Description
The aim of this book is to improve pyrosequencing protocols as well as instrumentation for better clinical use by describing improvements and novel applications of pyrosequencing technology. Divided into five parts, the book’s thirty chapters explore advances in pyrosequencing template preparation, pyrosequencing technology innovations, multiplex pyrosequencing based on barcodes, the miniaturization of pyrosequencing equipment, as well as various applications. As part of the Springer Protocols program, chapters contain the kind of detail and practical implementation advice to guarantee successful results in the lab. Comprehensive and thorough, Advances and Clinical Practice in Pyrosequencing serves as a valuable reference for researchers who are engaged in personalized medicine, disease control, and DNA diagnosis in numerous other fields. Part I: Template Preparation 1. Preparation of Single-Stranded DNA for Pyrosequencing by LATE-PCR Huiyong Yang, Chao Liang, Zhiyao Chen, Bingjie Zou, Qinxin Song, and Guohua Zhou 2. A Simplified Protocol for Preparing Pyrosequencing Templates Based on LATE-PCR Using Whole Blood as Starting Material Directly Yunlong Liu, Haiping Wu, Hui Ye, Zhiyao Chen, Qinxin Song, Bingjie Zou, Jianzhong Rui, and Guohua Zhou 3. Improvement of LATE-PCR to Prepare Pyrosequencing Template Qinxin Song, Huiyong Yang, Bingjie Zou, Hideki Kambara, and Guohua Zhou 4. Pyrosequencing Templates Generated by Nicking PCR Products with Nicking Endonuclease Qinxin Song, Haiping Wu, Guohua Zhou, and Hideki Kambara 5. Pyrosequencing Templates Generated by Asymmetric Nucleic Acid Sequence-Based Amplification (Asymmetric-NASBA) Huning Jia, Zhiyao Chen, Haiping Wu, Hui Ye, Bingjie Zou, Qinxin Song, and Guohua Zhou 6. Gel Immobilization of Acrylamide-Modified Single-Stranded DNA Template for Pyrosequencing Pengfeng Xiao, Huan Huang, Bingjie Zou, Qinxin Song, Guohua Zhou, and Zuhong Lu 7. Multiplex PCR Based on a Universal Biotinylated Primer to Generate Templates for Pyrosequencing Zhiyao Chen, Yunlong Liu, Hui Ye, Haiping Wu, Jinheng Li, Bingjie Zou, Qinxin Song, and Guohua Zhou Part II: Technology Innovation 8. A Novel Pyrosequencing Principle Based on AMP-PPDK Reaction for Improving the Detection Limit Guohua Zhou, Tomoharu Kajiyama, Mari Gotou, Akihiko Kishimoto, Shigeya Suzuki, and Hideki Kambara 9. Pyrosequencing Chemistry Coupled with Modified Primer Extension Reactions for Quantitative Detection of Allele Frequency in a Pooled Sample Guohua Zhou, Masao Kamahori, Kazunori Okano, Gao Chuan, Kunio Harada, and Hideki Kambara 10. A Gel-Free SNP Genotyping Method Based on Pyrosequencing Chemistry Coupled with Modified Primer Extension Reactions Directly from Double-Stranded PCR Products Guohua Zhou, Hiromi Shirakura, Masao Kamahori, Kazunori Okano, Keiichi Nagai, and Hideki Kambara 11. Improvement of Pyrosequencing to Allow Multiplex SNP Typing in a Pyrogram Guohua Zhou, Mari Gotou, Tomoharu Kajiyama, and Hideki Kambara 12. Improvement of P yrosequencing-Sensitive Based on the Capture of Free Adenosine 5′-Phosphosulfate with Adenosine Triphosphate Sulfurylase Haiping Wu, Wenjuan Wu, Zhiyao Chen, Weipeng Wang, Bingjie Zou, Qinxin Song, Guohua Zhou, and Hideki Kambara 13. Using Polymerase Preference Index to Design imLATE-PCR Primers for an Efficient Pyrosequencing Qinxin Song, Xiemin Qi, Yiyun Shen, Yiru Jin, Bingjie Zou, and Guohua Zhou Part III: Reagents Preparation 14. Preparation of Thermalstable Biotinlyted Firefly Luciferase and Its Application in Pyrosequencing Shuhui Zhu, Bingjie Zou, Haiping Wu, Yinjiao Ma, Ying Chen, Qinxin Song, and Guohua Zhou 15. Expression of Thermostable Recombinant Luciola lateralis