October 29, 2002
MEDIA CONTACT: Joanna Downer
Hopkins To Be Part of Major International Genetic Mapping Project
Researchers at the McKusick-Nathans Institute for Genetic Medicine at Johns Hopkins have been funded to participate in an international effort to catalogue human genetic variation, a project crucial in the hunt for genes involved in such common diseases as asthma, heart disease and diabetes.
With funds from the National Institutes of Health, the Hopkins scientists will analyze and interpret genetic information to help produce what is known as a "haplotype map," which will document individual sites of genetic variations called single nucleotide polymorphisms, or SNPs.
The "International HapMap" project will flag "chunks" of human DNA that contain multiple specific genetic variations and have been inherited as a unit over the course of human history. The project will document the patterns of variation common to populations in Nigeria, Japan, China and the United States.
"We expect these genetic 'chunks' to hold clues about the subtle genetic influences that result in complex diseases, illnesses in which genes and environment are involved," says Aravinda Chakravarti, Ph.D., director of the McKusick-Nathans Institute. "Since it's clear that more than one gene contributes to these diseases, we need to have a snapshot of multiple genes, their usual sequences and their common variations. The haplotype map will give us that big picture."
The Human Genome Project created a draft of the sequence of human DNA, but the HapMap is needed to fully understand, process and use that information in studying common genetic disorders, Chakravarti added.
Eighteen public and private groups in the United States, Japan, China, Nigeria, the United Kingdom and Canada are part of this effort. Initially, samples from 200 to 400 people in Nigeria, Japan, China and the United States will be included in the project.
"There are two challenges that must be met for a project like this to be successful," says Chakravarti. "First you have to determine the genetic variation in samples from many people. Then you have to analyze and interpret the data to create the map. We are very pleased to be able to take part in this crucial analysis."
DNA is made of just four types of building blocks. For most of the 3 billion "locations" along the genome, the sequence is identical from person to person, but occasionally there's a change (a mutation). These changes can be harmless, or they can lead directly or indirectly to some physical effect, whether a disease or a more benign result, such as a change in hair color.
It is estimated that there's an average of one genetic change per 800 sites in human DNA -- that's millions of individual changes to track. These genetic changes are clustered in some places, but appear throughout the genome and on every chromosome.
Researchers noticed that some fairly large sections of DNA are passed down from generation to generation as a unit, with a specific set of genetic variations within that unit. Because each of these so-called haplotype blocks is inherited as a whole, there are only a few common versions of each one.
Haplotypes essentially allow scientists to group sets of genetic mutations together. By determining which letter of DNA (A, T, G, or C) is present at just a few key locations within a haplotype block, the scientists know the entire sequence. The HapMap will determine common haplotypes and their places in the genome, literally creating a map of human haplotypes.
"Making and using the HapMap is going to dramatically speed the search for genes involved in common diseases, all of which are incredibly complex genetically," says Chakravarti. "This map will be created through collaborative ventures with scientists around the world, and we expect to use the finished product in our own disease research."
Patient populations are expected to have some genetic variations not seen in the samples used to create the HapMap, and hence have different haplotypes than most people. Already, rough haplotype-style information has revealed new genetic regions involved in disease, says Chakravarti.
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