Accelerating the Detection of Genomic Duplications and Deletions

Changes in genomic copy-number are the genetic fingerprints of many human cancers. The oncogenes that drive tumor growth produce an increased copy number and often reside in regions of DNA duplication. Suppressor genes that quell tumor growth yield a decreased copy number and typically appear in regions of DNA deletions.

Researchers use several methods to detect these genetic rearrangements, but most are based on either fluorescent in situ hybridization (FISH) or the quantitative analysis of polymerase chain reaction (PCR) products. FISH is popular and accurate but is time-consuming and provides limited resolution. Quantitative PCR methods are often more efficient but are technically demanding and difficult to design. Fortunately, there are faster, simpler alternatives that can also reveal mutations conventional methods may miss.

Testing two alternatives

To achieve faster throughput and better resolution, some scientists are turning to techniques such as multiplex amplifiable probe hybridization (MAPH) and multiplex ligation-dependent probe amplification (MLPA). These methods are based on quantitative amplification using a single pair of primers following probe hybridization to genomic DNA.

Recently, researchers used the Agilent 2100 bioanalyzer in combination with the DNA 500 LabChip kit to perform MAPH and MLPA. Their methods and results are summarized in the application note, "Rapid detection of genomic duplications and deletions using the Agilent 2100 bioanalyzer."

During resolution testing, peaks were readily distinguished with probe separation of greater than 20 base pairs (bp). In assessing the minimum concentration required for accurate analysis, just 0.5 ng/µl would yield a peak of approximately five units in height and a signal-to-noise ratio of at least 10. Subsequent experiments showed that the Agilent solution combined with MAPH or MLPA provided fast, simple detection of copy-number changes in genomic DNA.

Enhancing cancer research

Two recent product releases can improve the detection process. The DNA 1000 LabChip kit extends the analysis range to 1000 bp and matches the resolution of the DNA 500 kit across the same size range. The new expert software for the 2100 bioanalyzer accelerates analysis by providing color flagging of quantitative and qualitative results based on customizable peak table rules. These new additions enhance the capabilities of a system that is already recognized for its speed, reproducibility and ease-of-use in genomics research.

For more information

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