Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
The primary purpose of this volume is to demonstrate the range of applications of the Pyrosequencing technology in research and diagnostics and to provide detailed protocols. Beginning with an up-to-date overview of the biochemistry, the volume continues with quantitative analysis of genetic variation, ratio of expressed alleles at the RNA level, analysis of DNA methylation, global DNA methylation assays, specialized applications for DNA methylation analysis including loss of imprinting, single blastocyst analysis, allele-specific DNA methylation patterns, DNA methylation patterns associated with specific histone modifications. The volume further details tools and protocols for the detection of viruses and bacteria, and genetic and epigenetic analyses for forensics using Pyrosequencing. As a volume in the highly successful Methods in Molecular Biology series, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols and tips on troubleshooting and avoiding known pitfalls.
Comprehensive and adaptable, Pyrosequencing: Methods and Protocols, Second Edition will greatly aid doctorial students, postdoctoral investigators and research scientists studying different aspects of genetics and cellular and molecular biology.
Part I: Introduction1. The History of Pyrosequencing
ÒPål Nyrén
2. PyroMark® Instruments, Chemistry, and Software for Pyrosequencing® Analysis
Martin Kreutz, Gerald Schock, Julia Kaiser, Norbert Hochstein, and Ralf Peist
3. Software-Based Pyrogram® Evaluation
Guoli Chen, Matthew T. Olson, and James R. Eshleman
4. Quantitative Validation and Quality Control of Pyrosequencing® Assays
Ulrich Lehmann
Part II: Analysis of Genetic Variation
5. Extended KRAS and NRAS Mutation Profiling by Pyrosequencing®
Andreas Jung
6. Universal BRAF State Detection by the Pyrosequencing®-based U-BRAFV600 Assay
Alexander Skorokhod
7. Pyrosequencing®-based Identification of Low Frequency Mutations Enriched through Enhanced-ice-COLD-PCR
Alexandre How-Kit and Jörg Tos
8. Analysis of Mutational Hotspots in Routinely Processed Bone Marrow Trephines by Pyrosequencing®
Stephan Bartels and Ulrich Lehmann
9. Analysis of Copy Number Variation By Pyrosequencing® using Paralogous Sequences
Marianne Kristiansen Kringen
10. Prenatal Diagnosis of Chromosomal Aneuploidies by Quantitative Pyrosequencing®
Hui Ye, Haiping Wu, Yunlong Liu, Bingjie Zou, Tomoharu Kajiyama, Hideki Kambara, and Guohua Zhou
11. HLA-B and HLA-C Supratyping by Pyrosequencing®
Irene Vanni, Elisabetta Ugolotti, Patrizia Larghero, and Roberto Biassoni
12. Allele Quantification Pyrosequencing® at Designated SNP sites to Detect Allelic Expression Imbalance and Loss-of-heterozygosity
Chau-To Kwok and Megan P. Hitchins
Part III: Analysis of DNA Methylation Patterns
13. Quantitative DNA Methylation Analysis by Pyrosequencing®
Jessica Roessler and Ulrich Lehmann
14. Quantitative Methylation Analysis of the PCDHB Gene Cluster
Barbara Banelli and Massimo Romani
15. Assessment of Changes in global DNA Methylation Levels by Pyrosequencing® of Repetitive Elements
Ali M. Tabish, Andrea A. Baccarelli, Lode Godderis, Timothy M. Barrow, Peter Hoet1 and Hyang-Min Byun
16. Global Analysis of DNA 5-methylcytosine using the Luminometric
Methylation Assay, LUMA
Karin Luttropp, Louise K Sjöholm, and Tomas J Ekström
17. Limiting Dilution Bisulfite Pyrosequencing®: a Method for Methylation Analysis of Individual DNA Molecules in a Single or a Few Cells
Nady El Hajj, Juliane Kuhtz, and Thomas Haaf
18. Detection of Loss of Imprinting by Pyrosequencing®
Silvia Tabano, Eleonora Bonaparte, and Monica Miozzo
19. Analysis of DNA Methylation Patterns in Single Blastocysts by Pyrosequencing®
John Huntriss, Kathryn Woodfine, Joanna E Huddleston, Adele Murrell, and Helen Mary Picton
20. Allele-specific DNA methylation detection by Pyrosequencing®
Lasse Sommer Kristensen, Jens Vilstrup Johansen, and Kirsten Grønbæk
21. SNP-based Quantification of Allele-Specific DNA Methylation Patterns by Pyrosequencing®
Florence Busato and Jörg Tost
22. DNA Methylation Analysis of ChIP Products at Single Nucleotide Resolution byPyrosequencing®
Céline Moison, Fanny Assemat, Antoine Daunay, Paola B Arimondo, and Jörg Tost
Part IV: Bacterial Typing and Identification
23. Multiplex Pyrosequencing®: Simultaneous Genotyping Based on SNPs from Distant Genomic Regions
Piotr Wojciech Dabrowski, Kati Bourquain, and Andreas Nitsche
24. Detection of Drug-Resistant Mycobacterium tuberculosis
Anna Engström and Pontus Juréen
25. Application of Pyrosequencing® in Food Biodefense
Kingsley Kwaku Amoako
Part V: Forensics
26. Forensic Analysis of Mitochondrial and Autosomal Markers using Pyrosequencing®
Magdalena M. Bus, Hanna Edlund, and Marie Allen
27. Tissue-specific DNA Methylation Patterns in Forensic Samples Detected By Pyrosequencing®
Joana Antunes, Kuppareddi Balamurugan, George Duncan, and Bruce McCord
The primary purpose of this volume is to demonstrate the range of applications of the Pyrosequencing technology in research and diagnostics and to provide detailed protocols. Beginning with an up-to-date overview of the biochemistry, the volume continues with quantitative analysis of genetic variation, ratio of expressed alleles at the RNA level, analysis of DNA methylation, global DNA methylation assays, specialized applications for DNA methylation analysis including loss of imprinting, single blastocyst analysis, allele-specific DNA methylation patterns, DNA methylation patterns associated with specific histone modifications. The volume further details tools and protocols for the detection of viruses and bacteria, and genetic and epigenetic analyses for forensics using Pyrosequencing. As a volume in the highly successful Methods in Molecular Biology series, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.
