RFrAP: a computer program for analysis of complex HLA RFLPs. Assignment of restriction fragments to haplotypes by segregation analysis.

The availability of HLA class II cDNA probes has led to the development of a powerful method for the discrimination of genetic variation in this region of the major histocompatibility complex. There are problems with this approach which reduce its usefulness, including the hybridization of a probe with multiple restriction fragments (RFs) from the same locus or of two different cDNA probes with the same RF (cross-hybridizing). These problems may now be largely overcome by the relatively simple computer program presented here, which allows the entry, storage, and editing of phenotype data. It includes utilities for the automatic assignment of bands to haplotypes and also statistical functions to determine several types of correlations. The outputs are presented in a format familiar to HLA serologists and immunogeneticists. In addition, the data is stored in a manner that allows the user to easily prepare "ad hoc" figures and tables that illustrate the more complex relationships among bands and between them and other variables.

DQA1 restriction fragment length polymorphisms and insulin-dependent diabetes mellitus: a BglII fragment labels a subset of B8,DR3 haplotypes uniquely associated with insulin-dependent diabetes mellitus.

Class II restriction fragment length polymorphism studies of 38 pedigrees with multiple cases of insulin-dependent diabetes mellitus revealed the existence of a DQA1-related polymorphism that distinguishes two kinds of HLA-B8,DR3 haplotypes. One of these, characterized by the presence of DQA1-BglII 7.20 kb, was present in all 14 examples inherited by patients and in 6 of the 12 B8,DR3 haplotypes not so inherited. The apparently complete association between the presence of this fragment and the "affected" status of B8,DR3 haplotypes (p = 0.004) was confirmed in a separate group of 26 simplex pedigrees selected for the presence of this haplotype in the respective probands (combined p less than 0.0001).

Definition of IDDM-associated HLA DQ and DX RFLPs by segregation analysis of multiplex sibships.

Genetic variation of the DQ alpha and beta and of the DX alpha genes, detectable as RFLP in genomic DNA digests, has been suggested to improve the identification of individuals at high risk for insulin-dependent diabetes mellitus (IDDM). DNA from all members of 32 IDDM multiplex families was digested with six restriction endonucleases and the resulting fragments analyzed in Southern blots for hybridization with labeled cDNA probes for those genes. A computerized segregation analysis procedure was then used to assign fragments to haplotypes. Associations among fragments and between fragments and haplotypes characterized serologically and biochemically for their class II genes and IDDM-carrier status were calculated. The results indicate that the alleles of the DX alpha polymorphism maintain linkage disequilibrium with those of the DQ beta genes responsible for the well-known DQ beta 3.2-IDDM association, so that IDDM-carrier haplotypes carry disproportionally often both DQ beta 3.2 and DX alpha-TaqI-2.2kb. Thus, these RFLPs identify a DR-DQ-DX haplotype in high linkage disequilibrium, rather than the locus or loci that account for their high relative risk. However, four DR4-DQ beta 3.2 haplotypes that lack DX alpha-TaqI-2.2kb were encountered, two of which are "affected." These haplotypes suggest that the identification of the "disease locus" can be facilitated by the study of unusual haplotypes in which distinct IDDM-associated alleles occur separated from their neighbors of the standard genetic configurations.