Genotyping result evaluation method and system
A method and a system for evaluating results of differentiating genotype signals and noise signals when a DNA fragment containing a gene to be analyzed is amplified by PCR and detected by electrophoresis are provided. An outlier of genotyping results is detected based on the fact that, when using the same marker, the height ratio of a stutter peak to a true peak and the height ratio of a +A peak to a true peak are reproducible, and that a constant size value is obtained with the use of the same allele of the same marker. In addition, a waveform obtained in past processes with the use of the same marker or the same allele is obtained utilizing a database by focusing on reproducibility. Also, a database is extended so as to obtain improved evaluation ability in a manner such that appropriate waveform data from which an outlier is not obtained is additionally registered in a database.
1. A system for evaluating results of the length of a PCR amplification product of a DNA fragment containing a microsatellite, said system comprising:
a processor for:
(i) determining +A peaks derived from one or more detection signals of a PCR amplification product in which one adenine is added to the DNA fragment end and peaks excluding +A peaks based on the detection signals of the PCR amplification product; and
(ii) determining true peaks derived from the detection signals of the PCR amplification product of the DNA fragment and stutter peaks derived from the detection signals of the PCR amplification product in which a microsatellite repetitive sequence is increased or decreased by one unit or more based on the detection signals of the PCR amplification product;
a display for displaying (i) a graph of a detection signals of a PCR amplification product, in which the axes denote detection signal intensity and fragment length, respectively; and (ii) the results of the determination of +A peaks and peaks excluding +A peaks, the results of the determination of true peaks and stutter peaks, together with the graph; and
a storage device comprising a database of prior analysis results of the length of the PCR amplification product of the DNA fragment containing the same microsatellite obtained from each of a plurality of individuals,
wherein said processor determines +A peaks and true peaks, respectively, based on at least one of the following criteria:
(1) whether or not the height ratio of a true peak and a stutter peak subjected to determination differs by more than a predetermined value from ratios derived from a plurality of individuals stored in the database;
(2) whether or not the height ratio of a true peak and a +A peak subjected to determination differs by more than a predetermined value from ratios derived from a plurality of individuals stored in the database; and
(3) whether or not fragment lengths associated with true peaks, stutter peaks, and +A peaks subjected to determination differ by more than a predetermined value from those obtained from a plurality of individuals stored in the database.
2. The system according to claim 1 ,
wherein the database further stores experimental protocols for the analysis together with the analysis results of each individual, and
data stored in the database is used as criteria by the processor in evaluation of the detection signals when determining peaks only when the data was collected using the same experimental protocol as that used in producing the PCR application product.
3. The system according to claim 1 , wherein
analysis results generated by the processor when determining peaks are stored in the database when the results are analyzed and determined to be appropriate for inclusion in the database based on predetermined criteria.
4. The system according to claim 2 , wherein
analysis results generated by the processor when determining peaks are stored in the database when the results are analyzed and determined to be appropriate for inclusion in the database based on predetermined criteria.