Identifying Cancer Mutations
Determining the underlying cause of disease is a daunting task. In a 1994 Time magazine interview, Francis Collins, now director of the National Institutes of Health, said that locating a gene from scratch was like "trying to find a burned-out light bulb in a house located somewhere between the East and West coasts without knowing the state, much less the town or street the house is on." With its 3 billion base pairs distributed over 23 paired chromosomes, the human genome is an epic map to navigate. Nevertheless, an international effort to map the human genome at the individual DNA base pair level—the Human Genome Project—was initiated in 1990. The effort cost more than $2.7 billion, involved 20 research institutes and culminated in 2003 with the publication of the completed DNA sequence of the human genome.
An important byproduct of this effort has been significant improvements in DNA sequencing technology. These advances have led to the development of so-called next-generation sequencing instruments that can decode a human genome in several weeks—and at a cost of less than $100,000. In pioneering research using this technology, investigators from Washington University’s Genome Institute in 2008 reported they had unraveled the first complete genome of a cancer patient, a woman with acute myeloid leukemia. Since then, the same team of scientists has sequenced the genomes of additional cancer patients, including those with breast, lung, ovarian and glioblastoma, a type of brain tumor. These efforts and those of other scientists engaged in whole-genome sequencing of cancer genomes are providing an unprecedented look at the mutations that underlie cancer.
Next-generation DNA sequencing technology will be used in the St. Jude Children’s Research Hospital – Washington University Pediatric Cancer Genome Project to sequence the genomes of 600 pediatric cancer patients. This rapid-sequencing method involves chopping the DNA into millions of small fragments, about 200 base pairs in length. The fragments are amplified many times and then read, or decoded, simultaneously. Fluorescent markers indicate the position of each DNA letter, A, T, C or G.
As part of the new project, DNA will be isolated from both the cancer cells and a normal, healthy tissue sample from the same patient. The healthy cells give the scientists a reference DNA sequence to which they can compare genetic alterations in the patient's tumor cells. The scientists will look for genetic differences—points of single base changes in the DNA, insertions and deletions of bits of genetic material, variations in gene copy number and structural changes—in a patient's cancer genome compared with his or her normal genome.
Typically, hundreds of mutations may be linked to the cancer, but the challenge for researchers is to sift through massive amounts of genetic data to distinguish the dozen or so “driver” mutations—those that are thought to initiate and contribute to tumor growth—from the “passenger” mutations, which are random, background mutations that are not relevant to the disease.
The advantage of the whole-genome approach is that scientists can move beyond a list of genes that have been previously associated with cancer to explore the entire genome and find meaningful cancer-causing mutations. Such a project holds enormous potential for improving the diagnosis and treatment of childhood cancers.