Scientists Identify DNA That May Contribute to Each Person's Uniqueness

[Serephino]

Web address:
http://www.scienced aily.com/ releases/ 2010/08/
100811085416. htm
Scientists Identify DNA That May Contribute to Each Person's Uniqueness

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A new scan of the human genome has shed light on why people have such
a variety of physical traits and disease risks. (Credit: iStockphoto)
ScienceDaily (Aug. 13, 2010) — Building on a tool that they developed
in yeast four years ago, researchers at the Johns Hopkins University
School of Medicine scanned the human genome and discovered what they
believe is the reason people have such a variety of physical traits
and disease risks.

In a report published in the June 25 issue of Cell, the team
identified a near complete catalog of the DNA segments that copy
themselves, move around in, and insert themselves here and there in
our genome. The insertion locations of these moveable segments --
transposons -- in each individual's genome helps determine why some
are short or tall, blond or brunette, and more likely or less likely
to have cancer or heart disease. The Johns Hopkins researchers say
that tracking the locations of transposons in people with specific
diseases might lead to the discovery of new disease genes or mutations.

Using their specialized "chip" with DNA spots that contain all of the
DNA sequences that appear in the genome, researchers applied human DNA
from 15 unrelated people. The research team compared transposon sites
first identified in the original published human "index" genome and
found approximately 100 new transposon sites in each person screened.

"We were surprised by how many novel insertions we were able to find,"
says Jef Boeke, Ph.D., Sc.D., an author on the article, a professor of
molecular biology and genetics, and co-director of the High Throughput
Biology Center of the Institute for Basic Biomedical Sciences at Johns
Hopkins. "A single microarray experiment was able to reveal such a
large number of new insertions that no one had ever reported before.
The discovery taught us that these transposons are much more active
than we had guessed."

Each of the 15 different DNA samples used in the study was purified
from blood cells before it was applied to a DNA chip. Transposons
stick to spots on the DNA chip corresponding to where they're normally
found in the genome, letting the researchers locate new ones.

Boeke's group first invented the transposon chip in 2006 for use in
yeast. But, it was Kathleen Burns, M.D., Ph.D., now an assistant
professor of pathology at Johns Hopkins, who first got the chip to
work with human DNA. "The human genome is much larger and more
complex, and there are lots of look-a-like DNAs that are not actively
moving but are similar to the transposons that we were interested in,"
says Burns. The trick was to modify how they copied the DNA before it
was applied over the chip. The team was able to copy DNA from the
transposons of interest, which have just three different genetic code
letters than other look-alike DNA segments.

"We've known that genomes aren't static places, but we didn't know how
many transposons there are in each one of us; we didn't know how often
a child is born with a new one that isn't found in either parent and
we didn't know if these DNAs were moving around in diseases like
cancer," says Burns. "Now we have a tool for answering these
questions. This adds a whole dimension to how we look at our DNA."

Anna Schneider, Yunqi Lu, Tejasvi Niranjan, Peilin Shen, Matoya
Robinson, Jared Steranka, David Valle, Curt Civin, Tao Wang, Sarah
Wheelan and Hongkai Ji from Johns Hopkins Medicine are additional
authors on the manuscript.

Funding for this research was provided by grants from the National
Cancer Institute, the National Human Genome Research Institute, the
Brain Science Institute at Johns Hopkins School of Medicine and the
Goldhirsh Foundation and by a Career Award for Medical Scientists from
the Burroughs Wellcome Foundation.

This is just an interesting article I got in my email.  I admit I only skimmed it.  What I wonder is if this means they'll be able to test people to see if they're at risk for diseases like cancer.  If this is the case, I wonder, would you want to know?  Some things are treatable and even curable.  Some things are not.

Also, is this another step closer to using gene therapy to prevent diseases.  That would be a good use of gene therapy I think.   

[Oniya]

They already have genetic testing for certain forms of cancer - I found references to breast cancer, ovarian cancer, some types of gastrointestinal cancer, lung cancer, prostate, and colon cancer.  However, just because one is predisposed doesn't mean that one is doomed to develop cancer, and just because one isn't predisposed doesn't mean that lifestyle choices (smoking, drinking, fatty foods) won't affect one's chances of developing cancer.

[outsidethelines]

I thought it's been known for a little while now that DNA contributes to people's uniqueness? I learned at least a couple years ago that DNA contributed to physical attributes, temperament characteristics, and predispositions to other tendencies and medical issues.
It looks like they just got a bit scientific and learned more about the process, but the big picture here doesn't seem to be anything new.

Oniya is completely right in everything she said. I think the sort of gene therapy you're suggesting is a long way off-- altering genes/chromosomes and messing up in just the tiniest can have very severe consequences.

[DarklingAlice]

We have known about transposons for quite a while. The significance of the article is the development of the microarray chip and new options for analyzing the 'transposome' as it were.

As far as utility...well, Oniya certainly has a point. Beyond that, even the so called single allele disease is coming to be considered largely an object of myth. What we considered the promise of genomics and high-throughput gene analysis to be has largely been proven false over the years, and now most scientists pin their hopes on the headache inducingly more complex field of proteomics. Rather than giving us simple answers (as the media swore up and down it would do), the real legacy of the grandiose genome projects is to open up more questions, more avenues of research, and more techniques.

Which is not to say that gene therapy is not useful for relatively simple diseases like Cystic Fibrosis, thalassemias, and potentially a number of the poly-uridine repeat disorders. But even in those cases we must be careful as these diseases prove to be far more complex than the single gene disorders they at first appeared to be.

I know I have an article sitting around here somewhere on this topic...will see if I can upload it when Mrs. A and I get back from the gym.

EDIT:
Fortunately it was available free through NCBI already!
Human disease classification in the postgenomic era: A complex systems approach to human pathobiology

Examples of modular network representations of disease. Key: G, primary disease genome or proteome; D, secondary disease genome or proteome; E, environmental determinants; I, intermediate phenotype; P, pathophenotype.