Method for determining efficacy of chemotherapy treatment for a subject

A method of treating cancer in a subject that has previously received cytotoxic treatment selected from a chemotherapeutic, an adjuvant, a cytotoxic antibody and/or a radiation treatment regimen, the method comprising:

• quantifying an amount of RNA disruption in a biological sample obtained from the subject comprising cellular RNA at a time point after the subject has received cytotoxic treatment selected from a chemotherapeutic, an adjuvant, a cytotoxic antibody and/or a radiation treatment regimen, by:
• obtaining at least one electropherogram dataset corresponding to the biological sample comprising cellular RNA;
• determining values for features from the at least one electropherogram dataset by:
• (a) using two identifying ranges, which are regions that are defined to accommodate possible shifting of 18S and 28S peaks, by:
• defining default ranges as the two identifying ranges to search for the 18S and 28S peaks, and
• shifting the default ranges if a marker region is not at its expected location, where the expected location is a time associated with a first peak that is a dye-only peak that indicates a start of a run of a gel during electrophoresis for obtaining the at least one electropherogram dataset and the shifting is done so that the two identifying ranges include a shifted 18S peak and a shifted 28S peak, respectively, which correspond to an 18S rRNA peak and a 28S rRNA peak, respectively,
• (b) detecting the 18S and 28S peaks using the two identifying ranges, by:
• obtaining a plurality of electropherogram datasets corresponding to unique biological samples comprising cellular RNA at the time point during or after the treatment using a common analysis platform;
• identifying an electropherogram dataset corresponding to a standard sample;
• separating the plurality of electropherograms into an adjustment group and a standard group;
• identifying normal characteristics representative of a normal sample from the plurality of electropherograms in the standard group, the normal characteristics comprising the retention times for the 18S and the 28S peak from samples in the standard group which are defined as standard retention times;
• determining locations of peaks for the electropherograms in the adjustment group by determining retention times for the 18S and 28S peaks of the electropherograms in the adjustment group by locating peaks that are around the standard retention times;
• and
• determining values for features from the adjusted electropherograms and the electropherograms from the standard group, and
• (c) determining values for the features derived at least in part based on the determined 18S and 28S peaks, an intermediate region and a low C banding region, the intermediate region being between the determined 18S and 28S peaks and the low C banding region being an upper portion of a low banding region below and adjacent to the determined 18S peak;
• and
• determining an RDA score for the biological sample based on a 1) a ratio of intermediate region area to a sum of the 28S peak area and the 18S peak area;
• 2) a ratio of a low C banding region area to the sum of the 28S peak area and the 18S peak area;
• or 3) a ratio of a sum of the low C banding region area and the intermediate region area to the sum of the 28S peak area and the 18S peak area;
• determining if the amount of RNA disruption of the cellular RNA is increased or not increased by comparing the RDA score with a reference value, at least one threshold value or at least one threshold curve, wherein the subject is identified as a responder if the amount of RNA disruption is increased and a non-responder if the amount of RNA disruption is not increased;
• and
• administering the same cytotoxic treatment the subject previously received when the subject is determined to be a responder;
• or switching the cytotoxic treatment when the subject is determined to be a non-responder, wherein switching the cytotoxic treatment comprises administering an increased dose of the same cytotoxic treatment the subject previously received, administering one or more of radiation and a chemotherapeutic agent in addition to the cytotoxic treatment previously received by the subject, discontinuing the cytotoxic treatment previously received by the subject and initiating a different cytotoxic treatment regimen selected from a chemotherapeutic, an adjuvant, a cytotoxic antibody and/or a radiation treatment regimen.