Modifier Genes vs. Susceptibility Genes

The identification of gene modifiers may improve our ability to understand differences in the severity of disease.  Having such information may help guide decisions about therapy, for both patients and doctors.  The outcomes of a search for gene modifiers for cystic fibrosis are described by one of the authors:

"There are likely a number of gene modifiers in CF and other diseases, and this current paper describes one of the first robust examples," [Michael] Knowles said. "Some CF patients may do worse because of ’severe inflammation’ genes, whereas others may do worse because of differences in mucus genes. Still others might because of their growth and metabolism genes, etc… Thus, therapy might need to be targeted to a particular area or areas in individual patients. This is important not only for CF, but for other lung diseases as well because gene modifiers we discover in CF will be seen in other diseases, and there are already examples of that."

An editorial accompanying the article in the New England Journal of Medicine describes how modifier genes are different from susceptibility genes:

"Susceptibility genes and modifier genes are two biologic phenomena that few clinicians should ignore in the genome era. Susceptibility genes, which are genes with functional variants that affect the causes of disease, are routinely being identified for simple mendelian diseases and, more recently, for common genetic disorders. Modifier genes are distinct from susceptibility genes, in that they are genetic variants that affect the clinical manifestation of disease (as opposed to liability)…The identification of gene modifiers and their interactions in cystic fibrosis and other diseases has only just begun."

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Christina K. Haston and Thomas J. Hudson. "Finding Genetic Modifiers of Cystic Fibrosis" NEJM 353(14)1509-1511. October 6, 2005. (sorry subscribers only)

Drumm et al. "Genetic Modifiers of Lung Disease in Cystic Fibrosis" NEJM 353(14)1443-1453. October 6, 2005. (sorry subscribers only)

October 6, 2005 | Filed Under disease-management, education, variation | Comments Off 

Free Short Courses in Statistical Genetics

Several years of streaming video lectures on statisical genetics at the University of Alabama, Birmingham.  The courses range from basic genetics to bayesian methods.  Thanks UAB. 

October 3, 2005 | Filed Under education | 1 Comment 

Development of Sequencing Technology

Two grafs on the development of sequencing technology from a recent article in Bioscience Technology.

1) Sequencing technology is "frozen in time", still searching for a breakthrough:

Progress in gene sequencing has arisen more from improved methods than
ground-breaking instrumentation. Glenn Schulman, PharmD, marketing
manager at 454 Life Sciences (New Haven, CT) points out that gene
sequencing technology has become frozen in time circa 2000. “Things
pretty much stopped with capillary electrophoresis-based
instrumentation,” he says. “There have been incremental improvements,
but nothing truly enabling.”

2) Logarithmic Scaling of 454’s sequencing-by-synthesis technology (see image)

454’s progress has been phenomenal since it reported its first results,
on about 25 base pairs, in late 2001. Since then scale-up has been
logarithmic: 33 kbp in 2002, 2.8 Mbp in 2003, and about 20 million bp
today (about the size of a bacterial genome) in a 4.5 hour run. Dr.
Schulman sees no end in sight to Moore’s Law-type scaling, which could
result in sequencing a whole human genome — 30 Gbp — in a matter of
days or hours.

Resources:
Angelo DePalma. "Sequencing in the post-genomic age." Bioscience Technology.

Biotage’s Pyrosequencing (sequence-by-synthesis) tutorial …with video

April 18, 2005 | Filed Under education, technology | Comments Off 

Nosocomephobia

The fear of hospitals is everywhere.  If anything, at least awareness of major safety concerns is growing.  The fact that it pops-up in unexpected places, like in the preface of a book on telecom terminology, is evidence of this fact.  Here is the passage I speak of:

HOSPITALS ARE DANGEROUS PLACES
Hospitals are dangerous places.  If you ever have to go to one, NEVER go without someone who will personally supervise everything about your presence there, the whole time you’re there.  A skeptical spouse works better.

This is from the ninteenth edition of Newton’s Telecom Dictionary (2003).  The twentieth edition (2004) contains a similar passage.  No mention of the subject matter in the in the previous 18 editions(at least not in the 18th edition, when I became a Newton neophyte). 

For those of you unfamiliar with the book, do yourself a favor and buy a copy.  If you use a computer, you need it.  If this computer is on a network, you really need it.  Regardless of whether you are a novice or an illustrious member of the digiterati, it is a wonderful resource to have around.  Newton issues an updated book every year and I buy it every year.  I frequently find myself dipping into it in pursuit of one definition and not resurfacing for an hour.   

For those of you interested in nosocomephobia, why it exists, what to do about it, and other health care related commentary, check out The Piper Report.

