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Tag Archives: SNP

Biotech Trends Update — Personalized Medicine: The Limits of Genomic Analysis

A great report on GenomeWeb yesterday by Andrea Anderson reviews two JAMA papers that failed to show a clinically useful role for SNP genetic testing in predicting heart disease risk.  Instead,

“traditional risk information based on factors such as family history and plasma biomarker levels were better for predicting heart disease.”

Anderson ties these results back to a January paper in the British Medical Journal that found that

“non-genetic factors were more useful for predicting type 2 diabetes than a set of 20 SNPs.”

The GenomeWeb article quotes the lead author of one JAMA paper as finding the results “surprising and a little disappointing;” but I am inclined to think some context is missing, since only the most die-hard genetic determinist should be either surprised or disappointed. 

Two factors suggest that these conditions, and many others, will resist accurate prediction based on genomic sequence analysis:

  1. They are genetically complex.  The prospective studies looked at data sets with between 12 and 101 SNPs.  Simple calculations suggest that the number of genetic permutations is itself staggering, never mind the physiological complexity of multigenic interactions.
  2. There are massive environmental components. Diet and exercise, among many other factors, will have a tremendous impact on clinical outcomes.  These habits are learned, not inherited, and are even “contagious” within social groupings.

My bottom line: In an age when genomic sequences are becoming increasingly accessible, it should be reassuring to know that even your medical future is not written in stone.  We always suspected as much. Now we have the genetic data to prove it.

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Friday Science Review: February 12, 2010

New Discovery for Neonatal Diabetes: Researchers uncovered an important role for the Rfx6 gene.  Its integrity is required for normal development of the islets of Langerhans cells in the pancreas that produces important hormones including insulin.  Genetic mutations found in Rfx6 are the cause of severe neonatal diabetes where there are no insulin producing islets of Langerhans cells.  To prove the critical role of Rfx6 in directing the differentiation of early pancreatic cells, researchers disrupted the gene in mice and observed the development of an identical disorder as displayed in humans.   Identifying the gene is a key piece of the puzzle and will lead to new avenues to find treatments for all types of diabetes.  Dr. Constantin Polychronakos and his team at McGill University collaborated with researchers from UCSF and report their study in the on-line edition of Nature.

Controlling Stem Cell Fate: A genome-wide screen identified the PCL2 (polycomb-like 2) gene as a key decision maker in determining the fate of stem cells.  This is an important area of research because stem cell based therapies in regenerative medicine are on the rise but more thorough understanding of stem cell control is necessary for safety reasons.  In the absence of PCL2, stem cells can no longer differentiate into specialized cells regardless of adding stimulating factors to try to push it to differentiate.  Once they re-introduced PCL2 into the stem cells, they were able to drive differentiation again.  By mapping the network of genes that PCL2 regulates, they can trace the steps in the path of a stem cell in becoming one of the many cell types in our body.  University of Toronto scientist, Dr. William Stanford and his team describe their research in the journal Cell Stem Cell.

Stem Cell Prediction: This is a neat study.  Researchers generated an algorithm to predict the future of a stem cell – whether it divides and self-renew as stem cells or produce alternate cell types.  They recorded video of retinal progenitor cells under the microscope to ‘observe’ the cell’s characteristic dynamic behaviour and movements just prior to dividing.  This information was computed to generate a predictive algorithm that was tested to be (amazingly!) 99% accurate in identifying cells that will self-renew as stem cells and 87% correct in predicting a differentiation cell fate.  This may lead to new tools to help scientists isolate pure populations of stem cells for their future studies.  Dr. Michel Cayouette’s group at the Institut de Recherches Cliniques de Montréal presents their work in this week’s edition of Nature Methods.

Genomics of Flesh-eating Disease: The genomic sequences of Streptococcus bacterial strains from past epidemics in Ontario were determined in a study involving Canadian and US researchers.  They identified and compared single nucleotide polymorphisms (SNPs) between the strains and found that they were different by an average of only 49 SNPs.  Each strain, however, also contained unique sequences that could be used for tracking purposes in future outbreaks.  Some genes were highly variable, which is information that they can use to try to understand the bacterial virulence factors at play in gaining an advantage over the infected person.  These comparative pathogenomic studies are invaluable for microbial epidemiology research and for shedding light on new potential targets for antibiotic drugs.  Drs. Donald Low and Allison McGeer at Mount Sinai Hospital participated in the research that is reported in this week’s edition of the Proceedings of The National Academy of Sciences.

