Category Archives: Gene Medicine

WEDNESDAY, March 7 (HealthDay News) -- The genetic makeup of cancer cells differs significantly from region to region within a single tumor, according to new research that raises questions about the true potential of personalized cancer medicine.

With this treatment approach, doctors study a tumor's genetic makeup to determine which drugs would work best in a particular patient. But if the genetic mutations driving the cancer cells vary widely, a single tissue sample won't necessarily give the full picture.

This "targeted therapy" involves "sticking a needle into the primary tumor site and taking a small sliver of a tumor, doing a gene analysis, and creating a genetic profile of the tumor to predict how the tumor will behave," explained Dr. Dan Longo, an oncologist and deputy editor at the New England Journal of Medicine.

"What this paper tells us is that is an oversimplification of the complexity of tumors and their heterogeneity," he said. "If you look at different sites of the very same tumor and the very same person, one site might tell you a gene profile associated with a good prognosis and the other site will tell you a gene profile associated with a bad prognosis."

Longo wrote an editorial accompanying the new study, published in the March 8 issue of the New England Journal of Medicine.

In the study, scientists from Cancer Research UK London Research Institute took 13 biopsies, or tissue samples, from a patient whose kidney cancer had spread. The biopsies were from eight regions of the kidney tumor and four tumors in the chest and lungs.

Researchers also took normal tissue, sequenced the patient's genome and compared that to what they found in the biopsies.

Genetic analysis turned up 128 mutations in the tumors. But only about one-third, or about 40 of those mutations, were present in all of the biopsies.

"The majority of mutations are not shared in every biopsy," said senior study author Charles Swanton, a professor of cancer medicine at the research institute.

Swanton and his colleagues also analyzed tumor tissue samples from another three patients with kidney cancer. From a total of 30 biopsies from all four patients, 26 tissue samples had mutations that were highly heterogenous, or varied, from one another.

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Is Cancer Outwitting 'Personalized Medicine'?

BOSTON Scientists are reporting what could be very bad news for efforts to customize cancer treatment based on each persons genes.

They have discovered big differences from place to place in the same tumor as to which genes are active or mutated. They also found differences in the genetics of the main tumor and places where the cancer has spread.

This means that the single biopsies on which doctors rely to choose drugs are probably not giving a true view of the cancers biology. It also means that treating cancer wont be as simple as many had hoped.

By analyzing tumors in unprecedented detail, Were finding that the deeper you go, the more you find, said one study leader, Dr. Charles Swanton of the London Research Institutes Cancer Research UK. Its like going from a black-and-white television with four pixels to a color television with thousands of pixels.

Yet the result is a fuzzier picture of how to treat the disease.

The study is reported in Thursdays New England Journal of Medicine.

It is a reality check for overoptimism in the field devoted to conquering cancer with new gene-targeting drugs, Dr. Dan L. Longo, a deputy editor at the journal, wrote in an editorial.

About 15 of these medicines are on the market now and hundreds more are in testing, but they have had only limited success. And the new study may help explain why.

The scientists used gene sequencing to a degree that has not been done before to study primary tumors and places where they spread in four patients with advanced kidney cancer. They found that two-thirds of gene mutations they detected were not present in all areas of the same tumor. They also were stunned to see different mutations in the same gene from one part of a tumor to another.

That means a single biopsy would reveal only a minority of mutations. Still, its not clear whether doing more biopsies would improve accuracy, or how many or how often they should be done.

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Gene-based cancer research suffers setback, scientists say

BOSTON - Scientists are reporting what could be very bad news for efforts to customize cancer treatment based on each person's genes.

They have discovered big differences from place to place in the same tumour as to which genes are active or mutated. They also found differences in the genetics of the main tumour and places where the cancer has spread.

This means that the single biopsies that doctors rely on to choose drugs are probably not giving a true view of the cancer's biology. It also means that treating cancer won't be as simple as many had hoped.

By analyzing tumours in unprecedented detail, "we're finding that the deeper you go, the more you find," said one study leader, Dr. Charles Swanton of the Cancer Research UK London Research Institute in England. "It's like going from a black-and-white television with four pixels to a colour television with thousands of pixels."

Yet the result is a fuzzier picture of how to treat the disease.

The study is reported in Thursday's New England Journal of Medicine.

It is a reality check for "overoptimism" in the field devoted to conquering cancer with new gene-targeting drugs, Dr. Dan Longo, a deputy editor at the journal, wrote in an editorial.

About 15 of these medicines are on the market now and hundreds more are in testing, but they have had only limited success. And the new study may help explain why.

The scientists used gene sequencing to a degree that has not been done before to study primary tumours and places where they spread in four patients with advanced kidney cancer. They found that two-thirds of gene mutations they detected were not present in all areas of the same tumour. They also were stunned to see different mutations in the same gene from one part of a tumour to another.

That means a single biopsy would reveal only a minority of mutations. Still, it's not clear whether doing more biopsies would improve accuracy, or how many or how often they should be done.

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Gene study suggests treating cancer is more complex than many had hoped

LONDON (Reuters) - Taking a sample or biopsy from just one part of a tumour might not give a full picture of its genetic diversity and may explain why doctors, despite using genetically targeted drugs, are often unable to save patients whose cancer has spread, scientists said.

A study by British researchers found there are more genetic differences than similarities between biopsies taken from separate areas of the same tumour, and yet further gene differences in samples taken from secondary tumours.

