Viruses in the Genome

Carl Zimmer has an excellent post on viruses in the human genome.  Here is the juicy snip:

The human genome carries full-fledged retroviruses, as well as
viruses in various state of decay. Scientists have identified 98,000 of
these viruses, along with about 150,000 fragments of defunct viruses.
All told, they make up 8 percent of the human genome. In many cases,
the virus genes have disappeared altogether, leaving behind flanking
repeats, which have been duplicated to millions of copies that take up
about 40 percent of the genome. As a point of comparison, our "own"
genes–in other words, those that encode proteins that make up our
bodies and allow our bodies live–make up only about one percent of the
genome.

Some of these endogenous retroviruses are only found in some people
and not others. They must have invaded someone’s genome and then spread
to his or her descendants, but have not yet spread throug our entire
species. Others appear to be ubiquitous–meaning that they are ancient
passengers that had already spread throughout an ancestral population.

Read the whole piece.

Carl Zimmer, The Sixty-Million Year Virus. The Loom, March 13, 2006.

Norbert Bannert, and Reinhard Kurth. Retroelements and the human genome: new perspectives on an old relation. PNAS. October 5, 2004. vol. 101 (Suppl. 2) 14572-14579. [A nice open-access review article on human endogenous retroviruses (HERVS)]

Critics Circle: Genographic Project

First crop of critics of the Genographic Project have emerged.  Here is an overview:

  1. involving the public may not be useful, involving the public is expensive, the volume of respondents may be surprisingly high (Andrew Paterson, a scientist at the genetics and genomic biology group at the Sick Kids Research Institute)
  2. control over sample collection is weak, self-reporting is often inaccurate, look-out for contamination of samples (Steven Scherer, senior scientist at the genetics and genomic biology group at the Sick Kids Research Institute)
  3. should have gone the extra mile and made a biobank of the DNA samples (Kenneth K. Kidd, professor of genetics and psychiatry at Yale Med)
  4. should have used DNA Genotek’s Oragene kit rather than buccal swabs (company CEO Ian Curry)

Sarah Lysecki. "National Geographic’s DNA database raises doubts" itbusiness.ca, 4/18/2005.


Update 4/21/05

The Indigenous Peoples Council on Biocolonialism objects to the Genographic Project and Spencer Wells responds.

Genographic Video

Genographic_vid_1

See here.

Genomiography: Large-Scale Copy Variations

Groups of scientists working independently have shown very large differences exist in the genomiography (i.e. genomic geography) of healthy individuals. These differences are much more dramatic than the well-known single nucleotide kind of variation, SNPs. Dr. Stephen Scherer, co-principal investigator, senior scientist at Sick Kids, and associate professor at University of Toronto describes the discovery:

“Using new genome scanning technologies, we serendipitously found stretches of DNA sometimes hundreds of thousands of chemical bases (nucleotides) long that were present or absent in the genomes of healthy individuals. These large-scale copy variations, or LCVs, frequently overlap with genes and could explain why people are different…At first we were astonished and didn’t believe our results because for years we had been taught that most variation in DNA was limited to very small changes. Then we heard the Harvard group was making similar observations and ultimately we combined our data and came to the same conclusion.”


Dr. Charles Lee
, the other co-principal investigator and assistant prof at Harvard Medical School gives his take on the discovery:

“Because these newly discovered variants exist in the genomes of healthy individuals, their presence could lead to subtle differences affecting physical or behavioural traits by influencing the expression of specific genes, but they could also predispose to future disease…For example, the most common LCV involves amylase genes. Our study shows that some people may have 10 copies of this gene while others may have as much as 24 copies of this same gene. It would be really exciting if we found that an increased copy number of these genes was associated with increased susceptibility to pancreatic diseases or cancer. This would allow us to use these LCVs as disease markers.”

The press release at EurekaAlert! puts the discovery into perspective:

Early information from the Human Genome Project indicated that the DNA in the genome of any two individuals is 99.9 per cent identical with the 0.1 per cent variation arising primarily from some three million single nucleotide changes scattered amongst the chromosomes. The new data from the Sick Kids and Harvard groups revealed 255 regions (comprising more than 0.1 per cent) of the genome where large chunks of DNA are present in different copy numbers between individuals. Over 50 per cent of these alterations lead to changes in gene numbers and at least 14 regions overlapped with known sites associated with human disease.

These groups have put their data in publicly available database entitled the Database of Genomic Variants: A curated catalogue of large-scale variation in the human genome.


Primary Sources:

Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science 305, 525-528 (July 23, 2004).

Iafrate, A.J. et al. Detection of large-scale variation in the human genome. Published online in Nature Genetics August 1, 2004.

Press:
Kate Ruder, Large-Scale Differences Discovered in DNA of Healthy People. Genome News Network, August 6, 2004.

DNA variations surprise researchers
. EurakaAlert! August 1, 2004.

UPDATE: Genomiography promises to be a googlewhackblatt if only for a very short time. I suspect phylogenomiography will be a googlewhackblatt for much longer.