Mapping 250K/500K SNP assay

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14 GeneChip ® Mapping 500K Assay Manual 42. Klein, R.J., Zeiss, C., Chew, E.Y., Tsai, J.Y., Sackler, R.S., Haynes, C., Henning, A.K., Sangiovanni, J.P., Mane, S.M., Mayne, S.T., Bracken, M.B., Ferris, F.L., Ott, J., Barnstable, C., Hoh, J. Complement factor H polymorphism in age-related macular degeneration. Science 308:385-9 (2005). 43. Serono Identifies 80 Genes Involved in Multiple Sclerosis Using 100,000 SNPs. In: Affymetrix Microarray Bulletin; 2005; Issue 1: 1- 4; www.microarraybulletin.com. 44. Huang, J., Wei, W., Zhang, J., Liu, G., Bignell, G.R., Stratton, M.R., Futreal, P.A., Wooster, R., Jones, K. W., Shapero, M.H. Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics 1:287-99 (2004). 45. Nannya, Y., Sanada, M., Nakazaki, K., Hosoya, N., Wang, L., Hangaishi, A., Kurokawa, M., Chiba, S., Bailey, D. K., Kennedy, G.C., Ogawa, S. A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res 65:6071-9 (2005). 46. Wong, K.K., Tsang, Y.T., Shen, J., Cheng, R.S., Chang, Y.M., Man, T.K., Lau, C.C. Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA. Nucleic Acids Res 32:e69 (2004). 47. Zhao, X., Li, C., Paez, J.G., Chin, K., Janne, P.A., Chen, T.H., Girard, L., Minna, J., Christiani, D., Leo, C., Gray, J.W., Sellers, W.R., Meyerson, M. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res 64:3060-71 (2004). 48. Zhou, X., Mok, S.C., Chen, Z., Li, Y., Wong, D.T. Concurrent analysis of loss of heterozygosity (LOH) and copy number abnormality (CNA) for oral premalignancy progression using the Affymetrix 10K SNP mapping array. Hum Genet 115:327-30 (2004). 49. Rauch, A., Ruschendorf, F., Huang, J., Trautmann, U., Becker, C., Thiel, C., Jones, K.W., Reis, A., Nurnberg, P. Molecular karyotyping using an SNP array for genomewide genotyping. J Med Genet 41:916-22 (2004).
chapter 1 | Overview 15 50. Bignell, G.R., Huang, J., Greshock, J., Watt, S., Butler, A., West, S., Grigorova, M., Jones, K.W., Wei, W., Stratton, M.R., Futreal, P.A., Weber, B., Shapero, M.H., Wooster, R. High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 14:287-95 (2004). 51. Janne, P.A., Li, C., Zhao, X., Girard, L., Chen, T.H., Minna, J., Christiani, D.C., Johnson, B.E., Meyerson, M. High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines. Oncogene 23:2716-26 (2004). 52. Herr, A., Grutzmann, R., Matthaei, A., Artelt, J., Schrock, E., Rump, A., Pilarsky, C. High-resolution analysis of chromosomal imbalances using the Affymetrix 10K SNP genotyping chip. Genomics 85:392-400 (2005). 53. Lieberfarb, M.E., Lin, M., Lechpammer, M., Li, C., Tanenbaum, D.M., Febbo, P.G., Wright, R.L., Shim, J., Kantoff, P.W., Loda, M., Meyerson, M., Sellers, W.R. Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP. Cancer Res 63:4781-5 (2003). 54. Ishikawa, S., Komura, D., Tsuji, S., Nishimura, K., Yamamoto, S., Panda, B., Huang, J., Fukayama, M., Jones, K.W., Aburatani, H. Allelic dosage analysis with genotyping microarrays. Biochem Biophys Res Commun 333:1309-1314 (2005). 55. Zhao, X., Weir, B.A., LaFramboise, T., Lin, M., Beroukhim, R., Garraway, L., Beheshti, J., Lee, J.C., Naoki, K., Richards, W.G., Sugarbaker, D., Chen, F., Rubin, M.A., Janne, P.A., Girard, L., Minna, J., Christiani, D., Li, C., Sellers, W.R., Meyerson, M. Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis. Cancer Res 65:5561-70 (2005). 56. Garraway, L.A., Widlund, H.R., Rubin, M.A., Getz, G., Berger, A.J., Ramaswamy, S., Beroukhim, R., Milner, D.A., Granter, S.R., Du, J., Lee, C., Wagner, S.N., Li, C., Golub, T.R., Rimm, D.L.,
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: chapter 1 | Overview 13 35. Hu, N.,
Page 29 and 30: chapter 1 | Overview 17 64. Gabriel
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
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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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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
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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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Page 295 and 296:
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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