Chapter 6 Example of Use

To illustrate and show an example of mSignatureDB functionalities, we have applied our application to analyze two public datasets reporting somatic mutation catalogs on 106 cases of oral squamous cell carcinomas (OSCC) from India and 510 cases of head and neck squamous cell cancer (HNSC) from America , respectively. Our main focuses are on depicting the major differences of mutational signatures between American and India populations and facilitating users to explore all functionality of the database.

Two options can be chosen to perform comparative analysis between datasets.

6.1 Option 1: From the ‘Search’ page

As shown in the Figure of STEP 3, common signatures arise from aging (COSMIC signature 1), and the over-activity of APOBEC cytidine deaminases (COSMIC signature 2 and 13) can be identified through the heatmap. Furthermore, users can observe that smoking-related signature (COSMIC signature 4) plays key roles in the American population, whereas the tobacco chewing-related signature (COSMIC signature 29) is dominant in the Indian population. The result also demonstrates that risk factors can vary between countries and populations in head and neck cancer owing to different life habits or mutagen exposures. In addition to COSMIC signature 29, we noticed the prevalence of signature 24 in the Indian population, which is known to be correlated with aflatoxin exposure but was not emphasized by a previous publication.

6.2 Option 2: From the ‘Analysis’ page

6.2.1 Known signatures determination

6.2.2 de novo signatures analysis