Genome mapping
July 22, 2011
In a new study published Thursday in the journal Nature, a joint team of British and American scientists have published a complete genetic map of African-Americans.
The joint team from Oxford University in the United Kingdom and Harvard University in the United States analyzed genetic samples from about 30,000 individuals, gathered from five large health studies carried out by African-American cancer consortiums, among others.
By studying such a vast sample, the research showed that genetic mixing takes place slightly differently than people who are only of European ancestry. Scientists say that by better understanding this variability in a gene called PRDM9, that they may eventually be able to unlock a more fundamental understanding of the evolution of disease in all humans.
Mutation and recombination
Genetic diversity happens in two ways: mutation and recombination. These two processes are what make us each unique individuals, explained Simon Myers, one of the lead researchers in the mapping effort, at Oxford University in the United Kingdom.
Recombination, the biological process in which a new chromosome is stitched together from maternal and paternal DNA, "generates features for natural selection to try out," the lecturer in bioinformatics told Deutsche Welle.
In addition to adding to evolutionary understanding, the results "should motivate a search" for addressing profound congenital, or from-birth, diseases.
Analyzing thousands of African-American DNA samples from five major health studies, the mapping results have implications especially for people with West African ancestry. Until now, most such mapping efforts have focused on DNA from people of European descent.
Out of Africa
The prevailing theory on human evolution is that Homo sapiens evolved in Africa, and that at some point in the distant past, a group of perhaps a few thousand people emigrated off the continent, colonizing Asia, Europe, and ultimately the rest of the world.
Most Europeans, for example, are descended from this relatively small group, and therefore reflect a rather uniform genetic makeup.
European DNA therefore "represents only a subset of genetic diversity," Myers said. The biggest repository of genetic diversity remained on the ark of the initial continent, Africa.
When European and American slave traders landed on the shores of Africa, stealing away people for forced labor in far-away lands, this resulted in a new genetic diversity among the descendents of slaves, many of which also have European blood.
The fact of this genetic mixing, which occurred in a clear time window of about 200 years, set up the unique conditions that the geneticists used in their work.
According to Rolf Horstmann, who teaches molecular medicine at the Bernhard Nocht Institute for Tropical Medicine in Hamburg, the research highlights the genetic differences between African and European populations.
"This helps to further explain why (people of African descent) have more genetic diversity," he told Deutsche Welle. "We can see that genetic diversity is maintained over generations."
Horstmann, who was not part of the research study, added the findings could have implications in the study of hereditary diseases.
Recombination hotspots
The researchers focused their work on pinpointing the specific locations that genetic recombination occurs.
Recombination, or the biological process in which chromosomes are stitched together, only occurs at specific locations on the genome.
"This stitching is not random, but rather, intensely clustered," Myers explained. Where the stitching switches between maternal and paternal DNA, or recombination crossover, occurs at tens of thousands of "hotspots" all over the genome.
"The presence of a specific 'word,' or sequences of DNA bases, makes a hotspot more likely," Myers continued.
The team knew from previous work about this "word," but wondered just how it worked. The team's research found that a protein called PRDM9 scans across the genome for such words.
Once the protein "reads" this word, it "grabs physically hold of DNA and brings in recombinational machinery – that's where the crossover happens," Myers explained.
African-Americans, who average about 80 percent African origin, typically have all the same hotspots as Europeans – but they also have more. These extra hotspots are marked by a different genetic "word." About a third of recombination in African Americans occurs through this newly decoded word.
African-Americans essentially have a "more diverse set of hotspots than Europeans," Myers said.
Since the slave trade was focused on western sub-Saharan Africa, laregly among Bantu-language-speaking people, the findings probably hold true for people currently living in – or among people with ancestry from – those regions.
Beyond evolutionary understanding, the new genetic map holds further potential.
Mapping disease
Genetic maps, besides being general resources, can also be used to chart the origins of congenital disease.
"These hotspots are also where recombination goes wrong – they're the places where disease happens, the 'risky' part of genome," Myers added.
He noted that the next steps in this research include surveying for variation in this gene and finding more hotspots, along with understanding better how the PRDM9 protein works.
A completely independent study by researchers at the University of California in Los Angeles also developed a highly accurate genetic map of African Americans, though the team had a somewhat different focus and smaller sample.
Genetic disorders are rare, but diverse, and can be quite profound, Myers explained. They include, for example, some forms of anemia.
"Europeans have been well studied," Myers clarified. "This could help people of West African descent more than other maps have in the past," he added.
Author: Sonya Angelica Diehn and Gerhard Schneibel
Editor: Cyrus Farivar