Systems and methods for analyzing circulating tumor DNA

Patent metadata

Field	Value
Publication number	US-11560598-B2
Application number	US-201916525822-A
Country	US
Kind code	B2
Filing date	Jul 30, 2019
Priority date	Jan 13, 2016
Publication date	Jan 24, 2023
Grant date	Jan 24, 2023

Abstract

The invention provides oncogenomic methods for detecting tumors by identifying circulating tumor DNA. A patient-specific reference directed acyclic graph (DAG) represents known human genomic sequences and non-tumor DNA from the patient as well as known tumor-associated mutations. Sequence reads from cell-free plasma DNA from the patient are mapped to the patient-specific genomic reference graph. Any of the known tumor-associated mutations found in the reads and any de novo mutations found in the reads are reported as the patient's tumor mutation burden.

First claim

What is claimed is:

1. At least one non-transitory computer-readable storage medium storing processor-executable instructions that, when executed by a computer hardware processor, cause the computer hardware processor to perform a method for analyzing a sample containing cell-free plasma DNA from a patient, the method comprising:
creating, in the at least one non-transitory computer-readable storage medium, an initial genomic reference graph that represents a plurality of known human genomic sequences, the initial genomic reference graph comprising a directed graph having nodes and edges connecting the nodes, the nodes including a first node and a second node, wherein:
the first node is stored as a first object in the at least one non-transitory computer-readable storage medium,
the second node is stored as a second object in the at least one non-transitory computer-readable storage medium, and
a first edge of the edges is stored as a pointer from the first object to the second object in the at least one non-transitory computer-readable storage medium;

creating a patient-specific genomic reference graph for the patient from the initial genomic reference graph by augmenting the initial genomic reference graph using at least one non-tumor genomic sequence previously obtained by sequencing a sample containing non-tumor DNA from the patient;
aligning sequence reads, previously obtained by sequencing the sample containing the cell-free plasma DNA from the patient, to the patient-specific genomic reference graph to find at least one mutation in the cell-free plasma DNA relative to the non-tumor DNA from the patient; and
generating a report indicating that circulating-tumor DNA (ctDNA) in the patient includes the at least one mutation found in the cell-free plasma DNA.

2. The at least one non-transitory computer-readable storage medium of claim 1 , wherein creating the patient-specific genomic reference graph comprises:
aligning the at least one non-tumor genomic sequence to the initial genomic reference graph;
identifying mutations of the at least one non-tumor genomic sequence relative to the initial genomic reference graph; and
incorporating the identified mutations into the initial genomic reference graph to create the patient-specific genomic reference graph.

3. The at least one non-transitory computer-readable storage medium of claim 2 , wherein incorporating the identified mutations into the initial genomic reference graph comprises, for a mutation of the identified mutations:
creating a third node representing the mutation in the initial genomic reference graph; and
storing the third node as a third object in the at least one non-transitory computer-readable storage medium.

4. The at least one non-transitory computer-readable storage medium of claim 1 , wherein the report identifies a patient's tumor-related mutation population, wherein the tumor-related mutation population includes mutations in the cell-free plasma DNA relative to the non-tumor DNA from the patient.

5. The at least one non-transitory computer-readable storage medium of claim 4 , wherein:
the report further identifies one or more portions of the sequence reads that align to one or more known tumor-associated mutations in the patient-specific genomic reference graph.

6. The at least one non-transitory computer-readable storage medium of claim 4 , wherein the report identifies a first clone and a second clone present in a tumor in the patient.

7. The at least one non-transitory computer-readable storage medium of claim 5 , wherein the report identifies a driver mutation not present in the known human genomic sequences and present in the cell-free plasma DNA from the patient.

8. The at least one non-transitory computer-readable storage medium of claim 7 , further comprising adding the driver mutation as a known tumor-associated mutation of the one or more known tumor-associated mutations annotated in the patient-specific genomic reference graph.

9. The at least one non-transitory computer-readable storage medium of claim 4 , further comprising aligning a second set of sequence reads to the patient-specific genomic reference graph and producing a second report that identifies a patient's second tumor-related mutation population at a time different from an initial time associated with the patient's tumor-related mutation population, wherein the second report includes a comparison of the patient's second tumor-related mutation population to the patient's tumor-related mutation population.

10. A system comprising:
a computer hardware processor; and
at least one non-transitory computer-readable storage medium storing processor-executable instructions that, when executed by the computer hardware processor, cause the computer hardware processor to perform a method for analyzing a sample containing cell-free plasma DNA from a patient, the method comprising:
creating, in the at least one non-transitory computer-readable storage medium, an initial genomic reference graph that represents a plurality of known human genomic sequences, the initial genomic reference graph comprising a directed graph having nodes and edges connecting the nodes, the nodes including a first node and a second node, wherein:
the first node is stored as a first object in the at least one non-transitory computer-readable storage medium,
the second node is stored as a second object in the at least one non-transitory computer-readable storage medium, and
a first edge of the edges is stored as a pointer from the first object to the second object in the at least one non-transitory computer-readable storage medium;

creating a patient-specific genomic reference graph for the patient from the initial genomic reference graph by augmenting the initial genomic reference graph using at least one non-tumor genomic sequence previously obtained by sequencing a sample containing non-tumor DNA from the patient;
aligning sequence reads, previously obtained by sequencing the sample containing the cell-free plasma DNA from the patient, to the patient-specific genomic reference graph to find at least one mutation in the cell-free plasma DNA relative to the non-tumor DNA from the patient; and
generating a report indicating that circulating-tumor DNA (ctDNA) in the patient includes the at least one mutation found in the cell-free plasma DNA.

11. The system of claim 10 , wherein creating the patient-specific genomic reference graph comprises:
aligning the at least one non-tumor genomic sequence to the initial genomic reference graph;
identifying mutations of the at least one non-tumor genomic sequence relative to the initial genomic reference graph; and
incorporating the identified mutations into the initial genomic reference graph to create the patient-specific genomic reference graph.

12. The system of claim 11 , wherein incorporating the identified mutations into the initial genomic reference graph comprises, for a mutation of the identified mutations:
creating a third node representing the mutation in the initial genomic reference graph; and
storing the third node as a third object in the at least one non-transitory computer-readable storage medium.

13. The system of claim 10 , wherein the report identifies a patient's tumor-related mutation population, wherein the tumor-related mutation population includes mutations in the cell-free plasma DNA relative to the non-tumor DNA from the patient.

14. The system of claim 13 , wherein:
the report further identifies one or more portions of the sequence reads that align to one or more known tumor-associated mutations in the patient-specific genomic refere

Assignees

• Seven Bridges Genomics Inc

Inventors

• Lee Wan-Ping
• Locke Devin

Classifications

• G16B30/00

  ICT specially adapted for sequence analysis involving nucleotides or amino acids · CPC title

• C12Q2600/158

  Expression markers · CPC title

• C12Q2600/156

  Polymorphic or mutational markers · CPC title

• G16B5/10

  Boolean models · CPC title

• G16B5/00

  ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks · CPC title