Category Archives: Gene Medicine

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 startup 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 such as 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 centre that is jointly operated by the University of California, San Diego, and the University of California, Irvine.

Once you make the transition from a data poor to data rich environment, everything changes, said Smarr, who is a member of the Complete Genomics scientific advisory board.

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 startup 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 centre than a biology lab.

In 2005, when Clifford Reid, a successful Silicon Valley software entrepreneur, began to assemble his team, he approached Banyai and asked if he was interested in joining a gene sequencing startup. 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.

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Gene sequencing falls to $5,000

The AnMed Health Family Medicine Center, the practice site for the AnMed Health Family Medicine Residency Program, recently honored two of its former patients by dedicating its waiting room in their honor. Edison Thomas and his wife, Gene, were patients at the Family Medicine Center for 25 years. The couple was always pleased with the care they received from family medicine residents and faculty. To express their gratitude, the Thomases left a portion of their estate - $63,172 - to the Family Medicine Center. Mr. Thomas's two sisters surprised the Family Medicine Center with a check in October. After renovations, the Family Medicine Center unveiled The Mr. and Mrs. Edison C. Thomas Waiting Room on Feb. 3, 2012. "What a wonderful gesture of appreciation this gift is to recognize the 36 years of family medicine training and compassionate patient care rendered at our program," said Dr. Stoney Abercrombie, director of the AnMed Health Family Medicine Residency Program. Every day patients have the opportunity to give back to AnMed Health in honor of the caregivers who made a difference in their life. To find out how, call the AnMed Health Foundation at 864.512.3477 and ask about the Grateful Patient program. To learn more about planned giving, go online to http://www.anmedhealth.org/ourfoundation.

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AnMed Health Family Medicine Center names waiting room in honor of two former patients

A woman receives cancer treatment

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

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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 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.

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By analyzing tumors 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 color 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.

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Gene differences in tumors making cancer treatment difficult

Public release date: 8-Mar-2012 [ | E-mail | Share ]

Contact: Katherine Barnes katherine.barnes@kcl.ac.uk 44-207-848-3076 King's College London

Researchers at King's College London and Hiroshima University, Japan, have identified a specific gene linked to throat cancer following a genetic study of a family with 10 members who have developed the condition.

The study, published today in American Journal of Human Genetics, uncovered a mutation in the ATR gene, demonstrating the first evidence of a link between abnormality in this gene and an inherited form of cancer. The researchers say this finding raises new ideas about genetic factors linked to throat cancer and provides a platform for exploring the role of ATR more generally in cancer biology.

Scientists carried out a genome-wide linkage study in a US family with an unusual hereditary condition affecting 24 members of the family over five generations. Characteristics include developmental abnormalities of hair, teeth and nails as well as dilated skin blood vessels. Strikingly, nearly every person with the condition involved in the study had developed throat cancer (oropharyngeal squamous cell carcinoma) in their 20s or 30s.

The team took blood samples from 13 members of the affected family, as well as samples from 13 unaffected people. After analysing these samples they found a single mutation in ATR was present in all the people with the condition, but none of the unaffected people had the mutation. Ten of the 13 people with the condition had developed throat cancer.

Professor John McGrath from the King's College London Genetic Skin Disease Group at St John's Institute of Dermatology, based at Guy's Hospital, said: 'This is an intriguing study which not only provides a genetic explanation for an unusual syndrome, but also provides a unique novel insight into how the ATR gene may be associated with a specific form of cancer. It is a classic example of how we can use rare conditions to give us insight into more common diseases.

'Key known risk factors for developing throat cancer include consumption of alcohol and tobacco as well as viral infections such as HPV (humanpapilloma virus). But this is the first evidence connecting abnormalities in the ATR gene with susceptibility to this type of cancer. We know that ATR encodes a protein critical to the way cells repair their DNA, and is therefore a vital mechanism. We now plan to investigate the cancer pathways in more detail to try to find new treatments.'

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CONTACT Katherine Barnes International Press Officer King's College London Tel: +44 207 848 3076 Email: katherine.barnes@kcl.ac.uk

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New throat cancer gene uncovered by UK and Japanese scientists

THURSDAY, March 8 (HealthDay News) -- Researchers have identified five new genetic mutations associated with Crohn's disease in Jews of Eastern European descent (Ashkenazi Jews) and say their findings may help explain why Crohn's is nearly four times more prevalent in this group than in the general population.

Crohn's is an inflammatory bowel disease that causes swelling and irritation in the digestive tract. Symptoms include abdominal pain, diarrhea, rectal bleeding, weight loss, and fever.

Previous research pinpointed 71 genetic variants associated with Crohn's disease risk in people of European ancestry. In this new study, Mount Sinai School of Medicine researchers compared almost 2,000 Ashkenazi Jews with Crohn's disease to another 4,500 Ashkenazi Jews without the disease.

The team found 12 of the known risk variants and also discovered five new genetic risk regions on chromosomes 5q21.1, 2p15, 8q21.11, 10q26.3 and 11q12.1.

