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| Modern Genetic Analysis Chapter 12. Genomics Summary Eukaryotic genomes are complex, consisting of not only unique functional genes present once in the genome, but also families of tandem and dispersed function genes, as well as several types of noncoding and apparently nonfunctional repetitive sequences. Genomics is the branch of genetics that deals with the systematic molecular characterization of such genomes. Some of the methods used are traditional genetic-mapping procedures, but, in addition, specialized techniques have been developed for manipulating the large amounts of DNA in a genome. Genomic analysis is important for two reasons: first, it affords a way of obtaining an overview of the genetic architecture of an organism, and, second, it forms a set of basic information that can be used to find new genes such as those involved in human disease. Genomic analysis generally proceeds from low-resolution analysis to techniques with higher resolution. Initially, genes must be assigned to chromosomes, and this assignment can be achieved by a variety of techniques including linkage to standard markers, in situ hybridization, pulsed field gel electrophoresis, and humanrodent cell hybridization. The arrangement of loci along a chromosome can be determined by using various types of meiotic recombination mapping and (in humans) X-irradiated hybrids. Particularly useful are molecular markers that can fill in the gaps between genes of known phenotypic association. RFLPs, SSLPs, and RAPDs all provide heterozygous loci that can be used as molecular marker loci in mapping. The highest level of genomic resolution is the physical mapping of DNA fragments. Most useful are fragments that have been cloned in vectors that carry large DNA inserts, such as cosmids, YACs, and BACs. The goal of physical mapping is to produce a set of overlapping clones that encompass an entire chromosome or an entire genome. Sequence-tagged sites are particularly useful in aligning overlapping cosmids into contigs. As more clones are characterized, contigs grow to the size of entire chromosomes. Expressed sequence tags (ESTs) can slot functional genes into the genomic map. Genomic maps have been used in the positional cloning of human disease genes of unknown function. The maps have provided suitable starting points for chromosome walking and jumping. Genomic sequencing often reveals genes that have never been associated with a phenotype; such genes must be investigated by doing gene disruptions to check for a possible mutant phenotype. Functional genomics uses a variety of approaches such as the definition of all ORFs, gene knockouts to probe gene function, the yeast two-hybrid system to look for gene interaction, and DNA microarrays to determine which genes are transcribed.

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