ANÁLISIS DEL ÁRBOL DE FALLOS

Identifying and characterising recombination hotspots in the human genome is of great importance as such regions disrupt the underlying haplotype structure, which are the basis of association studies (section 1.12; Chapter 6 ). A hotspot map of the genome may confer many advantages to genetic association studies; although recombination breaks down association, the existence of a hotspot in one region implies that another region experiences low recombination. This understanding can be utilised by employing relevant densities of markers with respect to the hotspot distribution in a candidate region. Thus, areas of low recombination derived from association studies, that exhibit higher levels of association would require reduced marker coverage than regions o f higher recombination (provided frequency o f gene conversion are not high).

Recombination hotspot mapping, which ultimately investigates crossover distribution, is achieved in many ways, ranging from low resolution (visual mapping of chiasmata) to refined high resolution (sperm studies). Recombination can be detected by (i) examining a change in linkage of detectable markers in the progeny of a mating between differing individuals (discussed in section 1.8), (ii) by comparative genetic and physical mapping (section 1.11), (iii) by population based association

analysis (section 1.12) and (iv) by high resolution mapping in males using sperm (section 1.13).

1.8.1 Genetic and physical mapping

Hotspot mapping can be, in part achieved by the correlation o f genetic and physical distances of a given region, however the resolution of this approach is limited by the density of markers and the number o f individuals examined. Despite these limitations comparative genetic and physical maps have generated important understanding concerning meiotic recombination rates (Chapter 3).

1.8.2 Linkage analysis

Linkage is the tendency of genes, or other DNA sequences at specific loci, to be inherited together as a consequence o f their physical proximity on a single chromosome. In classical linkage analysis, elucidation of the arrangement o f genes on the chromosome of an organism was achieved by following the segregation pattern of two variable phenotypic traits through successive generations. This was done by observing how often the different forms o f the two traits are co-inherited, thereby making inferences on whether the genes responsible for the two traits are on the same chromosome (linked or not linked) or located on separate chromosomes. Today, linkage analysis has been used to assist in the mapping of the human genome and predominantly to construct a framework for the mapping of inherited disease genes. This task has been made easier by knowledge of the physical location of the markers used, a result of physical mapping efforts culminating in the finished Human Genome Project (section 1.14). A large number o f polymorphic DNA markers (section 1.8.2.2), of known location and distribution through the genome, now provide a powerful tool for positional cloning.

Intra-specific genetic variation o f markers is essential for linkage analysis. The analysis of family data for linkage requires families where one parent is a double heterozygote at the loci to be tested and where it is possible to observe segregation o f these markers on the offspring. Observations over several such families provide sufficient numbers o f known non-recombinant and recombinant individuals to make a direct estimate of the recombination fraction (0) between the two markers under consideration. Segregation analyses o f markers within a candidate region can provide

information on recombinant individuals through haplotype analysis and ultimately assist in identifying crossovers. The resolution of mapping hotspots in this way is limited by the number of informative polymorphic markers and informative meioses, but has been instrumental in many studies (sections 1.15.1 and 1.15.2; Chapter 5).

1.8.2.1 Genetic linkage maps

The first comparative genetic and physical map of chromosome 1 (Figure 1.5) assigned 23 loci using linkage, family data and chiasmata frequency at male meiosis (Cook and Hamerton, 1982). Since 1987 several updated genetic maps have been published, these are essential for detecting recombination events for localising Mendelian traits and disease-susceptibility genes to precise chromosomal regions and identifying recombination hotspots. The ‘genetic composition’ o f these maps have changed parallel to the evolution of polymorphic markers.

Earlier markers portrayed an uneven coverage consisting o f many gaps, especially at the telomeric and centromeric regions o f most chromosomes, which have been overcome with the development o f more markers. Collating mapping information has been instrumental in the development of genetic maps, made possible with the availability of a set of reference families from CEPH (Centre d ’ Études du

Polymorphisme Humain). CEPH (http://www.cephb.fr/), Genethon

(http://www.genethon.fr/genethon-cu.html), Whitehead Institute for Biomedical Research/MIT Centre for Genome Research (http://www-genome.wi.mit.edu/), Sanger Centre (http://webace.Snger.ac.uk/HGP/), Stanford Human Genome Centre (SHGC) (http://shgc-www.stanford.edu). Genetic Location Database (LDB) (http://cedar.genetics.soton.ac.uk/public_html/ldb.html) and Marshfield map (http://research.marshfieldclinic.org/genetics/Map_Markers/maps.html), all provide collaborative mapping information. The important use o f genetic maps in the sequencing of the draft Human Genome cannot be emphasised enough, since genetic maps have been one of the tools utilised in the assembly and validation o f sequenced segments of the genome (Matise et al, 2002).

1.8.2.2 Genetic markers

Polymorphic markers are variable regions in the DNA that exhibit a limited number o f sequence variations (or alleles) among the population making it possible to detect the co-segregation between the locus (which could be a disease locus

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