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Tag Archives: genome sequencing

Friday Science Review: April 16, 2010

An amazing week of Canadian research advancements…

Cancer Genome Project is Well Underway: The Ontario Institute for Cancer Research (OICR), who is leading the International Cancer Genome Consortium (ICGC), published a report this week in Nature outlining the international effort to sequence 25,000 cancer genomes – 500 genomes from each of the 50 most common cancers such as breast, colon, liver, lung, and pancreatic cancers.  Some partial datasets are already available to the global research community at www.icgc.org.  This is truly a Herculean effort that is only possible because of the international collaborative effort of over 200 members around the globe.  Whole cancer genome sequencing will provide a fundamental base to advance personalized medicine to the next level.  Here is the original OICR press release and you can read a more comprehensive ‘Scientific American’ style news feature article on the cancer genome project here in the same issue of Nature.

Seek and Destory: Non-Hodgkins lymphoma cancer is taking a big hit from a newly discovered compound that destroys lymphoma cells.  The small molecule compound targets and blocks a transcription factor called BCL6, which is responsible for half of non-Hodgkins lymphoma cases.  Scientists started with the 3D structure of the BCL6 protein and used computer-aided drug design to perform in silico screening of over a million compounds.  They eventually narrowed it down to this one compound that proved to be efficacious and also non-toxic.  Dr. Gilbert Prive at the University Health Network led the innovative project that demonstrates the success of a computational approach to drug design and the ability to target transcriptions factors with minimal side effects.  Read all about it! – in the free full text article in Cancer Cell.

Divide and Conquer: Cell division is a complicated process with the synchronized dance of chromosomes segregating to each new cell.  It is a poorly understood process but research is this field is advancing with the discovery of new essential proteins involved in cell divisionDr. Laurence Pelletier (Samuel Lunenfeld Research Institute) and his collaborators in Europe used a combination of RNAi tools and mass spectrometry techniques to identify the components of protein complexes involved in cell division.  As cancer cells are hyperactive dividing cells, this new information will also aid in the advancement of cancer targeting therapeutics.  The study appears in the journal Science.

The Missing Link: Many have suspected that there must be some link or relationship between stress, anxiety and depression.  Now there is molecular evidence that this is true.  The connection involves the interaction between corticotropin releasing factor receptor 1 (CRFR1) and certain types of serotonin receptors (5-HTRs).  CRFR1 activity leads to stress related anxiety and it also stimulates an increase in the number of 5-HTRs in the brain, which can lead to signaling abnormalities causing depression.  The team headed by Dr. Stephen Ferguson at the University of Western Ontario also developed a small molecule inhibitor that blocks 5-HTRs.  Let’s hope this inhibitor and knowledge of the molecular links lead to more effective treatments for these disorders.  Check out the free full-text article in Nature Neuroscience.

Smart Buggers:  Understanding how bacteria become resistant to last-resort antibiotic drugs just got a boost from a McMaster University study.  Vancomycin resistant methicillin-resistant staphylococcus aureus (VMRSA), also known as the hospital superbug, is a rapidly growing problem with limited effective solutions.  The research team identified the histidine kinase VanSsc protein as the direct vancomycin detector in bacteria, which then triggers the expression of three genes that provide the drug resistance.  This is the first important step in redesigning antibiotic drugs to effectively fight these little buggers.   Dr. Gerry Wright and his collaborators published their exciting work in Nature Chemical Biology.

Not Just a Bad Golf Shot: Scientists have identified mutations in the SHANK3 gene that are associated with schizophrenia.  SHANK3 is a scaffolding protein involved in the formation of the synapse and maintains the structure of nerve cells.  Dr. Guy Rouleau’s team at the Université de Montréal discovered the new mutations (R1117X and R536W) in two families with schizophrenia patients where one of these families had three affected brothers.  Further molecular and genetic studies in zebrafish models confirmed that the R1117X mutation causes behavioural defects.  Earlier studies linked SHANK3 mutations to autism, which suggests that there is a molecular connection between the two neurological disorders.  The findings are reported in this week’s edition of the Proceedings of the National Academy of Sciences.

