Genomics

The Happy mapping approach (Genomics)

1. Introduction In 1989, while a Ph.D. student at the University of Oxford, Paul Dear invented a new method for genome mapping, named “Happy mapping”, which reflected the use of polymerase on minute amounts of DNA in the procedure. This method is basically an in vitro adaptation of the radiation hybrid (RH) method (Cox etal., […]

Hitchhiking mapping (Genomics)

1. The principle of hitchhiking mapping Hitchhiking mapping is one approach toward the identification and characterization of genes with a beneficial effect in a given context (Schiotterer, 2002; Schiotterer, 2003). The underlying principle of hitchhiking mapping is that a beneficial mutation will either be lost or increased in frequency until it becomes fixed in the […]

The technology tour de force of the Human Genome Project (Genomics)

In the short span of a few years, genome sequencing centers around the world were required to undergo a transition that effectively doubled or tripled their normal yearly data production, in order to complete the Human Genome Project (HGP) well ahead of its anticipated completion date (Lander etal., 2001). Much of what enabled this increased […]

Digital karyotyping: a powerful tool for cancer gene discovery (Genomics)

Human beings are genetically diploid. Normally, there are 23 pairs of chromosomes in the nucleus of a somatic cell, and there are two copies of each gene at its specific genomic locus. However, chromosomal aneuploidy, and gene-specific amplification and deletion are commonly observed in human cancer cells. Although random chromosomal or subchromosomal changes can be […]

The Human Genome Project (Genomics)

1. Introduction The Human Genome Project (HGP) has seen many important milestones in its history, but perhaps the most significant was in February 1996 when all the participants (Table 1) agreed that they would do their utmost to ensure that the genome sequence would be freely available to all. They agreed that sequence data would […]

Genome assembly (Genomics)

1. Introduction Historians will undoubtedly rank the Human Genome Project (HGP) among the great achievements of humanity. HGP (see Article 24, The Human Genome Project, Volume 3) represented an advancement of more than an order of magnitude in size over preliminary “model organism” projects for Caenorhabditis elegans (C. elegans Sequencing Consortium, 1998) and Drosophila melanogaster […]

Noncoding RNAs in mammals (Genomics)

1. Introduction As the genome-sequencing revolution has progressed through more complex organisms, the first outcome of each new genome sequence has been an estimated gene count. What appears to be an obsession with enumeration has largely ignored the question of the definition of a gene. From a geneticist’s viewpoint, a gene is a unit of […]

Segmental duplications and the human genome (Genomics)

1. Introduction The process of gene and genome duplication has played a major role in evolution and has sparked the interest of scientists for decades. Susumu Ohno’s concept, through his highly influential topic “Evolution by gene duplication” (Ohno, 1970), focused on the collective effect of duplications, mutations, and natural selection, wherein an increase in gene […]

The distribution of genes in human genome (Genomics)

1. Genome compartmentalization Thirty years ago, we discovered that the bovine genome (neglecting satellite DNAs, which consist of tandemly repeated short sequences) was made of DNA molecules (about 30 kb in size in our work) of fairly uniform GC levels (GC is the molar percentage of guanine+cytosine in DNA). These DNA molecules belonged to a […]

Pseudogenes (Genomics)

Pseudogenes are genomic regions that derive from genes but have no function (Balakirev and Ayala, 2003; Mighell et al., 2000; Vanin, 1985; Zhang and Gerstein, 2004). Because they have been traditionally assumed to present no biological relevance, the identification and classification of pseudogenes has attracted little attention and was initially restricted to evolutionary studies. Over […]