Palo Alto Weekly

News - December 14, 2012

Genome project finds variations within ethnic groups

Research could help advance study of genetic diseases

by Sue Dremann

When it comes to a person's chances of getting a disease, one's ethnicity may not be as telling as some people believe, according to new research published by Stanford University School of Medicine scientists and others.

Individuals who are considered part of the same ethnic group can have very diverse ancestries due to migration that, over time, has mixed their genetic material with others', researchers said.

Chinese Americans in San Francisco's Chinatown, for example, theoretically could have a dramatically different rate of a particular disease than Chinese living in Beijing.

The research, which is part of the 1,000 Genomes Project, is redefining how ethnic groups might be identified. The project found several million genetic changes in 1,092 people from 14 populations in Europe, Africa, East Asia and the Americas. The variations could contribute to everything from metabolic rates and thyroid disease to pancreatic cancer. The study is the world's largest and most detailed catalog of human genetic variation. It was published in the journal Nature on Oct. 31, and more than 100 institutions and hundreds of individual scientists co-authored the research.

Ethnicity as it is generally thought of is a cultural designation, the scientists said. But that grouping doesn't necessarily explain causes of disease. Puerto Ricans, for example, have a high incidence of asthma, but Mexicans have a low incidence, according to research by collaborator Dr. Esteban Burchard, professor of biopharmaceutical sciences and medicine at University of California-San Francisco.

"Normally we would think of both these groups as 'Hispanic,' but they are on the extreme ends of the asthma spectrum," he said.

This genetic Noah's Ark is being used to study and potentially cure diseases, according to the U.S. National Institutes of Health. Changes in the structure of DNA can help explain an individual's susceptibility to disease, response to drugs or reaction to environmental factors such as air pollution or stress. Some genetic variations are beneficial: A rare genetic mutation that blocks human immunodeficiency virus (HIV) from infecting white blood cells protects people who carry the gene, scientists said.

The $120 million, five-year study will reveal a wealth of information for understanding human history and its movements, Stephen Sherry of the National Institutes of Health said in a statement.

"I view this project as a Lewis and Clark expedition to the interior of the human genome (the entirety of an organism's hereditary information). We knew the outlines and contours. Now we're trying to document all of the fine details such as the rivers and tributaries," he said.

In examining African Americans residing in the southwest United States, researchers found that they share more genetic variants with a group known as the Yoruba in Ibadan, Nigeria, than they do with the Luhya in Werbuye, Kenya.

Among East Asian populations, Han Chinese from Beijing share a particular genetic variation with Han Chinese in southern China more often than they do to Japanese in Tokyo. But the Japanese population, which lies due east of Beijing, shares the variation with the Beijing Chinese moreso than it does with the more-remote southern China group.

A study of three distinct Hispanic communities revealed the importance of limiting generalizations about cultural ethnic groups: Puerto Ricans living in Puerto Rico genetically have a large proportion of European genetic material, with small but nearly equal proportions of African and Native American material. They also have a small amount of genetic material termed "unassigned."

Colombians living in Medellin, Colombia, have a large proportion of European and a larger proportion nearly 25 percent of Native American genetic ancestry compared to the Puerto Rican group, the researchers found.

Among persons of Mexican ancestry living in Los Angeles, the genetic makeup is almost equally European and American Indian, with only a thin sliver of African ancestry and the largest percentage of "unassigned" genetic ancestry of any of the three populations.

Within continents, there can also be significant differences in the range of genetic variation. Europeans in general have the least amount of novel variations, while the African continent has the most, the researchers found. Among Europe's Iberian Spanish and Finnish populations, though, there are large numbers of rare genetic variations, perhaps because the populations haven't mixed with outside ethnic groups or because there has been breeding within a clan, researchers said.

Carlos Bustamante, a professor of genetics at Stanford and a principal investigator of the study, said the genome project is important because some ethnic groups' genetics have not been well-researched, and medically underserved populations could be helped by the information.

