September 2010- A Johns Hopkins-led collaboration that analyzed the key genetic culprit in a common, complex developmental defect revealed not only its specific molecular basis, but also showed how both rare and common mutations in both coding and non-coding sections of a gene can contribute to disease in unique and specific ways, leading to recognizable gene-trait associations.
The study, published July 1, 2010, in the American Journal of Human Genetics, focused on RET, the major gene in Hirschsprung disease, a disorder of the colon caused when nerve cells that move food through the intestines are absent. The team found the molecular basis of mutations in both the coding and the non-coding portion of the genome, specifically, both in the protein-encoded part and at a binding site for a transcription factor that regulates the RET gene.
“We found there are two classes of mutations in the same gene,” says Aravinda Chakravarti, Ph.D., professor of medicine, pediatrics and molecular biology and genetics at the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins. “One is qualitative and makes a mutant protein, and the other is quantitative that changes the amount of protein made. Ultimately the result is the same: not enough wild-type (normal) protein.”
The complexity of the inheritance of diseases usually is attributed to the numbers of genes involved. However, this study shows the importance of discerning which specific variants a patient has in the constituent genes.
Consequently, success in variant identification in complex disorders will strongly depend on which patients are studied, according to the authors.
“Our conclusions have significant implications for disease gene vs. disease variant/mutation discovery,” Chakravarti explains. “The patients we choose to study can uncover either rare or common variants and may be one major reason for recent debates on the frequency of mutant alleles and their genetic effects, and the success or failure of replication of genetic findings.”
Almost two decades of research into Hirschsprung has yielded a key genetic insight, he adds: “The genes responsible for diseases have a whole variety of mutations in them, and these different mutations have different effects that accumulate in different kinds of patients.”
Some cases of Hirschsprung disease occur in a familial way and others in an isolated way. No matter how the scientists segregated the disease — whether they looked at severe versions in females or less severe versions in males — all had mutations in the RET gene. However, different proportions of coding vs. non-coding mutations seemed to associate with severity of disease.
The scientists used DNA sequencing technology to distinguish disease-causing mutations from neutral variation and found that the non-coding enhancer variant was more frequent in the less severe common forms of the disease, while multiple, rare coding mutations were the norm in the less common and more severe forms in which longer segments of the colon were affected. Both rare and common mutations, individually and together, made contributions to the risk of Hirschsprung disease, according to the study.
“Frequency is often a silly argument: a non-issue that may explain little,” Chakravarti says. “What we should look for is the nature of the mutations. And depending on which patients we see, we may find either coding mutations or non-coding mutations.”
--by Maryalice Yakutchik