Advances and Clinical Practice in Pyrosequencing

ISBN-13: 9781493933068 / Angielski / Twarda / 2016 / 407 str.

Guohua Zhou; Qinxin Song

Opis

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."

Spis treści

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