January 9, 2012

$9.5 mill federal grant to support ‘asthma genome’ project

Search is on for genetic roots of diseases that afflict blacks disproportionately

A Johns Hopkins–led team of experts in genetics, immunology, epidemiology and allergic disease has embarked on a four-year effort to map the genetic code, or whole genome, of 1,000 people of African descent, including men and women from Baltimore.

Researchers say that their initial goal is to find genetic variations underlying asthma and to explain why the disease disproportionately afflicts blacks. As many as 20 percent of African-Americans have asthma, a disease often associated with allergies and marked by difficulty breathing, wheezing, coughing and tightness in the chest. Chronic asthma can lead to serious lung damage, and blacks are three times more likely than other American adults to be hospitalized or die from the condition.

Study principal investigator and immunogeneticist Kathleen Barnes says that the effort to sequence the genetic code of 500 asthmatics and 500 nonasthmatics “represents an exciting opportunity to disentangle the genetic basis of a host of other diseases, not just asthma, which have a hereditary component and uniquely or disproportionately affect minorities.”

Barnes, a professor in the Division of Allergy and Clinical Immunology in the Johns Hopkins University School of Medicine and in the university’s Bloomberg School of Public Health, and her team say that they will make their findings freely available to other researchers through the dbGAP national database of genomewide association studies, maintained by the National Library of Medicine, a member of the National Institutes of Health. The National Heart, Lung and Blood Institute, also part of the NIH, has provided the Johns Hopkins team with $9.5 million in study funding.

For part of the initiative, the researchers have contracted with Illumina Inc. of San Diego to create a commercially available customized gene chip, or DNA microarray test, dubbed the “African power chip,” to quickly find single mutations in genetic materials from blacks that may be associated with heightened disease risk.

Barnes says that her team’s findings should fill in serious gaps in the hunt for genetic variations posed by Illumina’s existing genotyping chip and a similar gene chip by Affymetrix Inc. of Santa Clara, Calif. Both chips were developed from whole genome sequencing of predominantly white European men and women and do not represent potential variations found mostly or only in minority groups.

“One of our biggest barriers as researchers trying to find the underlying genetic roots of disease in minority groups has been the persistent lack of microarray testing tools relevant to each racial profile, especially African-Americans,” said Barnes, who is director of Johns Hopkins’ Genetics Research Facility and its Lowe Family Genomics Core laboratory.

“Asthma is exacerbated by social factors, such as poverty, and inadequate education and access to medical care,” she said, “so separating out the genetic component is particularly complex but scientifically doable.” Barnes is also the Mary Beryl Patch Turnbull Scholar at Johns Hopkins.

Researchers plan to sequence the genomes of blacks selected from among an international group of people participating in existing genetic studies who have already been clinically diagnosed with asthma, or without, or who have other kinds of compromised lung function, and whose family histories are well-documented. The participants will be selected from 15 academic research centers across the United States, the Caribbean and South America, as well as from four additional research sites in Western Africa.

An estimated 20 million Americans have asthma, the most common chronic condition among American children. Each year, more than 4,000 Americans die from the condition, which also accounts for one-quarter of trips (some 2 million) to hospital emergency rooms for breathing problems.

Related website

Kathleen Barnes