Methods and computer program products for compression of sequencing data

Patent metadata

Field	Value
Publication number	US-2017194985-A1
Application number	US-201615368765-A
Country	US
Kind code	A1
Filing date	Dec 5, 2016
Priority date	Jan 31, 2012
Publication date	Jul 6, 2017
Grant date	—

Abstract

A compression method includes measuring a waveform associated with a chemical event occurring on a sensor array, wherein the waveform comprises at least one region associated with expected measured values and at least one region associated with unpredictable measured values; applying a first compression process to the waveform, the first compression process including an averaging of one or more frames in one or more portions of the waveform; applying a keyframe delta compression to the frame-averaged data; forming a compressed data structure including a keyframe and calculated differences subsequent to the keyframe; and storing one or more compressed data structures in memory.

First claim

1 .- 20 . (canceled)

21 . A compression method, comprising:
measuring a waveform associated with a chemical event occurring on a sensor array, the measuring including digitizing voltage signals using an analog to digital converter to produce a plurality of frames of measured values for the waveform, the voltage signals generated by the sensor array in response to the chemical event, wherein the chemical event is indicative of a number of nucleotide incorporations in a genetic sequencing reaction, wherein the waveform comprises at least one portion associated with expected measured values and at least one portion associated with unpredictable measured values; applying a first compression process to the waveform using a processor, the first compression process including an averaging of one or more frames in one or more portions of the waveform to form frame-averaged data, wherein a number of frames of the frame-averaged data is less than a number of frames in the plurality of frames of measured values; applying a keyframe delta compression to the frame-averaged data using the processor, wherein the keyframe delta compression comprises calculating a difference between a current frame of the frame-averaged data and a previous frame of the frame-averaged data associated with the waveform; forming a compressed data structure including a keyframe of the frame-averaged data and a plurality of the calculated differences subsequent to the keyframe, wherein the compressed data structure represents the keyframe and the plurality calculated differences in a number of bytes that is less than an original number of bytes representing the frame-averaged data; and storing one or more compressed data structures in a memory.

22 . The method of claim 21 , further comprising:
determining compression information corresponding to the one or more compressed data structures; and storing the compression information in the memory.

23 . The method of claim 22 , wherein the compression information includes the number of bytes for storing each of the one or more compressed data structures.

24 . The method of claim 23 , wherein the compression information includes a code indicating a change in the number of bytes for storing the one or more compressed data structures from a previous compressed data structure.

25 . The method of claim 21 , wherein the averaging comprises:
applying a first frame averaging to the at least one portion associated with the expected measured values, wherein the first frame averaging comprises averaging a first number of frames during the at least one portion associated with the expected measured values; and applying a second frame averaging to the at least one portion associated with the unpredictable measured values, wherein the second frame averaging comprises averaging a second number of frames during the at least one portion associated with the unpredictable measured values, the second number of frames being lower than the first number of frames.

26 . The method of claim 25 , further comprising:
applying a third frame averaging to a second portion of the waveform, wherein the second portion is associated with another portion of the waveform with expected measured values, and wherein the third frame averaging comprises averaging a third number of frames during the second portion, the third number of frames being higher than the second number of frames.

27 . The method of claim 21 , wherein the measuring the waveform comprises measuring the waveform of a dynamic response of an ion-sensitive field effect transistor (ISFET) array to a change in ionic strength of an analyte solution in fluid contact with the ISFET array.

28 . The method of claim 27 , wherein the measuring the waveform of the dynamic response of the ISFET array comprises associating the at least one portion with the unpredictable measured values to a stepwise increase in ion concentration in the analyte solution and associating the at least one portion with the expected measured values to at least one portion of the dynamic response outside of the stepwise increase in ion concentration.

29 . The method of claim 28 , wherein the averaging comprises applying a first frame averaging to the at least one portion associated with the expected measured values, wherein the first frame averaging comprises averaging a first number of frames during the at least one portion associated with the expected measured values, wherein the first number of frames results from measured values during the at least one portion of the dynamic response outside of the stepwise increase in ion concentration.

30 . The method of claim 28 , wherein the averaging comprises applying a second frame averaging to the at least one portion associated with the unpredictable measured values, wherein the second frame averaging comprises averaging a second number of frames during the at least one portion associated with the unpredictable measured values, wherein the second number of frames results from measured values during the stepwise increase in ion concentration in the analyte solution.

31 . A computer program product comprising a computer-usable medium having computer program logic recorded thereon that, when executed by one or more processors, compresses data from a sensor array, wherein the data comprise digitized voltage signals generated by the sensor array in response to a chemical event occurring on the sensor array to produce a plurality of frames of measured values of a waveform, wherein the chemical event is indicative of a number of nucleotide incorporations in a genetic sequencing reaction, the computer program logic comprising computer readable program code that enables a processor to:
obtain the plurality of frames of measured values of the waveform associated with the chemical event occurring on the sensor array, wherein the waveform comprises at least one portion associated with expected measured values and at least one portion associated with unpredictable measured values; apply a first compression process to the waveform, the first compression process including an averaging of one or more frames in one or more portions of the waveform to form frame-averaged data, wherein a number of frames of the frame-averaged data is less than a number of frames in the plurality of frames of measured values; apply a keyframe delta compression to the frame-averaged data, wherein the keyframe delta compression comprises calculating a difference between a current frame of the frame-averaged data and a previous frame of the frame-averaged data associated with the waveform; form a compressed data structure including a keyframe of the frame-averaged data and a plurality of the calculated differences subsequent to the keyframe, wherein the compressed data structure represents the keyframe and the plurality calculated differences in a number of bytes that is less than an original number of bytes representing the frame-averaged data; and store one or more compressed data structures in a memory.

32 . The computer program product of claim 31 , wherein the computer readable program code enables the processor to:
determine compression information corresponding to the one or more compressed data structures, and store the compression information in the memory.

33 . The computer program product of claim 32 , wherein the compression information includes the number of bytes for storing each of the one or more compressed data structures.

34 . The computer program product of claim 33 , wherein the compression information includes a code indicating a change in the number of bytes for storing

Assignees

• Life Technologies Corp

Inventors

• Sugnet Charles
• Cawley Simon
• Gupta Mohit
• Marjanovic Iztok
• Rearick Todd
• Beauchemin Mark
• Hubbell Earl

Classifications

• 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

• H03M7/30 Primary

  Compression (speech analysis-synthesis for redundancy reduction G10L19/00; for image communication H04N); Expansion; Suppression of unnecessary data, e.g. redundancy reduction · CPC title

• G06F19/24

  Physics · mapped topic

• G16B40/10

  Signal processing, e.g. from mass spectrometry [MS] or from PCR · CPC title