PubMed · 10939841
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R A Brooksbank. 2000. Repetitive strain.. https://doi.org/10.1016/s1357-4310(00)01719-6
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OBJECTIVE: Analyze the information contained in homozygous haplotypes detected with high density genotyping. METHODS: We analyze the genotypes of approximately 2,500 markers on chr 22 in 12 population samples, each including 200 individuals. We develop a measure of disequilibrium based on haplotype homozygosity and an algorithm to identify genomic segments characterized by non-random homozygosity (NRH), taking into account allele frequencies, missing data, genotyping error, and linkage disequilibrium. RESULTS: We show how our measure of linkage disequilibrium based on homozygosity leads to results comparable to those of R(2), as well as the importance of correcting for small sample variation when evaluating D'. We observe that the regions that harbor NRH segments tend to be consistent across populations, are gene rich, and are characterized by lower recombination. CONCLUSIONS: It is crucial to take into account LD patterns when interpreting long stretches of homozygous markers.
Trisomy 22 syndrome manifestations include cranial and facial anomalies. Ambiguous genitalia have been described in some fetus, but histological examination of the gonads has been rarely provided. We report here the first case of a male pseudohermaphrodite fetus with non-mosaic full trisomy 22 in amniocytes and presenting with ambiguous external genitalia, testes, and a uterus. In this case, we have further analyzed cytogenetically gonadal and uterine tissues. FISH analyses on paraffin-embedded gonads and uterus indicated the presence of two cell lines: XY and monosomy X, with 22%-50% of uterine cells having monosomy X, while 85%-100% of right and 77%-96% of left testicular cells were XY. The distribution of sex chromosomes observed in these tissues could explain the sexual differentiation observed in this fetus. On the other hand, this phenotype could also have resulted from cryptic anomalies in one or several genes implicated in sexual differentiation. Further evidence is thus needed before identifying the true cause of pseudohermaphroditism in our patient.
The genome-wide distribution of linkage disequilibrium (LD) determines the strategy for selecting markers for association studies, but it varies between populations. We assayed LD in large samples (200 individuals) from each of 11 well-described population isolates and an outbred European-derived sample, using SNP markers spaced across chromosome 22. Most isolates show substantially higher levels of LD than the outbred sample and many fewer regions of very low LD (termed 'holes'). Young isolates known to have had relatively few founders show particularly extensive LD with very few holes; these populations offer substantial advantages for genome-wide association mapping.