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NICHOLAS HOUSBY  \nOxagen Limited, Abingdon, United Kingdom  \nKLUWER ACADEMIC PUBLISHERS  \nNEW YORK, BOSTON, DORDRECHT, LONDON, MOSCOW  \neBook ISBN: 0-306-47595-2  \nPrint ISBN: 0-7923-7173-9  \n©2002 Kluwer Academic Publishers  \nNew York, Boston, Dordrecht, London, Moscow  \nPrint ©2001 Kluwer Academic Publishers Dordrecht  \nAll rights reserved  \nNo part of this eBook may be reproduced or transmitted in any form or by any means, electronic, mechanical, recording, or otherwise, without written consent from the Publisher  \nCreated in the United States of America  \nVisit Kluwer Online at: [http://kluweronline.com](http://kluweronline.com)  \nand Kluwer's eBookstore at: [http://ebooks.kluweronline.com](http://ebooks.kluweronline.com)  \nTABLE OF CONTENTS  \nINTRODUCTION xiii  \nPREFACE xv  \nCHAPTER 1  \nTJ. Griffin, LM. Smith  \nSingle-Nucleotide Polymorphism Analysis by MALDI-TOF Mass Spectrometry  \n1.Introduction  1  \n1.1. MALDI-TOF M~~S ~~ 2  \n2. Analysis of Peptide Nucleic Acid Hybridisation Probes  2  \n2.1. Design of PNA Hybridisation Probes  3  \n2.2. Analysis of Polymorphisms in Tyrosinase Exon 4  4  \n3. Direct Analysis of Invasive Cleavage Products  5  \n3.1. The Invader Assay  6  \n3.2. Direct Analysis of SNPs From Human Genomic DNA  8  \n4. Conclusions  11  \n5. Experimental Methods  11 5.1. PNA Probe Synthesis and Preparation 11 5.2. PCR Amplification of Exon 4 of the Tyrosinase Gene  11 5.3. Hybridisation of PNA Probes to Immobilised Gene Targets  12 5.4. MALDI-TOF MS Analysis of PNA Probes 12 5.5. Invader Squared Reaction  13 5.6. MALDI-TOF MS Sample Preparation of Cleavage Products 13  \n5.7. MALDI-TOF MS Analysis of Cleavage Products  14 6. Affiliations  14 7. References  14  \nCHAPTER 2  \nLA. Haff, AC. Belden, LR. Hall, PL. Ross, IP. Smirnov SNP Genotyping by MALDI-TOF Mass Spectrometry  \n1. Introduction  16  \n2. SNP Analysis by Single Base Extension of Primers  17  \n3. Materials and Methods 19  \n4. Design Considerations forthe SNP Genotyping Assay  19 4.1. Design of PCR Product  19 4.2. PCR Product Polishing  20 4.3. Primer Design Rules for Monoplex SNP Typing  20  \nviii  \n4.4. Mass Calculations 21 4.5. Primer Design Rules for Multiplexed Reactions  22  \n4.5.1. Multiplexing with Primer Pools of Six or Fewer Primers 22  \n4.5.2.Recommended Primer Pool Design: More Than Six Primers 23  \n4.6 Primer Quality  25 5. The Single Base Extension Reaction  26  \n5.1. Desalting of Primer Extension Reactions  27 5.2. MALDI-TOF Conditions  27  \n5.3. Determination of Bases Added to the Primer  27 6. Modification of the SNP Typing Assay to Support Allele Frequency Determination  28 7. Conclusions  31 8. References  32  \nCHAPTER 3  \nHubert Köster  \nMASSARRAY™ : Highly Accurate and Versatile High Throughput Analysis of Genetic Variations  \n1. Introduction  33 2. MassARRAY™ Technology  34 3. Methodology of MassARRAY™ Technology  36 4. Diagnostic Applications of MassARRAY™ Technology for Analysis of DNA Sequence Variations  38 5. Application of MassARRAY™ for Confirmation and Validation of Single Nucleotide Polymorphisms 43 6. Conclusions 45 7. Materials and Methods 47 8. Acknowledgements48 9. References  48  \nCHAPTER 4  \nS. Sauer, D. Lechner, IG. Gut  \nThe GOOD Assay  \n1. Introduction  50 2. SNP Genotyping by MALDI 50 3. How to Improve the Analysis of DNA by MALDI  51 4. Principles of the GOOD Assay  54  \nix  \n5. Variations of the GOOD Assay  57 6. Materials and Method of the GOOD Assay  60 7. Applications of the GOOD Assay 62 8. The Issue of DNA Quality  62 9. Physical Haplotyping by the GOOD Assay  62 10. Quantitation  62 11. Automation of the GOOD Assay  63 12. Outlook  64 13. References  65  \nCHAPTER 5  \nPH. Tsatsos, V. Vasiliskov, A. Mirzabekov  \nMicrochip Analysis of DNA Sequence by Contiguous Stacking of Oligonucleotides and Mass Spectrometry  \n1. Introduction  66  \n2. Magichip properties  67  \n2.1 Production of MAGIChip 67  \n2.2 Activation of Probes  67  \n2.3 Chemical Immobilisation of P","cbCaih8weSqwvzg8","https://ap.wps.com/l/cbCaih8weSqwvzg8","pdf",7325954,158,"English","# Introduction\n# Preface\n# Chapter 1\n## Single-Nucleotide Polymorphism Analysis by MALDI-TOF Mass Spectrometry\n# Chapter 2\n## SNP Genotyping by MALDI-TOF Mass Spectrometry\n# Chapter 3\n## MASSARRAY™: Highly Accurate and Versatile High Throughput Analysis of Genetic Variations\n# Chapter 4\n## The GOOD Assay\n# Chapter 5\n## Microchip Analysis of DNA Sequence by Contiguous Stacking of Oligonucleotides and Mass Spectrometry\n# Chapter 6\n## Short Oligonucleotide Mass Analysis (SOMA): an ESI-MS Application for Genotyping and Mutation Analysis\n# Chapter 7\n## Proteomics and Mass Spectrometry: Some Aspects and Recent Developments","[{\"question\":\"What genomic applications are covered in this book’s chapters?\",\"answer\":\"The chapters focus on SNP genotyping and mutation analysis workflows, including SNP detection using MALDI-TOF approaches, MassARRAY high-throughput analysis, microchip-based DNA sequencing strategies, and SOMA for genotyping and mutation detection.\"},{\"question\":\"Which mass spectrometry techniques are emphasized?\",\"answer\":\"The table of contents highlights MALDI-TOF mass spectrometry, MassARRAY technology, microchip-linked mass spectrometry monitoring, and electrospray ionisation mass spectrometry (ESI-MS) for short oligonucleotide mass analysis.\"},{\"question\":\"What kinds of experimental design and validation topics are included?\",\"answer\":\"The contents include design considerations for SNP genotyping assays, materials and methods sections for sample preparation and probe/procedural steps, and applications that support confirmation and validation of single nucleotide polymorphisms.\"}]","Mass Spectrometry and Genomic Analysis - Introduction - table of contents | PDF",1789974100,398]