Methods and apparatus for analysis of chromatographic migration patterns

Claim 1

A method of sharpening peaks in a signal representing a chromatographic distribution of components from a biochemical mixture separated by a chromatographic method comprising the steps of: providing a signal representing a chromatographic distribution of components from a biochemical mixture separated by a chromatographic method; transforming the signal from its original space domain to a cepstrum; manipulating the cepstrum with a lifter function selected to substantially reduce the amplitude of a portion of the cepstrum which is attributable to a blurring function, thereby producing a liftered cepstrum signal; and de-transforming the liftered cepstrum signal to produce a deconvolved lane signal in the original space domain.

Claim 2

A method of sharpening peaks in a signal representing a chromatographic distribution of components from a biochemical mixture separated by a chromatographic method comprising the steps of: providing a signal representing a chromatographic distribution of components from a biochemical mixture separated by a chromatographic method; transforming the signal from its original space domain to a cepstrum; manipulating the cepstrum with a lifter function selected to substantially reduce the amplitude of a portion of the cepstrum which is attributable to a blurring function, thereby producing a liftered cepstrum signal; and de-transforming the liftered cepstrum signal to produce a deconvolved lane signal in the original space domain.

Claim 9

A method of sharpening peaks in a signal representing a chromatographic distribution of components from a biochemical mixture separated by a chromatographic method comprising the steps of: providing a signal representing a chromatographic distribution of components from a biochemical mixture separated by a chromatographic method; generating an FS (frequency spectrum) signal by Fourier transformation of the signal; taking the log of the FS signal to produce a CLS (complex log-spectrum) signal; taking an inverse Fourier transform of the real portion of the CLS signal to produce a cepstrum signal; multiplying the cepstrum signal by a lifter function chosen to reduce the contribution of a blurring function, thereby producing a liftered cepstrum signal; subjecting the liftered cepstrum signal to Fourier transformation to produce an LLS (liftered log-spectrum) signal; adding the imaginary portion of the LS signal to the LLS signal to produce a liftered CLS signal; taking the inverse logarithm of the liftered CLS signal to produce a liftered FS (liftered frequency spectrum) signal; and taking the inverse Fourier transform of the liftered FS signal to produce a deconvolved signal.

Claim 10

A method of sharpening peaks in a signal representing a chromatographic distribution of components from a biochemical mixture separated by a chromatographic method comprising the steps of: providing a signal representing a chromatographic distribution of components from a biochemical mixture separated by a chromatographic method; generating an FS (frequency spectrum) signal by Fourier transformation of the signal; taking the log of the FS signal to produce a CLS (complex log-spectrum) signal; taking an inverse Fourier transform of the real portion of the CLS signal to produce a cepstrum signal; multiplying the cepstrum signal by a lifter function chosen to reduce the contribution of a blurring function, thereby producing a liftered cepstrum signal; subjecting the liftered cepstrum signal to Fourier transformation to produce an LLS (liftered log-spectrum) signal; adding the imaginary portion of the LS signal to the LLS signal to produce a liftered CLS signal; taking the inverse logarithm of the liftered CLS signal to produce a liftered FS (liftered frequency spectrum) signal; and taking the inverse Fourier transform of the liftered FS signal to produce a deconvolved signal.

Claim 20

A method of determining a nucleotide sequence of a DNA molecule from an electrophoretic migration pattern of a set of DNA sequencing lanes sufficient to establish the relative migration patterns of fragment groups respectively terminating in each one of the nucleotides designated A, T, G and C, comprising the steps of: providing a set of lane signals respectively encoding the migration patterns of each member of the set of sequencing lanes, and each lane signal having peaks representing the relative amounts of DNA fragments of different sizes present in the corresponding lane; identifying putative peaks in all of the lane signals and determining a putative spacing which is the average for all of the putative peaks; aligning the lane signals to establish a provisional ordering of the putative peaks; generating a three-dimensional matrix having a plurality of matrix elements, each matrix element taking the form of a coordinate pair comprising a spacing value for a specific occurrence of a peak pair, and the location in the signal of that specific occurrence, wherein a peak pair is defined as a pair of non-identical peaks which are adjacent each other in the provisional ordering; deriving a peak pair spacing function for each category of peak pair; selecting a reference lane; and adjusting the number of samples within each lane signal as needed to produce a spacing function for the lane signal which substantially matches the spacing function of the reference lane, thereby producing a set of fully aligned lane signals; and reading a DNA sequence from the order of peaks in the aligned lane signals