Comprehensive and adaptable, Pyrosequencing: Methods and Protocols, Second Edition will greatly aid doctorial students, postdoctoral investigators, and research scientists studying different aspects of genetics and cellular and molecular biology.
The History of Pyrosequencing
Ò.- Pyro Mark® Instruments, Chemistry and Software for Pyrosequencing® Analysis.- Software-Based Pyrogram
® Evaluation.- Quantitative Validation and Quality Control of Pyrosequencing
® Assays.- Extended KRAS and NRAS Mutation Profiling by Pyrosequencing®.- Universal BRAF State Detection by the Pyrosequencing®-based U BRAF
V600 Assay.- Pyrosequencing
®-based Identification of Low Frequency Mutations Enriched through Enhanced-
ice-COLD-PCR.- Analysis of Mutational Hotspots in Routinely Processed Bone Marrow Trephines by Pyrosequencing
®.- Analysis of Copy Number Variation By Pyrosequencing
® using Paralogous Sequences.- Prenatal Diagnosis of Chromosomal Aneuploidies by Quantitative Pyrosequencing
®.- HLA-B and HLA-C Supratyping by Pyrosequencing
®.- Allele Quantification Pyrosequencing® at Designated SNP sites to Detect Allelic Expression Imbalance and Loss-of-heterozygosity.- Quantitative DNA Methylation Analysis by Pyrosequencing®.- Quantitative Methylation Analysis of the
PCDHB Gene Cluster.- Assessment of Changes in global DNA Methylation Levels by Global Analysis of DNA 5-methylcytosine using the Luminometric Methylation Assay, LUMA.- Limiting Dilution Bisulfite Pyrosequencing
®: a Method for Methylation Analysis of Individual DNA Molecules in a Single or a Few Cells.- Detection of Loss of Imprinting by Pyrosequencing
®.- Analysis of DNA Methylation Patterns in Single Blastocysts by Pyrosequencing
®.- Allele-specific DNA methylation detection by Pyrosequencing
®.- SNP-based Quantification of Allele-Specific DNA Methylation Patterns by Pyrosequencing
®.- DNA Methylation Analysis of ChIP Products at Single Nucleotide Resolution byPyrosequencing
®.- Multiplex Pyrosequencing®: Simultaneous Genotyping Based on SNPs from Distant Genomic Regions.-Detection of Drug-Resistant
Mycobacterium tuberculosis.- Application of Pyrosequencing
® in Food Biodefense.- Forensic Analysis of Mitochondrial and Autosomal Markers using Pyrosequencing
®.- Tissue-specific DNA Methylation Patterns in Forensic Samples Detected By Pyrosequencing
®.
Prof. Dr. Ulrich Lehmann lehrte bis zu seiner Emeritierung am Geologisch-Paläontologischen Institut der Universität Hamburg.
