Finding the Genetic Signs of a Predisposition for Cancer

Cancer develops when good cells turn bad. This transformation typically happens when the body's protein-based signaling factors malfunction and either excite or fail to inhibit cell growth. Scientists know that these malfunctions, and therefore certain cancers, are more likely to occur in some people than in others—and researchers have spent decades looking for telltale signs of a predisposition for cancer.

Recent research enabled by the decoding of the human genome has shown that some signs of predisposition are visible at the genetic level. The driving concept behind this research is the notion that people with the same disease will also have the same genetic aberrations. The basic method of detection involves comparing the DNA sequences of diseased and healthy individuals, looking for genetic markers of the malady in question.

DNA sequencing analysis has been used for some studies, but the required time and expense make it an inefficient way to compare large populations. Still, this approach reveals the presence of changes in single nucleotides or "bases" within individual strands of DNA. Those changes, which may appear as a substitution or deletion in a base pair, are called single nucleotide polymorphisms (SNPs or "snips").

There are an estimated 3 million SNPs in the human genome. However, once researchers have identified a subset of SNPs potentially associated with a disease, they need to sequence only those sections of the genome. This targeted sequencing can identify the types of mutations associated with the cancer and pinpoint their exact locations. To further increase the efficiency of this approach, research labs are looking for screening tools that will accelerate the process of finding the most likely SNPs to sequence.

Evaluating a fast, accurate alternative

Many products and methods are currently used to screen for SNPs. The most widely used methods are DNA sequencing, denaturing high-performance liquid chromatography (dHPLC) and real-time polymerase chain reaction (PCR). These proven approaches are accurate, but they also tend to be costly, complicated and time consuming.

Recent research by a team in the US has demonstrated a high performance, low-cost alternative based on the Agilent 2100 bioanalyzer and the DNA 1000 LabChip^® kit. The team has shown that the Agilent solution can distinguish between normal and mutated DNA in specific genes, and do it quickly and accurately: the 2100 bioanalyzer can run 12 samples in about 30 minutes, and the system can resolve heterozygous mutations to within 10-15% of base pair (bp) length.

Increasing the speed and efficiency of screening

The team's methods and results are described in the Agilent application note, "Mutation and detection for the K-ras and P16 genes." Their work focused on the human K-ras gene, which is a member of the Ras family of guanosine triphosphates (GTPases). GTPase enzyme activity converts GTP-binding proteins from active to inactive form—one of the changes that makes good cells turn bad. Ras proteins suffer from impaired GTPase activity that renders the protein resistant to inactivation by the regulatory proteins that control cell growth.

This figure shows DNA sequence data that corresponds to Agilent 2100 bioanalyzer data. This size-range resolution could not be visualized on a gel slab.

Mutant, activated forms of the Ras proteins are frequently observed in cancer. Specifically, mutations in a region called K-ras gene codon 12 can lead to cancer of the colon, pancreas, liver, spleen, stomach or lungs. This type of mutated DNA sequence shows up as extra bands in an Agilent chip image (see figure). In this study, only mutated samples showed these extra bands. As described in the application note, the team used sequencing analysis to verify the presence of specific SNPs in their samples.

The researchers concluded that this type of fast, rapid screening assay could be employed in any molecular biology laboratory. They have also suggested that the 2100 bioanalyzer can be used for some SNP detection assays, thereby increasing the efficiency of the search for genetic markers that may signify a predisposition for certain cancers.

For more information

To learn more about uses of the Agilent 2100 bioanalyzer in cancer research, please see our compendium of application examples. For additional information about these and other Agilent life sciences products and resources, please visit the Life Sciences/Chemical Analysis main page.