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Chromosome 7 Sequenced—Again
  
By Kate Dalke


Featured Article.

Scientists who study chromosome 7 have plenty to smile about these days. Their favorite chromosome has been completely sequenced by two different groups and may be the best-characterized chromosome in the human genome.

This week, scientists from the International Human Genome Consortium, led by Washington University School of Medicine in St. Louis, announced the complete sequence of chromosome 7.



They sequenced 99.4 percent of this medically important chromosome, which carries the cystic fibrosis gene and genes associated with diseases such as autism and leukemia.

Just three months ago, another group of scientists, led by the University of Toronto, published their sequence of chromosome 7 in Science.

The genome consortium reports that its chromosome sequence is 99.9 percent accurate and represents another milestone in the Human Genome Project’s effort to precisely characterize each of our chromosomes. The finished sequences of chromosomes 14, 20, 21, 22, and Y have already been published.

The consortium identified 1,150 genes and 941 pseudogenes—DNA sequences that look like genes but don’t actually make proteins. The sequence appears in Nature.

A region of chromosome 7 associated with Williams-Beuren syndrome—a developmental disorder—proved particularly difficult to sequence. Duplicated sequences in this region can cause genes to be deleted and result in disease.

The consortium used data in public databases to sequence the chromosome. The Canadian group assembled 85 percent of the sequence using data from Celera Genomics in Rockville, Maryland, and 15 percent using sequences in public databases.

The Canadian group’s analysis of the chromosome included medically relevant information about individual patients and 10 years' of unpublished data from the Toronto laboratory. It also included some previously unreleased data from Celera.

In April, the Canadian group launched a Web site where scientists can submit updates and information about patients and chromosome-7 regions associated with disease. The site receives about 1,000 hits a day.

The groups reported different numbers of genes on the chromosome. The Canadian group found about 300 more genes than the consortium’s estimate of 1,150.


Repetitive sequences surrounding the Williams-Beuren syndrome region; colored boxes indicate large duplicated sequences. View larger

The consortium’s number may be lower because some DNA sequences that looked like genes turned out, upon further inspection, to be pseudogenes.

“They didn’t pin down the pseudogenes as well as we did,” says Richard K. Wilson of Washington University, who led the consortium’s study.

Differences between the chromosome sequences should be expected because the DNA came from different individuals.

The gene number is just one of many ways the two papers vary. The groups' interpretations of the sequences also differed because they used different supplemental data in their analysis of chromosome 7, such as the unpublished data from the Toronto lab.

Despite differences, the availability of two finished versions of chromosome 7 is good for researchers. “Further comparisons, combinations, and collations of the data can only benefit the entire community as a whole,” says Stephen W. Scherer of the University of Toronto, who led the Canadian team.

“Don’t think for a moment that because there are differences, somebody is necessarily right or wrong,” says Eric Green of the National Human Genome Research Institute in Bethesda, Maryland, who is a member of the consortium team and has studied chromosome 7 for 14 years.

In the years ahead, Green continues, the current practice of analyzing one chromosome at a time will become obsolete because there are better ways to understand the genetics of disease. Instead of studying the genome chromosome-by-chromosome, researchers will look for disease-causing regions and trends across the entire genome.

“We’re at the end of an era,” says Green. “The boundaries around chromosomes are dissipating.”

—Related Articles—

Genomics Meets Medicine on New Gene Map

Mapping the Williams Syndrome Region in Humans and Mice

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Hillier, L.W. et al. The DNA sequence of human chromosome 7. Nature 424, 157-164 (July 10, 2003). [The Science paper is not cited by the genome consortium.]
 
Scherer, S.W. et al. Human chromosome 7: DNA sequence and biology. Science 300, 767-772 (April 10, 2003).
 

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