Applied Biosystems 3500 User Manual

The software evaluates peaks in the data for each capillary. To be identied as a
possible allele, peaks must be within the following ranges (nominal allele size, or
reference bin size, is hard-coded):
Fragment analysis HID analysis
All markers between ±0.4 bp and ±0.5 bp of
nominal size for the allele
• All markers except TH01: ±0.7 bp of
nominal size for the allele
• TH01:
– Seven markers are ±0.7 bp of
nominal size for the allele
– Three markers are ±0.5 bp of
nominal size for the allele
For all peaks that are within the nominal size range, the software calculates the
A
verage Peak Height and the Sizing Precision. Peaks that meet the following
thresholds pass.
Result Description Threshold
Min Peak Height Minimum of peak heights for
observed allele peaks of the
included capillaries.
• Fragment: >175 RFU
• HID: >400 RFU
Sizing Precision Standard deviation of the observed
allele fragment sizes
<0.15 for expected alleles
Pass/Fail Alleles with a sizing precision and minimum peak height that do not
meet thresholds fail.
For information only
Nominal Size Expected allele fragment peak size (bp).
Mean Average fragment size for the observed allele peaks.
Peak Height % >
Min
Percentage of observed allele peaks with a peak height above the
minimum threshold.
Sizing Accuracy Difference between the expected allele size and the mean allele size.
1.
Examine the number of size standard and allele peaks found for each capillary.
2.
If all capillaries pass, click Accept Results.
If any capillaries fail, the Accept Results buon is dimmed. Ev
aluate the raw
data for failed capillaries to determine if the install check can be accepted with
the failed capillaries. If the run is acceptable, the software allows you to deselect
capillaries and recalculate results.
Pass/fail criteria
for the
fragment/HID
install check
Evaluate fragment
ins
tall standard
data
Chapter 6 Run calibrations and install checks
Run a fragment/HID install check
6
3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1
135

Applied Biosystems 3500 Specifications

General

Number of capillaries	8
Capillary Length	50 cm
Laser	Solid-state laser
Instrument Type	Capillary electrophoresis system
Technology	Capillary Electrophoresis (CE)
Weight	95 kg
Power Requirements	100–240 V