New Web Tool Helps Researchers Explore How the Genome Changes in Cancer

Scientists at Memorial Sloan-Kettering have launched a new web-based tool to make information from large-scale genome-sequencing projects easier for researchers to navigate and explore.

The publicly accessible tool — called the cBio Cancer Genomics Portal — empowers cancer biologists and clinicians to translate complex data gathered about gene alterations into new cancer insights and clinical applications, the inventors write in a report published in the May issue of the journal Cancer Discovery.

 

Gynecologic oncologist Douglas Levine (left) and postdoctoral research fellow Petar Jelinic are using the new web tool to explore genetic changes that occur in ovarian cancer.

“Now scientists can quickly extract the particular slice of information they need from genome databases without having to deal with the bulk of data that isn’t relevant to their research,” explains computational biologist Nikolaus Schultz, who led the development of the cBio Cancer Genomics Portal together with co-author Ethan Cerami. In addition, the resource facilitates the analysis of different types of data and presents the results in graphical summaries.

“Essentially, you can turn spreadsheets with millions of numbers into diagrams that reveal what happens to genes in cancer — without having to be an expert in genome analysis,” Dr. Schultz adds.

Information Overload

Investigators in the field have collaborated nationally and globally in recent years to catalog the myriad genetic changes that occur in tumors. For example, The Cancer Genome Atlas (TCGA) — a genome-sequencing project launched by the National Cancer Institute and the National Human Genome Research Institute in 2006 — is amassing genomic and clinical information from patients with more than 20 types of cancer.

A goal of these types of collaborations is to fast-track the understanding of the basic mechanisms of cancer — for example, by determining how certain alterations in the genome may initiate the formation of tumors, change the behavior of tumors after they have formed, or affect their response to therapy. Such knowledge could ultimately result in better methods to diagnose and control cancers, or prevent the disease from occurring in the first place.

But according to Chris Sander, Chair of the Sloan-Kettering Institute’s Computational Biology Program and one of the report’s authors, the speed of progress is now limited by the complex task of translating massive molecular data into insights that ultimately could benefit patients.

“The amount of detailed information from thousands of tumor samples stored in public genome databases is overwhelming and continues to grow rapidly as the result of national and international efforts,” Dr. Sander explains. When completed, The Cancer Genome Atlas will have mapped the genomes of more than 20,000 tumors, with diverse types of genetic changes documented for each sample.

“The community of cancer researchers is now tackling the challenge of translating the atlas into useful insights about the genes and physiological processes that are rewired in cancer, and the way these changes might affect disease outcome,” Dr. Sander adds.

Bridging a Knowledge Gap

The relationship between genes and cancer is inherently complicated. For example, the function of a gene can be affected by alterations of the DNA sequence, as well as by epigenetic changes, which leave the genetic code unchanged while modifying the activity of genes. Cancer is often the result of a complex mixture of genetic and epigenetic changes occurring in many genes over time.

To date, the new resource provides researchers easy access to five types of changes affecting thousands of cancer-associated genes, which have been mapped out in 17 diseases. The data has been generated by TCGA and by two independent Memorial Sloan-Kettering projects, which provided the first comprehensive analyses of gene changes in prostate cancer and sarcoma. Information generated in additional projects — including those coordinated by the International Cancer Genome Consortium — will soon be included.

“Our tool was designed to bridge a knowledge gap between computational and systems biologists on the one hand, and cancer researchers and disease experts on the other hand,” says Dr. Sander. “The feedback from the scientific community has been very enthusiastic.”

“It’s incredibly rewarding to know that more and more people are using our resource,” adds Dr. Schultz, “and to hear that it’s helping them capture the essence of what happens with the genome in cancer.”

This research was supported by the National Cancer Institute of the National Institutes of Health under award numbers NCI-U24CA143840 and NCI-R21CA135870.

 

Mskcc.org [en línea] NY (USA): mskcc.org, 05 de julio de 2012 [ref. 21 de junio de 2012] Disponible en Internet: http://www.mskcc.org/news/announcement/new-web-tool-helps-researchers-explore-how-genome-changes

Skin cancer drug hopes raised by study

A new treatment for advanced skin cancer almost doubles survival times, according to an international study.

Melanoma is aggressive and dangerous

Doctors say 132 patients in the US and Australia who were given the drug vemurafenib gained several extra months of life.

Research in the New England Journal of Medicine found those in the study lived an average of 16 months, compared with nine months on conventional treatment.

Vemurafenib (Zelboraf) has been approved for use in Europe.

The treatment is one of two drugs for late-stage melanoma, approved on fast-track in the US last year, which offer hope for patients with advanced melanoma.

Before that, there had been no new drugs for the cancer for more than a decade.

         Malignant melanoma

• Melanoma, also called malignant melanoma, is a type of skin cancer that is aggressive and dangerous
• Melanoma is relatively rare and makes up 10% of all skin cancer cases
• Melanoma is responsible for most deaths due to skin cancer
• About 2,000 people die every year in England and Wales from melanoma
• The main cause of melanoma is believed to be over-exposure to the sun
• Over using sunbeds and sun lamps may also increase the risk of developing melanoma

Vemurafenib is suitable for about half of patients with advanced melanoma as it targets tumours that express a certain gene mutation.

Dr Antoni Ribas, a professor of haematology/oncology and a researcher at the Jonsson Cancer Center at the University of California-Los Angeles, said: «This study shows that Zelboraf changes the natural history of this disease. This data is beyond what I would have expected.

«We’re seeing a significant number of patients with durable responses to the drug, and that the whole group of treated patients is living longer.

«These results tell us that this drug is having a very big impact, and this changes the way we treat metastatic melanoma.»

According to the European Medicines Agency, the drug has been recommended for approval in Europe, pending final authorisation by the European Commission.

Elizabeth Woolf, head of Cancer Research UK’s information website Cancer Help UK, said: «This is an interesting, impressive but relatively small trial of a promising new-generation melanoma drug, which Cancer Research UK is proud to have played a role in developing.»

But she said there were still questions that remain unanswered, not least the cost.

We’re getting somewhere with these targeted drugs but we have a whole raft of research still to do address the issue of resistance”

Kate Law. Cancer Research UK

«Everyone on the trial had the drug, so we cannot tell how large the benefits are, compared to people who didn’t have it, or had another treatment. And because the drug targets a particular gene fault, only half of all melanoma patients are eligible.

«About half of those treated seem to benefit, so it could potentially help roughly a quarter of patients with advanced melanoma overall.

«Looking at these uncertainties, and now that the drug is available to UK cancer patients, it will be interesting to see what price the manufacturer charges so as not to place too great a strain on already scarce NHS resources.»

Drug resistance

Cancer Research UK said once the drug was licensed in Europe, patients would be able to discuss treatment options with their doctor.

In England, patients will have to apply to the Cancer Drugs Fund, the charity said.

Kate Law, director of clinical and population research at Cancer Research UK, said the treatment was one of a new generation of cancer drugs targeted at patients with a specific genetic make-up.

While it offered hope, she said, it was not a cure as the cancer eventually became resistant to the drug.

She told the BBC: «This is not a cure – you’re talking an extra six months of life.

«We’re getting somewhere with these targeted drugs but we have a whole raft of research still to do to address the issue of resistance.»

Bbc.co.uk [en línea] Londres (UK): bbc.co.uk, 27 de febrero de 2012 [ref. 23 de febrero de 2012] Disponible en Internet: http://www.bbc.co.uk/news/health-17128925