Copy number variation (CNV) is a common mutation in which large chunks of DNA are either deleted from or added to the genome. Seemingly similar cells, especially cancer cells, often have significantly different genetic mutations. Detailed knowledge of these CNVs in individual cells can point to specific treatment regimens. An online tool that can help clinicians better differentiate the defects in individual tumor cells that appear to be similar, have been discovered by scientists. This open-source software is freely available online, and is expected to help scientists better define the nature of a cancer and other diseases and improve their treatment.
Michael Schatz, associate professor at Cold Spring Harbor Laboratory (CSHL) in New York, US, said, "You may think that every cell in a tumor would be the same, but that is actually not the case. We are realizing that there can be a lot of changes inside even a single tumor. If you are going to treat cancer, you need to diagnose exactly what subclass of cancer you have."
The study said, "The new interactive online program called 'Gingko' reduces the uncertainty of single-cell analysis and provides a simple way to visualize patterns in copy number mutations across populations of cells."
A powerful single-cell analytic technique for exploring CNV is whole genome sequencing. But, the challenge is that before sequencing can be done, the cell's DNA has to be amplified many times over. This process is rife with errors, with some arbitrary chunks of DNA being amplified more than that of others. In addition, because many laboratories use their own software to examine CNVs, there is little consistency in how researchers analyze their results.
To address these two challenges, Schatz and team created Gingko. This interactive, web-based program automatically processes sequence data, maps the sequences to a reference genome, and creates CNV profiles for every cell that can then be viewed with a user-friendly graphical interface.
The software appeared online in Nature Methods.