Scientists have developed an online tool that can help clinicians better differentiate the defects in individual tumor cells that appear to be similar.
The open-source software, which is freely available online, is expected to help scientists better define the nature of a cancer and other diseases and improve their treatment. Seemingly similar cells, especially cancer cells, often have significantly different genetic mutations and therefore detailed knowledge of these mutations; called copy number variations (CNVs), in individual cells can point to specific treatment regimens.
“The new interactive online programme called Gingko reduces the uncertainty of single-cell analysis and provides a simple way to visualise patterns in copy number mutations across populations of cells”, the study said.
Copy number variation is a common mutation in which large chunks of DNA are either deleted from or added to the genome. One powerful single-cell analytic technique for exploring CNV is whole genome sequencing. 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 others. In addition, because many labs use their own software to examine CNVs, there is little consistency in how researchers analyse their results.
To address these two challenges, the researchers created Gingko. The interactive, web-based programme 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.