Method of predicting response to therapy by assessing tumor genetic heterogeneity
AssigneeRoche Sequencing Solutions, Inc.
InventorsAarthi Balasubramanyam, Christine Ju, Xiaoju Ma, Thomas Muley, Felix Herth, Nalin Tikoo, Birgit Wehnl, Liu Xi, Stephanie J. Yaung
Life of this patent
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Abstract
The invention is a method of predicting response to therapy in a cancer patient by serial sampling the patient's cell-free tumor nucleic acids to determine a change in the number of mutations per amount of plasma.
Claims9
A method for determining whether a cancer patient has positively responded to a therapy regimen, the method comprising the steps of:
- (a) providing a blood plasma sample from the patient collected at a first time point during treatment regimen;
- (b) providing a blood plasma sample from the patient collected at a second time point during treatment regimen;
- (c) determining in the samples the sequence of at least a portion of each of the biomarkers listed in Table 1 or Table 2;
- (d) determining in the samples the ratio of the number of mutations detected in the biomarkers to the volume of the samples (MMPM);
- (e) determining that the patient has responded to the therapy regimen if the MMPM in the second sample is lower than in the first sample;
- or
- (f) determining that the patient has not responded to the therapy regimen if the MMPM in the second sample is not lower than in the first sample.
A method of treatment of a non-small cell lung cancer (NSCLC), small cell lung cancer (SCLC) and colorectal cancer (CRC) comprising the steps of:
- (a) providing a blood plasma sample from the patient collected at a first time point during treatment regimen;
- (b) providing a blood plasma sample from the patient collected at a second time point during treatment regimen;
- (c) determining in the samples the sequence of at least a portion of each of the biomarkers listed in Table 1 or Table 2;
- (d) determining in the samples the ratio of the number of mutations detected in the biomarkers to the volume of the samples (MMPM);
- (e) continuing the therapy regimen if the MMPM in the second sample is lower than in the first sample;
- or
- (f) altering the therapy regimen if the MMPM in the second sample is not lower than in the first sample.
A computer system designed to implement an algorithm for whether a cancer patient has positively responded to a therapy regimen, wherein the algorithm analyses sequencing data on one or more biomarkers obtained from at least two patient's blood samples collected at separate time points during the therapy regimen, the algorithm containing one or more steps selected from mutation detection, error correction, counting the number of mutations per sample and determining the ratio of the number of mutations in a sample to the sample volume (MMPM), determining whether MMPM has decreased at subsequent time points and reporting that the patient has responded to therapy if MMPM has decreased between subsequent time points and reporting that the patient has not responded to therapy if MMPM has not decreased between subsequent time points.
A computer system designed to implement an algorithm for selecting a therapy for a cancer patient wherein the algorithm analyses sequencing data on one or more biomarkers obtained from at least two patient's blood samples collected at separate time points during the therapy regimen, the algorithm containing one or more steps selected from mutation detection, error correction, counting the number of mutations per sample and determining the ratio of the number of mutations in a sample to the sample volume (MMPM), determining whether MMPM has decreased at subsequent time points and reporting suggested selection of the same therapy if MMPM has decreased between subsequent time points and reporting suggested selection of an alternative therapy if MMPM has not decreased between subsequent time points.
Dependencies are inferred from the claim text.