhD, division chief of genetics in the UC San Diego School of Medicine and a professor in the departments of Medicine and Bioengineering at UC San Diego. "Based on patient data, patients are placed into subtypes with associated treatments. For example, one subtype of cancer is known to respond well to drug A, but not drug B. Without subtyping, every patient looks the same by definition, and you have no idea how to treat them differently."

Recent advances in knowledge and technology have made it easier (and less expensive) to sequence individual genomes, especially in the treatment of cancer, which is fundamentally a disease of genes.

But genes are "wildly heterogeneous," said Ideker. It is in combination, influenced by other factors, that mutated genes cause diseases like cancer. Every patient's cancer is genetically unique, which can affect the efficacy and outcomes of clinical treatment.

"When you look at patients' data at the level of genes, everybody looks different," said Ideker. "But when you look at impacted and systems, groupings do appear. No genes are mutated in exactly the same place, but the mutations do appear in the same ."

Specifically, the scientists looked at – present in tumors but not healthy tissues – in data from lung, uterine and ovarian cancer patients compiled by The Cancer Genome Atlas, an on-going National Institutes of Health-funded program to gather and catalogue the genomes of thousands of cancer patients.

Ideker said the NBS approach has immediate clinical value. Genome sequencing of cancer patients is rapidly becoming a standard part of diagnosis. Clinicians can use NBS, he said, to better match treatment to cancer subtype. And by chronicling treatment outcomes, funneling those results back into the database, they can further refine and improve cancer therapies, making them as personalized as the individuals themselves.

Explore further: Кesearchers identify gene variations that may help predict cancer treatment response

More information: Nature Methods, DOI: 10.1038/nmeth.2651

Related Stories

Кesearchers identify gene variations that may help predict cancer treatment response

August 9, 2013
Researchers at the Moffitt Cancer Center have identified four inherited genetic variants in non-small cell lung cancer patients that can help predict survival and treatment response. Their findings could help lead to more ...

Major cancer genotyping study logs 5,000th tumor profile

September 12, 2013
More than 5,000 genetic profiles of tumor DNA have been completed in a large research study by scientists at Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Boston Children's Hospital designed to speed the ...

Researchers develop software tool for cancer genomics

August 26, 2013
Researchers at the Medical College of Wisconsin (MCW) have developed a new bioinformatics software tool designed to more easily identify genetic mutations responsible for cancers. The tool, called DrGaP, is the subject of ...

Study finds genomic differences in types of cervical cancer

August 23, 2013
A new study has revealed marked differences in the genomic terrain of the two most common types of cervical cancer, suggesting that patients might benefit from therapies geared to each type's molecular idiosyncrasies.

Three subtypes of gastric cancer suggest different treatment approaches

August 27, 2013
Stomach cancer, one of the leading causes of cancer death worldwide, actually falls into three broad subtypes that respond differently to currently available therapies, according to researchers at Duke-NUS Graduate Medical ...

Study finds genetic mutation in castration-resistant prostate cancer

August 29, 2013
The mutation occurs in the androgen-synthesizing enzyme 3βHSD1 in castration-resistant prostate cancer (CRPC), according to research published online today in Cell. This mutation enables the tumor to make its own supply ...

Recommended for you

Researchers discover novel mechanism linking changes in mitochondria to cancer cell death

February 20, 2018
To stop the spread of cancer, cancer cells must die. Unfortunately, many types of cancer cells seem to use innate mechanisms that block cancer cell death, therefore allowing the cancer to metastasize. While seeking to further ...

Stem cell vaccine immunizes lab mice against multiple cancers

February 15, 2018
Stanford University researchers report that injecting mice with inactivated induced pluripotent stem cells (iPSCs) launched a strong immune response against breast, lung, and skin cancers. The vaccine also prevented relapses ...

Induced pluripotent stem cells could serve as cancer vaccine, researchers say

February 15, 2018
Induced pluripotent stem cells, or iPS cells, are a keystone of regenerative medicine. Outside the body, they can be coaxed to become many different types of cells and tissues that can help repair damage due to trauma or ...

Team paves the way to the use of immunotherapy to treat aggressive colon tumors

February 15, 2018
In a short space of time, immunotherapy against cancer cells has become a powerful approach to treat cancers such as melanoma and lung cancer. However, to date, most colon tumours appeared to be unresponsive to this kind ...

Can our genes help predict how women respond to ovarian cancer treatment?

February 15, 2018
Research has identified gene variants that play a significant role in how women with ovarian cancer process chemotherapy.

First comparison of common breast cancer tests finds varied accuracy of predictions

February 15, 2018
Commercially-available prognostic breast cancer tests show significant variation in their abilities to predict disease recurrence, according to a study led by Queen Mary University of London of nearly 800 postmenopausal women.

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.