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We're only human? It's more complex than that, says gene study

Wed Nov 22, 1:07 PM ET

PARIS (AFP) - New investigations into the code for life suggest the assumption that humans are genetically almost identical is wide of the mark, and the implications could be resounding.

Current thinking, inspired by the results five years ago from the
Human Genome Project, is that the six billion humans alive today are 99.9 percent similar when it comes to genetic content and identity.

But major research work, published on Thursday, suggests we are genetically more diverse -- and the repercussions could be far-reaching for medical diagnosis, new drugs and the tale of human evolution itself.

Until now, analysis of the genome has focussed overwhelmingly on comparing flaws, or polymorphisms, in single "letters" in the chemical code for making and sustaining human life.

An international consortium of scientists has taken a different tack and believe they have uncovered a complex, higher-order variation in the code.

This better explains why some individuals are vulnerable to certain diseases and respond well to specific drugs, while counterparts swiftly fall sick or never respond to treatment, the authors believe.

Their focus has been to dig out deletions or duplications of code among relatively long sequences of individual DNA and then compare these so-called copy number variations (CNVs) across a range of volunteers of different ancestry.

The researchers were astonished to locate 1,447 CNVs in nearly 2,900 genes, or around one eighth of the human genetic code.

"Each one of us has a unique pattern of gains and losses of complete sections of DNA," said Matthew Hurles of Britain's Wellcome Trust Sanger Institute, one of the project's partners.

"One of the real surprises of these results was just how much of our DNA varies in copy number. We estimate this to be at least 12 percent of the genome."

"The copy number variation that researchers had seen before was simply the tip of the iceberg, while the bulk lay submerged, undetected. We now appreciate the immense contribution of this phenomenon to genetic differences between individuals."

Some of the missing or duplicated stretches are very long, suggesting that, like backroom switches in a protein factory, CNVs must have a big impact on gene expression.

Nearly 16 percent of genes that are known to be related to disease have CNVs, the group found.

These include genes involved in rare genetic disorders such as DiGeorge, Williams-Beuren and Prader-Willi syndromes and those linked with schizophrenia, cataracts, spinal muscular atrophy and atherosclerosis.

But kidney disease, Parkinson's, Alzheimer's and vulnerability to malaria and the human immunodeficiency virus (
HIV), which recent research has blamed on single-letter variations in the gene code, may also well be rooted in CNVs, the doctors believe.

"The stage is set for global studies to explore anew... the clinical significance of human variation," said Huntington Willard and Kevin Shianna of the Institute for Genome and Science Policy at Duke University in North Carolina, in a review of the research.

Evolution is another area that will come under new scrutiny.

The "Out of Africa" scenario, by which Homo sapiens emerged from east Africa and spread around the globe, will not be challenged, though.

Our origins are so recent that the vast majority of CNVs, around 89 percent, was found to be shared among the 269 people who volunteered blood as samples for the study.

These individuals included Japanese from Tokyo, Han Chinese from Beijing, Yoruba from Nigeria and Americans of Northern and Western European ancestry.

All the same, there are widespread differences in CNVs according to the three geographical origins of the samples.

This implies that, over the last 200,000 years or so, subtle variants have arisen in the genome to allow different populations of humans adapt to their different environments, Wellcome Trust Sanger said in a press release.

The research, which appears in the British journal Nature, is based on two technical breakthroughs, one in faster, accurate sequencing of DNA and the other in a powerful software programme to spot the CNVs.


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Dopuna: 24 Nov 2006 12:18

Humans show big DNA differences



Scientists have shown that our genetic code varies between individuals far more than was previously thought.

A UK-led team made a detailed analysis of the DNA found in 270 people and identified vast stretches in their codes to be duplicated or even missing.

A great many of these variations are in areas of the genome that would not damage our health, Matthew Hurles and colleagues told the journal Nature.

But others are - and can be shown to play a role in a number of disorders.

To date, the investigation of the human genome has tended to focus on very small changes in DNA that can have deleterious effects - at the scale of just one or a few bases, or "letters", in the biochemical code that programs cellular activity.

And for many years, scientists have also been able to look through microscopes to see very large-scale abnormalities that arise when whole DNA bundles, or chromosomes, are truncated or duplicated.

But it is only recently that researchers have developed the molecular "tools" to focus on medium-scale variations of the code - at the scale of thousands of DNA letters.

Big factor

This analysis of so-called copy number variation (CNV) has now revealed some startling results.

It would seem the assumption that the DNA of any two humans is 99.9% similar in content and identity no longer holds.

The researchers were astonished to locate 1,447 CNVs in nearly 2,900 genes, the starting "templates" written in the code that are used by cells to make the proteins which drive our bodies.

This is a huge, hitherto unrecognised, level of variation between one individual and the next.

"Each one of us has a unique pattern of gains and losses of complete sections of DNA," said Matthew Hurles, of the UK's Wellcome Trust Sanger Institute.

"One of the real surprises of these results was just how much of our DNA varies in copy number. We estimate this to be at least 12% of the genome.

"The copy number variation that researchers had seen before was simply the tip of the iceberg, while the bulk lay submerged, undetected. We now appreciate the immense contribution of this phenomenon to genetic differences between individuals."

Evolving story

The new understanding will change the way in which scientists search for genes involved in disease.

"Many examples of diseases resulting from changes in copy number are emerging," commented Charles Lee, one of the project's leaders from Brigham and Women's Hospital and Harvard Medical School in Boston, US.

"A recent review lists 17 conditions of the nervous system alone - including Parkinson's disease and Alzheimer's disease - that can result from such copy number changes."

Scientists are not sure why the copy variations emerge, but it probably has something to do with the shuffling of genetic material that occurs in the production of eggs and sperm; the process is prone to errors.

As well as aiding the investigation of disease and the development of new drugs, the research will also inform the study of human evolution, which probes genetic variation in modern populations for what it can say about their relationship to ancestral peoples.

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