Mapping 250K/500K SNP assay

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16 GeneChip ® Mapping 500K Assay Manual Meyerson, M.L., Fisher, D.E., Sellers, W.R. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 436:117-22 (2005). 57. Sebat, J., Lakshmi, B., Troge, J., Alexander, J., Young, J., Lundin, P., Maner, S., Massa, H., Walker, M., Chi, M., Navin, N., Lucito, R., Healy, J., Hicks, J., Ye, K., Reiner, A., Gilliam, T.C., Trask, B., Patterson, N., Zetterberg, A., Wigler, M. Large-scale copy number polymorphism in the human genome. Science 305:525-8 (2004). 58. Sharp, A.J., Locke, D.P., McGrath, S.D., Cheng, Z., Bailey, J.A., Vallente, R.U., Pertz, L.M., Clark, R.A., Schwartz, S., Segraves, R., Oseroff, V.V., Albertson, D.G., Pinkel, D., Eichler, E.E. Segmental duplications and copy-number variation in the human genome. Am J Hum Genet 77:78-88 (2005). 59. Tuzun, E., Sharp, A.J., Bailey, J.A., Kaul, R., Morrison, V.A., Pertz, L.M., Haugen, E., Hayden, H., Albertson, D., Pinkel, D., Olson, M.V., Eichler, E.E. Fine-scale structural variation of the human genome. 37:727-732 (2005). 60. Iafrate, A.J., Feuk, L., Rivera, M.N., Listewnik, M.L., Donahoe, P.K., Qi, Y., Scherer, S.W., Lee, C. Detection of large-scale variation in the human genome. Nat Genet 36:949-51 (2004). 61. Shriver, M.D., Kennedy, G.C., Parra, E.J., Lawson, H.A., Sonpar, V., Huang, J., Akey, J.M., Jones, K.W. The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs. Hum Genomics 1:274-86 (2004). 62. Shriver, M.D., Mei, R., Parra, E.J., Sonpar, V., Halder, I., Tishkoff, S.A., Schurr, T.G., Zhadanov, S.I., Osipova, L.P., Brutsaert, T.D., Friedlaender, J., Jorde, L.B., Watkins, W.S., Bamshad, M.J., Gutierrez, G., Loi, H., Matsuzaki, H., Kittles, R. A., Argyropoulos, G., Fernandez, J.R., Akey, J.M., Jones, K.W. Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation. Hum Genomics 2:81-89 (2005). 63. Cardon, L.R., Abecasis, G.R. Using haplotype blocks to map human complex trait loci. Trends Genet 19:135-40 (2003).
chapter 1 | Overview 17 64. Gabriel, S.B., Schaffner, S.F., Nguyen, H., Moore, J.M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., Liu-Cordero, S.N., Rotimi, C., Adeyemo, A., Cooper, R., Ward, R., Lander, E.S., Daly, M.J., Altshuler, D. The structure of haplotype blocks in the human genome. Science 296:2225-9 (2002). 65. Carlson, C.S., Eberle, M.A., Rieder, M.J., Yi, Q., Kruglyak, L., Nickerson, D.A. Selecting a maximally informative set of singlenucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 74:106-20 (2004). 66. Mueller, J.C., Lohmussaar, E., Magi, R., Remm, M., Bettecken, T., Lichtner, P., Biskup, S., Illig, T., Pfeufer, A., Luedemann, J., Schreiber, S., Pramstaller, P., Pichler, I., Romeo, G., Gaddi, A., Testa, A., Wichmann, H.E., Metspalu, A., Meitinger, T. Linkage disequilibrium patterns and tagSNP transferability among European populations. Am J Hum Genet 76:387-98 (2005). 67. Di, X., Matsuzaki, H., Webster, T.A., Hubbell, E., Liu, G., Dong, S., Bartell, D., Huang, J., Chiles, R., Yang, G., Shen, M.M., Kulp, D., Kennedy, G.C., Mei, R., Jones, K.W., Cawley, S. Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays. Bioinformatics 21:1958-63 (2005).
