Linkage of tuberculosis to chromosome 2q35 loci, including NRAMP1, in a large aboriginal Canadian family

Abstract

An epidemic of tuberculosis occurred in a community of Aboriginal Canadians during the period 1987-89. Genetic and epidemiologic data were collected on an extended family from this community, and the evidence for linkage to NRAMP1, a candidate gene for susceptibility to mycobacterial diseases, was assessed. Individuals were grouped into risk (liability) classes based on vaccination, age, previous disease, and tuberculin skin-test results. Under the assumption of a dominant mode of inheritance and a relative risk of 10, which is associated with the high-risk genotypes, a maximum LOD score of 3.81 was observed for linkage between a tuberculosis-susceptibility locus and D2S424, which is located just distal to NRAMP1, in chromosome region 2q35. Significant linkage was also observed between a tuberculosis-susceptibility locus and a haplotype of 10 NRAMP1 intragenic variants. No linkage to the major histocompatibility-complex region on chromosome 6p was observed, despite distortion of transmission from one member of the oldest couple to their affected offspring. The ability to assign individuals to risk classes was crucial to the success of this study.

Figure 1

Partial pedigree of the extended kindred. The five culture-negative cases (individuals 10, 13, 15, 21, and 22) had radiological abnormalities consistent with active tuberculosis; individuals 10 and 15 also had symptoms associated with tuberculosis. Not included in the pedigree are nine individuals from whom DNA was not available and among whom there were two infants classified as culture-negative cases (both had radiological abnormalities), three children classified as not having disease (all PPD negative; two were culture negative, and no culture was taken from the third), and four people with unknown disease phenotype. The order of the information below each circle is as follows: mycobacterial test result (c+ = M. tuberculosis culture positive; c− = M. tuberculosis culture negative; nd = no data), liability class, NRAMP1 haplotype, D2S424 alleles, and TNF haplotype. D2S424 alleles 1, 2, and 3 are 185, 181, and 157 bp, respectively. BCG indicates that the individual was vaccinated. For classification of disease phenotype and definition of liability classes, see the Subjects and Methods section; for NRAMP1 andTNF haplotypes, see tables 2 and 3, respectively.

Figure 2

YAC contig of the NRAMP1-gene region. The names of loci and chromosome 2–specific IRS probes are indicated at the top of the figure. YAC clones are represented as bars; the YAC address is given to the left of the bar. The blackened area of each bar indicates that the YAC was unambiguously identified by the probe listed directly above the YAC; the unblackened area of each bar indicates that the probe did not hybridize with the YAC; and the gray-shaded area of each bar indicates that the YAC was not tested for the presence of the probe. D2S1471 was not included in STS contig mapping; the order NRAMP1–VIL–D2S1471 was established by physical mapping in a PAC contig (Abel et al. 1998).

Figure 3

Sensitivity of LOD-score results to the diagnosis of an affected individual, for the NRAMP1 haplotype, two flanking microsatellite markers, and one intragenic polymorphism, D543N. LOD scores in all cases were maximized over the recombination fraction. Horizontal lines show the LOD scores for the original data. The order along the horizontal axis corresponds to the identification numbers of affected individuals in figure 1, with the exception of individuals 23 and 24, who were two culture-negative cases not shown in figure 1.