Gene Therapy is Still Alive: The promise of gene therapeutics to cure diseases may not have lived up to the hype presented a decade ago but there are still some hopeful successes using gene therapy.  One recent example comes from Laval University where researchers repaired the defective dystrophin gene responsible for Duchenne muscular dystrophy (DMD). In some cases of DMD, the dystrophin gene is misread causing a frame-shift mutation.  These frame-shift mutations may be targeted and repaired by enzymes called meganucleases.  A proof-of-principle project by Dr. Jacques Tremblay demonstrated that expression of specific meganucleases in the muscle of a DMD mouse model can restore the normal reading frame of a mutated dystrophin gene.  More details in this week’s edition of Gene Therapy.

Friday Science Review: March 19, 2010

Friday Science Review: January 15, 2010

A little sunflower power to brighten up a quiet week…

Understanding Cancer Therapy Resistance: A molecular contribution to resistance to cancer treatments is from the cellular protein Clusterin (CLU).   This cell survival protein is targeted by the antisense based OGX-011, one of OncoGenex Pharmaceutical’s leading compounds currently in phase 2 trials for prostate, lung and breast cancers.  In this recent research project, the mechanism of clusterin mediated treatment resistance was investigated by Dr. Martin Gleave’s team at the University of British Columbia.  They found that CLU enhances the degradation of two proteins, COMMD and I-kappaB, which in turn leads to an increase in the transcriptional activity of NF-kappaB to support cell survival.  These findings surely provide additional potential drug targets for Dr. Gleave, who is the founder of OncoGenex and currently serves as the Chief Scientific Officer.  The study is reported in Molecular Cancer Research.

Sunflower Genome: This is an award announcement to fund the $10.5M (USD) “Genomics of Sunflower” Project.  The contributions are from a ‘cross-border’ consortium including Genome Canada, Genome BC, the US Departments of Energy and Agriculture, and France’s INRA (National Institute for Agricultural Research).  An international team including University of British Columbia researchers and led by Dr. Loren Rieseberg will generate the reference genome that is approximately 3.5 billion bases long for the sunflower family, which includes 24,000 different species.  This agri-biotech project will support the future of the sunflower industry (its seed industry alone is worth $14B) by trying to identify genes that are responsible for agriculturally important traits such as seed-oil content, flowering, seed-dormancy, and wood producing-capacity as well as adapt to today’s changing environment and consumer tastes.

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Trends Update — DTC Genetic Tests: NOVA ScienceNOW Program Takes a Look

B&W_DNA_sequenceYesterday’s NOVA ScienceNOW program included a segment on direct-to-consumer genomics (H/T to GenomeWeb’s Daily Scan Blog).  The program was bullish on George Church’s Personal Genome Project; but it took a pretty dim view of the predictive value of current consumer technology.

The program was accessible and interesting, but it went overboard in making a cautionary point about current DTC genomics offerings.  It transitions directly from Neal deGrasse Tyson’s 23andMe results for heart disease and diabetes to Steven Pinker’s genomic scan, which showed that Pinker had “double the risk of baldness,” whereas Steven is anything but bald.  Well, sure, and the weather report yesterday said there was an 80% chance of rain but it didn’t rain.  That doesn’t mean I should stop checking weather reports, or even that I was stupid to pack an umbrella.  It’s just probabilities.  I guess I agree with the program in the sense that anyone who can’t spot that flaw shouldn’t be interpreting their own genomic data, but it seems like an oddly condescending way for them to make the point.

Kudos, though, for pointing out:

  1. the gaps in the Genetic Information Nondiscrimination Act; and 
  2. the low risk to tenured Harvard profs of revealing their sequence data, as they are likely shielded from many of the risks to other participants.

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Q3 Is Looking Up for Biotech: Emdeon, Cumberland, Domain, LOM BioQuest, OETF

light at the end of the tunnel smallThis week has seen a continued upswing for biotech and other health industry companies in the U.S. (with two IPOs) and in Canada (with great VC news and the pending appointment of an administrator for the Ontario Emerging Technologies Fund):

In the U.S.

Here in Canada

In the pipeline

With personalized medicine seeing increasing validation as a clinical strategy, genomics technology will be key.  News this week from Helicos Biosciences that an individual’s complete genome was sequenced in one month for just $50k in consumables is an important marker (har) on the road to regular full-genome scans as part of our medical toolkit.

