Download MSI Analysis System, Version 1.2 Technical Manual TM255

MSI Analysis System, Version 1.2
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1. Description......................................................................................................................................... 2
1.A. The MSI Analysis System............................................................................................................. 2
1.B. Microsatellite Instability Overview............................................................................................... 4
1.C. The Internal Lane Standard 600 .................................................................................................. 4
2. Product Components and Storage Conditions ........................................................................................ 5
3. DNA Extraction Methods ..................................................................................................................... 5
4. DNA Amplification Using the MSI Analysis System ................................................................................ 6
4.A. Amplification Setup .................................................................................................................... 6
4.B. Amplification Thermal Cycling ..................................................................................................... 8
5. Detection of Amplified Fragments Using the ABI PRISM® 310 Genetic Analyzer ...................................... 9
5.A. Matrix Generation ...................................................................................................................... 9
5.B. Sample Preparation .................................................................................................................. 10
5.C. Instrument Preparation ............................................................................................................ 10
6. Detection of Amplified Fragments Using the ABI PRISM® 3100 Genetic Analyzer
with Data Collection Software, Version 1.0.1 or 1.1 ............................................................................. 11
6.A. Spectral Calibration .................................................................................................................. 11
6.B. Sample Preparation .................................................................................................................. 12
6.C. Instrument Preparation ............................................................................................................ 12
7. Detection of Amplified Fragments Using the ABI PRISM® 3100 or 3100-Avant Genetic Analyzer with
Data Collection Software, Version 2.0, and the Applied Biosystems® 3130 or 3130xl Genetic Analyzer .... 15
7.A. Spectral Calibration .................................................................................................................. 15
7.B. Sample Preparation .................................................................................................................. 16
7.C. Instrument Preparation ............................................................................................................ 16
8. Data Analysis .................................................................................................................................... 17
8.A. MSI Analysis Overview ............................................................................................................. 17
8.B. Importing Panels and Bins Text Files for GeneMapper® Software, Versions 4.0 and 4.1 ................. 20
8.C. Creating an Analysis Method Using GeneMapper® Software, Versions 4.0 and 4.1 ......................... 21
8.D. Creating a Size Standard ........................................................................................................... 22
8.E. Processing Data ........................................................................................................................ 23
8.F. Reviewing the Size Standard ...................................................................................................... 23
8.G. Reviewing Analyzed Sample Data ............................................................................................... 23
9. Troubleshooting................................................................................................................................ 24
10. Appendix .......................................................................................................................................... 26
10.A. Reference ................................................................................................................................ 26
10.B. Related Products ...................................................................................................................... 26
10.C. Allele Frequencies for Mononucleotide Repeat Loci .................................................................... 27
10.D. Summary of Changes ................................................................................................................ 28
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TM255 · Revised 8/14
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