PATENT CLAIM ANALYSIS

Application Number: 15906404
Application Type: Utility
Filing Date: 2018-02
Publication Date: 2018-11
Patent Classification: ["702", "019000"]

Abstract:
The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.

Claim (Index 35):
A system for identifying a structural variation, the system comprising:\n at least one computer hardware processor; and at least one non-transitory computer-readable storage medium storing instructions that, when executed by the at least one computer hardware processor, cause the at least one computer hardware processor to perform:\n representing, in the at least one tangible, non-transitory computer-readable storage medium, a reference sequence and variation of the reference sequence as a reference graph, the reference graph comprising a plurality of nodes and edges, wherein conserved regions of the reference sequence are represented as single nodes and regions that vary are represented as alternate nodes, wherein at least one of the alternate nodes comprises a structural variation not present in the reference sequence; \n receiving one or more nucleotide sequence reads from a nucleic acid sample, wherein at least one sequence read comprises at least a portion of the structural variation; \n determining optimal-scoring alignments between the one or more sequence reads and one or more paths within the reference graph, wherein the determining comprises considering two or more alternative paths by looking backward to any prior nodes on the reference graph to find a maximum score for the one or more sequence reads; and \n identifying the structural variation as present in the nucleic acid sample based on the optimal-scoring alignments between the one or more sequence reads and the one or more paths.

Metadata:
- Claim Count in Document: 59.0
- Percentile: 88.0
- Lexical Diversity: 1.96552
- Patent Class: 702.0
- Transitional Phrase Type: open
- Component Type: 1
- Foreign Priority: False
- Related Applications: ['15196345', '14041850', '14811057', '14517406', '14016833']

Analysis Scores:
- 35 USC 101 Eligibility (BERT): 0.2257385765195186
- 35 USC 102 Novelty (BERT): 0.6429809203585428
- Combined Prediction Score: 0.267462810903421
- Mean Citation Score: 436.52065000000016
- Max Citation Score: 459.58737
- Similarity Product: 347.3955027980858

Labels:
- Claim Label 101: 1
- Claim Label 102: 1
- Claim Label 103: 1
- Claim Label 112: 1
- Combined Label: 1
- Label 101 Adjusted: 1

Dataset: test