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Trends in 2009: Direct-to-Consumer Genetic Tests Come to Canada

B&W_DNA_sequenceThis week saw the introduction of what I believe is Canada’s first personal genomics service offering.  Toronto’s Medcan Clinic paired up with California-based Navigenics to scan individuals’ genomes for a variety of disease markers.

Personal genomics is a burgeoning trend this year, which according to a special report in April’s Economist, will only be further boosted by a Moore’s Law-type improvement in sequencing power and price.  Available service offerings range from whole genome sequencing (e.g., Illumina and Knome) that costs tens of thousands of dollars to targeted scans typically offered for under $500 by a much wider variety of providers (Navigenics, 23andMe, deCODE and Pathway Genomics).

Regulation of DTC Testing:

In the U.S., the regulatory environment has settled down somewhat over the last 6 months, with most U.S. states regulating DTC genetics companies as clinical labs and the providers registering as such on a regular basis, including CLIA certification.  However, the HHS Secretary’s Advisory Committee on Genetics, Health and Society is due to meet in October to further discuss whether DTC genetic tests should be regulated as medical devices.  The CDC has released a report entitled “Good Laboratory Practices for Molecular Genetic Testing for Heritable Diseases and Conditions” setting out best practices both for testing and interpretation.

In Ontario, there are a number of regulatory considerations (thanks on these points for input from Will Chung, of our renowned Life Sciences team):

  1. Private labs and specimen collection centres require licenses and are governed by the Laboratory and Specimen Collection Centre Licensing Act (LSCCLA). However, blood collection at such facilities is governed by separate legislation which controls who may draw blood and for what purpose.
  2. The LSCCLA requires that only “legally qualified medical practitioners” are permitted to examine specimens, which means that patients may not directly order testing of their own blood at private licensed labs.
  3. Ontario’s Regulated Health Professions Act stipulates that communicating a “diagnosis” is a “controlled act” which may only be performed by a person authorized by a health profession Act, although it is not clear that DTC genomics results are a “diagnosis.”

Medscan seems to have navigated the regulatory waters, but time will tell how these laws are applied and/or modified.

In the EU, the European Society for Human Genetics advocates for pre-market review for “truthful labeling and promotion” as well as post-market evaluation of DTC genetic tests. In May, Germany passed a law restricting the availability of DTC genomics services by requiring testing to be carried out by a licensed doctor following the patient’s consent.”

How much protection do consumers need?

Many commentators are concerned with the public’s ability to understand these tests and distinguish between those that are clinically meaningful and those that are more … snake-oily.  Others object on the basis that there is little value added absent any available treatment — many preventive measures are things we already know we should do, like eat well, exercise, etc.  A number of groups, including advocacy group Genetic Alliance and the Genetics and Public Policy Center at Johns Hopkins University have called for a national registry of DTC genetic tests that would include performance data.

Others (and not just 23andMe’s founders) take a more libertarian view.  Ronald Bailey, the science columnist at Reason, agrees that people probably don’t need to be “protected against learning such information without the guidance of a knowledgeable physician or genetic counselor.”  In fact, a lawsuit in May brought by a girl born with Fragile X syndrome against the sperm bank that didn’t test for the predisposition may drive  higher demand for genetic testing in the fertility context which may in turn drive supply of services and diagnostic tools and may contribute to normalizing broader parental testing and pre-implantation screening.

Interestingly, a NEJM report a couple of weeks ago showed no lasting psychological damage from a genetic prognosis of increased Alzheimer’s risk.  By the time a year passed after the results, subjects who had an increased Alzheimer’s risk were no more depressed, anxious, or distressed than when they started the study.

Most importantly, 98% of patients in the Alzheimer’s study who tested positive said they would still get tested if offered the choice again.  98% is a lot. It suggests that DTC services will be increasingly popular, particularly as the price drops and the quality of the data, the analytics and the available counseling continue to improve.

Stay tuned to this page for further DTC genetics news and analysis.

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Personalized Medicine: The “SNP Doctor”

BIO SmartBrief picked up a story today about a device being tested called the mohel Snip Doctor, a hand-held diagnostic device that:

looks for known single nucleotide polymorphisms (SNPs) – single letter changes in the genetic code – that can affect an individual’s response to medical treatment.

While most current approaches to personalized medicine are mechanistic (e.g., HercepTest), this device raises the possibility of a correlative approach.  Of course, it’s only a temporary measure to hold us over until our full genomes are a normal part of our electronic medical records.

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