Why Do Children Get Cancer?
Although childhood cancer is rare, it is still the leading cause of death by disease in children age 14 and younger. Sadly, the genetic causes of some of the most devastating childhood cancers remain a mystery.
Innovative new research tools developed by Children’s Discovery Institute investigators Drs. Todd Druley and Robi Mitra will help solve that mystery.
Todd Druley, MD, PhD is a pediatric oncologist at St. Louis Children’s Hospital and Washington University School of Medicine who is determined to understand why cancerous tumors arise in children.
“Whenever I have to tell parents that their child has cancer, I invariably get the same two questions,” said Druley. The first is, ‘Will my child die?’ The second is, ‘How did this happen?’ In 90 percent of the cases, there is no answer for that second question.”
“From a genetics perspective we know that it takes between five to seven mutations in key genes to cause cancer,” said Druley. “We also know the rate at which mutations occur in the cells in our bodies. Given that, it is a near mathematical impossibility for a child to get cancer, and it’s why most adults do not get cancer until very late in life.”
The fact that children do develop tumors suggests that different mechanisms are at work in the development of cancerous tumors in youngsters. “Perhaps what enables the development of cancer in children is very subtle,” said Druley.
“It may be that in children’s cancer the genes or networks of genes that govern normal development are in some way disturbed by rare alternative forms of certain key genes. Maybe it’s the combined effect of five or 10 rare gene variants. If an individual carries one,or even two or three, there is no ill effect. But, if all of these rare forms of certain genes occur in one individual, the combination somehow derails the train.”
This rare gene variant hypothesis represents new thinking in the genetic investigation of disease,which has mostly concentrated on searching for common, single gene culprits. Unfortunately, identifying rare gene variants has been a difficult, costly and time-consuming task with current genetic research tools, and it’s why scientists know almost nothing about rare variants and their effects on disease.
In 2006, Druley set out to find a better way to search for rare variants. His first stop was the laboratory of Rob Mitra, PhD, an assistant professor in the Department of Genetics at Washington University. Dr. Mitra develops experimental and computational tools to understand complicated cellular processes.
In 2007, grants from the Children’s Discovery Institute enabled Druley and Mitra to begin the enormous task of developing a way to find and quantify all of the alternative forms of a given gene – even those that occur in less than one percent of humans.
“Essentially,” said Mitra, “you need to sequence DNA samples from thousands of individuals living in different locations around the globe to capture as many variations of the gene as possible. Then, you need sophisticated analytical tools to ferret out the very rare gene variants. With conventional sequencing and analytical methods, it would be an unimaginable project.”
Thanks to work done by Mitra and others in developing “next-generation” sequencing technologies, the project could be not only imagined, but carried out. Collaborator Elaine Mardis, PhD, who co-directs Washington University’s Genome Sequencing Center, offered access to the very latest next generation equipment that can generate massive amounts of DNA sequencing data at 100-times lower cost than traditional methods.
For the thousands of individual samples needed, the team looked to Dr. F. Sessions Cole, Park J. White Professor of Pediatrics at Washington University School of Medicine and Director of the Division of Newborn Medicine, who provided his collection of 25,000 heel blot (blood) samples from newborns in Missouri, South Korea, South Africa, and Norway.
Mitra and Druley’s challenge was to figure out how to turn those thousands of spots of dried blood on filter paper into data about the full spectrum of genetic variation. The most effective way to accomplish that was to pool the DNA from large groups of individuals, create thousands of copies of specific genes from that DNA pool, and then repeatedly sequence those genes.
The methods Druley and Mitra developed to achieve that task represent a major breakthrough in medical genetics research. The first “test run” of the new technology was a pooled sample of DNA from 1,111 individuals from Dr. Cole’s samples. A single gene from these same individuals had already been painstakingly sequenced one at a time over a three year period by Dr. Cole’s laboratory associates.
Those results would be used to confirm the accuracy of the new technology. With Druley and Mitra’s new methods, the sequencing that took Dr. Cole’s lab three years to do was completed in just four months at about 40-50 times less cost, and with pinpoint accuracy.
“What we sequenced in our test run was only a fraction of one percent of the entire genome of each of the 1,111 individuals” said Druley. “However, a pooled sequencing experiment of that size yields about 4.5 billion DNA bases to compare in order to sort out the rare gene variants.” It was a mountain of data, and no methods existed to analyze pooled samples.
A computational biology graduate student in Mitra’s lab, Francesco Vallania, rose to that challenge. Vallania designed and implemented a unique computational algorithm that will likely revolutionize the way massive volumes of data generated in these types of experiments will be handled in the future.
Finally, fellow Discovery Institute investigator, population geneticist Dr. Justin Fay, added his stamp to the project by designing a detailed way to sift through the results to determine which of the rare variants would be most likely to result in disease.
“We designed a way to find them; Justin designed a way to target the worst ones,” said Druley. The new tools the team developed will help identify a variety of rare, but important genetic variants related to disease. “I think we can now find the proverbial needles in the haystack that may be at the root of not only cancer, but a wide variety of other conditions as well,” said Druley.
Robi Mitra, PhD, and Todd Druley, MD, PhD