Resolution Algorithm - Thermo Scientific Applied Biosystems SeqStudio Genetic Analyzer User Manual

D
Appendix D Create and run an HID plate

Resolution algorithm

Resolution algorithm

214
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 configuration to the resolution power generated with a
SeqStudio ™ Genetic Analyzer/POP–1
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 different concentrations, which
directly relate to the viscosity and length of the polymer molecule. Different
concentrations are suited to different applications. For example:
• Sequencing analysis applications—Traditionally use POP-6
™
Polymers. POP-6 and POP-7
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
its polymer concentration and molecule size, POP-4
resolving power within the size range for forensic STR amplification kits and
runs faster.
About POP–1 Polymer
™
We are introducing POP–1
be used for all applications on the instrument.
For smaller fragments, POP–1
larger fragments, POP–1
In addition to providing higher resolution for expected STR fragment peaks, peaks
intrinsic to the amplification process in the n–1/n+1 position from the main allele may
resolve as shoulders with POP–1
™
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 benefit from the POP–1
™ Polymer configuration.
™
Polymers are composed of relatively longer
™
Polymer for the SeqStudio
™
Polymer resolves similarly to POP-7
™
Polymer resolves between POP-6
™
Polymer. Because of the limited resolving power of
™
Polymer.
SeqStudio Genetic Analyzer Instrument and Software User Guide
™
™ ™
and POP-7
™
Polymer. Because of
™
Polymer has single basepair
™
Genetic Analyzer, which can
™
Polymer. For
™ ™
and POP-7 Polymers.