Mapping complex genetic traits in humans: new methods using a complete RFLP linkage map.

It has been clear since the rediscovery of Mendel that humans obey laws of heredity identical with those of other organisms. The central features of Mendelism were observable in humans by following simply inherited common traits, including some diseases. However, the systematic study of human heredity using the standard concepts (complementation and recombination, tests of epistasis, etc.) has been infeasible in humans for two reasons: (1) because Homo sapiens is not an experimental animal that can be manipulated at will and (2) because few genetic markers had been found that were heterozygous often enough to allow random matings to be informative. The advent of recombinant DNA technology led to the suggestion (Botstein et al. 1980) that common polymorphisms in DNA sequence (conveniently observed as restriction fragment length polymorphisms, or RFLPs) could be used as generally informative genetic markers allowing the systematic study of heredity in humans, including the construction of a true linkage map of the entire human genome. The application of RFLP technology to simple Mendelian diseases has proceeded rapidly. RFLPs have been found closely linked to the autosomal dominant Huntington's disease (Gusella et al. 1983) and polycystic kidney disease (Reeder et al. 1985), the autosomal recessive cystic fibrosis (Knowlton et al. 1985; Tsui et al. 1985; Wainwright et al. 1985; White et al. 1985), and the X-linked recessive Duchenne muscular dystrophy (DMD) (Davies et al. 1983). In turn, closely linked DNA markers have made it possible to localize the disease genes to chromosomal regions (Gusella et al. 1983; Knowlton et al. 1985; Reeder et al. 1985; Wainwright et al. 1985; White et al. 1985), to undertake prenatal diagnosis of fetuses known to be at risk, and to begin chromosome walks in an attempt to clone the disease genes (Kunkel et al.; Worton et al.; all this volume). In addition, the RFLP linkages have shed light on the formal genetics of the disorders-showing, for example, that mutations at a single locus account for all (or almost all) cases of cystic fibrosis (Donis-Keller et al.; Tsui et al.; Williamson et al.; White et al.; all this volume) or of Huntington's disease (Gusella et al., this volume). These successes make clear that RFLPs can be found linked to any common human disease that shows simple Mendelian transmission and is caused by a single genetic locus. Much of what we want to know about human heredity, however, concerns traits whose underlying genetics is less favorable for analysis. Some apparently identical clinical conditions can result from mutations at any one of several g e n e s a circumstance called genetic heterogeneity. Some traits have incompletepenetrance, with only a fraction of those carrying the appropriate mutant genotype actually displaying the trait. Conversely, some genotypes predispose individuals to a disease, but those of normal genotype may be affected as well, just at a lower rate. Environment may play an important role in the expression of the trait. In addition, gene interactions can occur, in which a phenotype results from the interaction of alleles at more than one locus. These complexities can underlie even the most clearcut phenotypes. These complex modes of inheritance are common in genetically well-studied organisms, such as bacteria, yeast, nematodes, and fruit flies, and evidence is accumulating that humans are no different. Geneticists usually surmount the problems by isolating purebreeding stocks, each carrying a mutation at a single locus, and then arranging crosses at will. In the case of human genetics, however, we must take crosses as we find them. Unfortunately, even with RFLPs as markers, traditional methods for genetic linkage analysis are quite inefficient at mapping genetically complex traits: A prohibitively large sample may be required before linkage can be detected or other genetic properties tested. Furthermore, traditional linkage analysis absolutely requires families with two or more affected individuals. Yet, many traits of biological or medical interest are quite rare, with most cases being sporadic. Collecting enough pedigrees with multiple affected subjects may be impossible. It may thus appear, at first sight, that the vast majority of human heredity must remain refractory to genetic mapping, due to complexity or rarity. On the contrary, it is the main thesis of this paper that this need not be so. The important point is that studying the segregation patterns of a large number of mapped RFLPs simultaneously (rather than one at a time) can make it feasible to map many traits that are genetically complex and/or rare. We discuss below new mathematical techniques, unusual genetic resources, and clinical up-