Disease Gene Identification: Methods and Protocols

Part I: Introduction 1. Technological Issues and Experimental Design of Gene Association Studies Johanna K. DiStefano and Darin M. Taverna 2. Statistical Issues in Gene Association Studies Richard M. Watanabe 3. Identification of Causal Sequence Variants of Disease in the Next Generation Sequencing Era Christopher B. Kingsley Part II: Methods for Gene Identification 4. Microarray-Based Genome-Wide Association Studies Using Pooled DNA Szabolcs Szelinger, John V. Pearson, and David W. Craig 5. Medium-Throughput SNP Genotyping Using Mass Spectrometry: Multiplex SNP Genotyping Using the iPLEX(R) Gold Assay Meredith P. Millis 6. Targeted SNP Genotyping Using the TaqMan Assay Dorit Schleinitz, Johanna K. DiStefano, and Peter Kovacs 7. Bar-Coded, Multiplexed Sequencing of Targeted DNA Regions Using the Illumina Genome Analyzer Szabolcs Szelinger, Ahmet Kurdoglu, and David W. Craig Part III: Functional Characterization of Susceptibility Alleles and Loci 8. Site-Directed Mutagenesis Patricia E. Carrigan, Petek Ballar, and Sukru Tuzmen 9. Gene Expression Profiling of Tissues and Cell Lines: A Dual Color Microarray Method Sonsoles Shack 10. Methods for microRNA Microarray Profiling Aarati R. Ranade and Glen J. Weiss 11. Allelic Expression Profiling to Dissect Genome-Wide Association Study Signals Jonathan D. Gruber 12. Quantitative Polymerase Chain Reaction: Quantitative PCR Using the Comparative Cq Method Kimberly Yeatts 13. Genomic Analysis by Oligonucleotide Array Comparative Genomic Hybridization Utilizing Formalin-Fixed Paraffin Embedded Tissues Stephanie J. Savage and Galen Hostetter 14. RNA Mapping Protocols: Northern-Blot and Amplification of cDNA Ends Maria Lucrecia Alvarez and Mahtab Nourbakhsh 15. High Content RNA Interference Assay: Analysis of Tau Hyperphosphorylation as a Generic Paradigm RiLee H. Robeson and Travis Dunckley Part IV: Alternative Approaches 16. Integrative Systems Biology Approaches to Identify and Prioritize Disease and Drug Candidate Genes Vivek Kaimal, Divya Sardana, Eric E. Bardes, Ranga Chandra Gudivada, Jing Chen, and Anil G. Jegga 17. Identification of a Common Variant Affecting Human Episodic Memory Performance Using a Pooled Genome-Wide Association Approach: A Case Study of Disease Gene Identification Traci L. Pawlowski and Matthew J. Huentelman 18. RNAi-Based Functional Pharmacogenomics Sukru Tuzmen, Pinar Tuzmen, Shilpi Arora, Nathalie Meurice, Spyro Mousses, and David Azorsa 19. Genetic Predisposition to β-Thalassemia and Sickle Cell Anemia in Turkey: A Molecular Diagnostic Approach A. Nazli Basak and Sukru Tuzmen