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

Inventors

Van Rooyen, Pieter • Ruehle, Michael • Mehio, Rami

Assignees

Edico Genome Corp

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

A genomics analysis platform executes a sequence analysis pipeline using one or more first processing units and one or more programmable logic devices or one or more ASICs. The first processing units execute one or more software algorithms to perform one or more first genomic processing operations and access one or more first memory devices, while the hardwired digital logic circuits are programmatically configured into a physical configuration to perform one or more second genomic processing operations or one or more third genomic processing operations.

The programmable hardware devices are physically arranged as a set of processing engines including one or more mapping engines for the second genomic processing operations and one or more aligning engines for the third genomic processing operations. The platform couples the first processing units and the programmable hardware devices using physical electronic interconnects, enabling genomic data to be communicated between first memory devices and second memory devices in opposite directions.

The sequence analysis pipeline includes seed chaining and heuristic filtering to identify superior and inferior seed chains, optional one-change SNP editing when no seed hits occur, dynamic programming alignment using a Smith-Waterman or Needleman-Wunsch approach, wavefront scoring and banded alignment, localized de Bruijn graph assembly to generate candidate haplotypes, and pair-HMM modeling with M/I/D states. The platform outputs alignment information including a CIGAR string and alignment score parameters, and variant calling outputs variant call files with MAPQ and confidence estimates.

Claims Coverage

The document contains four independent claim groupings across programmable logic devices and ASICs. Together, they cover a genomics analysis platform that executes a sequence analysis pipeline with software-executed first genomic processing on first processing units, hardwired digital logic circuits arranged as mapping and aligning processing engines, and bidirectional genomic data exchange between first and second memory devices via physical electronic interconnects.

Across the independent claims, the core coverage is an architecture for executing a sequence analysis pipeline where software-executed first processing units access first memory devices, specialized hardware with hardwired digital logic circuits performs mapping and aligning processing engines, and bidirectional genomic data exchange between first and second memory devices is performed via physical electronic interconnects.

Stated Advantages

Documented Applications