# US 2019/0171963 A1 · Bioinformatics Systems, Apparatuses, and Methods Executed on a Quantum Processing Platform

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- Number: US 2019/0171963 A1
- Document ID: US20190171963A1
- Status: Published application
- Kind: A1
- Application number: 16/119,418
- Filed: 2018-08-31
- Published: 2019-06-06
- Earliest claimed: 2017-02-23
- Assignees: Edico Genome, Corp.
- Applicants: Edico Genome, Corp.
- Inventors: Pieter van Rooyen
- Web page: https://patentgrep.com/patent/US20190171963A1

## CPC

- G16B 30/00: ICT specially adapted for sequence analysis involving nucleotides or amino acids
- G06F 18/295: {Markov models or related models, e.g. semi-Markov models; Markov random fields; Networks embedding Markov models}
- G06N 7/01: Probabilistic graphical models, e.g. probabilistic networks
- G06N 10/40: Physical realisations or architectures of quantum processors or components for manipulating qubits, e.g. qubit coupling or qubit control
- G06V 10/85: {Markov-related models; Markov random fields}
- G06V 10/955: {using specific electronic processors}
- G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B 20/20: Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
- G16B 30/10: Sequence alignment; Homology search
- G16B 50/00: ICT programming tools or database systems specially adapted for bioinformatics
- G16B 50/10: Ontologies; Annotations
- G16B 50/30: Data warehousing; Computing architectures
- G16B 50/40: Encryption of genetic data
- G16B 50/50: Compression of genetic data
- G06F 16/137: {Hash-based (content-based indexing of textual data G06F16/31)}
- G16B 30/20: Sequence assembly
- G16B 40/00: ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G06F: ELECTRIC DIGITAL DATA PROCESSING (computer systems based on specific computational models G06N)
- G06N: COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06V: IMAGE OR VIDEO RECOGNITION OR UNDERSTANDING

## Abstract

A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data includes a quantum computing device formed of a set of hardwired quantum logic circuits interconnected by a plurality of superconducting connections to process information represented as a quantum state that is configured as a set of one or more qubits. The hardwired quantum logic circuits may be arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired quantum logic circuits to perform one or more steps in the bioinformatics analysis on the reads of genomic data. Each subset of the hardwired quantum logic circuits may be formed in a wired configuration to perform the one or more steps in the bioinformatics analysis.

## Claims

### Claim 1

A system for executing a sequence analysis pipeline on a plurality of reads of genomic data using an index of genetic reference data stored in a memory, each read of genomic data representing a sequence of nucleotides, the genetic reference data representing one or more genetic reference sequences, the system comprising:
a quantum computing device formed of a set of hardwired quantum logic circuits interconnected by a plurality of superconducting connections to process information represented as a quantum state that is configured as a set of one or more qubits, one or more of the plurality of superconducting connections comprising a memory interface for accessing the memory, the set of hardwired quantum logic circuits being arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired quantum logic circuits to perform one or more steps in the sequence analysis pipeline on the plurality of reads of genomic data, the set of processing engines comprising a mapping module in a first hardwired configuration to:
receive a read of genomic data via the memory interface of the one or more of the plurality of superconducting connections;
extract a portion of the read to generate a seed, the seed representing a subset of the sequence of nucleotides represented by the read;
calculate a first address within the index based on the seed;
access the address in the index in the memory;
receive a record from the address, the record representing position information in the genetic reference sequence;
determine, based on the record, one or more matching positions from the read to the genetic reference sequence; and
output at least one of the matching positions to the memory via the memory interface.