Hopkins is first US institution to obtain powerful genotyping system

August 14, 2003

Ahead of other U.S. academic institutions, The Johns Hopkins University School of Medicine and its McKusick-Nathans Institute of Genetic Medicine have pooled resources to obtain a commercial system capable of processing hundreds of DNA samples and determining up to 600,000 genotypes a day.

The $1.5 million system, purchased from Illumina Inc. (San Diego, Calif.), has been installed and tested and should be fully operational by September. Part of the shared genetics resources at Johns Hopkins, the system will use both premade panels of known genetic sequences and research-specific panels of genes, designed in-house, to identify genetic changes in DNA samples.

"In addition to offering a lower cost to researchers, our flexibility should set us apart from what is available from companies," says Alan Scott, Ph.D., director of Johns Hopkins' Genetics Resources Core Facility and one of the forces behind getting the new genotyping system. "Quite a few research programs here require genotyping hundreds to thousands of tissue samples, and other researchers may have been reluctant to take on such tasks because the work couldn't be done nearby. Now we'll be able to offer these services right here at Hopkins."

The new system, called "BeadLab" because of the technology it uses, can examine up to 96 different samples and determine more than 100,000 genotypes in a single experiment. A genotype is a description of an individual's sequence of genetic building blocks (A, G, T and C) and can be compared to others' to help scientists identify genes involved in disease.

Most of the human genome's 3 billion building blocks occur in the same order in all humans. But everyone also has occasional substitution of one genetic building block for another. If a particular spot has a common variation (i.e., some people have an "A" instead of the usual "C"), that position is said to have a single nucleotide polymorphism, or SNP (pronounced "snip"). Several million SNPs already are known.

Geneticists have successfully correlated SNPs or other mutations with the incidence of some rare diseases such as cystic fibrosis. But determining genetic contributors to and causes of such common diseases as cancer has been a difficult, piecemeal process because these conditions involve multiple genetic changes that combine to affect health or disease.

"This genotyping technology lets you rapidly survey what amounts to the entire human genome for regions linked to a condition, and then, separately, to delve into the fine detail of very small regions of DNA to figure out what's really happening," says Scott.

With the appropriate controls and experimental set-up by trained technicians, the system determines the genotypes of all the samples and produces a score that rates the accuracy of the result.

"These genotypes can then be correlated with patient characteristics, health, tissue type or whatever it is you're studying," says Aravinda Chakravarti, Ph.D., director of the McKusick-Nathans Institute. "Instead of spending years just to get genotype information across the genome, now we can spend our time analyzing the data, looking for multiple genes rather than finding them one at a time. With this system we're well on our way to being able to do large-scale studies of complex human genetic diseases and to investigating the biological basis of individuals' susceptibility to disease."

The Illumina system's BeadArray technology uses dimpled fiberoptic strands in bundles no thicker than a pencil lead, each holding tens of thousands of tiny beads. Each bead is labeled with one of up to 1,300 DNA tags to unmask the version of a specific SNP in the sample. The fiberoptic bundles are then arrayed as in a 96-well plate.

The new facility will be housed at the Johns Hopkins Bayview campus near the Center for Inherited Disease Research, a Johns Hopkins operation funded by a federal contract. As more researchers begin to need and use the technology, Scott hopes the system is used to determine roughly 200,000 genotypes per day.

Scott notes that the high-throughput genotyping system complements other services offered by the Genetics Resources Core Facility, including the DNA Fragment Analysis Lab and the DNA Analysis Facility. Both can determine research-specific genetic sequences that can't otherwise be studied.
On the Web:

The Genetics Resources Core Facility

Illumina, Inc.

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