Mutation Detection A Practical Approach

by Cotton, R. G. H.; Edkins, E.; Forrest, S.

• ISBN13: 9780199636570
• ISBN10: 0199636575
• Format: Hardcover
• Copyright: 1998-05-07
• Publisher: Oxford University Press

Summary

Mutation detection is increasingly undertaken in a wide spectrum of research areas: in medicine it is fundamental in isolating disease genes and diagnosis, and is especially important in cancer research; in biology, commercially important genes can be identified by the mutations they contain. But mutation detection is time-consuming and expensive. This volume offers the latest tried and tested protocols for a range of detection methods, from the labs of the leading researchers in the field.

Table of Contents

List of Contributors	xv	(4)
Abbreviations	xix
Introduction	1	(5)
Sue Forrest
References	6	(1)
1. Single-strand conformation polymorphism analysis	7	(18)
Kenshi Hayashi
Youji Kukita
Masakazu Inazuka
Tomoko Tahira
1. Introduction	7	(1)
2. PCR-SSCP using polyacrylamide slab gel	8	(9)
PCR Optimization and primer design	10	(1)
Pre-amplification and isolation by agarose gel electrophoresis	10	(1)
PCR using [(32)P]deoxynucleotide triphosphate	11	(1)
Removal of 3' appendage	12	(1)
SSCP gel electrophoresis	13	(2)
Interpretation of autoradiogram	15	(1)
Re-amplification and direct sequencing	15	(1)
Gel matrices other than polyacrylamide	16	(1)
Restriction endonuclease fingerprinting and dideoxy fingerprinting	17	(1)
3. Fluorescent SSCP in an automated DNA sequencer	17	(6)
Primer design in post-PCR fluorescent labelling	18	(1)
Fluorescent labelling by 3' exchange reaction	19	(2)
SSCP in capillary electrophoresis (CE-SSCP)	21	(2)
Data processing	23	(1)
Acknowledgements	23	(1)
References	23	(2)
2. Single-stranded conformation polymorphism and heteroduplex analysis	25	(10)
Bernard Gerrard
Michael Dean
1. Introduction	25	(2)
2. Optimization of the PCR reaction	27	(1)
3. SSCP sample prepration	28	(1)
4. Optimization of SSCP/HA detection	29	(2)
5. Multiplexing	31	(1)
6. Interpretation of results	32	(1)
7. Applications	33	(1)
8. Other methods	33	(1)
References	33	(2)
3. Comprehensive mutation detection with denaturing gradient gel electrophoresis	35	(28)
L.S. Lerman
Cherif Beldjord
1. Introduction	35	(3)
The scope of DGGE, its distinctive capabilities, and the nature of results	35	(3)
2. Background	38	(1)
3. Basic principle, the physical properties of DNA	39	(1)
4. Overview of the procedures in searching for mutants	40	(3)
Defining segments for scrutiny	40	(1)
Sample preparation	41	(1)
Gradient and velocity separations	41	(1)
Features of the gel patterns	42	(1)
Discrimination of zygozygosity	42	(1)
Comments	43	(1)
5. Use of the psoralen cross-link as a clamp	43	(2)
The psoralen protocol	44	(1)
6. Computational tools	45	(12)
What is a meltmap?	45	(3)
Meltmap protocol	48	(5)
Predicting electrophoretic separations	53	(3)
Computer operations for MUTRAV	56	(1)
7. Other members of the DGGE family	57	(2)
Gel separations in a uniform, partially denaturing environment	57	(1)
Capillary electrophoresis	57	(1)
The thermal gradient	57	(1)
The temperature ramp	58	(1)
2D length and gradient separations	58	(1)
8. End notes	59	(1)
Acknowledgments	59	(1)
References	59	(4)
4. Cleavage using RNase to detect mutations	63	(18)
H. Nagase
Y. Nakamura
1. Introduction	63	(1)
2. RNase protection assay for mutation detection	64	(15)
Evaluation of the sensitivity	64	(3)
Source material	67	(1)
PCR for RNase protection assay	68	(1)
RNA probe preparation	69	(4)
RNase protection	73	(2)
Detection of digested probe	75	(1)
Mutation detection by sequencing of the PCR products	76	(2)
Other modified methodologies for mutation detection	78	(1)
Acknowledgements	79	(1)
References	79	(2)
5. Cleavage of mismatched bases using chemical reagents	81	(18)
Francesco Giannelli
Peter M. Green
Susan J. Ramus
1. Introduction	81	(2)
2. Basic procedures	83	(7)
Comments on the basic procedures	89	(1)
3. Ultra fast chemical mismatch detection	90	(6)
Labelling	90	(1)
Solid phase	90	(5)
Comments	95	(1)
References	96	(3)
6. Mutation detection using T4 endonuclease VII	99	(14)
Rima Youil
1. Introduction	99	(1)
2. The biology of Endo VII	99	(3)
The role of Endo VII in vivo	99	(1)
Characterization of Endo VII	99	(1)
Action of Endo VII on heteroduplex DNA	100	(2)
3. Use of Endo VII for mutation detection	102	(5)
Enzyme mismatch cleavage	102	(1)
Amplification of reference and target DNA	102	(1)
Formation of heteroduplexes	103	(2)
Endo VII digestion of heteroduplex DNA	105	(1)
Analysis of cleavage products	105	(2)
4. Fluorescent EMC	107	(1)
5. Factors to consider in the EMC assay	107	(2)
Incubation time and temperature	107	(1)
Applicability of EMC to various genes and DNA types	107	(1)
Sensitivity	107	(1)
