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Genome Code Cracked for Breast and Colon Cancers

ed on the APC gene and others identified by the Hopkins group.

'Cancer scientists recognize that merely identifying pieces of DNA that have a role in the disease is a beginning, not an end to our work,' says Bert Vogelstein, M.D., an investigator at the Howard Hughes Medical Institute and co-director of the Ludwig Center at Johns Hopkins, 'but by using a more systematic method to identify genes that play an essential role in cancer, we will be able to guide that work.'

The Hopkins team began their project with 11 samples each from breast and colon cancers, removed from patients after surgery. Within each tumor cell, billions of individual chemicals called nucleotides pair together in a preprogrammed fashion to build the rungs of a DNA ladder that compose genetic instructions. Changes called mutations in the nucleotides can create coding errors that transform a normal cell into a cancerous one.

To locate the altered nucleotides, the scientists compared the genetic code of their tumor samples with normal ones. First, they used the Human Genome Project (HGP) to identify the sequences of best-known genes – more than 13,000 in all – roughly two-thirds of the total number of genes identified by the HGP. The actual number of human genes is still in dispute, but is estimated to be about 20,000.

Then, in each tumor, the scientists examined the DNA code of these 13,000 genes by dividing each gene into overlapping sections – about 10 per gene – to get 130,000 sections for analysis. Each segment was amplified through a process called polymerase chain reaction, purified, and its sequence determined using more than three million biochemical reactions. The sequences were fed through computer software that matches up normal sequences with those from tumor samples. The software highlighted more than 800,000 suspicious regions that were visually inspected, one by one, to verify that they were true mutations that altered protein code rath
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