Technology and Publications
Sequence Comparison
MitoTech has developed a new rule-based approach to DNA sequence alignment that is specifically designed for absolutely reproducible sequence comparisons and difference reporting nomenclature. These MitoTyper Rules were derived from the original Wilson Rules that were used to describe the differences between a mitochondrial sequence and a reference sequence. The MitoTyper rules are the new standard protocol for mtDNA type description by the Federal Bureau of Investigation.
The MitoTyper Rules and Validation
- Journal of Forensic Sciences, 2010 - Volume 55, Issue 5, September 2010, Pages: 1190–1195, Bruce Budowle, Deborah Polanskey, Constance L. Fisher, Bobi K. Den Hartog, Russell B. Kepler and John W. Elling
- Manuscript - Automated alignment and nomenclature for consistent treatment of polymorphisms in the human mitochondrial DNA control region
- FSI:GSS - Stabilizing mtDNA sequence nomenclature with an operationally efficient approach
- ISFG Presentation - 'Standardizing the Nomenclature for mtDNA Haplotypes with an Intuitive Hierarchal Execution Software Program'
There is some debate in the scientific community on the relative merits of rule-based alignment versus a phylogenetic based alignment. MitoTech investigated the difference in the type descriptions between the two approaches and determined that they are essentially equivalent.
Comparison of MitoTyper Rules and EMPOP Phylogenetic Sequence Alignment
- Journal of Forensic Sciences, 2010 - Volume 55, Issue 5, September 2010, Pages: 1190–1195, Bruce Budowle, Deborah Polanskey, Constance L. Fisher, Bobi K. Den Hartog, Russell B. Kepler and John W. Elling
- Manuscript - Comparison of Mitotyper rules and EMPOP Phylogenetic Sequence Alignment
Automated Data Analysis
MitoTech has developed an data analysis software system, MTexpert, that automates the assembly and analysis of mitochondrial DNA for forensic and data basing applications. MTexpert uses the MitoTyper Rules for sequence alignment and difference descriptions.
MTexpert
- MTexpert - Poster
- FSI:GSS - MTexpert, an automated software system for forensic mitochondrial DNA data analysis
MitoTech has developed the eFAST(tm) software with The University of North Texas Health Science Center Department of Forensic & Investigative Genetics. eFAST automates the quality assessment of each trace generated by the sequencing instrument - filtering the traces based on a hierarchy of quality analyses
eFAST
- eFAST description - NCJRS Final Report ~ 11Mb file
- Curtis P., Thomas J., Phillips N., and Roby R. Optimization of primer specific filter
metrics for the assessment of mitochondrial DNA sequence data. Mitochondrial DNA.
2010 Dec; 21(6):191-197. - Roby R., Phillips N., Thomas J., Kepler R., Elling J., and Eisenberg A. Quality
Assessment and Alert Messaging Software for Raw Mitochondrial DNA Sequence Data.
Conference Proceedings of the Sixteenth American Academy of Forensic Sciences 2010:
Seattle, WA; February 25, 2010. - Phillips N. eFAST© Software: Automated Quality Assessment, Alert Messaging, File
Distribution and Sample Tracking of Mitochondrial DNA Sequence Data. Proceedings of
the University of North Texas Health Science Center Eighteenth Annual Research
Appreciation Day 2010: Fort Worth, TX; April 23, 2010. - Roby R. Improving Efficiency in the (Mitochondrial) DNA Laboratory. The NIJ
Conference 2010: Washington, D.C.; June 16, 2010. - Phillips N. and Roby, R. Expert System Rules and Software Advancements for
Mitochondrial DNA Analysis. Conference Proceedings of the Seventeenth American
Academy of Forensic Sciences 2011: Chicago, IL.
Quality Analysis Tools
MitoTech has developed sequence comparison and cluster analysis tools that are useful for identifying unusual polymorphisms and segments of a new sample sequence. Unusual features can be checked carefully for accuracy before the sequence is accepted.
Cluster Analysis