Friday Science Review: October 23, 2009

A lucky find and two very different genomics projects…

Connective Tissue Disorder Linked to Defects in Ltbp4:  A McGill University researcher collaborating on two independent projects, one from Washington University School of Medicine and the other from New York University School of Medicine, made the coincidental link between the two after realizing that the tissue defects were identicalDr. Elaine Davis, an electron microscopy expert at McGill, analyzed tissue from children born with abnormally developed lungs, gastrointestinal and urinary systems, skin, skull, bones and muscles.  The underlying cause is a connective tissue disorder called cutis laxa that also causes skin to hang loosely from the body.  At the same time, Dr. Davis was analyzing tissue taken from Ltbp4 gene knockout mice from New York University when she realized that the connective tissue defects in the human and mouse samples were identical.  This connection was confirmed when they sequenced the Ltbp4 gene in human patients and discovered recessive mutations.  With this discovery, they now have a molecular target to understand the disease and to design therapeutic strategies.  The study is reported in The American Journal of Human Genetics.

A Deep-sea Microbe Genome: The microbe, SUP05, lives in the deep ocean “dead zone” where oxygenated water is minimal. It survives by using other compounds instead of oxygen, such as nitrates, sulphates and metals.  A recent surge in population suggests an expanding low-oxygen ocean ecosystem and is an indicator of global climate change.  University of British Columbia professor Dr. Steve Hallam and his research group analyzed the entire genome of SUP05 and identified a number of genes mediating carbon assimilation, sulfur oxidation, and nitrate respiration.  This study provides the first insight into the metabolism of these microbes and their effects on nutrients and gases in the deep-ocean ecosystem and will also lead to further understanding of their ecological and biogeochemical role.  The report appears in this week’s edition of Science.

Allelic Expression Genomic Map: Illumina genomics technology was used in this study to map global allelic expression differences associated with cis-acting variants.  Cis-acting elements can affect gene expression and variations due to single nucleotide polymorphisms (SNPs) explain a large percentage of the phenotypic differences in the population.  It is very informative to have this global map of the cis-acting variants and helps researchers identify variants associated with diseases.  To demonstrate this, they finely mapped cis-regulatory SNPs in a region in chromosome 8 associated with lupus.  The study was performed by Dr. Tomi Pastinen and his Genome Quebec team at McGill University and the report was published in Nature Genetics.

DNA Repair Suppresses c-Myc Lymphoma:  Overexpression of c-Myc in B cells is associated with lymphomas but requires secondary mutation events for the disease to develop.  In this study, immunologist Dr. Alberto Martin and his research team at the University of Toronto identified that the DNA repair protein, Msh2, plays an important role in mitigating c-Myc associated cancer.   To demonstrate this, they generated mice that overexpress c-Myc but with Msh2 mutations such that they are deficient in DNA mismatch repair.  These mice rapidly develop B cell lymphomas, which suggests that Msh2-dependent DNA repair actively suppresses c-Myc associated oncogenesis.  The report appears in the early edition of The Proceedings of the National Academy of Sciences.

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Friday Science Review: September 11, 2009

Two great medical discoveries…

Stayin’ Alive:  During a stroke, for example, neurons deprived of oxygen undergo cell death.  In a recent discovery lead by Dr. Michael Tymianski’s team at the Krembil Neuroscience Centre at Toronto Western Hospital, the protein TRPM7 was found to play a critical role in mediating this detrimental effect.   After suppressing TRPM7 expression in a localized region of a rat’s brain, they simulated a stroke by cutting off blood flow to the brain for 15 minutes.  The subsequent analysis revealed a complete lack of tissue damage compared to rat brains expressing TRPM7.  The resistance to death by cells lacking TRPM7 even preserved the brain’s cognitive function and memory performance following the ‘stroke’.  This may have tremendous implications for preventing further cell damage following ischemia in any tissue and is not necessarily limited to the brain, although it is yet to be tested elsewhere in the body

Details of the discovery are reported in the latest edition of Nature Neuroscience.

Insulin Resistance Gene Discovery: An international effort led by Dr. Robert Sladek and Dr. Constantin Polychronakos at McGill University performed a genome-wide comparison and identified a single nucleotide variation in the genetic region near the IRS1 gene that is associated with insulin resistance and hyperinsulinemia.

Dr. Sladek explains it best:

“It’s a single-nucleotide polymorphism (SNP, pronounced ‘snip’), a single letter change in your DNA,” said Sladek. “What’s interesting about this particular SNP is that it’s not linked genetically to the IRS1 gene in any way; it’s about half-a-million base-pairs away, in the middle of a genetic desert with no known genes nearby. In genetic terms, it’s halfway from Montreal to Halifax. And yet we can see that it causes a 40-per-cent reduction in the IRS1 gene, and even more important, a 40-per-cent reduction in its activity. Which means that even if insulin is present, it won’t work.”

IRS1 is known to be the key signalling protein involved in the cell’s initial response to insulin.  This recently discovered variant allele affects the level of IRS1 protein expressed and reduces the capacity of the cells to respond to insulin. Unlike other diabetes risk genes that affect insulin production in the body, this is the first that is known to suppress insulin stimulation in the cells.

The research article appears in the early online edition of Nature Genetics.

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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