That might help explain why, despite recent development of a wave of highly targeted drugs designed to tackle cancers of specific genetic types, the prognosis remains poor for many patients with so-called solid-tumour disease like breast, lung, or kidney cancer that has spread to others parts of the body.

But the researchers, whose study was partly funded by charity Cancer Research UK and published in the New England Journal of Medicine, said it also pointed to a way forward.

The team carried out the first ever genome-wide analysis of the genetic changes or faults in different regions of the same tumour.

They looked at four patients with cancer in their kidneys, taking samples from different regions of the primary tumour and also from other organs where the tumour had spread.

They found that the majority of gene faults, around two-thirds, were not the same in one sample as in another, even when the biopsies were taken from the same tumour.

Samples taken from secondary tumours - which are a result of the disease spreading to other parts of the body - had yet more different genetic faults, suggesting that basing treatment decisions on just one primary tumour sample is not sufficient.

"We've known for some time that tumours are a patchwork of faults, but this is the first time we've been able to use cutting-edge genome sequencing technology to map out the genetic landscape of a tumour in such exquisite detail," said Charles Swanton, of University College London's cancer institute, who led the study and presented its results at a briefing in London on Tuesday.

He said they had uncovered "an extraordinary amount of diversity" at a genetic level both within tumours and within a single patient, with more differences between biopsies from the same tumour than similarities.

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Cancer gene mutation more complex than previously thought -study

Taking a sample or biopsy from just one part of a tumor might not give a full picture of its genetic diversity and may explain why doctors, despite using genetically targeted drugs, are often unable to save patients whose cancer has spread, scientists said.

A study by British researchers found there are more genetic differences than similarities between biopsies taken from separate areas of the same tumor, and yet further gene differences in samples taken from secondary tumors.

That might help explain why, despite recent development of a wave of highly targeted drugs designed to tackle cancers of specific genetic types, the prognosis remains poor for many patients with so-called solid-tumor disease like breast, lung, or kidney cancer that has spread to others parts of the body.

But the researchers, whose study was partly funded by charity Cancer Research UK and published in the New England Journal of Medicine, said it also pointed to a way forward.

The team carried out the first ever genome-wide analysis of the genetic changes or faults in different regions of the same tumor.

They looked at four patients with cancer in their kidneys, taking samples from different regions of the primary tumor and also from other organs where the tumor had spread.

They found that the majority of gene faults, around two-thirds, were not the same in one sample as in another, even when the biopsies were taken from the same tumor.

Samples taken from secondary tumors - which are a result of the disease spreading to other parts of the body - had yet more different genetic faults, suggesting that basing treatment decisions on just one primary tumor sample is not sufficient.

"We've known for some time that tumors are a patchwork of faults, but this is the first time we've been able to use cutting-edge genome sequencing technology to map out the genetic landscape of a tumor in such exquisite detail," said Charles Swanton, of University College London's cancer institute, who led the study and presented its results at a briefing in London on Tuesday.

He said they had uncovered "an extraordinary amount of diversity" at a genetic level both within tumors and within a single patient, with more differences between biopsies from the same tumor than similarities.

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Cancer gene mutation more complex than previously thought

MOUNTAIN VIEW, Calif. -- In Silicon Valley, the line between computing and biology has begun to blur in a way that could have enormous consequences for human longevity.

Bill Banyai, an optical physicist at Complete Genomics, has helped make that happen. When he began developing a gene sequencing machine, he relied heavily on his background at two computer networking start-up companies. His digital expertise was essential in designing a factory that automated and greatly lowered the cost of mapping the three billion base pairs that form the human genome.

The promise is that low-cost gene sequencing will lead to a new era of personalized medicine, yielding new approaches for treating cancers and other serious diseases. The arrival of such cures has been glacial, however, although the human genome was originally sequenced more than a decade ago.

Now that is changing, in large part because of the same semiconductor industry manufacturing trends that opened up consumer devices like the PC and the smartphone: exponential increases in processing power and transistor density are accompanied by costs that fall at an accelerating rate.

As a result, both new understanding and new medicines will arrive at a quickening pace, according to the biologists and computer scientists.

"For all of human history, humans have not had the readout of the software that makes them alive," said Larry Smarr, director of the California Institute of Telecommunications and Information Technology, a research center that is jointly operated by the University of California, San Diego, and the University of California, Irvine, who is a member of the Complete Genomics scientific advisory board. "Once you make the transition from a data poor to data rich environment, everything changes."

Complete Genomics, based in Mountain View, is one of more than three dozen firms hastening to push the cost of sequencing an entire human genome below $1,000. The challenge is part biology, part chemistry, part computing, and in Complete Genomics' case, part computer networking.

Complete Genomics is a classic Silicon Valley start-up story. Even the gene sequencing machines, which are housed in a 4,000-square-foot room bathed in an eerie blue light, appear more like a traditional data center than a biology lab.

In 2005 ,when Clifford Reid, a successful Silicon Valley software entrepreneur, began to assemble his team, he approached Dr. Banyai and asked if he was interested in joining a gene sequencing start-up. Dr. Reid, who was also trained in physics and math, had spent a year as an entrepreneur-in-residence at the Massachusetts Institute of Technology, where he had become a convert to bioinformatics, the application of computer science and information technologies to biology and medicine.

Dr. Banyai had even less experience in biology.

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Cost of Gene Sequencing Falls, Raising Hopes for Medical Advances