Mapping 250K/500K SNP assay

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190 GeneChip ® Mapping 500K Assay Manual EXAMINING THE RAW PROBE DATA EXPORT Information on raw probe intensity can be obtained by selecting a SNP identifier from within the .chp file and choosing the Probe Intensity option in the Run menu. Probe intensity data is displayed for each probe in bar, line, or trace graph format. SNP call data can be exported for use in third party software products as either a tab delimited file or linkage formats compatible with MERLIN, GeneHunter, or Haploview software (new for GTYPE 4.0). If pedigree information is included in your experiment file, use GTYPE to export the genotype calls and pedigree information to a file in either MERLIN, GeneHunter, or Haploview format. For more information on these formats, please refer to the GeneChip ® Genotyping Analysis Software User’s Guide. Before using the linkage analysis export tool, the following must be done: Assign a sample template with pedigree attributes to the samples. Import sample attribute data. To export data for linkage analysis: 1. Click the SNP Export button in the Genotyping Views shortcut bar, or select Tools → Genotype → SNP Export... from the menu bar. 2. Click the MERLIN, GeneHunter, or Haploview tab to select the export format. Specify sample attributes containing pedigree information. For information on sample attribute values for these formats, please consult the GeneChip ® Genotyping Analysis Software User’s Guide.
chapter 7 | Analysis Workflow 191 3. Select the file set, project, sample, experiments, or analysis data in the data tree and drag them to the Samples box. 4. (Optional) Choose any filters that need to be applied to the data. The SNP filters allow you to filter out SNPs that do not meet the particular requirements of your experiment from the export. You can filter by: • Allele Frequency • Hardy-Weinberg Probability Value • Mendelian error rate When filtering on Mendelian error, you have the option to remove the erroneous SNPs from the export files, or to set calls for erroneous SNPs to NoCalls for families with inheritance errors. You may want to use the second option if exporting multiple families at once. 5. Select output file names and choose the path to save the files. Click Export to export your data. Consult the GeneChip ® Genotyping Analysis Software User’s Guide for directions specific to each format type. To batch export genotyping calls: The Tab Delimited export tool allows batch export of genotyping calls from large data sets simultaneously into tab delimited files. This feature can be combined with File Sets to provide a flexible method of analyzing custom groupings of large data sets. The data is exported in a tab-delimited text file with the following columns: • Affymetrix SNP ID • Genotype 1. Click the SNP Export button in the Genotyping Views shortcut bar, or select Tools → Genotype → SNP Export… from the menu bar. 2. Choose the Tab Delimited tab.
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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
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Introduction This chapter contains
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Reagent Preparation Wash A: Non-Str
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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
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Page 185 and 186: Table 6.3 (Continued) Common error
Page 187 and 188: Table 6.4 (Continued) Common Error
Page 189 and 190: Table 6.5 (Continued) Other Problem
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Page 193 and 194: Introduction Software Requirements
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Page 197 and 198: Figure 7.3 Dynamic Model Mapping Al
Page 199 and 200: Table 7.1 Dynamic Model Mapping Alg
Page 201: FILE SETS chapter 7 | Analysis Work
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
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Page 245 and 246: Consumables Required GENECHIP ® AR
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Page 249 and 250: Appendix B Thermal Cycler Programs
Page 251 and 252: 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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