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COELIAC DISEASE IN THE SAHARAWI
DQB1 genes and dot blot analysis of amplified DNA with sequence specific
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oligonucleotide probes (SSO) were carried out as previously reported . The DQA1
alleles were inferred using the known patterns of linkage disequilibrium from the
DRB1-DQB1 haplotypes.
Parental haplotypes were reconstructed using a program written by Frank
Dudbridge available at ftp://ftp-gene.cimr.cam.ac.uk/pub/software/.
A possible drawback of case-control analyses is their sensitivity to problems related
to genetic stratification. In order to circumvent this problem, 82 affected family-based
control, (AFBAC) DQA1-DQB1 haplotypes have been selected from all the families in
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which the parents were available, as described for single alleles by Thomson . The
AFBAC frequencies are based on the chromosomes that are never transmitted from the
parents to affected children and provide a source of controls which is not sensitive to
population stratification unless very recent. The control frequencies were also enriched
by 18 chromosomes deriving from 9 unaffected and unrelated Saharawi individuals.
The pseudo-controls (AFBAC) and control frequencies were nearly identical and
therefore were merged (total controls equal to 100 chromosomes). Using these control
haplotype frequencies and assuming Hardy-Weinberg equilibrium, we also established
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the control genotype frequencies as previously described . The frequencies of the HLA
class II haplotypes and genotypes obtained in patients and in controls, were then
compared using a 2 x 2 chi-squared Pearson test. The odds ratios ORs) were calculated
using the Wolf formula [a x d)/(b x c)]; when one element of this equation was 0 we used
the Haldane formula: RR=[2a + 1) 2d +1)]/[2b +1) 2c +1)], where a is the number of
patients possessing the HLA antigen; d is the number of controls lacking the particular
HLA antigen; b the number of patients lacking the particular antigen; c the number of
controls possessing the particular HLA antigen. In the association analyses performed
in this study, we considered only the probands in the 8 families with more than one
affected sibling. A correction for number of tests performed was applied by multiplying
the P values for the tested markers present in more than 1 patient or 1 control
(respectively 10 haplotypes and 8 genotypes).
We also evaluated the evolutionary relationship between the Saharawis and the
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other human groups. To this aim we performed a multi-dimensional scaling analysis
carried out using the correlation matrix of the haplotype frequencies reported in the
various populations and determined with a gene counting procedure.
Who are the Saharawis?
In order to obtain a visual output of the DRB1-DQA1-DQB1 haplotype distribution
worldwide and obtain information about the evolutionary relationships between the
various human groups we performed a multi-dimensional scaling analysis. The results
of this analysis are shown in Fig.1. The first dimension splits Eastern and Western world
populations. The Asian and the African appear to be the most differentiated human
groups, with the Kogi and Cayapa native American populations as the most
differentiated within the Asian group. The Caucasians are closely grouped and are
located between the African and the Asian range of variability. The second dimension
explains the diversity of the Caucasian group, which includes the North-African and the
Saharawi samples. More specifically, the Saharawi population appears to be located in