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Tag Archives: Genetics

Friday Science Review: January 29, 2010

A productive week of international collaborations leading to new drugs or targets…

Genetic Map of Yeast: A large-scale, genome-wide interaction map of yeast genes was constructed in an international study.  The extensive network of genetic interactions lays out a functional map of the cell where similar biological processes can be grouped together. Yeast has been studied in the past and present because their molecular signaling is similar to human cells and is easy to manipulate.  The detailed “genetic atlas” in this project, a first for any organism, provides important information to better understand genetic functions in relation to diseases.  Their technique also allowed the scientists to map interactions between genes and chemicals, which will aid in choosing drug targets by predicting the extent of the interaction with other genes and how it may affect the cell.  The multi-national project was led by University of Toronto researchers Drs. Brenda Andrews and Charles Boone.  Details of the yeast map study appear in the prestigious journal, Science.

Mutations in Lymphomas: The identity of new mutations associated with specific types of lymphomas is described in this latest Nature Genetics article.  Sequencing of genes involved in the NF-kappaB signalling pathway led to the identification of recurrent mutations affecting the EZH2 histone methyltransferase enzyme.  The oncogene is the second member of this enzyme group found to be mutated in different types of cancer.  Mutations were found in over 21% of a lymphoma subtype, affecting amino acid Tyrosine 641 that renders the enzyme with lower activity.  Dr. Marco Marra at the Michael Smith Genome Sciences Centre (BC Cancer Agency) conducted the sequencing project.

Stopping Alzheimer’s Disease: Inhibition of ACAT1, an enzyme directly involved in cholesterol metabolism, significantly decreases the accumulation of amyloid plaques when tested in a mouse model of Alzheimer.  To gain deeper knowledge of how this works, researchers deleted the ACAT1 gene in mice predisposed to develop Alzheimer’s disease.  The brains of these mice had fewer amyloid plaques with improved cognitive function.  The key finding is that without ACAT1 function, cholesterol accumulates in a subcellular compartment of the cell where it is converted and no longer available to be involved in amyloid plaque formation.  These data supports the use of ACAT1 inhibitors in the battle against Alzheimer’s disease and lends insight into future improvement.  Dr. Nabil Seidah at the Institut de Recherches Cliniques de Montréal collaborated with researchers in the U.S. and published the study in the Proceedings of the National Academy of Sciences.

New Treatment to Stop Malaria: Two enzymes important to the survival of Plasmodium falciparum, the parasite causing malaria, have been discovered in an international collaboration aimed at stopping the drug-resistant parasite.  Malaria parasites invade red blood cells and digest the proteins for fuel to grow and divide until they burst out of the red blood cell and repeat the process again.  The discovery of the parasitic enzymes, PfA-M1 and PfA-M17, which are keys to the digestive process in red blood cells, was the first step in designing therapeutic drugs.  Building three-dimensional structures of the enzymes was the next step in determining how best to target and inhibit the enzyme.  The study suggests that blocking PfA-M1 and Pfa-M17 would prevent the parasite from feasting on the red blood cell and represents a new wave of promising anti-malarial drugs.  McGill University’s Dr. John Dalton led the international research project and is reported in this week’s The Proceedings of the National Academy of Sciences.

Vitamin D fights Crohn’s Disease: Vitamin D deficiency in individuals may contribute to the development of Crohn’s disease, as suggested in this new research report.  Mismanagement of intestinal bacteria triggers an inflammatory response that develops into the autoimmune disorder.  The action of Vitamin D, as the study suggests, is to directly promote the expression of NOD2, which signals to the body of a microbial invasion.  NOD2 then activates NF-kappaB to induce expression of DEFB2 (defensin beta2), an anti-microbial peptide.  To further support Vitamin D’s role, both DEFB2 and NOD2 have been linked to Crohn’s disease in earlier studies.  This is significant to the management of the disease because Vitamin D deficiency is easy to test for through a simple blood test and Vitamin D supplements (and sunlight!) are readily available.  Dr. John White and his team at McGill University and the Université de Montréal published their study in the Journal of Biological Chemistry.

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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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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