Method and system for DNA sequence determination and mutation detection with reference to a standard

A method for detecting mutations in a sample nucleic acid polymer having a putatively known genetic sequence comprising the steps of:

• (a) obtaining at least one sample fragment pattern representing the positions of a selected nucleic acid base within the sample nucleic acid polymer;
• (b) determining one or more normalization coefficients for the sample fragment pattern, said normalization coefficients being selected to provide a high degree of overlap between a normalized fragment pattern obtained by applying the normalization coefficients to the sample fragment pattern and a standard fragment pattern representing the positions of the selected nucleic acid base in a standard nucleic acid polymer actually having the known sequence;
• (c) applying the normalization coefficients to the sample fragment pattern to obtain the normalized fragment pattern;
• (d) dividing the normalized fragment pattern into a plurality of windows;
• and
• (e) determining the correlation between each window and the standard fragment pattern;
• wherein a difference between the correlation for any window and predetermined standard correlation values reflects the presence of a mutation within that window.

A method for classifying a sample of a nucleic acid as a particular species within a group of commonly-amplifiable nucleic acid polymers, comprising the steps of:

• (a) obtaining at least one sample fragment pattern representing the positions of a selected nucleic acid base within the sample nucleic acid polymer;
• (b) for each commonly-amplifiable species within the group, determining a set of one or more normalization coefficients for the sample fragment pattern, said normalization coefficients being selected to provide a high degree of overlap between a normalized fragment pattern obtained by applying the normalization coefficients to the sample fragment pattern and a standard fragment pattern representing the positions of the selected nucleic acid base within a standard nucleic acid polymer actually belonging to one of the commonly amplifiable species;
• (c) applying the sets normalization coefficients to the sample fragment pattern to obtain a plurality of trial fragment patterns;
• and
• (d) correlating the trial fragment patterns with the corresponding standard fragment patterns, wherein the sample is classified as belonging to the species for which the trial fragment pattern has the highest correlation with its corresponding standard fragment pattern, provided that the correlation is over a pre-defined threshold.

A method for detecting a variation in the sequence of a sample nucleic acid polymer from a standard sequence, comprising the steps of:

• (a) obtaining an experimental data trace reflecting separation of polynucleotide fragments derived from the sample nucleic acid on an electrophoresis gel;
• (b) normalizing the experimental data trace to maximize the correlation of the experimental data trace with a standard data trace reflecting separation of polynucleotide fragments derived from the standard sequence;
• and
• (c) determining the correlation between the normalized experimental data trace and the standard data trace in a plurality of windows, wherein a correlation for any one window which is significantly different from the correlation for other windows is indicative of the presence of a variation in the sequence of the sample nucleic acid polymer.