Luciferase and Its Function on Setting up of Heat-Stable Pyrosequencing System &nb sp; Shu Xu, Bingjie Zou, Qinxin Song, and Guohua Zhou 16. Expression and Purification of ATP Sulfurylase from Saccharomyces cerevisias in Escherichia coli and Its Application in Pyrosequencing Juan Luo, Wenjuan Wu, Bingjie Zou, Qinxin Song, and Guohua Zhou 17. Characterization of Recombinant Escherichia coli Single-Strand Binding Protein and Its Application in Pyrosequencing Jianping Wang, Bingjie Zou, Qinxin Song, and Guohua Zhou 18. Expression of PPDK from Microbispora Rosea Subsp. aerata in E. coli and Its Application in Pyrosequencing Bingjie Zou, Qinxin Song, and Guohua Zhou Part IV: Pyrosequencing-Bas ed Bio-Barcodes 19. Construction of 3-Plex Barcodes for Differential Gene Expression Analysis with Pyrosequencing Xiaodan Zhang, Haiping Wu, Zhiyao Chen, Guohua Zhou, and Hideki Kambara 20. Development of Pyrosequencing-Based Multiplex Bioassay by Designing Barcodes Encoded with Artificially Designed Sequences Zhiyao Chen, Xiaodan Zhang, Xiqun Liu, Bingjie Zou, Haiping Wu, Qinxin Song, Hideki Kambara, and Guohua Zhou 21. Quantitatively Discriminating Multiplexed LAMP Products with Pyrosequencing-Based Bio-Barcodes Chao Liang, Yanan Chu, Sijia Cheng, Haiping Wu, Bingjie Zou, Qinxin Song, and Guohua Zhou 22. Multiplex Ligation-Dependent Sequence-Tag Amplification Coupled with Pyrosequencing for Copy Number Variation (CNV) Analysis ; Haiping Wu, Bingjie Zou, Qinxin Song, and Guohua Zhou Part V: Instrumentation 23. Pyrosequencer Miniaturized with Capillaries to Deliver Deoxynucleotides Guohua Zhou, Masao Kamahori, Kazunori Okano, Kunio Harada, and Hideki Kambara 24. Pyrosequencer with a Sensor of Photo-Diode Array Hideki Kambara and Guohua Zhou 25. Pyrosequencing on Acryl-Modified Glass Chip Huan Huang, Haiping Wu, Pengfeng Xiao, Bingjie Zou, Qinxin Song, and Guohua Zhou 26. Pyrosequencing On-Chip Based on a Gel-Based Solid-Phase Amplification Huan Huang, Pengfeng Xiao, Zongtai Qi, Bingjie Zou, Qinxin S ong, and Guohua Zhou Part VI: Clinical Practice 27. Prenatal Diagnosis of Trisomy 21 by Quantitatively Pyrosequencing Heterozygotes Using Amniotic Fluid as Starting Material of PCR Hui Ye, Haiping Wu, Huan Huang, Yunlong Liu, Bingjie Zou, Qinxin Song, and Guohua Zhou 28. Comparative Gene Expression Analysis of Breast Cancer-Related Genes by Multiplex Pyrosequencing Coupled with Sequence Barcodes Qinxin Song, Hua Jing, Haiping Wu, Bingjie Zou, Guohua Zhou, and Hideki Kambara 29. MicroRNA Quantification by Pyrosequencing with a Sequence-Tagged Stem-Loop RT Primer Hua Jing, Qinxin Song, Zhiyao Chen, Bingjie Zou, Minsheng Zhu, Guohua Zhou, and Hideki Kambara 30. Analysis of Genetically Modified Organisms by Pyrosequencing on a Portable Photodiode-Based Bioluminescence Sequencer Qinxin Song, Guijiang Wei, Bingjie Zou, and Guohua Zhou 31. Genotyping of Pathogenic Serotypes of S. Suis with Pyrosequencing Huiyong Yang, Huan Huang, Haiping Wu, Bingjie Zou, Qinxin Song, Guohua Zhou, and Hideki Kambara 32. Differential Gene Expression Analysis of Breast Cancer by Combining Sequence-Tagged Reverse-Transcription PCR with Pyrosequencing Xiaodan Zhang, Haiping Wu, Zhiyao Chen, Bingjie Zou, Qinxin Song, and Guohua Zhou 33. Detection of Avian Influenza A Virus by Pyrosequencing Weipeng Wang, Haiping Wu, Bingjie Zou, Qinxin Song, and Guohua Zhou 34. Genotyping of Alcohol Dehydrogenase Gene by Pyroseque ncing Coupled with Improved LATE-PCR Using Human Whole Blood as Starting Material Zheng Xiang, Yunlong Liu, Xiaoqing Xing, Bingjie Zou, Qinxin Song, and Guohua Zhou 35. Pyrosequencing on a Single Cell Qinxin Song, Huiyong Yang, Bingjie Zou, Hideki Kambara, and Guohua Zhou