September 24, 2004 | Filed Under education | Comments Off 

Education: Six Weeks to Genomic Awareness

Around 6 hours of streaming lectures entitled, "Six Weeks to Genomics Awareness" are available here.  This lecture series was created by the University of Michigan Center for Genomics and Public Health and other collaborators.

Here are the lecture topics:
Module 1, Introduction to Genomics, Part 1: The Human Genome
Module 1, Introduction to Genomics, Part 2: Genes in Their Cellular Context
Module 1, Introduction to Genomics, Part 3: Genetic Mutation
Module 1, Introduction to Genomics, Part 4: Pedigree Analysis
Module 2, Genes in Populations, Part 1: Population Genetic Perspectives
Module 2, Genes in Populations, Part 2: Genotype-Phenotype Relationships
Module 3, Genetic Testing, Part 1: What is Genetic Testing?
Module 3, Genetic Testing, Part 2: The Challenges
Module 4, Gene-Environment Interactions, Part 1: Definitions and Examples
Module 4, Gene-Environment Interactions, Part 2: Pharmacogenetics
Module 5: Ethical, Legal and Social Issues
Module 6: An Overview ofState and National Resources

August 12, 2004 | Filed Under education | Comments Off 

Giving credit where it is due

The Dolan DNA Learning Center at Cold Spring Harbor is working with Clemson University to create a South Carolina DNA Learning Center.  From this news story:

"The mission of the Dolan DNA Learning Center is to prepare students and families to thrive in the gene age," said [David A.] Micklos, [executive director of the Dolan DNA Learning]. "We envision a day when all elementary students are exposed to principles of genetics and disease risk; when all high school students have the opportunity to do hands-on experiments with DNA; and when all families have access to genetic information they need to make informed health care choices. The center at Clemson will serve South Carolina, preparing students and families for the future."

Legislators should be added to this list of people that need to prepare for the future.  After a presentation at the Annual Meeting of Women in Biotechnology in late 2002, ethicist Arthur Caplan took a question from the audience about whether genetic testing would someday become routine during visits to the doctor.  Here is part of his response:    

"And molecular medicine will [get absorbed into the diagnostic culture] too. Someday if we don’t screw this up, I do believe you will go to the doctor’s office and get your molecular printout and be told that these drugs are bad for you, and those drugs are good for you, and this is a risk thing for you, and you should do this and that for your lifestyle change, and all that. And that’s great; I think that day is great. But I think it’s far off. People are not, we just mapped the genome. Most people don’t know where their genes are. Most people don’t want to eat genes. Most people think. I went and talked to a group of legislators about something and I asked them where their genes are, and about a quarter of them thought they were in their gonads. It’s partial credit. About a quarter of them thought they were in their brains. Which is very optimistic. And then, half of them knew they were kind of scattered around their bodies.

   

But I always laugh, I’m sorry to insult journalism here for a second, but you know all those pictures they show you of DNA on Time magazine? No o ne knows where that stuff is.  They have no idea. It’s like, and then we have this DNA thing and we replace it, and this is what genetic engineering is. We take the segment and we move it over here. And people are thinking, where is that? Where is that going on? I mean, is that like in my head or in my testicles or what are they talking about? I mean, they don’t know. So, a while for that to come. A while is what I would say. Not soon. The industry has to position itself for a lot of ignorance. A lot of fear, and some fear-mongering. There are critics of genetics out there all
over the place who want to use that to slow the industry down. For a variety of reasons."

It is important, as a society, to encourage some degree of scientific literacy.  For individuals eager to maximize personal well being, health literacy is an obstacle even for the educated.  These two indexes are of course interrelated. 

Here is the info for Caplan’s paper quoted above:
Arthur Caplan "Are We Ready for Mass Genetic Testing: Ethical and Social Hurdles" Annual Meeting of Women in Biotechnology. October 16, 2002. (Meeting transcript in pdf)

April 22, 2004 | Filed Under education, genetic-testing, opinion-research | Comments Off 

Exhibit: Art of Larry Gonick

The Bancroft Library at UC Berkeley has an online exhibit of original artwork from Cartoon Guide to Genetics (1991). 

(Thanks to The Eyes Have It for the pointer)

March 24, 2004 | Filed Under education, visualization | Comments Off 

Newly Designed GenInfo Newsletter

HumGen has published another informative issue of the GenInfo newsletter.

March 9, 2004 | Filed Under education | Comments Off 

DNA at PBS

DNA series on PBS.  Check your local listings here.

 

January 18, 2004 | Filed Under education | Comments Off 

HealthMaps

Another information thepary oriented product, this one from InterMap Systems is called the HealthMap Platform.  Check out this page to download a flash demo.

January 13, 2004 | Filed Under education, medical-consumerism | Comments Off 

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