Granted Patent B2

US 12,633,374 · App. 17/339,368 · Granted May 19, 2026

Inventors: Kenneth Pritzker (Toronto, CA); Amadeo Mark Parissenti (Sudbury, CA); Laura Pritzker (Toronto, CA); Mu Zhu (Waterloo, CA); Xiaohui Wang (Oakville, CA); Stacey Santi (Copper Cliff, CA); Rashmi Narendrula (Sudbury, CA); Baoqing Guo (Sudbury, CA)

Assignee: RNA Diagnostics Inc.

G16B25/10C12Q1/68C12Q1/6886G01N27/44791G16B25/00C12Q2600/142

Abstract

Claims (35)

1 . 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.

2 . The method of claim 1 , wherein the method comprises defining default ranges as the two identifying ranges to search for the 18S and 28S peaks and adjusting the default ranges if a marker region is not at its expected location, preferably the default ranges comprise about 39.5 seconds to about 44.95 seconds for the 18S peak and about 45.05 seconds to 53.5 seconds for the 28S peak.

3 . The method of claim 1 , wherein separating the plurality of electropherograms into an adjustment group and a standard group comprises determining a standard sample for the plurality of electropherogram datasets where the standard sample has the smallest standard score defined by a ratio of a sum of intermediate area, a lower B banding region area and a lower C banding region area to a sum of 18S peak area and 28S peak area.

4 . The method of claim 3 , wherein the separating act further comprises assigning a given electropherogram dataset to the adjustment group if retention times for at least one of the 18S and 28S peaks of the given electropherogram dataset differ by more than a certain time threshold to retention times of corresponding at least one of the 18S and 28S peaks of the standard sample.

5 . The method of claim 1 , wherein the method comprises comparing the RDA score to multiple thresholds, each threshold being arranged to correspond to an RDA zone which identifies a clinical zone boundary to determine or predict effectiveness of the treatment.

6 . The method of claim 1 , wherein the biological sample is obtained after the subject has received a first cycle of a chemotherapeutic, adjuvant and/or radiation treatment or after the subject has received 2, 3, 4 or more cycles of the chemotherapeutic, adjuvant and/or radiation treatment or after completion of the chemotherapeutic, adjuvant and/or radiation treatment regimen.

7 . The method of claim 1 , where the RDA score is indicative of responsiveness to the cytotoxic treatment and correlates to a decrease in RNA integrity of at least by 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80% or at least 90% wherein the reference value is a pretreatment value.

8 . The method of claim 1 , wherein the cancer is selected from breast cancer, optionally HER2+ positive breast cancer, prostate cancer, lung cancer, sarcomas, colon cancer, leukemia, lymphoma, multiple myeloma or ovarian cancer and/or the cytotoxic treatment comprises chemotherapeutic treatment selected from taxanes, anthracyclines and vinca alkaloids optionally vinblastine, alkylating agents optionally cisplatin and nucleoside analogs optionally 5-FU and combinations thereof, or from anthracyclines, paclitaxel, docetaxel and epirubicin and combinations thereof.

9 . The method of claim 5 , wherein one of the thresholds corresponds to a selected negative predictive value (NPV) and defines a boundary between RDA zone 2 and RDA zone 3 and another of the threshold corresponds to a selected positive predictive value (PPV) and defines the boundary between RDA zone 1 and the RDA zone 2.

10 . The method of claim 9 , wherein the RDA zones represent one of an increased likelihood of a complete response, a partial response and no response to the treatment.

11 . The method of claim 9 , wherein the RDA zone 1 refers to a range of the RDA scores where the NPV is at least 0.8, at least 0.85, at least 0.9, at least 0.95, at least 0.96, at least 0.97, at least 0.98 or greater.

12 . The method of claim 9 , wherein the RDA zone 2 refers to a range of the RDA scores that fall between the RDA zone 1 and the RDA zone 3, and the RDA zone 2 is an intermediate or indeterminate zone.

13 . The method of claim 9 , wherein the RDA zone 3 refers to a range of the RDA scores where the PPV is at least 0.15, at least 0.16, at least 0.17, at least 0.18, at least 0.19, at least 0.2 or greater.

14 . The method of claim 5 , wherein a subject is identified or predicted as having an increased likelihood of responding or not responding to the treatment depending on which of the RDA zone the RDA score falls within.

15 . The method of claim 1 , wherein a first reference value is a scalar value that is determined based on conducting ROC analysis on a database of experimental results to identify responders with a desired high Positive Predictive Value (PPV) and a desired low false positive rate.

16 . The method of claim 15 , wherein a second reference value is a scalar value that is determined based on conducting ROC analysis on a database of experimental results to identify non-responders with a desired high Negative Predictive Value (NPV) and a desired low false negative rate.

17 . The method of claim 16 , wherein the first and second references values are selected such that a distance therebetween is minimized.

18 . The method of claim 1 , wherein the cancer is breast cancer.

Assignments (2)

Continuity (4)

References Cited (174)