Finding mutations: the basics
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| Main Author: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Oxford [u.a.]
IRL Press
1997
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XII, 136 S. Ill., graph. Darst. |
| ISBN: | 0199636117 |
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| 100 | 1 | |a Hawkins, J. R. |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Finding mutations |b the basics |c J. R. Hawkins |
| 264 | 1 | |a Oxford [u.a.] |b IRL Press |c 1997 | |
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| 650 | 4 | |a Laboratory Techniques and Procedures | |
| 650 | 4 | |a Mutation | |
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Record in the Search Index
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| adam_text | Contents
Abbreviations xii
CHAPTER I Introduction to mutation detection I
1. Introduction to mutations and their detection 1
1.1 History 2
1.2 Mutation diagnosis versus mutation scanning 3
1.3 Application of the polymerase chain reaction 4
1.4 Outcomes of mutation 5
2. Mutation nomenclature 6
2.1 Chromosomal rearrangement nomenclature 6
2.1.1 Translocations 6
2.1.2 Inversions 6
2.1.3 Deletions 6
2.2 Submicroscopic mutation nomenclature 7
2.2.1 Point mutations 7
2.2.2 Deletions and insertions 8
2.2.3 Splice mutations 8
3. Experimental considerations 9
3.1 Efficacy of detection required 10
3.2 Availability of time, personnel, and specialist equipment 10
3.3 Safety considerations 10
3.4 Overall strategy 11
References 11
CHAPTER 2 Logistics 12
1. Substrate for analysis: DNA or RNA? 12
1.1 Availability of transcripts 12
1.2 Leaky transcription 13
1.3 Substrate choice in mutation diagnosis 13
1.4 Potential pitfalls associated with cDNA 13
1.5 Significance of gene structure 14
2. Analysis of old material 15
2.1 Paraffin embedded samples 15
3. Preparation and storage of samples and reagents 16
3.1 Storage of tissue samples 16
3.2 Storage of DNA and RNA samples 17
3.3 Storage of PCR reagents 17
Further reading 17
References 18
viii ? Contents
CHAPTER 3 The detection of rearrangements 19
1. The detection of large chromosomal rearrangements by microscopy 19
1.1 Chromosome banding 19
1.2 Fluorescent in situ hybridization 21
1.3 In situ hybridization to nonmetaphase
chromosomes 21
2. The detection of small rearrangements by blotting 22
2.1 Southern blotting 22
2.2 Northern blotting 23
3. Detection of small deletions, insertions, and expansions 23
3.1 RT PCR amplification 23
3.2 PCR amplification of exons 23
3.3 PCR detection of trinucleotide repeat expansions 24
Further reading 25
References 26
CHAPTER 4 Diagnostic mutation detection methods 27
1. Allele specific oligonucleotide hybridization 27
1.1 Introduction 28
1.2 The dot blot methodology 30
1.2.1 Attachment of amplified DNA to the membrane 30
1.2.2 Labelling the oligonucleotide 31
1.2.3 Hybridization (in ordinary buffer) 31
1.2.4 Hybridization in TMAC Buffer 32
1.3 Modifications of ASO hybridization 32
1.3.1 The reverse dot blot 32
1.3.2 Multiplex ASO analysis 33
1.3.3 Nonisotopic labelling 33
2. Allele specific PCR 33
2.1 Introduction 34
2.1.1 Primer design considerations 35
2.1.2 Multiplex analysis 36
2.2 Methodology 37
2.2.1 Dual colour labelling 37
3. Oligonucleotide ligation assay 37
3.1 The theory 38
3.1.1 Solid supports 40
3.1.2 Dual colour assay 40
3.1.3 OLA methodology 40
3.2 Ligase chain reaction 41
3.2.1 LCR methodology 42
4. Primer introduced restriction analysis 42
4.1 The principles 42
4.2 Methodology 44
5. Mini sequencing 44
5.1 Principles 45
5.1.1 Methodology 46
Finding Mutations: The Basics ? ix
5.1.2 Detection methods 47
5.1.3 Detection of mosaicism 47
6. 5 nuclease assay 47
6.1 The principles 48
6.2 Strategies for mutation detection 49
6.3 Experimental design considerations 51
7. Comparison of diagnostic methods 52
Further reading 53
References 53
CHAPTER 5 Scanning mutation detection methods 56
1. Single strand conformation assay 56
1.1 Single strand DNA conformation 57
1.1.1 SSCP gel variables 57
1.1.2 Other variables 60
1.2. SSCP methodology 62
1.2.1 The SSCP gel 63
1.2.2 Loading and running the gel 65
1.3 The result 67
1.3.1 Problems 68
1.4 Application of fluorescence technology to SSCP 68
2. RNase cleavage 69
2.1 The theory 69
2.1.1 Riboprobe synthesis 70
2.2 RNase cleavage methodology 73
2.2.1 Riboprobe synthesis 73
2.2.2 Handling RNA 73
2.2.3 Generating the heteroduplex 74
2.2.4 RNase cleavage 74
2.2.5 Preparing the gel 75
2.2.6 Running the gel 75
2.3 The result 75
2.3.1 Problems 75
2.4 Nonisotopic RNase cleavage 76