Claim 21

A method of determining a nucleotide sequence of a DNA molecule from an electrophoretic migration pattern of a set of DNA sequencing lanes sufficient to establish the relative migration patterns of fragment groups respectively terminating in each one of the nucleotides designated A, T, G and C, comprising the steps of: providing a set of lane signals respectively encoding the migration patterns of each member of the set of sequencing lanes, and each lane signal having peaks representing the relative amounts of DNA fragments of different sizes present in the corresponding lane; identifying putative peaks in all of the lane signals and determining a putative spacing which is the average for all of the putative peaks; aligning the lane signals to establish a provisional ordering of the putative peaks; generating a three-dimensional matrix having a plurality of matrix elements, each matrix element taking the form of a coordinate pair comprising a spacing value for a specific occurrence of a peak pair, and the location in the signal of that specific occurrence, wherein a peak pair is defined as a pair of non-identical peaks which are adjacent each other in the provisional ordering; deriving a peak pair spacing function for each category of peak pair; selecting a reference lane; and adjusting the number of samples within each lane signal as needed to produce a spacing function for the lane signal which substantially matches the spacing function of the reference lane, thereby producing a set of fully aligned lane signals; and reading a DNA sequence from the order of peaks in the aligned lane signals

Claim 32

A method of aligning the members of a set of lanes of a DNA sequencing electrophorogram, comprising the steps of: providing a set of lane signals respectively encoding the migration patterns of each member of the set of sequencing lanes, and each lane signal having peaks representing the relative amounts of DNA fragments of different sizes present in the corresponding lane; establishing a provisional alignment of the lanes; generating a three-dimensional matrix having matrix elements in the form of coordinate pairs, each coordinate pair comprising a peak pair spacing value for an individual occurrence of that peak pair, and the signal position of the individual occurrence; deriving a peak pair spacing function for each category of peak pair, and fitting the spacing function to a straight line; selecting a reference lane; and adjusting the number of samples within each lane signal as needed to produce a spacing function for the lane signal which substantially matches the spacing function of the reference lane.

Claim 33

A method of aligning the members of a set of lanes of a DNA sequencing electrophorogram, comprising the steps of: providing a set of lane signals respectively encoding the migration patterns of each member of the set of sequencing lanes, and each lane signal having peaks representing the relative amounts of DNA fragments of different sizes present in the corresponding lane; establishing a provisional alignment of the lanes; generating a three-dimensional matrix having matrix elements in the form of coordinate pairs, each coordinate pair comprising a peak pair spacing value for an individual occurrence of that peak pair, and the signal position of the individual occurrence; deriving a peak pair spacing function for each category of peak pair, and fitting the spacing function to a straight line; selecting a reference lane; and adjusting the number of samples within each lane signal as needed to produce a spacing function for the lane signal which substantially matches the spacing function of the reference lane.

Claim 37

A method of determining a DNA sequence from an electrophorogram of a set of nucleic acid sequencing lanes, comprising the steps of: providing a set of lane signals, each representing a corresponding one of a set of sequencing lanes and comprising a peak signal function convolved with a blurring function, the peak signal function comprising peaks reflective of the relative amounts of particular fragments in the sequencing lane; processing by blind deconvolution each of said lane signals to reduce the contribution of the blurring function to each lane signal, thereby producing a set of corresponding deconvolved lane signals; mutually aligning said lane signals to establish an ordering of peaks among the respective lanes; and reading a nucleic acid sequence from the order of peaks in the aligned lane signals.

Claim 38

A method of determining a DNA sequence from an electrophorogram of a set of nucleic acid sequencing lanes, comprising the steps of: providing a set of lane signals, each representing a corresponding one of a set of sequencing lanes and comprising a peak signal function convolved with a blurring function, the peak signal function comprising peaks reflective of the relative amounts of particular fragments in the sequencing lane; processing by blind deconvolution each of said lane signals to reduce the contribution of the blurring function to each lane signal, thereby producing a set of corresponding deconvolved lane signals; mutually aligning said lane signals to establish an ordering of peaks among the respective lanes; and reading a nucleic acid sequence from the order of peaks in the aligned lane signals.