Bustamante led a working group that developed computer algorithms to study admixing, in which two or more formerly separate populations begin to mix. The results allowed researchers to deconstruct an individual's ancestry based on recent genetic additions.

Each human being carries a handful of rare variations that could contribute to disease, and each person has a few hundred more rare variants that are likely to have a detrimental effect on how genes work, said Gilean McVean, professor of statistical genetics at the University of Oxford in England, and a co-leader of the project's analysis group.

But that doesn't mean an individual will come down with a disease.

"It's fortunate that most of us usually carry only one copy of these variants, since two copies might lead to disease," he said.

The final phase of the study, which began in 2007, will involve more than 2,500 people from 26 populations. Ultimately, the researchers hope to identify and compile variations in human genes occurring in at least one in 50 people.

Staff Writer Sue Dremann can be emailed at sdremann@paweekly.com.

Comments

Posted by Bob, a resident of Another Palo Alto neighborhood
on Dec 8, 2012 at 10:01 am

This is an incredibly interesting project—but it's not clear how the research will necessarily be linked to "disease", given that there are thousands of "diseases", and hundreds, perhaps thousands, of genetic differences in all of the "ethnic" groups found on the planet.

Moreover, this work will generate so much data that no living human being will be able to assimilate very much of the results of this research. There is so much computation needed that these folks ought to get themselves a couple super computers to help reduce the time to do the data reductions, and statistical inference work that is needed to make meaningful predictions.

Well .. best of luck to them .. this is a really difficult area of endeavor.


Posted by Lohengrin, a resident of Community Center
on Dec 9, 2012 at 1:34 pm

Even WASPs can have mixed ethnicity and not know it. After I had double pneumonia several years ago, I had an irregular heartbeat as an after-effect for a while, as well as an unusually high cholesterol level for a vegan. Some genetic blood tests were done by a local cardiologist and a lab named Berkeley Heartlab, I found I had markers in my blood for genetic diseases found in nationalities I did not know I was a part of!! The reason for my high cholesterol in spite of my lack of animals in my diet, was a Celtic genetic marker found in my blood that causes my liver to produce more cholesterol than I need. I never even knew I had Scottish, Irish, or Welsh blood in my lines! I grew up,thinking I was German and Swedish all this time.


Posted by Lohengrin, a resident of Community Center
on Dec 9, 2012 at 1:39 pm

The importance of knowing this occurred to me when I realized I might have passed this defect on to my son, who was unaware of Celtic roots. He had his doctor refer him to Berkeley Heartlab where tests revealed that he, too had the marker for high cholesterol. As a result, he was put on medication for this in his twenties.


Posted by maguro_01, a resident of Mountain View
on Dec 10, 2012 at 12:02 pm

AFAIK, "Hispanic" is a US invention, a social construct, lumping together a lot of people who speak close spins on Spanish and usually have brown eyes.

A friend who worked in social services for the city of Chicago once told me that Chicago started out with Mexican neighborhoods, Salvadoran neighborhoods, Columbian neighborhoods, and so on. The people did not particularly identify with one another. Then after Hispanics were invented they found themselves given a common identity and interests. So naturally such social constructs would not coincide with any genetic map.

Native Americans must have been subject to being similarly pushed together in spite of their varied histories and linguistic diversity. One wonders if "unassigned" might reflect the waves of migration from Asia to the Americas over thousands of years (??).

It will be interesting to follow this project and others. Here in California it's well worth the expense given the increasingly diverse population from everywhere. We read that it's not just disease or susceptibility to disease but organ transplants and so on also. Some demographics are apparently underserved.


Posted by MIDTOWN, a resident of Midtown
on Dec 10, 2012 at 4:17 pm

In addition to my grown children from a second marriage, I've been able to reach two from a previous marriage to inform them about my parents' medical histories and mine. They and their children should know about any potential inheritance of disease or susceptibility to disease. Heart problems, diabetes, and other diseases may have a genetic origin that your grandchildren might not suspect. GIVE THEM A BREAK! If you can reach them, let them know.


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