Inhaltsverzeichnis
Part I: Introduction1. The History of PyrosequencingÒ
Pål Nyrén
2. PyroMark® Instruments, Chemistry, and Software for Pyrosequencing® Analysis
Martin Kreutz, Gerald Schock, Julia Kaiser, Norbert Hochstein, and Ralf Peist
3. Software-Based Pyrogram® Evaluation
Guoli Chen, Matthew T. Olson, and James R. Eshleman
4. Quantitative Validation and Quality Control of Pyrosequencing® Assays
Ulrich Lehmann
Part II: Analysis of Genetic Variation
5. Extended KRAS and NRAS Mutation Profiling by Pyrosequencing®
Andreas Jung
6. Universal BRAF State Detection by the Pyrosequencing®-based U¿BRAFV600 Assay
Alexander Skorokhod
7. Pyrosequencing®-based Identification of Low Frequency Mutations Enriched through Enhanced-ice-COLD-PCR
Alexandre How-Kit and Jörg Tos
8. Analysis of Mutational Hotspots in Routinely Processed Bone Marrow Trephines by Pyrosequencing®
Stephan Bartels and Ulrich Lehmann
9. Analysis of Copy Number Variation By Pyrosequencing® using Paralogous Sequences
Marianne Kristiansen Kringen
10. Prenatal Diagnosis of Chromosomal Aneuploidies by Quantitative Pyrosequencing®
Hui Ye, Haiping Wu, Yunlong Liu, Bingjie Zou, Tomoharu Kajiyama, Hideki Kambara, and Guohua Zhou
11. HLA-B and HLA-C Supratyping by Pyrosequencing®
Irene Vanni, Elisabetta Ugolotti, Patrizia Larghero, and Roberto Biassoni
12. Allele Quantification Pyrosequencing® at Designated SNP sites to Detect Allelic Expression Imbalance and Loss-of-heterozygosity
Chau-To Kwok and Megan P. Hitchins
Part III: Analysis of DNA Methylation Patterns
13. Quantitative DNA Methylation Analysis by Pyrosequencing®
Jessica Roessler and Ulrich Lehmann
14. Quantitative Methylation Analysis of the PCDHB Gene Cluster
Barbara Banelli and Massimo Romani
15. Assessment of Changes in global DNA Methylation Levels by Pyrosequencing® of Repetitive Elements
Ali M. Tabish, Andrea A. Baccarelli, Lode Godderis, Timothy M. Barrow, Peter Hoet1 and Hyang-Min Byun
16. Global Analysis of DNA 5-methylcytosine using the Luminometric
Methylation Assay, LUMA
Karin Luttropp, Louise K Sjöholm, and Tomas J Ekström
17. Limiting Dilution Bisulfite Pyrosequencing®: a Method for Methylation Analysis of Individual DNA Molecules in a Single or a Few Cells
Nady El Hajj, Juliane Kuhtz, and Thomas Haaf
18. Detection of Loss of Imprinting by Pyrosequencing®
Silvia Tabano, Eleonora Bonaparte, and Monica Miozzo
19. Analysis of DNA Methylation Patterns in Single Blastocysts by Pyrosequencing®
John Huntriss, Kathryn Woodfine, Joanna E Huddleston, Adele Murrell, and Helen Mary Picton
20. Allele-specific DNA methylation detection by Pyrosequencing®
Lasse Sommer Kristensen, Jens Vilstrup Johansen, and Kirsten Grønbæk
21. SNP-based Quantification of Allele-Specific DNA Methylation Patterns by Pyrosequencing®
Florence Busato and Jörg Tost
22. DNA Methylation Analysis of ChIP Products at Single Nucleotide Resolution byPyrosequencing®
Céline Moison, Fanny Assemat, Antoine Daunay, Paola B Arimondo, and Jörg Tost
Part IV: Bacterial Typing and Identification
23. Multiplex Pyrosequencing®: Simultaneous Genotyping Based on SNPs from Distant Genomic Regions
Piotr Wojciech Dabrowski, Kati Bourquain, and Andreas Nitsche
24. Detection of Drug-Resistant Mycobacterium tuberculosis
Anna Engström and Pontus Juréen
25. Application of Pyrosequencing® in Food Biodefense
Kingsley Kwaku Amoako
Part V: Forensics
26. Forensic Analysis of Mitochondrial and Autosomal Markers using Pyrosequencing®
Magdalena M. Bü, Hanna Edlund, and Marie Allen
27. Tissue-specific DNA Methylation Patterns in Forensic Samples Detected By Pyrosequencing®
Joana Antunes, Kuppareddi Balamurugan, George Duncan, and Bruce McCord
Klappentext
The primary purpose of this volume is to demonstrate the range of applications of the Pyrosequencing technology in research and diagnostics and to provide detailed protocols. Beginning with an up-to-date overview of the biochemistry, the volume continues with quantitative analysis of genetic variation, ratio of expressed alleles at the RNA level, analysis of DNA methylation, global DNA methylation assays, specialized applications for DNA methylation analysis including loss of imprinting, single blastocyst analysis, allele-specific DNA methylation patterns, DNA methylation patterns associated with specific histone modifications. The volume further details tools and protocols for the detection of viruses and bacteria, and genetic and epigenetic analyses for forensics using Pyrosequencing. As a volume in the highly successful Methods in Molecular Biology series, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols and tips on troubleshooting and avoiding known pitfalls.nComprehensive and adaptable, Pyrosequencing: Methods and Protocols, Second Edition will greatly aid doctorial students, postdoctoral investigators and research scientists studying different aspects of genetics and cellular and molecular biology.
Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
