Adaptive compression and modification of nanopore measurement data

• US 10,102,338 B2
• Filed: 09/24/2015
• Issued: 10/16/2018
• Est. Priority Date: 09/24/2015
• Status: Active Grant

• Current Assignee: Roche Sequencing Solutions, Inc. (Roche Holding AG)
• Original Assignee: Genia Technologies, Inc. (Roche Holding AG)
• Inventors: Fernandez-Gomez, Santiago, Tian, Hui, Maney, Bill, Rajaraman, Jayalakshmi
• Primary Examiner(s): Negin, Russell Scott
• Application Number:
  US14/864,408
• Publication Number:
  US 20170091381A1
• Time in Patent Office: 1,118 Days
• Field of Search: None
• CPC Class Codes: G01N 33/48721 Investigating individual macromolecules, e.g. by translocation through nanopores Coulter counters in general G01N15/12; fabrication methods for nanoscale apertures B81B1/00; sequencing of nucleic acids C12Q1/68
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

A system includes a plurality of nanopore cells. Data corresponding to nanopore states of the plurality of nanopore cells is received. The data is analyzed to determine a compressed output size of the data given at least one compression technique. It is determined whether the compressed output size exceeds a data budget. In the event it is determined that the compressed output size exceeds the data budget, the data is modified. The modified data is outputted.

Claims

1. A system, comprising:

a plurality of nanopore cells; and

a processor configured to;

receive data corresponding to nanopore states of the plurality of nanopore cells;

analyze the data to determine a compressed output size of the data given at least one compression technique;

determine whether the compressed output size exceeds a data budget;

in response to a determination that the compressed output size exceeds the data budget, modify the data and output the modified data; and

detect that the received data indicates that a state of a nanopore has changed from a threaded state to an open-channel state prior to an end of a bright period of an AC voltage source signal cycle and no longer indicates the threaded state of the nanopore in a previously received data.

2. The system of claim 1, wherein the system is included in a biochip.

3. The system of claim 1, wherein the plurality of nanopore cells is included in a biochip and the processor is included in a chip separate from the biochip.

4. The system of claim 1, wherein receiving the data includes receiving for each nanopore cell a one bit indicator indicating a nanopore state of the nanopore cell.

5. The system of claim 4, wherein receiving the data includes combining together a plurality of one bit indicators into a bit array.

6. The system of claim 1, wherein analyzing the data includes selecting a selected compression technique among a plurality of compression techniques.

7. The system of claim 6, wherein the plurality of compression techniques are non-lossy compression techniques.

8. The system of claim 6, wherein selecting the selected compression technique includes determining an entropy of the data and determining that the selected compression technique best compresses data with the determined entropy.

9. The system of claim 1, wherein determining whether the compressed output size exceeds the data budget includes determining whether the compressed output size exceeds a threshold size.

10. The system of claim 1, wherein it is determined that the compressed output size exceeds the data budget based on a determination that an amount of data included in an output buffer exceeds a threshold level.

11. The system of claim 1, wherein the modifying the data includes removing a portion of the data.

12. The system of claim 1, wherein the processor is further configured to, in response to a determination that an uncompressed size of the data meets the data budget, output the data as uncompressed.

13. The system of claim 1, wherein in response to a determination that a non-lossy compressed version of the modified data does not meet the data budget, the modified data is compressed using a lossy compression technique to meet the data budget.

14. A method, comprising:

receiving data corresponding to nanopore states of a plurality of nanopore cells;

analyzing the data to determine a compressed output size of the data given at least one compression technique;

determining whether the compressed output size exceeds a data budget;

in response to a determination that the compressed output size exceeds the data budget, modify the data and output the modified data; and

detecting that the received data indicates that a state of a nanopore has changed from a threaded state to an open-channel state prior to an end of a bright period of an AC voltage source signal cycle and no longer indicates the threaded state of the nanopore in a previously received data.

15. The method of claim 14, wherein the method is performed using a biochip.

16. The method of claim 14, wherein the plurality of nanopore cells is included in a biochip and at least a portion of the method is performed by a chip separate from the biochip.

17. The method of claim 14, wherein receiving the data includes receiving for each nanopore cell a one bit indicator indicating a nanopore state of the nanopore cell.

18. The method of claim 17, wherein receiving the data includes combining together a plurality of one bit indicators into a bit array.

19. The method of claim 14, wherein analyzing the data includes selecting a selected compression technique among a plurality of compression techniques.

20. The method of claim 19, wherein the plurality of compression techniques are non-lossy compression techniques.

21. The method of claim 19, wherein selecting the selected compression technique includes determining an entropy of the data and determining that the selected compression technique best compresses data with the determined entropy.

22. The method of claim 14, wherein determining whether the compressed output size exceeds the data budget includes determining whether the compressed output size exceeds a threshold size.

23. The method of claim 14, wherein it is determined that the compressed output size exceeds the data budget based on a determination that an amount of data included in an output buffer exceeds a threshold level.

24. The method of claim 14, wherein the modifying the data includes removing a portion of the data.

25. The method of claim 14, further comprising, in response to a determination that an uncompressed size of the data meets the data budget, outputting the data as uncompressed.

26. The method of claim 14, wherein in response to a determination that a non-lossy compressed version of the modified data does not meet the data budget, the modified data is compressed using a lossy compression technique to meet the data budget.

27. A computer program product, the computer program product being embodied in a non-transitory computer readable storage medium and comprising computer instructions for:

receiving data corresponding to nanopore states of a plurality of nanopore cells;

analyzing the data to determine a compressed output size of the data given at least one compression technique;

determining whether the compressed output size exceeds a data budget;

in response to a determination that the compressed output size exceeds the data budget, modify the data and output the modified data; and

detecting that the received data indicates that a state of a nanopore has changed from a threaded state to an open-channel state prior to an end of a bright period of an AC voltage source signal cycle and no longer indicates the threaded state of the nanopore in a previously received data.