Scientists consider themselves lucky when an inherited disease is due to a single gene, like Huntington disease, for example. But most inherited diseases arise from a number of genetic changes that add up to trouble, making it difficult for geneticists to find everything that's to blame.

Now, for what is believed to be the first time, scientists have unraveled the complicated genetics of an inherited intestinal disease, opening the door to revealing complete genetic pictures of other complex diseases. Their results provide stirring reminders that it's important to consider all parts of a gene, not just those that carry instructions for a protein, when looking for contributors to disease.

In the April 15 advance online edition of Nature Genetics, the scientists report that three regions--parts of chromosomes 3, 10 and 19--are crucial for causing Hirsch-sprung disease and together explain its complicated inheritance pattern. Looking for changes within those regions, the scientists discovered that more often than not the protein-encoding parts were unchanged.

"Just because coding sequences aren't changed doesn't mean a gene isn't involved," says Aravinda Chakravarti, director of the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins and whose laboratory (while at Case Western Reserve University in Cleveland) led the U.S. effort. "Many diseases likely have genetics similar to Hirschsprung disease, and we've shown that such complex genetic contributors can be discovered with a carefully designed study."

Hirschsprung disease, in which nerves that normally control the bowel are missing, occurs in about one in 5,000 births. Because the way the disease pops up in family trees is complex, researchers collected and analyzed samples from parents and children in 49 families, each with at least two affected siblings.

The scientists found that three crucial regions explain the inheritance of the "short-segment" form of Hirschsprung disease, which is both more common and more genetically complex than the "long-segment" form, even though it has less affected intestine. They expect the three regions to correspond to three genes, although only one has been identified so far.

The key to their success, the researchers say, is combining a large amount of reliable clinical data with a thorough investigation of the genetics. The study first mapped the disease to regions of chromosomes, then identified changes within those regions. Because the scientists frequently found no changes in protein-encoding parts of the chromosome 10 region, the results underscore the importance of what often is ignored: The part of a gene that carries instructions for making a protein (the coding sequence) isn't the only part that can contribute to disease.

"Mapping gives you an independent way of saying that this gene is involved in a disease, even if there are no changes in the coding sequence," Chakravarti says. "This disease and many others are complex not just because they involve more than one gene but because the molecular mechanisms behind the genes' involvement are--quote--unusual."

While changes in the coding regions can alter the structure and function of the resulting protein, changes in "noncoding" sequences can affect sites for regulation, carry instructions for alternative ways to read the gene or can otherwise alter gene function and expression, Chakravarti says.

Computers scanned and analyzed the better part of each participant's genome to find changes that might explain how short-segment Hirschsprung is passed from generation to generation. In particular, the scientists looked for "overshared" genetic regions in siblings with the disease, reasoning that these regions would be present more often than one would expect by chance alone.

Of the many genetic differences found, additional computer analysis revealed that the changes within particular regions of chromosomes 3, 10 and 19 explain both familial and nonfamilial cases of short-segment Hirschsprung disease, the scientists say.

With more experiments, they proved that the region on chromosome 10 is a gene called RET, which already was implicated in long-segment Hirschsprung disease. The researchers expect to find a single gene in each of the other two regions but can't rule out the possibility of additional genes, they say.

"There are many complex inherited diseases out there," Chakravarti says. "With carefully designed studies that include both mapping and looking for particular genetic changes, we've shown it's possible to dissect the genetics of a complex disease."

Funding for the study was provided by the U.S. National Institutes of Health, Johns Hopkins University School of Medicine, Case Western Reserve University, University Hospitals of Cleveland, Association Francaise contre les Myopathies, INSERM and the Fondation pour la Recherche Medicale.