Improved visibility of character conflicts in quasi-median networks with the EMPOP NETWORK software.
OBJECTIVE
To provide a valuable tool for graphical representation of mitochondrial DNA (mtDNA) data that enables visual emphasis on complex substructures within the network to highlight possible ambiguities and errors.


METHODS
We applied the new NETWORK graphical user interface, available via EMPOP (European DNA Profiling Group Mitochondrial DNA Population Database; www.empop.org) by means of two mtDNA data sets that were submitted for quality control.


RESULTS
The quasi-median network torsi of the two data sets resulted in complex reticulations, suggesting ambiguous data. To check the corresponding raw data, accountable nodes and connecting branches of the network could be identified by highlighting induced subgraphs with concurrent dimming of their complements. This is achieved by accentuating the relevant substructures in the network: mouse clicking on a node displays a list of all mtDNA haplotypes included in that node; the selection of a branch specifies the mutation(s) connecting two nodes. It is indicated to evaluate these mutations by means of the raw data.


CONCLUSIONS
Inspection of the raw data confirmed the presence of phantom mutations due to suboptimal electrophoresis conditions and data misinterpretation. The network software proved to be a powerful tool to highlight problematic data and guide quality control of mtDNA data tables.
Bettina
B
Zimmermann
Alexander W
AW
Rock
Arne
A
Dur
Walther Parson, Institute of Legal Medicine, Medical University, Mullerstrasse 44, A-6020 Innsbruck, Austria, walther.parson@i-med.ac.at.
Walther
W
Parson
D016172:DNA Fingerprinting / Q000379:methods*; D004272:DNA, Mitochondrial / Q000235:genetics*; D030561:Databases, Nucleic Acid; D005828:Genetics, Population / Q000379:methods*; D006239:Haplotypes; D006801:Humans; D020407:Internet; D008928:Mitochondria / Q000235:genetics*; D009154:Mutation; D011786:Quality Control; D012984:Software
D004272:DNA, Mitochondrial