References 8 GeneChip ® <strong>Mapping</strong> <strong>500K</strong> Assay Manual 1. Botstein, D., White, R. L., Skolnick, M., Davis R.W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314-31 (1980). 2. Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh W., al. e: Initial sequencing and analysis of the human genome. Nature 409:860-921 (2001). 3. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A., al. e: The sequence of the human genome. Science 291:1304-51 (2001). 4. Botstein, D., Risch, N. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 33 Suppl:228-37 (2003). 5. Carlson, C.S., Eberle, M.A., Kruglyak, L., Nickerson, D.A.: <strong>Mapping</strong> complex disease loci in whole-genome association studies. Nature 429:446-52 (2004). 6. Wang, D.G., Fan, J.B., Siao, C.J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spencer, J., et al. Large-scale identification, mapping, and genotyping of singlenucleotide polymorphisms in the human genome. Science 280:1077-82 (1998). 7. Kruglyak, L., Nickerson, D.A. Variation is the spice of life. Nat Genet 27:234-6 (2001). 8. Gibbs, R.A., Belmont, J.W., Hardenbol, P., Willis, T.D., Yu, F., Yang, H., Ch'ang, L-Y, Huang, W., Liu, B., Shen, Y., al. e: The International HapMap Project. Nature 426:789-96 (2003). 9. Sachidanandam, R., Weissman, D., Schmidt, S.C., Kakol, J.M., Stein, L.D., Marth, G., Sherry, S., Mullikin, J.C., Mortimore, B.J., Willey, D.L., Hunt, S.E., Cole, C.G., Coggill, P.C., Rice, C.M., Ning, Z., Rogers, J., Bentley, D.R., Kwok, P.Y., Mardis, E.R., Yeh, R.T., Schultz, B., Cook, L., Davenport, R., Dante, M., Fulton, L., Hillier, L., Waterston, R.H., McPherson, J.D.,
chapter 1 | Overview 9 Gilman, B., Schaffner, S., Van Etten, W.J., Reich, D., Higgins, J., Daly, M.J., Blumenstiel, B., Baldwin, J., Stange-Thomann, N., Zody, M.C., Linton, L., Lander, E.S., Altshuler, D. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928-33 (2001). 10. Syvanen, A.C. Toward genome-wide <strong>SNP</strong> genotyping. Nat Genet 37 Suppl:S5-10 (2005). 11. Ardlie, K.G., Kruglyak, L., Seielstad, M. Patterns of linkage disequilibrium in the human genome. Nat Rev Genet 3:299-309 (2002). 12. Hinds, D.A., Stuve, L.L., Nilsen, G.B., Halperin, E., Eskin, E., Ballinger, D.G., Frazer, K.A., Cox, D.R. Whole-genome patterns of common DNA variation in three human populations. Science 307:1072-9 (2005). 13. Hirschhorn, J.N., Daly, M.J. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6:95-108 (2005). 14. Pharoah, P.D., Dunning, A.M., Ponder, B.A., Easton, D.F. Association studies for finding cancer-susceptibility genetic variants. Nat Rev Cancer 4:850-60 (2004). 15. Patil, N., Berno, A.J., Hinds, D.A., Barrett, W.A., Doshi, J.M., Hacker, C.R., Kautzer, C.R., Lee, D.H., Marjoribanks, C., McDonough, D.P., Nguyen, B.T., Norris, M.C., Sheehan, J.B., Shen, N., Stern, D., Stokowski, R.P., Thomas, D.J., Trulson, M. O., Vyas, K.R., Frazer, K.A., Fodor, S.P., Cox, D.R. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294:1719-23 (2001). 16. Crawford, D.C., Carlson, C.S., Rieder, M.J., Carrington, D.P., Yi, Q., Smith, J.D., Eberle, M.A., Kruglyak, L., Nickerson, D.A. Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am J Hum Genet 74:610-22 (2004). 17. Dawson, E., Abecasis, G.R., Bumpstead, S., Chen, Y., Hunt, S., Beare, D.M., Pabial, J., Dibling, T., Tinsley, E., Kirby, S., Carter, D., Papaspyridonos, M., Livingstone, S., Ganske, R., Lohmussaar, E., Zernant, J., Tonisson, N., Remm, M., Magi, R., Puurand, T.,
- Page 1 and 2: GeneChip ® Mapping 500K Assay Manu
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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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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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WHAT YOU CAN DO NEXT chapter 4 | 96
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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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LOCATION AND DURATION • Main Lab
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Hybridizing Samples Using Heat Bloc
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chapter 4 | 96-Well Plate Protocol
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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 4 | 96-Well Plate Protocol
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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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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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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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NETAFFX SNP ANNOTATION chapter 7 |
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CALL RATE chapter 7 | Analysis Work
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B2 OLIGO PERFORMANCE chapter 7 | An
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Chapter 8 Troubleshooting
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Assay Recommendations 211 Genotypin
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Problem Likely Cause Solution Faint
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Problem Likely Cause Solution Posit
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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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appendix A | Reagents, Equipment, a
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appendix A | Reagents, Equipment, a
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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
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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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appendix C | Low Throughput Protoco
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appendix C | Low Throughput Protoco
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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 C | Low Throughput Protoco
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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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appendix D | Reagents, Instruments,
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appendix D | Reagents, Instruments,
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Fragmentation and Labeling appendix
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appendix D | Reagents, Instruments,