Table of Contents

Introduction : gene discovery-from positional cloning to genomic cloning.
High throughput gene expression analysis and the identification of expression QTLs.
DNA methylation in the pathogenesis of autoimmunity.
Ccell-based analysis with microfluidic chip.
Missing dimension : protein turnover rate measurement in gene discovery.
Bioinformatics tools for the prediction of gene function.
Determination of genomic locations of targeted genetic loci.
Mutation discovery using high throughput mutation screening technology.
Candidate screening through gene expression profile.
Candidate screening through high-density SNP array.
Gene discovery through direct genome sequencing.
Candidate screening through bioinformatics tools.
Using an integrative strategy to identify mutations.
Determination of the function of a mutant in a gene.
Confirmation of a mutation by multiple molecular approaches.
Confirmation of a mutation by microRNA.
Confirmation of function of a gene by translational approaches.
Confirmation of single nucleotide mutations.
Initial identification and confirmation of a QTL gene.
Gene discovery of crop diseases in the post genome era.
Impact of whole genome genetic element analysis on gene discovery of disease models.
Impact of whole genome protein analysis on gene discovery of disease models. This book provides readers with new paradigms on the mutation discovery in the post-genome era. The completion of human and other genome sequencing, along with other new technologies, such as mutation analysis and microarray, has dramatically accelerated the progress in positional cloning of genes from mutated models. In 2002, the Mouse Genome Sequencing Consortium stated that "The availability of an annotated mouse genome sequence now provides the most efficient tool yet in the gene hunter's toolkit. One can move directly from genetic mapping to identification of candidate genes, and the experimental process is reduced to PCR amplification and sequencing of exons and other conserved elements in the candidate interval. With this streamlined protocol, it is anticipated that many decades-old mouse mutants will be understood precisely at the DNA level in the near future." The implication of such a statement should be similar to the identification of mutated genes from human diseases and animal models, when genome sequencing is completed for them. More than five years have passed, but genes in many human diseases and animal models have not yet been identified. In some cases, the identification of the mutated genes has been a bottleneck, because the genetic mechanism holds the key to understand the basis of the diseases. However, an integrative strategy, which is a combination of genetic mapping, genome resources, bioinformatics tools, and high throughput technologies, has been developed and tested. The classic paradigm of positional cloning has evolved with completely new concepts of genomic cloning and protocols. This book describes new concepts of gene discovery in the post-genome era and the use of streamlined protocols to identify genes of interest. This book helps identify not only large insertions/deletions but also single nucleotide mutations or polymorphisms that regulate quantitative trait loci (QTL).