The Technology
Recently, a new technique has been developed to size DNA fragments based
on co-migrating locus marker fragments called Locus Specific Brackets
(LSBs). There are several advantages to LSBs. First, since standard
size fragments co-migrate with the sample DNA, a separate dye-color dedicated
to the Internal Lane Standard (ILS) is not necessary. Secondly, run-to-run
sizing precision is improved because sample DNA and LSB fragments are
subject to the same environmental conditions in the capillary. Lastly,
electrophoretic mobility over the 100-400bp range of typical forensic
STR markers is nearly linear; therefore allelic ladder samples are not
necessary for repeat unit identification.
Co-migrating LSB Peaks in TH01
LSBs bracket the two alleles in this locus resulting
in approximately 0.1 basepair size resolution. |
How it works
In order for LSB data to be analyzed with GeneMarker HID, the data must
first be aligned and then an Internal Lane Standard created for each sample.
We have developed our JelMarker image reading software to align LSB data
and convert four-color raw data files (.fsa) into five-color (.sg1) files
containing an ILS. These five-color data files are then uploaded to GeneMarker
HID for profile determination.
Aligned LSB Dataset in JelMarker
Converting the raw trace files to a synthetic gel image
allows JelMarker to automatically align the LSBs and add an ILS to each
sample. |
The Results
JelMarker’s successful alignment of LSB fragments and the subsequent
STR analysis in GeneMarker HID prove to be very promising new techniques
for the forensic community. Not only will the well space taken up by allelic
ladders become available but additional dye colors for more loci positions
could be implemented. The result is a more discriminatory test for forensic
profile analyses.
Final Allele Report in GeneMarker HID
The final Allele Report in GeneMarker HID globally displays all loci in
all dye colors with a special auto-scaling feature to automatically magnify
even the smallest peaks. |
Acknowledgements
We would like to thank Christine Picard, M.S. and Jeffrey Wells, Ph.D.
of West Virginia University for providing LSB data and their continuing
collaboration with SoftGenetics.
References
1. Genetics and genomics of core short tandem repeat loci used
in human identity testing. JM Butler. Journal of Forensic Science. 2006.
51 (253-265).
2. Inferring ethnic origin by means of an STR profile. AL Lowe, A Urquhart,
LA Foreman, IW Evett. Forensic Science International. 2001. 119 (17-22).
3. Automated DNA profiling employing multiplex amplification of short
tandem repeat loci. CP Kimpton, P Gill, A Walton, A Urquhart, ES Millican,
M Adams. PCR Methods and Applications. 1993. 3 (13-22).
4. Evaluation of an automated DNA profiling system employing multiplex
amplification of four tetrameric STR loci. C Kimpton, D Fisher, S Watson,
M Adams, A Urquhart, J Lygo, P Gill. International Journal of Legal Medicine.
1994. 106 (302-311).
Application Notes
- LSB Application Note [PDF]
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