Celiac Disease

This volume provides detailed molecular analysis of the associated pathways and cell types involved in Celiac Disease, and embraces new technologies such as next generation sequencing. The book is divided into three parts: Part I gives a background overview with a number of reviews to describe the history and nature of the disease, its diagnosis, the role of animal models, and study designs for investigating genetic susceptibility. Part II describes molecular techniques, including tissue culture, isolation and cloning of relevant cell types, high content analysis of biopsies, and HLA genotyping. The final part of the book begins with an outline of scripting for data management, focusing on tools that are freely available to researchers who wish to explore them. It also describes analysis pipelines for bioinformatics prediction of antigenicity, quality control and analysis of GWAS data, and transcriptome analysis by next generation sequencing. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and thorough, Celiac Disease: Methods and Protocols brings together novel and more traditional methods in molecular biology and immunology, in order to provide a tool-kit for all stages for Celiac Disease research-from the practicalities of identifying, obtaining, stabilizing and maintaining high quality samples, to molecular analysis and bioinformatics.

Celiac Disease: Background and Historical Context. - Celiac Disease: Diagnosis. - Generating Transgenic Mouse Models for Studying Celiac Disease. - Study Designs for Exploring the Non-HLA Genetics in Celiac Disease. - 24 Hour Ex Vivo Culture of Coeliac Duodenal Biopsies. - Isolation and Cloning of Gluten-Specific T Cells in Celiac Disease. - Flow Cytometric Analysis of Human Small Intestinal Lymphoid Cells. - Adaptation of a Cell-Based High Content Screening System for the In-depth Analysis of Celiac Biopsy Tissue. - HLA Genotyping: Methods for the Identification of the HLA-DQ2, -DQ8 Heterodimers Implicated in Celiac Disease (CD) Susceptibility. - Detecting Allelic Expression Imbalance at Candidate Genes Using 5' Nuclease Genotyping Technology. - Gene Expression Profiling of Coeliac Biopsies and Peripheral Blood Monocytes Using Taqman Assays. - Cloning Gene Variants and Reporter Assays. - Epigenetic Methodologies for the Study of Celiac Disease. - Candidate Gene Knockdown in Celiac Disease. - Perl One-Liners: Bridging the Gap Between Large Data-Sets and Analysis Tools. - Bioinformatic Analysis of Antigenic Proteins. - Quality Control Procedures for Genome Wide Association Studies using the Immunochip Platform. - Quality Control and Analysis of NGS RNA Sequencing Data.