DNA-Match software for fragment analysis
The powerful programme DNA-Match reads and processes DNA-fragment analysis files measured on ABI (Applied Biosystems) DNA-Sequencers.
The whole system is written under the Mathematica programming language. Mathematica 4.1 or higher must be installed on the computer (or network) were DNA-Match shall be used.
Mathematica and DNA-Match run under various computer operating systems (Windows, Mac-OS, Linux and Unix). DNA-Match not only allows the assignment (allele calling) but also includes a powerful statistical analysis tool to interpret the measured e.g. multiplex microsatellite data. All data can be exported to other programmes or databases using a general .csv format which can easily be adjusted.
Most of the processing can be automated but any step can also be done manually. Besides an automatic quality control the graphical interface visualizes all measured data and is an excellent tool for the operator.
Compared to DNA-sequence analysis modern DNA-fragment analysis needs several special features for reliable genotyping. Measured fragment data can not be used like sequence data without further processing.
The processing comprises:
- samples with allelic ladders
- positive and negative controls.
Using a file name descriptor DNA-Match will recognise allelic ladders and control samples from the file name itself. Known and questioned samples are divided in two subgroups inside DNA-Match (control system and fragment analysis). Questioned samples are also identified by the file names (ABI-format) and the electropherograms are visualised and processed in the fragment analysis part.
Various sets of microsatellite markers with the alleles' expected bp values can be saved in a database. Several sophisticated functions programmed in an expert system assist the assignment of peaks from allelic ladders.
Two or more different colours are used to display bins for present fragments/peaks (pink) and absent but possible peaks (grey). Expected peaks in a positive control have pink coloured bins (vertical bar).
A peak on a wrong position in a positive control therefore is easily rerecognised.
Fragment analysis, genotyping
The allele assignment of the questioned samples is done with the expected bp values stored in database files. Every user can easily create his own database files for a set of markers (PCR multiplex system). As the measured bp values for a given marker always vary over time - depending on physical and chemical conditions - allelic ladder bp values are used to correct the bp values obtained for the questioned samples.
For the assignment one can use a single allelic ladder or mean values obtained through averaging over several allelic ladders. Advanced graphical display utilities allow an excellent insight in the performance of the sequencer and the PCR conditions - in general an insight in the quality of the measured data.
Genotypes determined for a case, e.g. a paternity case father, mother, child can be handed over to the statistical genetics programme.
Statistical formulas can be easily programmed for the problem to be solved.
Routines to calculate paternity indexes (PI) for father/mother/child or father/child are ready to use.
Likelihood ratios for any possible case can be calculated.
Two different sets of multiplex kits for one sample can be compared automatically to detect e.g. sample contamination, sample mix up or primer site mutations or other features.
Database / export functions
All determined data from the electropherograms can be exported via .csv data. Files in CSV format can be read from many programmes (spreadsheet calculators, databases etc.).