Granted Patent B2

US 12,386,895 · App. 17/000,054 · Granted Aug 12, 2025

Inventors: Alexander Frieden (Somerville, MA); Caleb J. Kennedy (Arlington, MA); Xavier S. Haurie (Belmont, MA)

Assignee: Laboratory Corporation of America Holdings

G06F16/9024G06F16/9038G16B20/20G16B20/40G16B50/00G16B50/30G16B20/00

Abstract

Claims (64)

1. A system for describing genetic information, the system comprising:

a memory configured to store:

a graph database comprising at least:

an allele node storing a first relationship record identifier (ID) and an allele pointer to allele information about an allele, the allele information included in genomic information of a sample obtained from an individual,

a mutation node storing a second relationship record ID and a first mutation pointer to mutation information about a mutation in the allele, and

a clinical significance node storing the second relationship record ID and a first mutation pointer to clinical significance information about the mutation; and

wherein each of the allele node, mutation node, and clinical significance node has a first fixed size; and

a relationship data structure comprising at least:

a first relationship record located by the first relationship record ID comprising an allele node ID, a mutation node ID, a first relationship type between the allele node and the mutation node, and a first pointer to a second relationship record, and

the second relationship record located by the second relationship record ID comprising the mutation node ID, a clinical significance node ID, a second relationship type between the mutation node and the clinical significance node, and a second pointer to the first relationship record; and

wherein each of the first relationship record and the second relationship record has a second fixed size; and

a processor coupled to the memory, the processor configured to:

receive updated information about the mutation and updated information about the clinical significance of the mutation;

generate an updated mutation node having the first fixed size in the graph database, the updated mutation node comprising a third relationship record ID and a second mutation pointer to the updated information about the mutation;

generate an updated clinical significance information node having the first fixed size in the graph database, the updated clinical significance information node comprising a fourth relationship record ID and a second clinical significance pointer to the updated information about the clinical significance of the mutation;

generate a third relationship record having the second fixed size in the relationship data structure, the third relationship record comprising an updated mutation node ID, the mutation node ID, a third relationship type of the updated mutation node and the mutation node, and a third pointer to the mutation node, wherein a location of the third relationship record in the relationship data structure is determined based on the third relationship record ID and the second fixed size;

generate a fourth relationship record having the second fixed size in the relationship data structure, the fourth relationship record comprising an updated clinical significance node ID, the updated mutation node ID, a fourth relationship type of the updated clinical significance and updated mutation node, and a fourth pointer to the updated mutation node, wherein a location of the fourth relationship record in the relationship data structure is determined based on the fourth relationship record ID and the second fixed size, wherein the first relationship record through the fourth relationship record make up a relationship chain in the relationship data structure; and

generate a report of a clinical significance of the mutation in the allele based on the first through fourth relationship records by traversing the relationship chain in the relationship data structure using the first through fourth relationship record IDs.

2. The system of claim 1 , wherein traversing the relationship chain comprises:

selecting one of the allele node, the mutation node, the clinical significance node, the updated clinical significance node, and the updated mutation node as a starting node;

determining a location of the starting node in the graph database based on an identifier of the starting node and the first fixed size a size of ; and

determining locations of other nodes in the graph database based on the relationship chain including the first through fourth relationship records.

3. The system of claim 1 , wherein, to generate the report, the processor is further configured to:

receive a query to retrieve information regarding the mutation, wherein the query indicates a starting node to start the query, and wherein the starting node is one of the allele node, the mutation node, the clinical significance node, the updated mutation node, or the updated clinical significance node;

determine relevant nodes from at least one of the allele node, the mutation node, the clinical significance node, the updated mutation node, or the updated clinical significance node for generating the report of the clinical significance of the mutation; and

starting at the starting node, traverse the relevant nodes to generate the report of the clinical significance of the mutation based on the relationship chain in the relationship data structure.

4. The system of claim 1 , wherein a plurality of edges connect the allele node, the mutation node, the clinical significance node, the updated clinical significance node, and the updated mutation node, based on the first through fourth relationship record IDs in the relationship chain.

5. The system of claim 1 , wherein the information about the mutation includes a description of the mutation as a variant of a reference human genome.

6. The system of claim 1 , wherein the data including the updated information includes sequence read data.

7. The system of claim 1 , wherein the data including the updated information is received as a ASTA file, FASTQ file, Sequence Alignment Map (SAM) file, Binary Alignment Map (BAM) file, or VCF file.