"This is the largest study to date, and the first to discover the unique risk factors of Crohn's disease in the Ashkenazi Jewish population," study leader Inga Peter, an associate professor of genetics and genomic sciences, said in a Mount Sinai news release.

"The prevalence of this disease is so much higher in Ashkenazi Jews, and the involvement of genetic variants predominant in this population might help understand why that is," she added.

The researchers also found that the genetic structure of the newly-identified regions associated with Crohn's disease risk in Ashkenazi Jews was much less diverse than that of non-Jewish Europeans.

"Not only did we discover different risk factors for Ashkenazi Jews, but we found that some previously known risk factors are more potent to this population," Peter said. "Armed with this new information, we can begin to analyze the specific signals in order to pinpoint causal genetic mutations, discover why they are malfunctioning, and eventually develop novel treatment approaches."

The study is published March 8 in the online edition of PLoS Genetics.

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Gene Mutations Linked to Crohn's Disease in Ashkenazi Jews

Two key patent cases that no doubt will impact the future of personalized medicine are pending review by the US Supreme Court. What will the Court decide?

By Courtenay C. Brinckerhoff | March 7, 2012

The debate over the patenting of technologies related to diagnostic and personalized medicine continues to swell with no resolution in sight. The Supreme Court heard oral arguments in Mayo Collaborative Services v. Prometheus Laboratories, Inc. last December, but has not yet issued a decision. Just last month, the US Patent and Trademark Office held public hearings to gather information for the study on genetic testing that it will use to prepare a report for Congress on this issue. And, the Supreme Court is deciding whether to review the Federal Circuit decision in Association for Molecular Pathology v. Myriad Genetics, Inc. (the BRCAI/gene patenting case), although current speculation is that the Court may defer any action on this case until it issues its decision in Prometheus. While each of these proceedings raises different legal issues, they all relate to the ability to obtain or enforce patent rights on genes, tests, and methods used in personalized medicine.

Personalized medicine is the new frontier of healthcare. It offers the promise of treatments that are tailored to a patients individual situation, including the patients genetic makeup, the specific variation of the disease the patient suffers from, and the patients specific response to a given course of treatment. With personalized medicine, a patient can be given the most effective treatment, improving prognosis and saving considerable time and money on ineffective treatments. As noted on the US Food and Drug Administrations Pharmacogentics webpage, [p]harmacogenomics can play an important role in identifying responders and non-responders to medications, avoiding adverse events, and optimizing drug dose.

The question being debated is whether these advances are most likely to flourish within the patent system or outside of it. Do patents promote investment in personalized medicine or stifle innovation by suppressing competition? Do patients benefit from patented therapies, or do they suffer without treatments because they are too expensive? The Founding Fathers established the patent system in the US Constitution as an incentive to promote the Progress of Science and useful Arts, but should a different paradigm apply to medical inventions?

Companies working in this field cite the high cost of developing and validating personalized medicine therapies, and emphasize the need to obtain a return on their successful investments. Without the promise of some period of market exclusivity during which they can profit from their years of research, companies will not have any incentive to work in this fieldor any resources to do so.

On the other side of the debate, some doctors organizations and patient groups believe that the patent system is bad for the healthcare system. They say that it drives up costs and may prevent patients from obtaining a second opinion, because the patent owner can prevent others from administering patented tests. Many believe that research would continueat universities and institutions like the National Institutes of Healthand that more people would benefit because the advances would be available on a more widespread basis.

At its heart, this debate may be more of a public policy question than a legal one. People deciding this issue must keep in mind that most university research is funded by government grants and that NIH is a federal agency. We may want taxpayer money to support this kind of research, but it raises the same specter of big government and taxpayer burden as health care reform. Is a country that may not be ready to provide universal access to proven therapies willing to invest substantial amounts in research programs that may take years to yield any benefits?

Turning back to the law, the US Court of Appeals for the Federal Circuit has refused to draw a line that categorically prohibits patents on personalized medicine. In Prometheus, the court found that methods of optimizing the dose of a specific type of drug was patent-eligible subject matter, not an improper attempt to patent a natural phenomenon. In Myriad, the court found that isolated DNA associated with an aggressive form of breast cancer could also be patented without violating the prohibition against patents on products of nature because DNA does not naturally occur in an isolated form. Although the Supreme Court could reach a different conclusion in either or both cases, its refusal to categorically prohibit business method patents suggests that it may also approach this issue in a similar fashioncautiously and on a case-by-case basis. That would leave it to Congress to decide if a different approach is needed (such as compulsory licensing as discussed at the Patent Office hearing), or if the current incentives and rewards are striking an adequate balance between private investment and public benefit.

Courtenay C. Brinckerhoff is a partner at Foley & Lardner LLP, vice chair of the firms Chemical, Biotechnology & Pharmaceutical Practice, and editor of Foleys PharmaPatentsBlog.com. The opinions expressed here do not represent those of Foley & Lardner LLP or its clients.

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Opinion: On the Gene Patent Debate