Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform

Patent metadata

Field	Value
Publication number	US-2016306922-A1
Application number	US-201615201175-A
Country	US
Kind code	A1
Filing date	Jul 1, 2016
Priority date	Jan 17, 2013
Publication date	Oct 20, 2016
Grant date	—

Abstract

A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit that may be connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits may be arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the bioinformatics analysis on the reads of genomic data. Each subset of the hardwired digital logic circuits may be formed in a wired configuration to perform the one or more steps in the bioinformatics analysis.

First claim

What is claimed is:

1 . A system for performing a bioinformatics analysis on genomic data using genetic reference sequence data, where each of the genomic data and the genetic reference sequence data represent a sequence of nucleotides, the system comprising:
a cloud computing cluster having one or more servers; a memory associated with the one or more servers for storing the genomic data and the genetic reference sequence data; and a field programmable gate array (FPGA) housed in at least one of the one or more servers, the FPGA comprising a set of hardwired digital logic circuits, the hardwired digital logic circuits being interconnected by a plurality of physical electrical interconnects, one or more of the plurality of physical electrical interconnects comprising a memory interface to access the memory, the hardwired digital logic circuits being arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the bioinformatics analysis on the genomic data, the set of processing engines comprising a first wired configuration to access the genomic data and the genetic reference sequence data, compare the sequence of nucleotides in the genomic data to the sequence of nucleotides of the genetic reference sequence data to determine one or more similarities or differences between the sequence of nucleotides in the genomic data and the sequence of nucleotides in the genetic reference sequence data, and generate one or more diagnostic evaluations based on the one or more similarities or differences.

2 . The system according to claim 1 , further comprising a database connected with the cloud computing cluster for receiving result data comprising the one or more similarities or differences from the set of processing engines, and for storing the result data in one or more electronic health records.

3 . The system according to claim 2 , wherein the cloud computing cluster is further configured to access the one or more electronic health records from the database to perform a tertiary analysis on the result data.

4 . The system according to claim 3 , wherein the tertiary analysis comprises one or more of diagnostic, prophylactic and/or therapeutic evaluation analysis.

5 . The system according to claim 1 , wherein the bioinformatics analyses comprises a cancer evaluation analysis.

6 . The system according to claim 4 , wherein the tertiary analysis is configured to predict a potential of an occurrence of a diseased state.

7 . The system according to claim 6 , wherein the diseased state comprises cancer.

8 . The system according to claim 7 , further comprising one or more application programming interfaces (APIs) that provide accessibility to the cloud computing cluster by one or more third party applications via a communications network.

9 . A system for executing a portion of a bioinformatics analysis pipeline on genomic data using genetic reference sequence data, where each of the genomic data and the genetic reference sequence data represent a sequence of nucleotides, the system comprising:
a cloud computing cluster having a plurality of servers; a memory associated with the plurality of servers for storing the genomic data and the genetic reference sequence data; and a bioinformatics analysis pipeline platform connected with the memory via an application programming interface (API), the bioinformatics analysis pipeline platform comprising a data analysis module to access the genomic data and the genetic reference sequence data from the memory, compare the sequence of nucleotides in the genomic data to the sequence of nucleotides of the genetic reference sequence data, to determine one or more similarities or differences between the sequence of nucleotides in the genomic data and the sequence of nucleotides in the genetic reference sequence data, and to generate one or more diagnostic evaluations representing the one or more similarities or differences.

10 . The system according to claim 9 , further comprising a database connected with the cloud computing cluster for receiving result data comprising the similarities or differences from the data analysis module, and storing the result data in one or more electronic health records.

11 . The system according to claim 10 , wherein the cloud computing cluster is further configured to access the one or more electronic health records from the database to perform a tertiary analysis on the result data.

12 . The system according to claim 11 , wherein the tertiary analysis comprises one or more of diagnostic, prophylactic and/or therapeutic evaluation analysis.

13 . The system according to claim 12 , wherein the one or more of diagnostic, prophylactic and/or therapeutic evaluation analysis comprises a cancer evaluation analysis.

14 . The system according to claim 11 , wherein the tertiary analysis is configured to predict a potential of an occurrence of a diseased state.

15 . The system according to claim 14 , wherein the diseased state comprises cancer.

16 . The system according to claim 15 , wherein the cloud computing cluster is accessible by one or more third party applications via the API.

17 . A genomics processing system for executing a portion of a genetic sequence analysis pipeline, the system comprising:
a cloud computing cluster having one or more servers, the cloud computing cluster having a memory associated with the one or more servers for storing a plurality of reads of genomic data and genetic reference sequence data, each read of genomic data and the genetic reference sequence data representing a sequence of nucleotides; a computing system that executes one or more third party applications for executing the portion of the genetic sequence analysis pipeline using the plurality of reads of genomic data and the genetic reference sequence data stored in the memory; and a sequence analysis pipeline platform connected with the memory and the computing system via one or more application programming interfaces (APIs), the sequence analysis pipeline platform comprising a diagnostic evaluations module to access, in response to the one or more third party applications executed by the computing system, the genomic data and the genetic reference sequence data from the memory, compare the sequence of nucleotides in the genomic data to the sequence of nucleotides of the genetic reference sequence data, to determine one or more differences between the sequence of nucleotides in the genomic data and the sequence of nucleotides in the genetic reference sequence data, and to generate one or more diagnostic evaluations representing the one or more similarities or differences.

18 . The system according to claim 17 , further comprising a database connected with the cloud computing cluster for receiving result data comprising the similarities or differences from the diagnostic evaluations module, and storing the result data in one or more electronic health records.

19 . The system according to claim 18 , wherein the computing system is further configured to access the one or more electronic health records from the database to perform a tertiary analysis on the result data.

20 . The system according to claim 19 , wherein the tertiary analysis comprises one or more of diagnostic, prophylactic and/or therapeutic evaluation analysis.

21 . The system according to claim 20 , wherein the one or more of diagnostic, prophylactic and/or therapeutic ev

Assignees

• Edico Genome Corp

Inventors

• Van Rooyen Pieter
• Ruehle Michael
• Mehio Rami
• Hahm Mark

Classifications

• G06F19/322

  Physics · mapped topic

• G06F19/3431

  Physics · mapped topic

• G06F19/3418

  Physics · mapped topic

• G06F19/24

  Physics · mapped topic

• G06F17/18

  for evaluating statistical data {, e.g. average values, frequency distributions, probability functions, regression analysis (forecasting specially adapted for a specific administrative, business or logistic context G06Q10/04)} · CPC title