Identification and use of circulating nucleic acid tumor markers
AssigneeThe Board of Trustees of the Leland Stanford Junior University
InventorsMaximilian Diehn, Arash Ash Alizadeh, Aaron M. Newman, Scott V. Bratman
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Abstract
Methods for creating a selector of mutated genomic regions and for using the selector set to analyze genetic alterations in a cell-free nucleic acid sample are provided. The methods can be used to measure tumor-derived nucleic acids in a blood sample from a subject and thus to monitor the progression of disease in the subject. The methods can also be used for cancer screening, cancer diagnosis, cancer prognosis, and cancer therapy designation.
Claims29
A method of detecting somatic mutations in a sample of cfDNA of a subject suffering from a cancer, wherein the somatic mutation is associated with cancer, the method comprising:
- (i) obtaining a first cell-free DNA (cfDNA) sample comprising circulating tumor DNA (ctDNA) comprising somatic mutations from the subject,
- (ii) performing hybrid capture on the first cfDNA sample using a selector set comprising a plurality of oligonucleotides to enrich for cfDNA corresponding to genomic regions known to contain tumor-specific somatic mutations identified in (b) to produce a hybrid captured first cfDNA sample,
- (iii) sequencing the hybrid captured first cfDNA sample to generate sequencing information;
- and
- (iv) analyzing the sequence information of the hybrid captured first cfDNA sample to detect ctDNA in the sample;
- wherein:
- the method is capable of detecting a percentage of ctDNA that is less than or equal to 2% of total cfDNA,
- the cancer is lymphoma, and
- the selector set is produced according to a method comprising:
- (a) performing a sequencing reaction on a plurality of tumor samples and a plurality of non-tumor samples from a population of subjects suffering from the cancer;
- (b) comparing the sequencing information of the plurality of tumor samples to sequencing information from the plurality of non-tumor samples from the population of subjects to identify fifty or more somatic mutations specific to the sequencing information of the plurality of tumor samples;
- and
- (c) producing the selector set corresponding to the 50 or more genomic regions comprising the one or more mutations specific to the sequencing information of the plurality of tumor samples.
A method of detecting somatic mutations in a sample of cfDNA of a subject suffering from a cancer, wherein the somatic mutation is associated with cancer, the method comprising:
- (i) obtaining a first cell-free DNA (cfDNA) sample comprising circulating tumor DNA (ctDNA) comprising somatic mutations from the subject,
- (ii) performing hybrid capture on the first cfDNA sample using a selector set comprising a plurality of oligonucleotides to enrich for cfDNA corresponding to genomic regions known to contain tumor-specific somatic mutations identified in (b) to produce a hybrid captured first cfDNA sample,
- (iii) sequencing the hybrid captured first cfDNA sample to generate sequencing information;
- and
- (iv) analyzing the sequence information of the hybrid captured first cfDNA sample to detect ctDNA in the sample;
- wherein:
- the method is capable of detecting a percentage of ctDNA that is less than or equal to 2% of total cfDNA,
- the cancer is non-Hodgkin lymphoma (NHL), and
- the selector set is produced according to a method comprising:
- (a) performing a sequencing reaction on a plurality of tumor samples and a plurality of non-tumor samples from a population of subjects suffering from the cancer;
- (b) comparing the sequencing information of the plurality of tumor samples to sequencing information from the plurality of non-tumor samples from the population of subjects to identify fifty or more somatic mutations specific to the sequencing information of the plurality of tumor samples;
- and
- (c) producing the selector set corresponding to the 50 or more genomic regions comprising the one or more mutations specific to the sequencing information of the plurality of tumor samples.
Dependencies are inferred from the claim text.