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Genome doesn’t start with ’G’: Study of the largest and last chromosome of the human genome published

The Wellcome Trust Sanger Institute and colleagues in the UK and USA today publish the longest and final chapter in what has been called The Book of Life -- the text and study of our human genetic material. Published in Nature, the report of the sequence of human chromosome 1 is the final chromosome analysis from the Human Genome Project.

The sequence has been used to identify more than 1000 new genes and is expected to help researchers find novel diagnostics and treatments for many diseases. In the past year alone, genes involved in a dozen diseases, including cancer and neurological disease, have been identified using the freely available chromosome 1 sequence and DNA resources.

"The sequence we have generated, like that produced by our collaborators throughout the Human Genome Project, has driven biomedical discovery," said Dr Simon Gregory, Assistant Professor from Duke University, who led the project while at the Sanger Institute. "This moment, the publication of the sequence from the last and largest human chromosome, completes the story of the HGP and marks the growing wave of biological and medical research founded on the human genome sequence.

Human chromosomes are numbered from the largest (chromosome 1) to the smallest (chromosomes 22 and 21). Chromosome 1 represents around 8% of our genome and contains about twice as many genes as the average chromosome. Each chromosome is composed of many millions of genetic letters or bases, called A, C, T and G. The first genetic letter of chromosome 1 sequence, and hence the beginning of our genome, is "C".

But sequence must be mined to be of benefit: for example, differences in the sequence between individuals will help develop an understanding of diseases associated with this chromosome. Almost 4500 single-letter changes in the genetic code (called SNPs) were identified that could lead to changes in protein activity. In addition, 90 SNPs were found that would result in a shortened -- and possibly inactive -- protein. Although some 15 SNPs are associated with already known protection from malaria and predisposition to porphyria, the function of these newly located SNPs is yet to be discovered.

"A catalyst for our gene discoveries", is how Dr Brian Schutte, Associate Professor of Pediatrics at the University of Iowa, describes the sequence of chromosome 1. "We suspected a gene for a rare human orofacial clefting disease lay on chromosome 1, but had not identified it. Our collaboration with the Sanger Institute led to much more rapid discovery of the gene involved, and also helped show that this gene contributes 12% risk for the common form of cleft lip and palate.

"Our experience demonstrates that sequencing efforts accelerate gene discovery of not only rare genetic disorders, but also common diseases that place the greatest burden on our healthcare system."

As well as the fine-grain variation represented by SNPs, the team localized genes to a number of larger ’chunks’ of DNA that differed between individuals. These chunks are as large as 1 million bases. Some of the regions have been previously implicated in how we vary in our interaction with the environment around us. For example, variations in the region around the GSTM1 gene can alter our susceptibility to cancer-causing chemicals or toxins and influence the toxicity or efficacy of certain drugs.

Chromosome 1 is particularly susceptible to rearrangement and it is thought that disruption to genes within these rearrangements play a role in several cancers and in mental retardation: deletion of regions of chromosome 1 is found in 1/5000 to 1/10,000 live births. The high-quality sequence has already helped researchers around the world to home in on genes that affect a range of cancers.

"The Human Genome Project has provided us with a wealth of information about our genes and their many variations," said Dr Mark Walport, Director of the Wellcome Trust. "It is a vital resource for answering important questions about health and disease. We have been a committed partner in the project since 1992 both in supporting the research and ensuring the results are freely accessible to all.

"The completion of the project, with the publication of the Chromosome 1 sequence, is a monumental achievement that will benefit the research community for years to come and is a credit to all involved."

When seeking funding from the Wellcome Trust for their efforts to sequence the human genome in 1995, the Sanger Institute management wrote: "Sequencing is not an end in itself: it is not the solution of the genome, but merely the baseline information that allows the real aim -- the biology -- to proceed faster". The chromosome 1 project stands as a reflection of that view. Genome sequence powers research to help us understand the biology of our genome and the medical consequences of sequence variation.

Don Powell | alfa
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