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.
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.
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.