High-density linkage or genetic maps developed by computer analysis of raw genotyping data show the relative positions of closely spaced DNA markers. High-throughput platforms have been developed for the rapid analysis of large numbers of genetic markers (millions per day). Two types of commonly used genetic markers are single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs), or microsatellites.
Long-range physical maps chart the features of chromosomes.
-Fluorescent in situ hybridization, or FISH, locates a cloned locus to a particular band on a particular chromosome.
-DNA hybridization and fingerprinting order the clones of a genomic library into overlapping clusters that span the chromosomes of the species. One approach to assigning chromosomal positions uses the markers of a high-density linkage map and sequence tagged sites (STSs) as hybridization probes to obtain overlapping, large-insert clones that span the chromosomes. Gaps between the clusters of clones (contigs) can be filled in by surveying new large insert libraries with STS markers from either contig end. Another approach does not rely on linkage mapping and genetic markers. Instead, physical analysis begins with the complete set of individual clones in a whole-genome library. Researchers establish fingerprints for each of the clones and make a computer search to determine overlaps in fingerprints that indicate overlaps in the corresponding clones. With a large enough number of clones, it is possible to
-Researchers use restriction mapping and hybridization probes to characterize the fine details of each clone in a contig.
-Computers combine the information for individual clones into detailed whole chromosome physical maps.
Long-range sequence maps, compiled from the sequences of subclones, provide a readout of every nucleotide in each chromosome. The subclones are derived either from previously mapped large insert clones (hierarchical shotgun approach) or directly from the genome (whole-genome shotgun approach).
Linkage, physical, and sequence maps can be readily integrated because the markers for the linkage and physical maps (SSRs, SNPs, STSs) use sequence-based PCR primers that generate unique molecular addresses in the genome and thus can be specifically localized on the genome.
A variety of major insights have emerged from analyses of human and model organism genomes.
The number of human genes, approximately 40,000 is surprisingly low.
Genes fall into two major classes: noncoding RNA genes, generally representing RNA molecular machines; and protein-coding genes encoding the protein structural components and molecular machines. The collection of proteins in a particular cell is a proteome, and the collection of mRNAs, a transcriptome. Transcriptomes and proteomes are dynamic and change throughout the time spans of development and physiological responses. Proteins are often composed of one or more domains that encode discrete functions.
Repeat sequences constitute more than 50% of the human genome. Some repeat sequences have evolved to become genes or control sequences. Others may catalyze chromosomal rearrangements and translocations.
Evolution can occur by the lateral transfer of genes from one organism to another. Humans, for example, may have 200 or more genes derived recently from bacteria.
The different human races have very few, if any, uniquely distinguishing genes. Genetically, there appears to be a single race of humans.
The sequences of microbes, plants, and animals all employ the same genetic code and show a remarkable similarity among many basic biological systems. This affirms the idea that we all descended from a single common ancestor.
The Human Genome Project has catalyzed the development of the DNA sequencer, DNA arrays, and the use of the mass spectrometer for genomics and proteomics. These instruments have been integrated into high-throughput platforms for DNA sequencing and genotyping, as well as for mRNA and protein analysis.
The Human Genome Project has spawned paradigm changes in our approaches to biology and medicine. Systems approaches, in which researchers study all the elements of a system, complement the more classical biological approaches, in which researchers analyze one gene or protein at a time. Predictive medicine will allow researchers to correlate polymorphisms with disease predisposition and eventually formulate probabilistic health-history predictions for each individual. Preventive medicine will place the defective genes in their biological systems and develop ways to avoid their limitations with, for example, drugs, diet, gene therapy, or stem cell therapy. The potential of predictive/preventive medicine raises social, ethical, and legal questions for which there are no easy answers.
