Mapping 250K/500K SNP assay

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REPORT 186 GeneChip ® Mapping 500K Assay Manual A Mapping Algorithm report is automatically generated when cell intensity data is analyzed from Mapping arrays. The report is automatically displayed when you use the Batch Analysis window to analyze data. The Mapping Algorithm Report has several important indicators that must be checked for each array in order to assess the quality of the data. A saved Mapping Algorithm can be opened by: 1. Clicking the Open button in the main toolbar, or selecting File → Open from the main menu. The Open dialog box appears. Figure 7.4 Open dialog box 2. From the Data of Type drop-down list, select Reports (*.RPT). 3. Select the Mapping Algorithm report from the displayed list. 4. Click OK to open the report. The report contains information that can be used to assess the performance of the sample. Refer to Table 7.1 for the report components and description.
Table 7.1 Dynamic Model Mapping Algorithm Report Components Report Component Description Total number of SNPs Number of SNPs on array. Total number of QC Probes Number of QC SNPs on array. Probe array type Affymetrix probe array model number. chapter 7 | Analysis Workflow 187 SNP Performance A list of the analyzed samples, with the following information: Sample An identifier assigned to the analyzed samples. Gender Gender of the sample determined by the DM algorithm. SNP Call Rate Number of SNP calls/Total number of SNPs on the array. AA Call Rate The number of AA calls for the sample/Total number of SNPs on the array. AB Call Rate The number of AB calls for the sample/Total number of SNPs on the array. BB Call Rate The number of BB calls for the sample/Total number of SNPs on the array. QC Performance A list of the analyzed samples, with the following information: Sample An identifier assigned to the analyzed samples. Median PM (QC Probe Set ID) MCR (DM Mapping only) MDR (DM Mapping only) Common SNP Patterns (DM Mapping only) Median Intensity Value for perfect match cells for the QC probe sets. MPAM algorithm Call Rate. This is used to determine whether a sample is contaminated. MPAM algorithm Discrimination Rate. This is used to determine whether a sample is contaminated. Calls for a selected set of SNPs, displayed as a list of the analyzed samples with the allele calls for the common SNPs.
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GeneChip ® Mapping 500K Assay Manu
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Contents CHAPTER 1 Overview 1 ABOUT
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contents v Equipment and Consumable
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contents vii Reagents Required 118
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contents ix CHAPTER 8 Troubleshooti
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contents xi STEP 4: PCR 257 Reagent
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Chapter 1 Overview
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About This Manual This manual is a
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chapter 1 | Overview 5 LD patterns
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Figure 1.1 GeneChip ® Mapping Assa
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chapter 1 | Overview 9 Gilman, B.,
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chapter 1 | Overview 11 23. Schaid,
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chapter 1 | Overview 13 35. Hu, N.,
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chapter 1 | Overview 15 50. Bignell
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chapter 1 | Overview 17 64. Gabriel
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Chapter 2 Laboratory Setup
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Introduction to Laboratory Setup Pl
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Main Lab Pre-PCR Clean Room chapter
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Chapter 3 Genomic DNA General Requi
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Introduction This chapter describes
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Sources of Human Genomic DNA chapte
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chapter 3 | Genomic DNA General Req
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Chapter 4 96-Well Plate Protocol
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ABOUT THIS PROTOCOL 96-Well Plate P
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chapter 4 | 96-Well Plate Protocol
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PREPARING THE WORK AREA FOR EACH ST
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PROGRAM YOUR THERMAL CYCLERS chapte
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EQUIPMENT AND CONSUMABLES REQUIRED
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ALIQUOTING PREPARED GENOMIC DNA To
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Negative Controls chapter 4 | 96-We
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Table 4.7 Nsp I Digestion Master Mi
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Stage 3: Ligation ABOUT THIS STAGE
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REAGENTS REQUIRED chapter 4 | 96-We
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DILUTE THE SAMPLES To dilute the sa
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Stage 4: PCR ABOUT THIS STAGE chapt
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About Controls chapter 4 | 96-Well
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B P1 P2 P3 Figure 4.2 Transferring
