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

Patent metadata

Field	Value
Publication number	US-9342652-B2
Application number	US-201514948372-A
Country	US
Kind code	B2
Filing date	Nov 22, 2015
Priority date	Jan 17, 2013
Publication date	May 17, 2016
Grant date	May 17, 2016

Abstract

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.

First claim

We claim as our invention the following:

1. A structured application-specific integrated circuit (ASIC) for analyzing genetic sequence data from an electronic data source that provides digital signals representing a plurality of reads of genomic data, each of the plurality of reads of genomic data comprising a sequence of nucleotides, and using a memory storing one or more genetic reference sequences associated with genomic data and an index of the one or more genetic reference sequences, the structured ASIC comprising:
a master slice that includes a set of digital logic circuits; and
one or more configurable metal layers formed on the master slice, each of the one or more configurable metal layers having a set of wired connections, the wired connections of the one or more configurable metal layers being arranged to interconnect a subset of the digital logic circuits to form a set of processing engines, the set of processing engines comprising:
a mapping engine to access the index of the one or more genetic reference sequences from the memory to map the read to one or more segments of the one or more genetic reference sequences based on the index; and
an alignment engine to access the one or more genetic reference sequences from the memory to align the read to one or more positions in the one or more segments of the one or more genetic reference sequences from the mapping engine.

2. The structured ASIC according to claim 1 wherein the set of processing engines further comprises a sorting engine to sort each aligned read according to the one or more positions in the one or more genetic reference sequences.

3. The structured ASIC according to claim 1 wherein a portion of the set of digital logic circuits is hardwired in the master slice as a base calling engine to analyze the genetic sequence data from the electronic data source to determine a most likely nucleotide at each position sequenced by the sequencer, and to estimate a confidence of the most likely nucleotide.

4. The structured ASIC according to claim 1 wherein a portion of the set of digital logic circuits is hardwired in the master slice as one or more embedded processor cores.

5. The structured ASIC according to claim 4 wherein one or more processing engines of the set of processing engines are connected to the one or more embedded processor cores via the one or more configurable metal layers formed on the master slice.

6. The structured ASIC according to claim 1 wherein the set of processing engines further comprises a primary analysis pipeline engine, the primary analysis pipeline engine executing on the genomic data one or more of: signal processing, image processing, base calling, and base call quality estimation.

7. The structured ASIC according to claim 6 wherein a portion of the set of digital logic circuits in the master slice is hardwired as a primary analysis pipeline engine accelerator to accelerate processing by the primary analysis pipeline engine.

8. The structured ASIC according to claim 1 wherein a first portion of the set of digital logic circuits in the master slice is hardwired as a base calling engine, and wherein a second portion of the set of digital logic circuits in the master slice is hardwired as one or more embedded processor cores, the base calling engine to analyze the genetic sequence data from the electronic data source to determine a most likely nucleotide at each position sequenced by the sequencer, and to estimate a confidence of the most likely nucleotide.

9. The structured ASIC according to claim 8 wherein one or more processing engines of the set of processing engines are connected to the one or more embedded processor cores via the one or more configurable metal layers formed on the master slice.

10. The structured ASIC according to claim 1 wherein the set of processing engines further comprises a base calling engine to analyze the genetic sequence data from the electronic data source to determine a most likely nucleotide at each position sequenced, and to estimate a confidence of the most likely nucleotide.

11. The structured ASIC according to claim 1 wherein the set of processing engines further comprises one or more embedded processor cores.

12. A structured application-specific integrated circuit (ASIC) for analyzing genetic sequence data from an electronic data source that provides digital signals representing a plurality of reads of genomic data, each of the plurality of reads of genomic data comprising a sequence of nucleotides, and using a memory storing one or more genetic reference sequences associated with genomic data and an index of the one or more genetic reference sequences, the structured ASIC comprising:
a master slice comprising a plurality of digital logic circuits; and
a plurality of configurable metal layers formed on the master slice, each of the plurality of configurable metal layers having a plurality of wired connections arranged to interconnect a subset of the plurality of digital logic circuits to form a mapping engine and an alignment engine, wherein the mapping engine is configured to access the index of the one or more genetic reference sequences from the memory to map the read to one or more segments of the one or more genetic reference sequences based on the index, and wherein the alignment engine is configured to access the one or more genetic reference sequences from the memory to align the read to one or more positions in the one or more segments of the one or more genetic reference sequences from the mapping engine.

13. A structured application-specific integrated circuit (ASIC) for analyzing genetic sequence data from an electronic data source that provides digital signals representing a plurality of reads of genomic data, each of the plurality of reads of genomic data comprising a sequence of nucleotides, and using a memory storing one or more genetic reference sequences associated with genomic data and an index of the one or more genetic reference sequences, the structured ASIC comprising:
a master slice comprising a plurality of digital logic circuits; and
a plurality of configurable metal layers formed on the master slice, each of the plurality of configurable metal layers having a plurality of wired connections arranged to interconnect a first subset of the plurality of digital logic circuits to form a plurality of processing engine comprising a base calling engine, a mapping engine, an alignment engine and a sorting engine.

14. The structured ASIC according to claim 13 wherein the base calling engine is configured to analyze the genetic sequence data from the electronic data source to determine a most likely nucleotide at each position sequenced by the sequencer, and to estimate a confidence of the most likely nucleotide.

15. The structured ASIC according to claim 14 wherein the a sorting engine is configured to sort each aligned read according to the one or more positions in the one or more genetic reference sequences.

16. The structured ASIC according to claim 14 wherein the mapping engine is configured to access the index of the one or more genetic reference sequences from the memory to map the read to one or more segments of the one or more genetic reference sequences based on the index.

17. The structured ASIC according to claim 16 wherein the alignment engine is configured to access the one or more genetic reference sequences from the memory to align the read to one or more positions in the one or more segments of the one or more genetic reference sequences from the mapping engine.

Assignees

• Edico Genome Corp

Inventors

• Van Rooyen Pieter
• Mcmillen Robert J
• Ruehle Michael

Classifications

• G06F13/4265

  on a point to point bus (G06F13/4247, G06F13/4282 take precedence) · CPC title

• G16B30/00

  ICT specially adapted for sequence analysis involving nucleotides or amino acids · CPC title

• H03K19/17736

  Structural details of routing resources · CPC title

• G06F13/16

  for access to memory bus (G06F13/28 takes precedence) · CPC title

• G16B40/00

  ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding · CPC title