PATENT CLAIM ANALYSIS

Application Number: 15907263
Application Type: Utility
Filing Date: 2018-02
Publication Date: 2018-07
Patent Classification: ["702", "019000"]

Abstract:
A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline. Additionally, a second integrated circuit is also provided, where each second integrated circuit forming a field programmable gate array (FPGA), the FPGA being configured by firmware to arrange a set of hardwired digital logic circuits that are interconnected by a plurality of physical interconnects to perform a second set of genomic processing steps of the sequence analysis pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second set of genomic processing steps. A shared memory is also provided.

Claim (Index 1):
An integrated circuit for executing a sequence analysis pipeline on a read of genomic data, derived from a genetic sequence of a subject, using one or more of a reference genetic sequence and a candidate haplotype sequence to determine a probability of observing the read of genomic data assuming the candidate haplotype sequence is a true representation of the subject's genetic sequence, each read of genomic data, the genetic reference sequence, and the candidate haplotype sequence representing a sequence of nucleotides, the integrated circuit being formed of a set of reconfigurable hardwired digital logic circuits that are interconnected by a plurality of physical electrical interconnects, one or more of the plurality of physical electrical interconnects comprising a memory interface for the integrated circuit to access a memory, the reconfigurable hardwired digital logic circuits being arranged as a first set of processing engines, the first set of processing engines to perform a plurality of steps in the sequence analysis pipeline on the read of genomic data and the candidate haplotype sequence, the first set of processing engines comprising a candidate haplotype generation and analysis module in a first hardwired configuration to:\n receive from the memory, via at least one of the plurality of physical electrical interconnects, a plurality of aligned reads of genomic data; form a pile up out of the plurality of aligned reads of genomic data; generate a graph of potential candidate haplotype sequences from the pile up of reads of genomic data to produce a generated graph; extract a candidate haplotype sequence from the generated graph of potential haplotype sequences to produce an extracted contiguous candidate haplotype sequence; select a read of genomic data for sequence analysis; compare the sequence of nucleotides of the contiguous candidate haplotype sequence to the sequence of nucleotides of the read of genomic data; perform a Hidden Markov Model (HMM) operation on each of the nucleotide sequences of the read of genomic data and the contiguous candidate haplotype sequence; and determine a probability of observing the read of genomic data assuming the candidate haplotype sequence is a true representation of the subject's genetic sequence.

Metadata:
- Claim Count in Document: 80.0
- Percentile: 88.0
- Lexical Diversity: 2.40506
- Patent Class: 702.0
- Transitional Phrase Type: open
- Component Type: 1
- Foreign Priority: False
- Related Applications: ['15497149', '15059221', '15643381', '15094939', '15700018']

Analysis Scores:
- 35 USC 101 Eligibility (BERT): 0.2913823342052846
- 35 USC 102 Novelty (BERT): 0.5743129925534839
- Combined Prediction Score: 0.3196754000401045
- Mean Citation Score: 430.74245
- Max Citation Score: 477.48706
- Similarity Product: 408.2571374966622

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