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Table 4.16 PCR Master Mix ADD PCR M
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WHAT YOU CAN DO NEXT chapter 4 | 96
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POOL THE PCR PRODUCTS chapter 4 | 9
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Figure 4.5 Loading Optical Plates w
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Process Control Metrics Evaluate th
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Table 4.24 PROBLEM: Average Sample
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IMPORTANT INFORMATION ABOUT THIS ST
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Figure 4.6 Work Area Set Up for Sta
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Stage 8: Labeling ABOUT THIS STAGE
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LOCATION AND DURATION • Main Lab
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Hybridizing Samples Using Heat Bloc
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Table 4.37 Hybridization Master Mix
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Load the Samples onto Arrays chapte
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Figure 4.8 Applying Tough-Spots ®
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Chapter 5 Washing, Staining, and Sc
Page 147 and 148: Introduction This chapter contains
Page 149 and 150: Reagent Preparation Wash A: Non-Str
Page 151 and 152: Experiment and Fluidics Station Set
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Page 161 and 162: HANDLING THE GENECHIP ® PROBE ARRA
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Page 167 and 168: Introduction This chapter provides
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Page 179 and 180: White Clamp Figure 6.7 Releasing pe
Page 181 and 182: Figure 6.8 Troubleshooting decision
Page 183 and 184: PROBLEMS AND SOLUTIONS Table 6.3 Co
Page 185 and 186: Table 6.3 (Continued) Common error
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Page 189 and 190: Table 6.5 (Continued) Other Problem
Page 191 and 192: Chapter 7 Analysis Workflow
Page 193 and 194: Introduction Software Requirements
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Page 197: Figure 7.3 Dynamic Model Mapping Al
Page 201 and 202: FILE SETS chapter 7 | Analysis Work
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Page 205 and 206: NETAFFX SNP ANNOTATION chapter 7 |
Page 207 and 208: CALL RATE chapter 7 | Analysis Work
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Page 215 and 216: B2 OLIGO PERFORMANCE chapter 7 | An
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Page 221 and 222: Chapter 8 Troubleshooting
Page 223 and 224: Assay Recommendations 211 Genotypin
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Page 227 and 228: Problem Likely Cause Solution Faint
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Page 231 and 232: Table 8.2 PROBLEM: Average Sample O
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Page 235 and 236: Appendix A Reagents, Equipment, and
Page 237 and 238: Reagents, Equipment, and Consumable
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Page 245 and 246: Consumables Required GENECHIP ® AR
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Appendix B Thermal Cycler Programs
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ABOUT THIS APPENDIX 500K DIGEST 500
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500K FRAGMENT 500K LABEL 500K HYB a
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Appendix C Low Throughput Protocol
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Introduction The Affymetrix GeneChi
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BEFORE YOU BEGIN appendix C | Low T
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STEP 2: Restriction Enzyme Digestio
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DIGESTION PROCEDURE PRE-PCR CLEAN A
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STEP 3: Ligation REAGENTS AND EQUIP
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PCR STAGING AREA appendix C | Low T
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STEP 4: PCR REAGENTS AND EQUIPMENT
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PCR PROCEDURE PRE-PCR CLEAN ROOM ap
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MAIN LAB appendix C | Low Throughpu
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STEP 5: PCR Purification and Elutio
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appendix C | Low Throughput Protoco
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STEP 7: Fragmentation REAGENTS AND
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FRAGMENTATION PROCEDURE 1. Pre-heat
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LABELING PROCEDURE MAIN LAB appendi
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STEP 9: Target Hybridization REAGEN
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HYBRIDIZATION PROCEDURE appendix C
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Appendix D Reagents, Instruments, a
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Appendix D
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appendix D | Reagents, Instruments,
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* Adaptor, Nsp 5' ATTATGAGCACGACAGA
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Table D.4 Reagents Supplied by Affy
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Fragmentation and Labeling appendix
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Mapping 250K/500K SNP assay

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