Section II: Troubleshooting a CEQ System Problem
4
CEQ™ 8000 Series Genetic Analysis System
Section II: Troubleshooting a CEQ System Problem
Is it an instrument problem or a chemistry problem?
A systematic approach to troubleshooting should be adopted to effectively diagnose
problems with the CEQ System. The first test that should be done on the CEQ System
is to run the CEQ Sequencing Test Sample. Upon successful completion of CEQ
Sequencing Test Sample analysis, sequencing of the pUC18 control DNA should be
performed. Finally, customer samples should be sequenced. These three tests rely on
the analysis of
Raw Data signal, Current profiles and Analyzed Data integrity
.
Listed below are more detailed descriptions of the tests in the 3-step diagnostic
process.
Diagnostics using CEQ Sequencing Test Sample
The CEQ Sequencing Test sample is used to confirm the integrity of the instrument
and various reagents used by the system. This test uses a “pre-made” DNA sequencing
reaction prepared using the same pUC18 DNA template as that provided in the CEQ
2000 DTCS kit. The CEQ Sequencing Test Sample should produce data that has a
beginning fluorescence of approximately 50,000–120,000 units and then declines
gradually until the end of the run (viewed in the Raw Data view of the Sequencing
Analysis application). In addition, the current profiles should also be normal (see
section “Current Profiles – Normal Current Profile” on page 2). Finally, the actual base
calls are checked to see if the instrument passes the system specification of 98%
accuracy at 700 bases (if using the LFR-1 method). You should perform the Service
Alignment with the control template pUC18dG. If the CEQ Sequencing Test Sample
provides acceptable results (good raw data signal, normal current profile and meets the
system specifications of 98% accuracy at 700 bases), then the CEQ instrument and
reagents are fine and further diagnostics of the sequencing chemistry are needed. If the
CEQ Sequencing Test Sample does not yield an acceptable result try testing the other
system consumables such as the separation gel, the capillary array and another lot of
the CEQ Sequencing Test Sample. The individual components should be tested in
separate experiments to identify the faulty component. If an acceptable result is still
not achieved after substituting all new components call the Beckman Coulter Field
Service Representative for service on the CEQ system.