8. The system of claim 1 , wherein the mutation information is obtained by sequencing the sample.

9. A method for describing genetic information, the method comprising:

receiving, by one or more computing devices, updated information about a mutation of an allele to be stored in a data storage device including a graph database and a relationship data structure, wherein the graph database comprises a first plurality of nodes storing a first relationship record identifier (ID) and an allele pointer to allele information about the allele, a second relationship record ID and a first mutation pointer to mutation information about the mutation of the allele, and the second relationship record ID and a first clinical significance pointer to clinical significance information of the mutation, wherein each node in the first plurality of nodes has a first fixed size;

generating, by the one or more computing devices, a first new node having the first fixed size in the graph database comprising a third relationship record ID and a second mutation pointer to updated information about the mutation, in response to receiving the updated information about the mutation;

determining, by the one or more computing devices, updated clinical significance information of the mutation based on the updated information about the mutation;

generating, by the one or more computing devices, a second new node having the first fixed size in the graph database comprising a fourth relationship record ID and a second clinical significance pointer to the updated clinical significance information of the mutation, wherein the first new node and the second new node are added to the plurality of nodes of the graph database;

forming, by the one or more computing devices, a relationship chain in the relationship data structure, the relationship chain comprising a second plurality of nodes storing an allele node ID, a mutation node ID, a clinical significance node ID, a first new node ID, and a second new node ID, wherein each node in the second plurality of nodes has a second fixed size; and

generating, by the one or more computing devices, a report of a clinical significance of the mutation in the allele by traversing the relationship chain in the relationship data structure using the first through fourth relationship record IDs.

10. The method of claim 9 , wherein traversing the relationship chain comprises:

selecting, by the one or more computing devices, one of the first plurality of nodes as a starting node;

determining, by the one or more computing devices, a location of the starting node in the graph database based on an identifier of the starting node and the first fixed size; and

determining, by the one or more computing devices, locations of other nodes in the graph database based on the relationship chain.

11. The method of claim 9 , wherein generating the report comprises:

receiving, by the one or more computing devices, a query to retrieve information regarding the mutation, wherein the query indicates a starting node to start the query;

determining, by the one or more computing devices, relevant nodes from the at least one of the first plurality of nodes for generating the report of the clinical significance of the mutation; and

starting at the starting node, traversing, by the one or more computing devices, the relevant nodes to generate the report of the clinical significance of the mutation based on the relationship chain in the relationship data structure.

12. The method of claim 9 , wherein a plurality of edges connect the first plurality of nodes based on the first through fourth relationship record IDs in the relationship chain.

13. The method of claim 9 , wherein the information about the mutation includes a description of the mutation as a variant of a reference human genome.

14. The method of claim 9 , wherein the updated information about the mutation includes sequence read data.

15. A non-transitory computer-readable medium having instructions stored thereon, execution of which, by one or more processors of a device, cause the one or more processors to perform operations comprising:

receiving updated information about a mutation of an allele to be stored in a data storage device including a graph database and a relationship data structure, wherein the graph database comprises a first plurality of nodes storing a first relationship record identifier (ID) and an allele pointer to allele information about the allele, a second relationship record ID and a first mutation pointer to mutation information about the mutation of the allele, and the second relationship record ID and a first clinical significance pointer to clinical significance information of the mutation, wherein each node in the first plurality of nodes has a first fixed size;

generating a first new node having the first fixed size in the graph database comprising a third relationship record ID and a second mutation pointer to updated information about the mutation, in response to receiving the updated information about the mutation;

identifying updated clinical significance information of the mutation based on the updated information about the mutation;

generating a second new node having the first fixed size in the graph database comprising a fourth relationship record ID and a second clinical significance pointer to the updated clinical significance information of the mutation, wherein the first new node and the second new node are added to the first plurality of nodes of the graph database;

forming a relationship chain in the relationship data structure, wherein the relationship chain comprises a second plurality of nodes storing an allele node ID, a mutation node ID, a clinical significance node ID, a first new node ID, and a second new node ID, wherein each node in the second plurality of nodes has a second fixed size; and

generating a report of a clinical significance of the mutation in the allele by traversing the relationship chain in the relationship data structure using the first through fourth relationship record IDs.

16. The non-transitory computer-readable medium of claim 15 , wherein the operations for traversing the relationship chain further comprise:

selecting one of the first plurality of nodes as a starting node;

determining a location of the starting node in the graph database based on an identifier of the starting node and the first fixed size ; and

determining locations of other nodes in the graph database based on the relationship chain.

17. The non-transitory computer-readable medium of claim 15 , wherein the operations for generating the report further comprise:

receiving a query to retrieve information regarding the mutation, wherein the query indicates a starting node to start the query;

determining relevant nodes from at least one of the first plurality of nodes for generating the report of the clinical significance of the mutation; and

starting at the starting node, traversing the relevant nodes to generate the report of the clinical significance of the mutation based on the relationship chain in the relationship data structure.

Assignments (7)

Continuity (3)

References Cited (400)