The following interview was conducted by Sue Herricks, a biology
teacher employed by the Champaign School District, at the University
of Washington Health Sciences Building on July 20, 2001. The focus
of the interview was computational aspects of DNA analysis.
Lee: Initially typing for the Disappeared was done with HLA and blood typing. However, with the advances in technology, mtDNA (mitochondrial DNA) and autosomal DNA are used for matching. HLA typing is now used in police work because they have such an extensive data base. It is not commonly used for identification of missing or dead children. Normally they child is matched as closely as possible with mtDNA and then this match is reinforced with autosomal DNA matches when possible.
Herricks: What role has scientific visualization and/or bioinformatic software analysis played in the Disappeared efforts thus far?
Lee has worked with two programs, both of which have some problems in mitochondrial DNA information analysis. The two programs are BLAST and CLUSTALW. BLAST is the program Lee uses. Some problems occur when trying to match mt DNA sequences. It is not uncommon for multiple single base pairs to be inserted in either the HVI or HVII sections, which are commonly used for matching. These multiple repeats do not allow for accurate matching of the remaining base pairs (e.g. ACTG will not line up correctly with the insertion of CCC in the second sample ACCCTG. BLAST and other sequence matching programs are not able to overlook insertions or deletions (not as common) and therefore mathematically cannot match up the two strands. Lee is working on altering the BLAST program so that mtDNA matching can be done with such deletions or insertions. It is not yet ready to be shared. However a program available only for use at the University of Washington has been developed.
CLUSTALW has the same problems discussed in using BLAST.
Herricks: Is there a particular biometric software analysis tool you believe to be best suited for student alignment and analysis of DNA sequences?
For student alignment sequences Lee suggested that teachers use mtDNA from the NCBI, which can be accessed at http://www.NCBI.mlm.gov . There are many types of mtDNA sequences that can be accessed, including human sequences. The human mtDNA has about 400 nucleotide pairs. Lee further suggests that teachers use the mtDNA template, the Anderson sequence (a fictitious sequence made from combining many examples of human mtDNA), and then create our own sequences from that. (Blast search for mito will bring up many examples.) Also, Lee showed Herricks examples of mtDNA sequences in which the computer program could not read the gel, resulting in mismatching of sequences. Those errors are not "covered in the software" and need to be looked at by a laboratory technician, who determine whether the sample needs to be rerun.
