Systems and methods for analyzing circulating tumor DNA
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.
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 reference graph.
15. The system of claim 13 , further operable to align a second set of sequence reads to the patient-specific genomic reference graph and produce 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.
16. A method for analyzing a sample containing cell-free plasma DNA from a patient, the method comprising:
using at least one processor to perform:
creating, in 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.
17. The method of claim 16 , 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.
18. The method of claim 17 , 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 least one non-transitory computer-readable storage medium.
19. The method of claim 16 , 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.
20. The method of claim 19 , further operable to align a second set of sequence reads to the patient-specific genomic reference graph and produce 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.