Thermo Scientific Applied Biosystems SeqStudio Genetic Analyzer - Resolution Algorithm

Resolution algorithm
A resolution algorithm, unique when running an HID application, is incorporated
into SeqStudio
™
Data Collection Software v1.2. The purpose of the algorithm is to
align the resolution power traditionally generated with a 3500/3500xL Genetic
Analyzer/POP-4
™
Polymer conguration to the resolution power generated with a
SeqStudio
™
Genetic Analyzer/POP–1
™
Polymer conguration.
About POP
™
polymer matrices
POP
™
polymer matrices separate DNA fragments of a known size range, at a desired
resolution and run time. Polymers are available in dierent concentrations, which
directly relate to the viscosity and length of the polymer molecule. Dierent
concentrations are suited to dierent applications. For example:
• Sequencing analysis applications—Traditionally use POP-6
™
and POP-7
™
Polymers. POP-6
™
and POP-7
™
Polymers are composed of relatively longer
molecules that provide greater DNA-to-polymer interaction and cause DNA
fragments to move through the polymer more slowly. This design results in a
longer run time and the increased resolution that is required for sequencing.
• Fragment analysis applications—Traditionally use POP-4
™
Polymer. Because of
its polymer concentration and molecule size, POP-4
™
Polymer has single basepair
resolving power within the size range for forensic STR amplication kits and
runs faster.
About POP–1
™
Polymer
We are introducing POP–1
™
Polymer for the SeqStudio
™
Genetic Analyzer, which can
be used for all applications on the instrument.
For smaller fragments, POP–1
™
Polymer resolves similarly to POP-7
™
Polymer. For
larger fragments, POP–1
™
Polymer resolves between POP-6
™
and POP-7
™
Polymers.
In addition to providing higher resolution for expected STR fragment peaks, peaks
intrinsic to the amplication process in the n–1/n+1 position from the main allele may
resolve as shoulders with POP–1
™
Polymer. Because of the limited resolving power of
POP-4
™
Polymer, these shoulders were not always visible in our legacy data sets.
The resolution algorithm is applied during data collection. The algorithm maintains
similar resolution for smaller fragments across the 3500/3500xL Genetic Analyzer and
SeqStudio
™
Genetic Analyzer, but allows for the improved resolution for larger
fragments that benet from the POP–1
™
Polymer.
Appendix D Create and run an HID plate
Resolution algorithm
D
214
SeqStudio
™
Genetic Analyzer Instrument and Software User Guide