3. Chemical cleavage of mismatches 76
3.1 The theory of chemical cleavage of mismatch 77
3.1.1 Mutation mapping 78
3.2 Probing strategies 79
3.2.1 Heteroduplex formation 80
3.2.2 Determination of zygosity 81
3.2.3 The fume hood 81
3.3 Methodology 82
3.3.1 Probe preparation 82
3.3.2 Preparing the solutions 83
3.3.3 The CCM procedure 83
3.4 The result 85
3.4.1 Problems 86
3.5 Application of fluorescence technology to CCM 86
x ? Contents
4. Denaturing gradient gel electrophoresis 87
4.1 Theory of DGGE 88
4.1.1 DGGE gel systems 89
4.1.2 GC clamps and chemical clamps 92
4.1.3 DGGE fragment design 92
4.2 Methodology 94
4.2.1 Fragment design 94
4.2.2 Generating the heteroduplex 94
4.2.3 Reagents 95
4.2.4 Preparing the gel 95
4.2.5 Running the gel 98
4.3 The result 99
5. Heteroduplex analysis 100
5.1 The theory 100
5.2 Practical considerations 101
5.2.1 Gel type 102
5.2.2 Fragment size 102
5.3 Fragment visualization 102
5.3.1 Ethidium bromide staining 102
5.3.2 Silver staining 102
5.3.3 Radiolabelling 103
5.3.4 Band behaviour on gels 103
5.4 Generating the heteroduplex 104
5.5 Methodology 104
5.5.1 Reagents 104
5.5.2 Making the gel 105
5.5.3 Running the gel 105
5.5.4 Staining the gel 105
5.6 The result 106
5.6.1 Problems 106
6. The protein truncation test 106
6.1 The theory 107
6.1.1 PCR amplification 108
6.1.2 In vitro transcription and translation 109
6.1.3 Electrophoresis 109
6.1.4 Mutation detection and mapping 109
6.2 Methodology 109
6.2.1 Coupled transcription/translation 110
6.2.2 Pouring and running the gel 110
6.3 The result 111
6.3.1 Problems 111
7. Fluorescence based DNA sequencing 111
7.1 Alternative methods of DNA sequencing 112
7.1.1 Cloned versus direct sequencing 112
7.1.2 Isotopic versus fluorescent sequencing 113
7.1.3 Dye primers versus dye terminators 114
7.1.4 Conventional sequencing versus cycle sequencing 116
7.2 DNA sequencing as a mutation detection technique 116
Finding Mutations: The Basics ? xi
8. Choosing a method 117
Further reading 118
References 119
CHAPTER 6 The future 122
1. Protein dependent mutation detection 122
1.1 Mismatch cleavage by resolvases 123
1.2 Mismatch recognition by DNA repair enzymes 123
1.2.1 MutS 124
1.2.2 In vivo use of repair enzymes 124
1.3 Structure specific nuclease analysis of single stranded DNA 125
2. Sequencing by hybridization 125
3. Mutation detection by functional assays 127
4. Denaturing high performance liquid chromatography 128
Further reading 128
References 128
Glossary 131
Index 135
|
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| indexdate | 2024-07-09T18:14:36Z |
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| isbn | 0199636117 |
| language | English |
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| spelling | Hawkins, J. R. Verfasser aut Finding mutations the basics J. R. Hawkins Oxford [u.a.] IRL Press 1997 XII, 136 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Mutaties gtt Genetics Genetics Technique Laboratory Techniques and Procedures Mutation Mutation (Biology) Research Methodology Genmutation (DE-588)4156638-5 gnd rswk-swf Nachweis (DE-588)4115334-0 gnd rswk-swf Genmutation (DE-588)4156638-5 s Nachweis (DE-588)4115334-0 s DE-604 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=007904346&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Hawkins, J. R. Finding mutations the basics Mutaties gtt Genetics Genetics Technique Laboratory Techniques and Procedures Mutation Mutation (Biology) Research Methodology Genmutation (DE-588)4156638-5 gnd Nachweis (DE-588)4115334-0 gnd |
| subject_GND | (DE-588)4156638-5 (DE-588)4115334-0 |
| title | Finding mutations the basics |
| title_auth | Finding mutations the basics |
| title_exact_search | Finding mutations the basics |
| title_full | Finding mutations the basics J. R. Hawkins |
| title_fullStr | Finding mutations the basics J. R. Hawkins |
| title_full_unstemmed | Finding mutations the basics J. R. Hawkins |
| title_short | Finding mutations |
| title_sort | finding mutations the basics |
| title_sub | the basics |
| topic | Mutaties gtt Genetics Genetics Technique Laboratory Techniques and Procedures Mutation Mutation (Biology) Research Methodology Genmutation (DE-588)4156638-5 gnd Nachweis (DE-588)4115334-0 gnd |
| topic_facet | Mutaties Genetics Genetics Technique Laboratory Techniques and Procedures Mutation Mutation (Biology) Research Methodology Genmutation Nachweis |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=007904346&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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