LOS COMPONENTES DE UN SISTEMA DE GESTIÓN

Gene mapping for autosomal recessive conditions has lagged behind that of autosomal dominant and X-linked disorders. This is mainly due to the fact that inordinate numbers of nuclear families with autosomal recessive disorders are needed to have a high likelihood of showing linkage (Wong et al. 1986).

As long ago as 1908 Sir Archibald Garrod observed that a large proportion o f patents with the recessive inborn error of metabolism, alkaptonuria, were the offspring of

consanguineous matings (Garrod, 1908). In 1953 Smith made the important

observation that the offspring of consanguineous unions would not only be homozygous by descent but also be homozygous for genetic markers close to the disease locus (Smith, 1953) (Figure 13). Smith's obsei*vation lead to the proposal by Lander and Botstein in 1987 that an autosomal recessive trait could be mapped by looking for areas of consistent homozygosity in the offspring of consanguineous

matings (Lander and Botstein, 1987). This approach, termed 'homozygosity

mapping', relies on the fact that in a child of a consanguineous union a fraction of the genome will be homozygous by descent (LTBD) This fraction (F) is known as the coefficient of inbreeding and is defined as the chance that a given locus will be HBD. F will vary depending on the degree of the relationship between the parents: F=l/4 for siblings, F=l/16 for 1st cousins and F=l/64 for 2nd cousins. Lander and Botstein postulate that in a population in Hardy-Weinberg equilibrium, the probability (a ) of a child with a recessive disease be homozygous by descent at the disease locus is Fq/Fq + (1 -F)q2 where q is the disease allele frequency. If q is small compared to F, then a is close to 1. Thus while the region surrounding the disease locus is HBD with a probability of = 1 unlinked regions are HBD with a probability of F. Assuming an

infinitely polymorphic marker, everytime homozygosity for any allele is observed in an affected child an odds ratio o f a :F is obtained supporting the hypothesis that the disease gene is linked to the marker compared to the hypothesis that it is unlinked. Thus for the afilected progeny of a 1st cousin marriage finding homozygosity for such a marker gives odds of 16; 1 in favour of linkage. If the marker is tightly linked then it is theorectically possible to obtain significant odds for proving linkage with only three such affected children (16^: 1).

4/4 3/4 +/+

a

a

In practice, the number of affected progeny required to achieve a LOD score > 3 depends not only on the coefficient of consanguinity but also on the spacing of the genetic markers used and their probability o f being homozygous at random in the population from which the child comes. Lander and Botstein have produced an algorithm to compute the number of inbred progeny needed to map a rare recessive disease by homozygosity mapping as a function of these variables (Figure 14). For example, using polymorphic markers with a 50% chance of being homozygous spaced at 10 cM intervals 10 progeny of 1st cousin matings are required. As the frequency of the disease allele in the population increases in relation to F then a will decrease and thus to map less rare conditions more affected progeny affected progeny will be required (Figure 14). The great advantage of this technique is that it allows rare recessive conditions, for which families with multiple affected individuals are scarce, to be mapped using a small number of affected individuals. It depends firstly on the ability to obtain DNA from inbred families and secondly on the availability o f a complete genetic map of evenly spaced highly polymorphic markers.

The latter criterion was fu fit led by the shift in the early 1990s from restriction fragment length polymorphism (RFLP) based mapping to the use of highly polymorphic short tandem repeat polymorphisms (STRPs) which are easily amplified by PCR. In 1992, Weissenbach and colleagues produced a "second generation", STRP based, linkage map of the human genome (Weissenbach et al. 1992) reporting dinucleotide markers at 10 cM intervals. By 1994 this map had been extended to include more than 2000 markers(Gyapay et al. 1994).

40 30 h = 0, 20 10 10 20 30

D istance b etw een c o n sec u tiv e RFLPs [cM]

40 •o « i s

If

li

F i g u r e 14. N u m b e r o f i n b r e d p r o g e n y n e e d e d t o m a p a r e c e s s i v e trait as a f u n c t i o n o f

d i s e a s e a n d allele f r e q u e n c y ( t r o m L a n d e r a n d B o t s t e i n , 1987).

The frequency of consanguineous marriage varies considerably depending on the geographical isolation and/or the cultural norms of the population. In many Muslim cultures for example Pakistan and most Middle Eastern and North African countries consanguineous marriage is very common and is considered socially supportive (Darr and Modell, 1988). In Britain the rate of cousin marriage in the Caucasian population is around 1 in 200 (Emei-y and Mueller (eds), 1992). However in certain ethnic groups it is considerably higher than this. A survey o f British Pakistani mothers in West Yorkshire suggests that over 50% were married to their 1st cousins (Darr and Modell, 1988).

The region of HBD surrounding the disease gene in an affected child depends on the degree o f relationship between the parents: for 1st cousins the median length is = 28cM (Lander and Botstein, 1987). Although this is a large genetic distance if n affected 1st cousin progeny are studied the region o f overlap will be on average 2%hi cM thereby localising the disease gene to several cMs. For 2nd cousins or more distant degrees of relationship between the parents the median region o f HBD will be shorter and so unless vei-y closely spaced markers are used regions o f overlapping HBD may be missed.

The percentage of the genome which is homozygous by descent depends on F, the coefficient o f inbreeding, but additionally on the prior coefficient o f inbreeding (F^) within the populaton as a whole. In a population where consanguineous marriage has been the usual pattern over many generations F^ may significantly increase the total value of F and therefore reduce the power of a pedigree to generate a likelihood of linkage (Mueller and Bishop, 1993). The disease allele frequency {q) is also likely to be relatively high in this type of population and therefore the probability that all affecteds in the population will be HBD at the disease locus will be < I.

A major problem complicating the use of homozygosity mapping is genetic heterogeneity. Theorectically if linkage is not found under the assumption of homogeneity it should be possible to search for more than one locus simultaneously

provided that at least one is HBD in the majority o f inbred affecteds (Lander and Botstein, 1987). The numbers of inbred progeny required to perform a simultaneous search have been estimated by Lander and Botstein. In practice, the problem has been overcome by using large inbred kindreds from isolated populations.