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Genomics

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Genomics is the study of an organism's genome and the use of the genes. It deals with the systematic use of genome information, associated with other data, to provide answers in biology, medicine, and industry.

Genomics has the potential of offering new therapeutic methods for the treatment of some diseases, as well as new diagnostic methods. For example, for women newly diagnosed with breast cancer, a genomic test called Oncotype DX assesses a patient’s individual risk of breast cancer recurrence and likely benefit from chemotherapy, which can help doctors make more informed and more personalized treatment decisions. Other applications are in the food and agriculture sectors.

The major tools and methods related to genomics are bioinformatics, genetic analysis, measurement of gene expression, and determination of gene function.

History

Genomics appeared in the 1980s and took off in the 1990s with the initiation of genome projects for several species. The related field of genetics is the study of genes and their role in inheritance.

The first genome to be sequenced in its entirety was that of bacteriophage Φ-X174; (5,368 bp) in 1980. The first free-living organism to be sequenced was that of Haemophilus influenzae (1.8Mb) in 1995, and since then genomes are being sequenced at a rapid pace. A rough draft of the human genome was completed by the Human Genome Project in early 2001 amid much fanfare.

The growth of the "omics"

Main article: -omics

The original use of the suffix "ome" (from the Greek for 'all', 'every' or 'complete') was "genome", which refers to the complete genetic makeup of an organism. Because of the success of large-scale quantitative biology projects such as genome sequencing, the suffix "ome" has been extended to a host of other contexts. For instance, proteome refers to the totality of proteins (expressed genes that are translated) in an organism, tissue type or cell. Proteomics is now well-established as a term for studying the proteome.

Look also: List of omics topics in biology

Comparative genomics

Main article: Comparative genomics

Comparison of genomes has resulted in some surprising biological discoveries. If a particular DNA sequence or pattern is present among many members of a clade, that sequence is said to have been conserved among the species. Evolutionary conservation of a DNA sequence may imply that it confers a relative selective advantage to the organisms that possess it. Conservation also suggests that sequence has functional significance. It may be a protein coding sequence or regulatory region. Experimental investigation of some of these sequences has shown that some are transcribed into small RNA molecules, although the functions of these RNAs were not immediately apparent.

The identification of similar sequences (including many genes) in two distantly related organisms, but not in other members of one of the clades, has led to the theory that these sequences were acquired by horizontal gene transfer. This phenomenon is most prominent in bacteria, although it also seems that genes were transferred from Archaea to Eubacteria. It has also been noticed that bacterial genes exist in eukaryotic nuclear genomes and that these genes generally encode mitochondrial and plastid proteins, giving support to the endosymbiotic theory of the origin of these organelles. This theory holds that the mitochondria and chloroplast organelles found in many animal and plant genomes were originally free-living bacteria that were absorbed by an ancestral eukaryote, and that subsequently became an integral part of the eukaryotic cell.

Genetic similarity

It is often stated that a particular organism shares X percent of its DNA with humans. This number indicates the percentage of base pairs that are identical between the two species. Here is a list of genetic similarity to humans, with sources, where known.

These numbers were found in various secondary sources, and were likely derived from differing methodologies (such as DNA-DNA hybridization or sequence alignment) which might give different results applied to the same pair of species. Therefore, they should be regarded only as rough approximations.

Species Similarity Source
Human 99.9% quoted by U.S.A. President Clinton, Jan 2000, State of the Union address; also Human Genome Project
100% identical twins
Chimpanzee 98.4% sources: Americans for Medical Progress; Jon Entine in the San Francisco Examiner
98.7% Richard Mural of Celera Genomics, quoted on MSNBC
Bonobo equal to chimpanzee
Gorilla 98.38% based on study of intergenic nonrepetitive DNA in Am J Hum Genet. (2001) Feb;682:444-56
Mouse 98% source: Americans for Medical Progress
85% comparing all protein coding sequences, NHGRI
Dog 95% Jon Entine in the San Francisco Examiner
C. elegans 74% Jon Entine in the San Francisco Examiner
Banana 50% source: Americans for Medical Progress
Daffodil 35% Steven Rose in The Guardian 22 January 2004

See also


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