Edico Genome Corporation

Intel Corporation

Lsi Corporation

Illumina Corporation

Other

Tarari, Inc.

Michael D Ruehle

Pieter Van Rooyen

Robert J McMillen

Rami Mehio

Mark Hahm

Eric Jon Ojard

Gavin Stone

Amnon Ptashek

Varun Jain

Johann Felix Wilhelm Schlesinger

Nayan Amrutlal Suthar

Viraj Deshpande

Sean Truong

Severine Catreux

Jacobus De Beer

John Cooper Roddey

Rahul Indarbhan Khinvasara

Jason E Cosky

Vinay Janardan Naik

Umesh Ramkrishnarao Kasture

Qiyan Sun

Adam Scislowicz

Arun Visvanath

Robert Mcmillen

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.

Bioinformatics systems, apparatuses, and methods for performing secondary and/or tertiary processing

Methods, systems, and apparatuses, including computer programs for identifying a gene fusion in a biological sample are disclosed. The method can include actions of obtaining first data that represents a plurality of aligned reads, identifying a plurality of fusion candidates included within the obtained first data, filtering the plurality of fusion candidates to determine a filtered set of fusion candidates, for each particular fusion candidate of the filtered set of fusion candidates: generating, by one or more computers, input data for input to a machine learning model that includes extracted feature data that to represents the particular fusion candidate, providing the generated input data as an input to the machine learning model that has been trained to generate output data representing a likelihood that a fusion candidate is a valid gene fusion, and determining whether the particular fusion candidate corresponds to a valid gone fusion based on the output data.

Rapid detection of gene fusions

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.

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

Methods, systems, and apparatuses, including computer programs for generating and using a hash table configured to improve mapping of reads are disclosed that include obtaining a first seed of K nucleotides from a reference sequence, generating a seed extension tree having a nodes, wherein each node of the nodes corresponds to (i) an extended seed that is an extension of the first seed and has a nucleotide length of K* and (ii) one or more locations, in a seed extension table, that include data describing reference sequence locations that match the extended seed, and for each node: storing interval information at a location of the hash table that corresponds to an index key for the extended seed, wherein the interval information references one or more locations in the seed extension table that include reference sequence locations that match the extended seed associated with the node.

Flexible seed extension for hash table genomic mapping

Bioinformatics systems, apparatuses, and methods for generating a De Brujin graph

A system, method and apparatus for executing a sequence analysis pipeline 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 connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are 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 sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

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

A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes a 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 connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are 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 sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

Genomic infrastructure for on-site or cloud-based DNA and RNA processing and analysis

A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes a structured ASIC 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 structured ASIC connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are 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 sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

Disclosed is a method and system for matching a complex NFA state comprising a spinner followed by a character class sequence which may be represented by the general regular expression form [S] {N,M}[A][A] . . . [Ak&#x2212;]. An input transition activates the spinner and the spin count increments with successive matches of the spin class [S]. When the spin count is between N and M, sequence matching begins. Several base sequence CCLs are compared in parallel with a corresponding window of input symbols. If all match, a signal enters a delay line until the end of the base sequence. When the signal exits the delay line, extended sequence CCLs are accessed from a table sequentially and compared with successive input symbols. After the final extension CCL matches, an output transition is signaled. For short sequences, unused base sequence CCLs may be configured with look-ahead classes.

Complex NFA state matching method that matches input symbols against character classes (CCLS), and compares sequence CCLS in parallel

Growing community of inventors

Santa Clara, CA, United States of America

Michael D Ruehle