Gene Mapping Based On Identity By Descent

The high frequency of NICC in an isolated rural area in the Tyrol suggested a founder effect (i.e., the affected individuals are all descendants of a common ancestor who introduced the NICC mutation into the population many generations ago) (Fig. 2). If there had been a lack of selective pressure against this mutant allele, the allele could have spread through the population so that a large majority of individuals would have inherited the same mutant gene identical by descent (IBD) either as a gene carrier or as a patient. In theory, the location of the gene mutation in patients should be revealed by homozygosity mapping, a mapping approach based on the inheritance of two identical copies of the disease locus by the affected child from a common ancestor (i.e., homozygosity by descent [HBD])

The size of the region around a disease locus that shows HBD in an affected inbred individual is determined by the number of meiotic steps that separate the affected individual from the common ancestor who carried a single copy of the disease gene on one of his/her chromosomes. In every meiotic step, recombination will lead to a reduction of the shared chromosomal segment (see Fig. 3). This mapping method therefore works extremely well when the patient is the product of a first- or second-cousin marriage (first cousins are separated by four meiotic steps, and second cousins by six meiotic steps) (Fig. 4). Relatively large regions (i.e., haplotypes) of approx 20-30 centiMorgans (cM) around the disease locus can be expected to be IBD in patients produced from these marriages

(45). The sensitivity with which homozygous regions can be detected is based on the resolution of the genetic markers used for mapping studies. Currently, most marker maps for genomewide mapping studies are spaced 5-10 cM apart. As the number of meiotic steps between a patient and a common founder increases, the homozygous region around the disease gene mutation becomes more difficult to observe. This is expected to be the case for Tyrolean NICC (13,33,34). Nevertheless, disease chromosomes should still share a reasonable amount of DNA around their disease mutation (e.g., chromosomes A and B in Fig. 2). These conserved regions of IBD around disease mutations can be identified by a search for haplotypes shared between individual patients.

More recently, founded populations (approx 8-15 generations ago) have become excellent resources for mapping rare diseases with a simple inheritance pattern: We can search for segments that are shared by patients and then demonstrate that this sharing is IBD (Fig. 4). This haplotype sharing approach has been extremely useful in mapping a number of rare disease genes, including the gene involved in benign recurrent hepatic cholestasis (BRIC) (46), Byler's disease (47), and North American childhood cirrhosis (48). The BRIC gene, for example, was localized to chromosome 18 by performing a genomewide screen on only three patients from a religiously isolated fishing community in the Netherlands. Although the chromosomes of these three BRIC patients had undergone at least six meioses since their shared origin, the BRIC haplotype was still shared over a region of more than 20 cM (46).

Fig. 2. A schematic representation of the effects of a founder effect in a population that expanded mainly by reproduction. The chromosome with the disease mutation (indicated by an asterisk) is transmitted by the founder through many generations; because of recombination, the size of the DNA flanking the mutation (in black) has been reduced. In the current population—consisting of normal, carriers, and affected individuals—each mutation is identical to the one that was already present in the founder of the population. However, the size of the ancestral DNA flanking the mutation (depicted in black) is different on each chromosome. The two bars represent a pair of homologous chromosomes.

Fig. 2. A schematic representation of the effects of a founder effect in a population that expanded mainly by reproduction. The chromosome with the disease mutation (indicated by an asterisk) is transmitted by the founder through many generations; because of recombination, the size of the DNA flanking the mutation (in black) has been reduced. In the current population—consisting of normal, carriers, and affected individuals—each mutation is identical to the one that was already present in the founder of the population. However, the size of the ancestral DNA flanking the mutation (depicted in black) is different on each chromosome. The two bars represent a pair of homologous chromosomes.

Fig. 3. The principle of homozygosity mapping. Homozygosity for the disease mutation (indicated by an asterisk) is the result of the inheritance of two copies of the mutant gene. Because this mutation was originally present in one of the two founders of this family, the two copies of the mutant gene (and its surrounding DNA) are identical by descent. The patient is therefore not only homozygous for the mutation responsible for the disease but also for the DNA directly flanking the mutation (i.e., the black region).

Fig. 3. The principle of homozygosity mapping. Homozygosity for the disease mutation (indicated by an asterisk) is the result of the inheritance of two copies of the mutant gene. Because this mutation was originally present in one of the two founders of this family, the two copies of the mutant gene (and its surrounding DNA) are identical by descent. The patient is therefore not only homozygous for the mutation responsible for the disease but also for the DNA directly flanking the mutation (i.e., the black region).

Fig. 4. The suitability of the different identity by descent methods is determined by the number of meiotic steps that separate patients or chromosomes from each other.
Fig. 5. The situation found in the Tyrolean NICC families. Haplotype sharing around the disease mutation can only be carried out using the obligate gene carriers (i.e., the patients' parents).

The situation for the Tyrolean NICC is, however, more complicated. The disease is lethal when left untreated, although now treatment can be either medication (e.g., D-penicillamine) or a liver transplantation. In the Tyrol, there is only one patient who has received a liver transplant and who is still alive and available for study (unpublished). All of the remaining patients have died from liver cirrhosis (13). Nevertheless, pairs of parents were identified who had had at least one NICC child (thus, both the parents must be obligate carriers for the NICC mutation on one of their chromosomes and, consequently, each parent was expected to have one copy of a [partly] shared haplotype [Fig. 5]). For families A, B, C, and I (34), the number of meiotic steps between the parents ranged from 5 to 19. Such relationships should result in IBD sharing of about 6 cM (for 20 meiotic steps) to more than 20 cM (for 5 meiotic steps) (45).

0 0

Post a comment