Life scientists use novel technique to produce genetic map for African Americans

July 23, 2011 in Genetics

UCLA life scientists and colleagues have produced one of the first high-resolution genetic maps for African American populations. A genetic map reveals the precise locations across the genome where DNA from a person's father and mother have been stitched together through a biological process called "recombination." This process results in new genetic combinations that are then passed on to the person's children.

The new map will help disease geneticists working to map in African Americans because it provides a more accurate understanding of recombination rates among that population, said the senior author of the research, John Novembre, a UCLA assistant professor of ecology and and of bioinformatics. The map could help scientists learn the roots of these diseases and discover genes that play a key role in them.

The study was published July 20 in the online version of the journal Nature Genetics and will be published in the print edition at a later date.

"Research aimed at finding disease variants will be improved by this tool, which could lead to better medications to help ameliorate the effects of those disease variants," Novembre said. "Health researchers can use a recombination map to refine where a might be."

Prior to this research, which was conducted by scientists from seven institutions, recombination had mainly been studied in European populations.

"Now we have a map for African Americans that researchers can use as a tool, instead of using a European map or an African map," said Novembre, a member of UCLA's Interdepartmental Program in Bioinformatics.

A second, independent study, led by David Reich at Harvard University and Simon Myers at Oxford University, used a similar approach to infer an African American recombination map. That research was published this week in Nature.

"While recombination rates between populations are very similar when you look at the broadest scales of the genome, we start to see variation in recombination between populations when we zoom in," said Daniel Wegmann, a UCLA postdoctoral scholar in Novembre's laboratory and the lead author of the study. "There are clear differences in recombination between Africans and Europeans, and African Americans tend to have a map that is a mixture between the African and European map, reflecting the mixture that took place between these two groups.

"If the position of a mutation is unknown and you want to pinpoint a gene linked to a disease, then recombination is important to help reveal in what region the gene lies," Wegmann said.

The mixture of African and European typical in the DNA of African Americans is reflected in recombination rates, Novembre said.

"No high-resolution recombination map has been inferred before for populations where the individuals have ancestry from different parts of the globe," Novembre said. "African Americans represent a unique combination of African and European ancestry. We found that if you know an African recombination rate for one region of the genome and you know the European rate, the African American rate sits about 80 percent of the way between the two. That is interesting, because the ancestry of African American DNA, on average, is 80 percent from African ancestral sources and 20 percent from European ancestral sources. The recombination rate reflects the ancestry."

The used an innovative method involving population genetic models in which they scanned the individual genomes of 2,565 African Americans, as well as 299 African Caribbeans, to study where in the genome each had African ancestry, where they had European ancestry, and where the "switch points" were that mark the location where the ancestry of a DNA segment changes.

Novembre and colleagues studied the ancestry of DNA segments to reconstruct where recombinations have occurred.

"The key is to uncover the ancestry of each segment of the genome," Novembre said. "Switch points enable us to identify recombination 'hot spots,' where recombination rates are high."

Explaining recombination, Novembre said, "When we pass on DNA to our children, we stitch together the DNA we received from our mother and father. The resulting DNA alternates between DNA from your mother and from your father, and the recombination points are the boundaries. Those points could be chosen uniformly across the whole chromosome, but studies have found that recombinations occur in some locations in the chromosome more than in others. Locations in the chromosome have particular recombination rates — the rate at which break points occur in that location.

"It is difficult to identify, by studying chromosomes directly, where the stitch points are between maternal and paternal DNA," he said. "In individuals of mixed ancestry, however, such as and African Caribbeans, we can identify switch points between African ancestry and European ancestry. These switch points mark locations where recombinations have occurred at some point in the past."

"There are regions of our map that differ from what we would expect," Wegmann said. "We see locations where there are deficiencies in recombination, and they line up with the locations of mutations that rearrange the genome and flip a piece of DNA to invert it. When you have a normal copy of the DNA and an inverted copy of the DNA, one from your mother and one from your father, this inversion suppresses recombination."

Of some 3 billion base pairs in a person's genome, the scientists were able to resolve recombination rates down to 50,000 base pairs of the DNA — an impressive figure.

Comparing this African American recombination map with that of other populations enables researchers to locate recombination hot spots, which have highly elevated rates of recombination.

In addition to the applications for disease mapping, the research provides broad insights into the fundamental of recombination.

"We want to learn how recombination rates vary across the genome," Novembre said.

Provided by University of California - Los Angeles

5 /5 (1 vote)  

Rank 5 /5 (1 vote)
Relevant PhysicsForums posts

More news stories

Researchers identify first drug targets in childhood genetic tumor disorder

Two mutations central to the development of infantile myofibromatosis (IM)—a disorder characterized by multiple tumors involving the skin, bone, and soft tissue—may provide new therapeutic targets, according to researchers ...

Genetics created 12 hours ago | popularity 3 / 5 (2) | comments 0 | with audio podcast

Patenting the human genome

Can human genes be patented? That was the question posed by Alan J. Snyder, vice president and associate provost for research and graduate studies at Lehigh, and Lee Kaplan, scientific director of cellular and molecular genetics ...

Genetics created 19 hours ago | popularity 4 / 5 (1) | comments 0

Researchers complete largest genetic sequencing study of human disease

Researchers from Queen Mary, University of London have led the largest sequencing study of human disease to date, investigating the genetic basis of six autoimmune diseases.

Genetics created May 22, 2013 | popularity 4.5 / 5 (4) | comments 0 | with audio podcast

Researchers develop model for better testing, targeting of malignant peripheral nerve sheath tumors

University of Minnesota Medical School researchers from the Masonic Cancer Center, University of Minnesota, in partnership with the University's Brain Tumor Program, have developed a new mouse model of malignant peripheral ...

Genetics created May 20, 2013 | popularity 5 / 5 (1) | comments 0 | with audio podcast

Researchers identify new circadian clock component

Northwestern University scientists have shown a gene involved in neurodegenerative disease also plays a critical role in the proper function of the circadian clock.

Genetics created May 16, 2013 | popularity 3 / 5 (1) | comments 1 | with audio podcast


Engineered cytomegalovirus protects monkeys from HIV equivalent

(Medical Xpress)—A new study by researchers in the US has shown that an ancient virus can be modified to help in the fight against the simian immunodeficiency virus SIV, which is the equivalent in monkeys ...

Hormone levels may provide key to understanding psychological disorders in women

Women at a particular stage in their monthly menstrual cycle may be more vulnerable to some of the psychological side-effects associated with stressful experiences, according to a study from UCL.

Going live: Immune cell activation in multiple sclerosis

Biological processes are generally based on events at the molecular and cellular level. To understand what happens in the course of infections, diseases or normal bodily functions, scientists would need to ...

Help at hand for people with schizophrenia

How can healthy people who hear voices help schizophrenics? Finding the answer for this is at the centre of research conducted at the University of Bergen.

Alzheimer's disease, the soft target of the euthanasia debate

(Medical Xpress)—The way Alzheimer's disease is portrayed by advocacy groups and the media is having undue influence on the euthanasia debate, according to a Deakin University nursing ethics professor.

Depression raises diabetics' risk of severe low blood sugar episodes

(Medical Xpress)—Patients with diabetes who are depressed are much more likely to develop episodes of dangerously low blood sugars, or hypoglycemia, than are those who are not depressed, a new study has ...