Disease Gene Identification: Methods and Protocols

Part I: Introduction1. Technological Issues and Experimental Design of Gene Association StudiesJohanna K. DiStefano and Darin M. Taverna2. Statistical Issues in Gene Association StudiesRichard M. Watanabe3. Identification of Causal Sequence Variants of Disease in the Next Generation Sequencing EraChristopher B. KingsleyPart II: Methods for Gene Identification4. Microarray-Based Genome-Wide Association Studies Using Pooled DNASzabolcs Szelinger, John V. Pearson, and David W. Craig5. Medium-Throughput SNP Genotyping Using Mass Spectrometry: Multiplex SNP Genotyping Using the iPLEX® Gold AssayMeredith P. Millis6. Targeted SNP Genotyping Using the TaqMan AssayDorit Schleinitz, Johanna K. DiStefano, and Peter Kovacs7. Bar-Coded, Multiplexed Sequencing of Targeted DNA Regions Using the Illumina Genome AnalyzerSzabolcs Szelinger, Ahmet Kurdoglu, and David W. CraigPart III: Functional Characterization of Susceptibility Alleles and Loci8. Site-Directed MutagenesisPatricia E. Carrigan, Petek Ballar, and Sukru Tuzmen9. Gene Expression Profiling of Tissues and Cell Lines: A Dual Color Microarray MethodSonsoles Shack10. Methods for microRNA Microarray ProfilingAarati R. Ranade and Glen J. Weiss11. Allelic Expression Profiling to Dissect Genome-Wide Association Study SignalsJonathan D. Gruber12. Quantitative Polymerase Chain Reaction: Quantitative PCR Using the Comparative Cq MethodKimberly Yeatts13. Genomic Analysis by Oligonucleotide Array Comparative Genomic Hybridization Utilizing Formalin-Fixed Paraffin Embedded TissuesStephanie J. Savage and Galen Hostetter14. RNA Mapping Protocols: Northern-Blot and Amplification of cDNA EndsMaria Lucrecia Alvarez and Mahtab Nourbakhsh15. High Content RNA Interference Assay: Analysis of Tau Hyperphosphorylation as a Generic ParadigmRiLee H. Robeson and Travis DunckleyPart IV: Alternative Approaches16. Integrative Systems Biology Approaches to Identify and Prioritize Disease and Drug Candidate GenesVivek Kaimal, Divya Sardana, Eric E. Bardes, Ranga Chandra Gudivada, Jing Chen, and Anil G. Jegga17. Identification of a Common Variant Affecting Human Episodic Memory Performance Using a Pooled Genome-Wide Association Approach: A Case Study of Disease Gene IdentificationTraci L. Pawlowski and Matthew J. Huentelman18. RNAi-Based Functional PharmacogenomicsSukru Tuzmen, Pinar Tuzmen, Shilpi Arora, Nathalie Meurice, Spyro Mousses, and David Azorsa19. Genetic Predisposition to beta-Thalassemia and Sickle Cell Anemia in Turkey: A Molecular Diagnostic ApproachA. Nazli Basak and Sukru Tuzmen