Page 1 and 2: GeneChip ® Mapping 500K Assay Manu
Page 3 and 4: Contents CHAPTER 1 Overview 1 ABOUT
Page 5 and 6: contents v Equipment and Consumable
Page 7 and 8: contents vii Reagents Required 118
Page 9 and 10: contents ix CHAPTER 8 Troubleshooti
Page 11 and 12: contents xi STEP 4: PCR 257 Reagent
Page 13 and 14: Chapter 1 Overview
Page 15 and 16: About This Manual This manual is a
Page 17 and 18: chapter 1 | Overview 5 LD patterns
Page 19 and 20: Figure 1.1 GeneChip ® Mapping Assa
Page 21 and 22: chapter 1 | Overview 9 Gilman, B.,
Page 23 and 24: chapter 1 | Overview 11 23. Schaid,
Page 25 and 26: chapter 1 | Overview 13 35. Hu, N.,
Page 27: chapter 1 | Overview 15 50. Bignell
Page 31 and 32: Chapter 2 Laboratory Setup
Page 33 and 34: Introduction to Laboratory Setup Pl
Page 35 and 36: Main Lab Pre-PCR Clean Room chapter
Page 37 and 38: Chapter 3 Genomic DNA General Requi
Page 39 and 40: Introduction This chapter describes
Page 41 and 42: Sources of Human Genomic DNA chapte
Page 43 and 44: chapter 3 | Genomic DNA General Req
Page 45 and 46: Chapter 4 96-Well Plate Protocol
Page 47 and 48: ABOUT THIS PROTOCOL 96-Well Plate P
Page 49 and 50: chapter 4 | 96-Well Plate Protocol
Page 51 and 52: PREPARING THE WORK AREA FOR EACH ST
Page 53 and 54: PROGRAM YOUR THERMAL CYCLERS chapte
Page 55 and 56: EQUIPMENT AND CONSUMABLES REQUIRED
Page 57 and 58: ALIQUOTING PREPARED GENOMIC DNA To
Page 61 and 62: Negative Controls chapter 4 | 96-We
Page 63 and 64: Table 4.7 Nsp I Digestion Master Mi
Page 65 and 66: Stage 3: Ligation ABOUT THIS STAGE
Page 67 and 68: REAGENTS REQUIRED chapter 4 | 96-We
Page 71 and 72: DILUTE THE SAMPLES To dilute the sa
Page 73 and 74: Stage 4: PCR ABOUT THIS STAGE chapt
Page 75 and 76: REAGENTS REQUIRED chapter 4 | 96-We
Page 77 and 78: 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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chapter 4 | 96-Well Plate Protocol
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WHAT YOU CAN DO NEXT chapter 4 | 96
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EQUIPMENT AND CONSUMABLES REQUIRED
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POOL THE PCR PRODUCTS chapter 4 | 9
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REAGENTS REQUIRED chapter 4 | 96-We
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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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EQUIPMENT AND CONSUMABLES REQUIRED
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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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REAGENTS REQUIRED chapter 4 | 96-We
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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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Experiment and Fluidics Station Set
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chapter 5 | Washing, Staining, and
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HANDLING THE GENECHIP ® PROBE ARRA
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Chapter 6 Fluidics Station Care and
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Introduction This chapter provides
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chapter 6 | Fluidics Station Care a
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White Clamp Figure 6.7 Releasing pe
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Figure 6.8 Troubleshooting decision
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PROBLEMS AND SOLUTIONS Table 6.3 Co
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Table 6.3 (Continued) Common error
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Table 6.4 (Continued) Common Error
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Table 6.5 (Continued) Other Problem
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Chapter 7 Analysis Workflow
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Introduction Software Requirements
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Figure 7.2 GTYPE main window with t
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Figure 7.3 Dynamic Model Mapping Al
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Table 7.1 Dynamic Model Mapping Alg
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FILE SETS chapter 7 | Analysis Work
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chapter 7 | Analysis Workflow 191 3
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NETAFFX SNP ANNOTATION chapter 7 |
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CALL RATE chapter 7 | Analysis Work
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chapter 7 | Analysis Workflow 197 G
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chapter 7 | Analysis Workflow 199 F
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chapter 7 | Analysis Workflow 201 S
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B2 OLIGO PERFORMANCE chapter 7 | An
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chapter 7 | Analysis Workflow 205 3
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chapter 7 | Analysis Workflow 207 W
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Chapter 8 Troubleshooting
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Assay Recommendations 211 Genotypin
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chapter 8 | Troubleshooting 213 10.
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Problem Likely Cause Solution Faint
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Problem Likely Cause Solution Posit
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Table 8.2 PROBLEM: Average Sample O
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When to Contact Technical Support c
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Appendix A Reagents, Equipment, and
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Reagents, Equipment, and Consumable
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appendix A | Reagents, Equipment, a
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Page 243 and 244:
Page 245 and 246:
Consumables Required GENECHIP ® AR
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Supplier Contact List Table A.10 Su
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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
Page 257 and 258:
Introduction The Affymetrix GeneChi
Page 259 and 260:
BEFORE YOU BEGIN appendix C | Low T
Page 261 and 262:
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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