Method of genotyping by determination of allele copy number

A method of processing photometric data comprising:

• (a) providing a plurality of fragments of DNA, a detector, and photometric data obtained using the detector from the DNA fragments;
• (b) adjusting a baseline of the photometric data;
• (c) reducing spectral noise;
• (d) identifying a peak in the photometric associated with each one of a plurality of the DNA fragments;
• (e) sizing the DNA fragments;
• (f) estimating spectral intensity for each fragment;
• (g) normalizing the spectral intensities;
• (h) genotyping each fragment using the normalized spectral intensities.

A method of discriminating a genotype comprising:

• (a) providing a plurality of samples that each have a plurality of DNA fragments from a plurality of loci, a plurality of DNA fragment standards, a detector, and photometric data obtained from the plurality of DNA fragments and the plurality of DNA fragment standards using the detector;
• (b) performing a baseline adjustment to the photometric data;
• (c) removing spectral overlap in the photometric data;
• (d) transforming the photometric data from a time domain into a frequency domain using a Fourier transform, truncating a portion of the transformed photometric data, and thereafter transforming the transformed photometric data remaining after truncation from the frequency domain back into the time domain using an inverse Fourier transform;
• (e) identifying a plurality of peaks in the photometric data and fitting a Gaussian peak to each one of the plurality of peaks;
• (f) performing a plurality of locally weighted quadratic regressions on the plurality of peaks to produce a plurality of molecular weight sizing functions;
• (g) estimating the molecular weight of each one of the plurality of DNA fragments using one of the plurality of molecular weight sizing functions;
• (h) binning the molecular weights of the plurality of DNA fragments;
• (i) designating each locus having a fragment present in each one of the samples as putatively monomorphic;
• (j) estimating a spectral intensity for each one of the plurality of DNA fragments;
• (k) designating the putative monomorphic locus having the least amount of variability in spectral intensity as a reference monomorphic locus;
• (l) determining a normalizing coefficient using the spectral intensities of the DNA fragment of the reference monomorphic locus;
• (m) using the normalizing coefficient to normalize the spectral intensities of all of the plurality of DNA fragments;
• and
• (n) using the normalized spectral intensities to genotype the plurality of DNA fragments.

A method of discriminating a genotype comprising:

• (a) providing a plurality of samples that each have a plurality of DNA fragments at a plurality of loci, a plurality of DNA fragment standards, a detector, and photometric data obtained from the plurality of DNA fragments and the plurality of DNA fragment standards using the detector;
• (b) identifying a plurality of peaks in the photometric data;
• (c) performing a plurality of locally weighted quadratic regressions on the plurality of peaks to produce a plurality of molecular weight sizing functions;
• (d) estimating the molecular weight of each one of the plurality of DNA fragments using one of the plurality of molecular weight sizing functions;
• (e) binning the molecular weights of the plurality of DNA fragments;
• (f) designating each locus that has a DNA fragment present in each one of the samples as putatively monomorphic;
• (g) estimating a spectral intensity for each one of the plurality of DNA fragments;
• (h) designating the putative monomorphic locus having the least amount of variability in spectral intensity as a reference monomorphic locus;
• (i) determining a normalizing coefficient using the spectral intensities of the DNA fragment of the reference monomorphic locus;
• (j) using the normalizing coefficient to normalize the spectral intensities of all of the plurality of DNA fragments;
• and
• (k) using the normalized spectral intensities to genotype the plurality of DNA fragments.

A method of discriminating a genotype comprising:

• (a) providing a plurality of samples that each have a plurality of DNA fragments at a plurality of loci, a plurality of DNA fragment standards, a detector, and photometric data obtained from the plurality of DNA fragments and the plurality of DNA fragment standards using the detector;
• (b) transforming the photometric data from a time domain into a frequency domain using a Fourier transform, truncating a portion of the transformed photometric data, and thereafter transforming the data remaining after truncation from the frequency domain back into the time domain using an inverse Fourier transform;
• (c) identifying a plurality of peaks in the photometric data and fitting an idealized peak to each one of the plurality of peaks;
• (d) determining a plurality of molecular weight sizing functions using the photometric data from the plurality of DNA fragment standards;
• (e) estimating the molecular weight of each one of the plurality of DNA fragments using one of the plurality of molecular weight sizing functions;
• (f) binning the molecular weights of the plurality of DNA fragments;
• (g) designating the locus having the least amount of variability as a reference monomorphic locus;
• (h) normalizing all of the DNA fragments using a normalization coefficient determined using the reference monomorphic locus;
• (i) genotyping the plurality of DNA fragments.

A method of discriminating a genotype comprising:

• (a) providing a plurality of samples that each have a plurality of DNA fragments at a plurality of loci, a plurality of DNA fragment standards, a detector, and photometric data obtained from the plurality of DNA fragments and the plurality of DNA fragment standards using the detector;
• (b) estimating a molecular weight for each one of the plurality of DNA fragments;
• (c) binning the molecular weights;
• (d) designating the locus having the least amount of variability as a reference monomorphic locus;
• (e) normalizing the DNA fragments using a normalization coefficient obtained from the reference monomorphic locus;
• (f) genotyping the plurality of DNA fragments.

A method of discriminating among genotypes comprising:

• (a) providing a plurality of samples that each have a plurality of DNA fragments at a plurality of loci, a plurality of DNA fragment standards, a detector, and data obtained from the plurality of DNA fragments and the plurality of DNA fragment standards using the detector;
• (b) transforming the data from a time domain into a frequency domain using a Fourier transform, truncating a portion of the transformed data, and thereafter transforming the data remaining after truncation from the frequency domain back into the time domain using an inverse Fourier transform;
• and
• (c) genotyping the plurality of DNA fragments.

A method of discriminating among genotypes comprising:

• (a) providing a plurality of samples that each have a plurality of DNA fragments disposed in a gel matrix from a plurality of loci, a plurality of DNA fragment standards, a detector, and data obtained from the plurality of DNA fragments and the plurality of DNA fragment standards using the detector;
• (b) estimating spectral intensity of each one of the plurality of DNA fragment using a generalized surface-fitting function to model the distribution of DNA fragments in a gel matrix;
• and
• (c) assigning a genotype to each one of the plurality of DNA fragments.

A method of discriminating among genotypes comprising:

• (a) providing at least one amplicon, a detector, and photometric data obtained using the detector from the at least one amplicon;
• (b) compensating for error in the data;
• and
• (c) using the error-compensated data to determine whether the genotype of the at least one amplicon is a homozygote or heterozygote;
• (d) using the error-compensated data to determine the original copy number of DNA templates from which the at least one amplicon was derived.