Systems and methods for generating, visualizing and classifying molecular functional profiles

Abstract

Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for a biological sample; determining a molecular-functional (MF) profile for a subject using the data; determining visual characteristics GUI elements using the data; generating a GUI personalized to the subject using the determined visual characteristics; and presenting the generated personalized GUI to a user.

1 . A method, comprising:
 obtaining first RNA expression data for a first biological sample from a subject having, suspected of having, or at risk of having cancer;   determining, using the first RNA expression data, first gene group expression levels for the subject corresponding to respective gene groups in a set of gene groups, the set of gene groups comprising gene groups associated with cancer malignancy and different gene groups associated with cancer microenvironment;   identifying, using the first gene group expression levels for the subject, at least one anti-cancer therapy to administer to the subject;   administering to the subject the at least one anti-cancer therapy identified using the first gene expression levels for the subject;   obtaining second RNA expression data for a second biological sample from the subject, the second biological sample obtained from the subject after administration of the at least one anti-cancer therapy to the subject;   determining, using the second RNA expression data, second gene group expression levels for the subject corresponding to respective gene groups in the set of gene groups; and   determining, using the first gene group expression levels and the second gene group expression levels, efficacy of treating the subject using the at least one anti-cancer therapy.   
     
     
         2 - 20 . (canceled)