Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
Inventors
Van Rooyen, Pieter • Ruehle, Michael • Mehio, Rami • Hahm, Mark
Assignees
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Publication Number
US-10691775-B2
Publication Date
2020-06-23
Expiration 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.
Core Innovation
The invention provides a system for performing a bioinformatics analysis on genomic data from a subject using genetic reference sequence data, where both the genomic data and the genetic reference sequence data represent sequences of nucleotides. The system includes a cloud computing cluster with one or more servers, memory associated with the servers for storing the genomic data and the genetic reference sequence data, and a field programmable gate array (FPGA) housed in at least one server. The FPGA comprises a set of hardwired digital logic circuits interconnected by physical electrical interconnects, including a memory interface to access the memory.
The hardwired digital logic circuits are arranged as a set of processing engines to perform one or more steps in the bioinformatics analysis. The processing engines access the genomic data and the genetic reference sequence data, compare the sequence of nucleotides to determine one or more similarities or differences, and produce results data storable in the memory. The cloud computing cluster is configured to access, retrieve, and process the results data.
The processed results data are used to generate one or more diagnostic, prophylactic and/or therapeutic evaluations based on the similarities or differences. The invention also provides a cancer diagnostic system that performs a cancer diagnostic analysis and generates one or more diagnostic evaluations including an identification or likelihood of cancer.
Claims Coverage
The independent claims cover a cloud computing cluster with memory and FPGA-based hardwired digital logic processing engines that compare subject genomic nucleotide sequences to genetic reference sequence data to produce results data, then generate diagnostic, prophylactic and/or therapeutic evaluations. Four inventive features are present.
Cloud/fpga processing engines for nucleotide comparison
A cloud computing cluster with servers and memory storing genomic data and genetic reference sequence data, and an FPGA housed in at least one server with hardwired digital logic circuits interconnected by physical electrical interconnects including a memory interface, the hardwired circuits arranged as processing engines to access the data, compare nucleotide sequences, determine similarities or differences, and produce results data storable in memory.
Cloud processing of results data to generate evaluations
The cloud computing cluster accesses, retrieves, and processes the results data to generate diagnostic, prophylactic and/or therapeutic evaluations based on similarities or differences.
Bioinformatics pipeline platform with fpga
A bioinformatics analysis pipeline platform with a data analysis module and memory interface, where an FPGA is configured to perform comparing steps between genomic data and genetic reference sequence data to produce results data stored in memory, and the cloud computing cluster generates diagnostic, prophylactic and/or therapeutic evaluations representing the similarities or differences.
Cancer diagnostic system with identification or likelihood of cancer
A cancer diagnostic system in which FPGA processing engines compare nucleotide sequences to produce results data comprising similarities or differences, and the cloud computing cluster generates diagnostic evaluations including an identification or likelihood of cancer.
Across the independent claims, the shared inventive structure is a cloud computing cluster with memory and FPGA-based hardwired digital logic processing engines that compare nucleotide sequences to produce results data, followed by cloud processing to generate diagnostic, prophylactic and/or therapeutic evaluations, including diagnostic evaluations identifying or indicating likelihood of cancer.
Stated Advantages
Generates one or more diagnostic, prophylactic and/or therapeutic evaluations based on similarities or differences between genomic data and genetic reference sequence data.
Cancer diagnostic evaluations include an identification or likelihood of cancer based on similarities or differences.
Documented Applications
Producing diagnostic, prophylactic and/or therapeutic evaluations from bioinformatics analysis results based on similarities or differences between a subject’s genomic data and genetic reference sequence data.
Performing a cancer diagnostic analysis on genomic data to generate diagnostic evaluations including identification or likelihood of cancer.
Executing one or more third party applications for a portion of a genetic sequence analysis pipeline over stored reads and reference sequence data, and generating diagnostic evaluations.
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