Bioinformatics systems, apparatus, and methods executed on an integrated circuit processing platform
Inventors
Rooyen, Pieter Van • McMillen, Robert • Ruehle, Michael
Assignees
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Publication Number
US-11043285-B2
Publication Date
2021-06-22
Expiration Date
Abstract
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.
Core Innovation
The invention describes an apparatus and system for bioinformatics sequence analysis that includes genomic reads, a genetic reference sequence, and an index of the genetic reference sequence stored in one or more memory devices. An integrated circuit formed of configurable digital logic circuits is interconnected by physical electrical interconnects and uses a memory interface to access the memory devices and output data back to memory for storage. The digital logic circuits are configured as a set of processing engines, and a controller coordinates access through the physical electrical interconnects.
A mapping module accesses the index of the genetic reference sequences from memory using the physical electrical interconnects and maps the reads to one or more segments of the genetic reference sequence to produce mapped reads. An alignment module then accesses the genetic reference sequence and a selected mapped read from memory, aligns the mapped reads to positions in the segments to produce aligned reads, and stores data describing the aligned reads in the one or more memory devices.
The invention further characterizes the index and mapping interaction as hash-table-based access in which seeds are extracted and hashed to generate lookup addresses used to access the reference index, including locating corresponding positions in the genetic reference sequences. The alignment may be performed as gapped alignment, and the document also describes hardware-oriented alignment scoring using a wave front and scoring cells implementing a banded dynamic programming approach, with match/mismatch and indel penalties, linear and affine gap penalties, optional base quality score dependent scoring, and backtrace reconstruction for aligned read representations such as CIGAR strings.
Claims Coverage
The independent claims define two inventive features in an apparatus and a system, centered on configurable digital logic circuits interconnected via physical electrical interconnects and a memory interface, with mapping and alignment modules that access reads, a genetic reference sequence, and an index, and store mapped and aligned read data in memory.
Integrated circuit with memory-interface physical electrical interconnects for mapping and storing intermediate results
An apparatus or system with an integrated circuit formed of configurable digital logic circuits interconnected by physical electrical interconnects, where one or more of the physical electrical interconnects comprise a memory interface to access memory devices and to output data for storage in the memory devices.
Mapping module accessing genetic reference index to map reads to reference segments
A mapping module configured to access, from memory, the index of the one or more genetic reference sequences using the physical electrical interconnects, map reads stored in the memory to one or more segments of the one or more genetic reference sequences to produce mapped reads, and store data describing the mapped reads in the one or more memory devices.
Alignment module aligning mapped reads to reference positions
An alignment module configured to access, from memory, the one or more genetic reference sequences and a selected mapped read, align mapped reads stored in memory to one or more positions in the one or more segments of the one or more genetic reference sequences to produce aligned reads, and store data describing the plurality of aligned reads in the one or more memory devices.
Controller or computer access to obtain aligned reads
A controller configured to access the one or more memories using the physical electrical interconnects and provide data describing the aligned reads to a computer, and/or a computer configured to access the one or more memories to obtain the plurality of aligned reads.
The independent claims require configurable digital logic engines connected via physical electrical interconnects that serve as a memory interface, implementing a two-stage pipeline: mapping reads using a genetic reference index to produce mapped reads stored in memory, and aligning the mapped reads to reference positions to produce aligned reads stored in memory for access by a controller or computer.
Stated Advantages
Not explicitly described in patent.
Documented Applications
Not explicitly described in patent.
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