Systems and methods for genetic analysis
Inventors
Frieden, Alexander • Kennedy, Caleb J. • Haurie, Xavier S.
Assignees
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Publication Number
US-12386895-B2
Publication Date
2025-08-12
Expiration Date
Abstract
The invention relates to using a graph database in genetic analyses to link mutation data to extrinsic data. Entities such as mutations, patients, samples, alleles, and clinical information are individually represented and stored as nodes and relationships between entities are also individually represented and stored. Each node and relationship can be stored using a fixed-size record and nodes can be flexibly invoked to represent any entity without disrupting the existing data. Systems and methods of the invention may be used for obtaining data representing a mutation in an individual and using a node in a graph database to store a description of the mutation. The node has stored within it a pointer to an adjacent node that provides information about a clinical significance of the variant. The graph database can be queried to provide a report of the clinical significance of the mutation.
Core Innovation
The invention describes a system and method for describing genetic information using a graph database and a relationship data structure. The graph database stores an allele node, a mutation node, and a clinical significance node, where each node has a first fixed size, and the allele node stores an allele pointer to allele information about an allele included in genomic information of a sample obtained from an individual.
The mutation node stores a second relationship record ID and a first mutation pointer to mutation information about a mutation in the allele, and the clinical significance node stores the second relationship record ID and a first mutation pointer to clinical significance information about the mutation. A relationship data structure includes first and second relationship records that are located by the first and second relationship record IDs, respectively, and include node IDs, relationship types, and pointers between relationship records.
The system receives updated information about a mutation and updated information about clinical significance, generates an updated mutation node and an updated clinical significance information node in the graph database, and generates third and fourth relationship records that form a relationship chain. A report of a clinical significance of the mutation in the allele is generated by traversing the relationship chain in the relationship data structure using the first through fourth relationship record IDs.
Claims Coverage
The independent claims (clm-00001, clm-00009, clm-00015) cover fixed-size graph nodes and fixed-size relationship records for genetic information, including mutation update handling and generating a clinical-significance report by traversing a relationship chain using relationship record identifiers.
Fixed-size allele, mutation, and clinical significance nodes with pointer identifiers
The system comprises a memory storing a graph database including an allele node, a mutation node, and a clinical significance node, wherein each node has a first fixed size and stores relationship record identifiers and pointers to allele information, mutation information, or clinical significance information.
Fixed-size relationship records forming a relationship chain navigable by record IDs
A relationship data structure comprises relationship records located by relationship record IDs, each having a second fixed size and storing node IDs, relationship types, and pointers between relationship records to form a relationship chain.
Update mutation and clinical significance by generating new fixed-size nodes and relationship records
The processor receives updated information about the mutation and updated information about the clinical significance of the mutation, generates updated fixed-size nodes, and generates third and fourth relationship records having the second fixed size and forming a relationship chain in the relationship data structure.
Generate a clinical significance report by traversing the relationship chain using relationship record IDs
The processor generates a report of a clinical significance of the mutation in the allele based on the relationship records by traversing the relationship chain in the relationship data structure using the first through fourth relationship record IDs.
Across the claims, the coverage centers on storing genetic information in a graph database with fixed-size nodes linked by fixed-size relationship records, updating mutation and clinical significance information by adding new nodes and relationship records, and generating a clinical significance report by traversing the relationship chain using relationship record identifiers.
Stated Advantages
Scalable query/report time independent of total database size.
Ability to insert novel entities and relationships during active variant curation.
Rapid generation of clinical-significance reports.
Documented Applications
Use with NGS-based carrier screening and genetic analysis, where mutations, alleles, patients, samples, clinical and literature entities are modeled in a graph database.
Generating clinical-significance reports by traversing relationship chains for variant classifications.
Performing allele-frequency queries using the modeled graph entities and relationships.
Linking variant-related entities to literature references and patient samples for clinical reporting and update tracking when variant classifications change.
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