• Thu, Nov 23 2006

Breaking News: The Genome is Complex

Or It’s Not Just Single Nucleotide Polymorphisms, Stupid

As I was telling Bryan Appleyard this morning over at Thought Experiments, anybody who knows anything about genetics knows that it’s a subject so complex that it’s almost impossible to decipher. That doesn’t mean we won’t be able to understand the genome and all the systems that interact with it, but it does mean that progress is a lot slower than people would like. And sometimes the impatience turns into hype.

Adding to the complexity, scientists have recently discovered that variations between individual humans as well as between the human species and other animals may be greater than previously believed; instead of being 99.9% genetically identical to your neighbor with the crazy hat, the figure may be closer to 99.5% (of course the figures vary depending on the formula you use further increasing the complexity). These revelations come from a new understanding of differences in copy number variants (CNVs), “large segments of DNA that either have an extra or missing part, as opposed to a single pair [of genes].”

Stephen Scherer, senior scientist at the Toronto Hospital for Sick Children, in The Toronto Star:

We were shocked at the number of these things that we found. We knew they existed, but we never predicted this many of them.

He was “shocked,” people!! But maybe it’s the media shock effect at play here.

From the Copy Number Variation (CNV) Project:

We do not know what proportion of genetic disease is caused by copy number variation (CNV), but we suspect that it is appreciable. We already know that many genetic diseases that occur in families result from these kinds of mutation, we also know that there are Copy Number Variants that protect against HIV infection and malaria. The contribution of CNV to the common, complex diseases (e.g. diabetes, heart disease) is presently unknown.

Evidence already exists that changes to the genome occur on all scales. For instance, we know that missing or additional chromosomes cause disease, e.g., trisomy 21. Other diseases, like leukemia, can be caused by chromosome translocation, where whole segments of chromosomes break off and attach itself to another chromosome in the wrong place.

So although I’ve been accused many times of oversimplifying genetics, this is one instance where I am innocent. The genome is already interesting and complex enough without the need to overdramatize it.

From The Independent:

Why does this matter?

One practical benefit is that it could lead to a new understanding of some of the most difficult, incurable diseases. Although it adds an extra layer of complexity to our understanding of the human genome, the discovery could lead eventually to new insights and medical treatments of conditions ranging from childhood disorders to senile dementia. Scientists are predicting for instance that the knowledge could lead to new diagnostic tests for such diseases as cancer.

Researchers working on the Copy Number Variation (CNV) Project have laid out their investigative questions:

  • How much copy number variation (CNV) exists between human genomes?
  • How best can CNVs be incorporated into whole genome association studies?
  • What is the contribution of copy number variation to genetic disease?
  • What is the relative contribution of different mutational mechanisms to CNV?
  • What is the genomic impact of CNV on gene expression?
  • What role has copy number variation played in recent human evolution?

Now THAT’S complex.

NB: This week’s Nature podcast has more about CNV’s.

news@nature.com, November 22, 2006

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