4th April 2005

Deletion, Duplication and Detail

Uncovering Variation in the Human Genomes

Exon copy-number changes in medically relevant disease genes. Representative results of exon array CGH for patient DNA samples. The grey arrows highlight the copy-number changes. A, Female Pelizaeus-Merzbacher disease carrier showing a triplication of the entire PLP1 gene. B, Male patient (EA12) with Duchenne Muscular Dystrophy (DMD) showing the deletion of exon 51 of the DMD gene, which is only 388 base-pairs in size.

Exon copy-number changes in medically relevant disease genes. Representative results of exon array CGH for patient DNA samples. The grey arrows highlight the copy-number changes. A, Female Pelizaeus-Merzbacher disease carrier showing a triplication of the entire PLP1 gene. B, Male patient (EA12) with Duchenne Muscular Dystrophy (DMD) showing the deletion of exon 51 of the DMD gene, which is only 388 base-pairs in size.

Hidden behind the phrase 'The Book of Life' to describe the human genome is the essential fact that there is not one human genome, but billions of human genomes. Much variation arises from single differences in genetic letters, scattered through our DNA. However, an unknown amount of variation results from the loss or the duplication of DNA regions. Removal or duplication of a gene or part of a gene can be the causative DNA alteration in some individuals with genetic disorders, but we do not know how extensive these changes are found in normal populations and what their true incidence is likely to be in disease or disease susceptibility.

In a major new development, published in the American Journal of Human Genetics on Monday April 4, 2005, researchers from the Wellcome Trust Sanger Institute and colleagues describe a new method called 'Exon Array CGH' (comparative genome hybridization) to detect loss or gain of DNA regions across the genome using a DNA 'chip' or array method.

The resolution of the method is 100-fold higher than existing array-based techniques, meaning that variation in regions as small as 150 base-pairs - a fraction of a gene - can be detected quantitatively. This has not been possible before: using current technology, deletions or duplications must be more than 15,000 base-pairs.

"In our study with previously defined patient samples, this new technology was 100% accurate and makes possible new diagnostic tools for disease where deletions or duplications of part, or all, of a gene plays an important role," said Dr David Vetrie, Investigator at the Wellcome Trust Sanger Institute. "Our new method will also revolutionize array studies of variation in gene copy number between individuals."

The Sanger Institute uses specially prepared single-stranded DNA elements arrayed on a glass slide as a panel of dots to probe for the presence, absence or change in number of defined regions of the genome. In the current study, the protein-coding parts (called exons) of five genes were arrayed: the genes included the largest in the human genome, dystrophin, involved in Duchenne Muscular Dystrophy (DMD). Deletion or duplication of regions of the 2.4 million base pair DMD gene constitute approximately two-thirds of all known mutations in individuals with this disorder; even the gain or loss of a single exon of 150 bp can be reliably detected using this method.

"The sensitivity of the method amazed us," continued Dr Vetrie. "Array studies are an extremely efficient mechanism to study many genomic regions at one time. What has been lacking to date is a route to increase the resolution to allow us to search with the accuracy we need across the genome. This method solves that problem."

In exon-array CGH, the presence or absence of protein-coding regions in DNA is detected using DNA chips. In the analysis of the patient sample shown, a yellow/green colour indicates two copies of the exon in the human genome, orange indicates one copy of the exon, and red indicates the complete absence of the exon.

In exon-array CGH, the presence or absence of protein-coding regions in DNA is detected using DNA chips. In the analysis of the patient sample shown, a yellow/green colour indicates two copies of the exon in the human genome, orange indicates one copy of the exon, and red indicates the complete absence of the exon.

The research has focussed on protein-coding exons of genes, but can also be used to investigate regions involved in regulating genes and regions that interact with proteins, a key component of gene regulation. The study can also be expanded to provide a resource to scan through the genome looking at each gene, or to focus in on regions of interest to define individual genes implicated in disease.

"With the human genome sequence came opportunities to marvel at how similar we are as well as to uncover the variation between us - variation that can have dramatic implications for human health," said Professor Jim Lupski, Cullen Professor of Molecular and Human Genetics and Professor of Paediatrics, Baylor College of Medicine, Houston. "The robust and sensitive method reported here will play an important role in the route from DNA sequence to disease study."

From development and validation of the system, Dr Vetrie's team is now developing new DNA chips to look at other interesting genes in the human genome which have clinical significance. They are also applying the same principles to identify regulatory regions in the human genome through the ENCODE project and in other studies aimed at understanding the regulatory mechanisms which occur during mammalian blood development.

This new method boosts our ability to screen for genome variation in all inherited diseases as well as in cancers. It will bring a new understanding of an important source of variation that is only superficially understood.


Notes to Editors

Participating Centres

  • Human Genetics and Microarray Facility, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
  • DNA Laboratory, Genetics Centre, Guy's and St. Thomas' NHS Foundation Trust, London Bridge, United Kingdom
  • Center for Human Genetics, U.Z. Gasthuisberg, Herestraat 49, Leuven, Belgium
  • Department of Genetics and Pathology, Rudbeck Laboratory, Dag Hammarskjölds väg 20, Uppsala University, Uppsala, Sweden
  • Clinical and Molecular Genetics, Institute of Child Health, London, United Kingdom

Publication details

  • Exon array CGH: detection of copy-number changes at the resolution of individual exons in the human genome.

    Dhami P, Coffey AJ, Abbs S, Vermeesch JR, Dumanski JP, Woodward KJ, Andrews RM, Langford C and Vetrie D

    American journal of human genetics 2005;76;5;750-62

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The Wellcome Trust Sanger Institute, which receives the majority of its funding from the Wellcome Trust, was founded in 1992. The Institute is responsible for the completion of the sequence of approximately one-third of the human genome as well as genomes of model organisms and more than 90 pathogen genomes. In October 2006, new funding was awarded by the Wellcome Trust to exploit the wealth of genome data now available to answer important questions about health and disease.

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The Wellcome Trust is the most diverse biomedical research charity in the world, spending about £450 million every year both in the UK and internationally to support and promote research that will improve the health of humans and animals. The Trust was established under the will of Sir Henry Wellcome, and is funded from a private endowment, which is managed with long-term stability and growth in mind.

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