Method for enhancing DNA base-calling accuracy
OwnerChangSheng Liu, Jiang Raoinventors
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Abstract
One embodiment of the present invention relates to a method of treating data derived from a separation of a nucleic acid sample. The data, which include features indicating the presence of different nucleic acid fragments in the sample are transformed on the basis of spacings between the features to obtain transformed data having a substantially constant spacing between features. Another embodiment of the present invention relates to an electrophoresis separations apparatus having at least one separation volume, a detector, and a processor. The processor is configured to transform the separations data based upon the spacing between features to obtain transformed data having a substantially constant spacing between features.
Claims21
A method of processing separations data, comprising:
- providing first data derived from a separation of a plurality of first nucleic acid fragments, the first data comprising first features, each first feature indicating the presence of a first nucleic acid fragment terminating in one of a plurality of different bases;
- and
- transforming the first data based upon first spacings between the first features to obtain transformed data having first transformed spacings between first features, wherein first transformed spacings between successive first features corresponding to first nucleic acid fragments terminating with one of the bases are integer multiples of a constant k.
An electrophoresis separation apparatus having at least one separation lane, a detector, and a processor, wherein the processor is configured to:
- obtain intensity-time data from the electrophoretic separation, the intensity-time data comprising peaks, each peak associated with the presence of a nucleic acid fragment terminating in one of a plurality of different bases;
- and
- transform the data based upon first spacings between the peaks to obtain transformed data having transformed spacings between peaks, wherein transformed spacings between successive peaks corresponding to nucleic acid fragments terminating with one of the bases are integer multiples of a constant k.
A method of processing data derived from a separation of a nucleic acid sample, comprising:
- obtaining separations data, the data comprising peaks indicating the presence of different nucleic acid fragments in the sample;
- calculating a normalized spacing between first and second members of each of a plurality of pairs of peaks by determining a spacing in time or distance between the first and second members of each pair and normalizing the spacing based on a number of peaks intermediate the first and second members;
- and
- transforming the separations data based upon the normalized spacings to obtain transformed data having a substantially constant spacing between adjacent peaks.
An electrophoresis separation apparatus having a plurality of separation lanes for separating a respective nucleic acid sample, a detector, and a processor, wherein the processor is configured to:
- obtain respective intensity-time data from each separation lane, the intensity-time data comprising peaks, each peak associated with the presence of a nucleic acid fragment terminating in one of a plurality of different bases;
- transform respective intensity data based upon spacings between the peaks to obtain respective transformed data having transformed spacings between peaks, wherein transformed spacings between successive peaks corresponding to nucleic acid fragments terminating with one of the bases are integer multiples of a constant k;
- and
- comparing the transformed data from different separation lanes to determine differences between the nucleic acid samples.
A method of processing separations data, comprising:
- providing separations data from the separation of a nucleic acid sample comprising a plurality of nucleic acid fragments, the separations data comprising peaks, each peak indicative of the presence of a nucleic acid fragment terminating in one of a plurality of different bases;
- and
- transforming the separations data based upon spacings between first and second members of respective pairs of the peaks, wherein the spacing between the first and second members of each pair is normalized by a respective number N determined from the number of peaks intermediate the first and second members.
Dependencies are inferred from the claim text.