DNA fragment length	108	(1)
Detection of multiple mutations within a single DNA fragment	108	(1)
Stability of Endo VII	109	(1)
6. Application to solid phase and non-radioactive format	109	(1)
7. EMD(TM): a commercial kit	109	(1)
8. Future prospects	110	(1)
Acknowledgements	111	(1)
References	111	(2)
7. Detection of mutations by hybridization with sequence-specific oligonucleotide probes	113	(18)
Randall K. Saiki
Henry A. Erlich
1. Introduction	113	(2)
The two formats	113	(1)
General considerations	114	(1)
2. Immobilized specimen filters	115	(5)
Designing solution-based sequence-specific oligonucleotide probes	115	(1)
Preparation of immobilized specimen filters	116	(1)
Immobilized specimen filter hybridization	117	(2)
Reusing immobilized specimen filters	119	(1)
3. Immobilized probe filters	120	(6)
Designing immobilized sequence-specific oligonucleotide probes	122	(1)
The probe tailing reaction	122	(1)
Preparation of immobilized probe filters	123	(1)
Immobilized probe filter hybridization	124	(1)
Reusing immobilized probe filters	125	(1)
4. DNA chips	126	(1)
5. Applications	127	(1)
6. Summary/perspectives	128	(1)
References	129	(2)
8. DNA detection and sequence distinction through oligonucleotide ligation	131	(10)
Ulf Landegren
Martina Samiotaki
Marek Kwiatkowski
Juri Parik
Mats Nilsson
Anette Hagberg
Gisela Barbany
1. Introduction	131	(1)
2. Background	132	(1)
A brief history of ligation assays	132	(1)
Target sequence distinction by DNA ligases	132	(1)
The oligonucleotide ligation assay (OLA)	132	(1)
3. DNA sequence distinction by PCR followed by OLA	133	(4)
PCR amplification	133	(1)
Ligation reaction	134	(1)
Binding of ligation products to solid support	134	(2)
Detection of ligation products	136	(1)
4. Comments on the OLA protocol	137	(1)
Design of ligation probes	137	(1)
Detection by time-resolved fluorometry	137	(1)
Properties of the oligonucleotide ligation assay	138	(1)
References	138	(3)
9. Detection of sequence variation using primer extension	141	(20)
Ann-Christine Syvanen
1. Introduction	141	(1)
2. Principle of the solid phase minisequencing method	142	(1)
3. Design and synthesis of primers	142	(2)
4. Guidelines for PCR amplification	144	(1)
5. The solid phase minisequencing method in practice	145	(5)
Affinity capture	145	(1)
The minisequencing primer extension reaction	146	(3)
Interpretation of the result	149	(1)
6. Quantitative PCR analysis by solid phase minisequencing	150	(2)
7. Minisequencing with colorimetric detection	152	(2)
8. Multiplex, fluorescent minisequencing	154	(3)
9. Conclusion	157	(2)
References	159	(2)
10. Selective amplification of specific alleles	161	(28)
Cynthia D.K. Bottema
Steve S. Sommer
1. Introduction	161	(2)
Principle	161	(2)
2. Parameters of PASA	163	(3)
Point of mismatch and oligonucleotide length	163	(2)
Detection limit	165	(1)
3. PASA protocol	166	(7)
DNA extraction	167	(1)
PCR amplification of specific alleles	168	(2)
Optimization of PASA	170	(3)
4. Implementation of PASA	173	(5)
Generality of PASA	174	(1)
Applications	175	(3)
5. Modifications of PASA	178	(8)
Simultaneous detection of allele-specific products	179	(4)
Sensitivity of PASA	183	(2)
Other adaptations of PASA	185	(1)
6. Conclusions	186	(1)
References	186	(3)
11. The protein truncation test (PTT)	189	(22)
Rob B. van der Luijt
Riccardo Fodde
Johan T. den Dunnen
1. Introduction	189	(1)
2. Mutation detection using PTT	189	(10)
3. Strategy	199	(2)
Forward primer	200	(1)
Reverse primer	200	(1)
Segmented set	200	(1)
4. Examples	201	(4)
PTT using genomic samples; FAP	201	(1)
PTT using RNA samples: DMD/BMD	202	(3)
5. Examples	205	(2)
Contaminations	205	(1)
No amplification	205	(1)
No translation products	205	(1)
Background translation products	206	(1)
Missing mutations	206	(1)
6. Conclusions	207	(2)
References	209	(2)
12. Functional assay of the p53 tumour suppressor gene	211	(12)
Thierry Frebourg
Jean-Michel Flaman
Anne Estreicher
Richard Iggo
1. Introduction	211	(1)
2. Detection of human p53 mutations in yeast	212	(1)
3. Overview of the assay	212	(4)
mRNA extraction	212	(3)
cDNA synthesis	215	(1)
PCR amplification of p53 cDNA	215	(1)
4. Yeast transformation	216	(3)
5. Interpretation of results	219	(1)
6. Conclusion	220	(1)
Acknowledgements	221	(1)
References	221	(2)
13. Advances in direct DNA sequencing for mutation scanning	223	(14)
Joakim Lundeberg
Cecilia Williams
Asfhin Ahmadian
Mathias Uhlen
1. Introduction	223	(1)
2. Solid phase sequencing	224	(1)
3. Solid phase DNA sequencing for p53 mutation scanning	225	(6)
Sample preparation	225	(1)
Nested multiplex in vitro amplification	226	(5)
4. DNA sequencing of the amplified fragments	231	(3)
5. Discussion	234	(1)
Acknowledgements	235	(1)
References	235	(2)
List of Suppliers	237	(4)
Index	241