Linkage disequilibria among (CA)n polymorphisms in the human dystrophin gene and their implications in carrier detection and prenatal diagnosis in Duchenne and Becker muscular dystrophies

Development of Microsatellite Marker System to Determine the Genetic Diversity of Experimental Chicken, Duck, Goose, and Pigeon Populations

Poultries including chickens, ducks, geese, and pigeons are widely used in the biological and medical research in many aspects. The genetic quality of experimental poultries directly affects the results of the research. In this study, following electrophoresis analysis and short tandem repeat (STR) scanning, we screened out the microsatellite loci for determining the genetic characteristics of Chinese experimental chickens, ducks, geese, and pigeons. The panels of loci selected in our research provide a good choice for genetic monitoring of the population genetic diversity of Chinese native experimental chickens, ducks, geese, and ducks.

SNPs at 3'-UTR of the bovine CDIPT gene associated with Qinchuan cattle meat quality traits

The CDIPT is crucial to the fatty acid metabolic pathway, intracellular signal transduction and energy metabolism in eukaryotic cells. We detected three SNPs at 3'-untranslated regions (UTR), named 3'-UTR_108 A > G, 3'-UTR_448 G > A and 3'-UTR_477 C > G, of the CDIPT gene in 618 Qinchuan cattle using PCR-RFLP and DNA sequencing methods. At each of the three SNPs, we found three genotypes named as follows: AA, AB, BB (3'-UTR_108 A > G), CC, CD, DD (3'-UTR_448 G > A) and EE, EF, FF (3'-UTR_477 C > G.). Based on association analysis of these SNPs with ultrasound measurement traits, individuals of genotype BB had a significantly larger loin muscle area than genotype AA. Individuals of genotype CC had significantly thicker back fat than individuals of genotype DD. Individuals of genotype EE also had significantly thicker back fat than did individuals of genotype FF. We conclude that these SNPs of the CDIPT gene could be used as molecular markers for selecting and breeding beef cattle with superior body traits, depending on breeding goals.

Interferon gamma receptor 1 gene polymorphism in patients with tuberculosis in China

The aim of the study was to examine the influence of the CA microsatellite polymorphisms of interferon gamma receptor 1 on patients with tuberculosis (TB) in the south-eastern Chinese population. Genomic DNA from patients with TB (n = 155) and ethnically matched controls (n = 89) were genotyped by short tandem repeat-PCR method. The allele frequency of (CA)(25) was 1.70-fold higher among patients than that among controls (95% CI 1.07-2.70) (P = 0.025). Compared with the non-(CA)(25)/non-(CA)(25) reference group, the risk to TB of the carriers of (CA)(25)/(CA)(25) genotypes were 6.46-fold (95% CI 1.40-29.74) (P = 0.0017) higher. On the contrary, the allele frequency of (CA)(26) was 0.29-fold lower in patients than that in controls (95% CI 0.11-0.76) (P = 0.012). Genotypes with (CA)(26) allele were at 0.35-fold (95% CI 0.13-0.98) (P = 0.045) lower to the risk of TB, compared with that of the non-(CA)(26)/non-(CA)(26) in the reference group. The above results indicated that the allele (CA)(25) appeared to be susceptible to TB, while the allele (CA)(26) to be protective towards TB. Our data also suggest that the CA repeat was a highly polymorphic marker and could be used for linkage and association analysis.

Carrier detection and prenatal molecular diagnosis in a Duchenne muscular dystrophy family without any affected relative available

In this paper we report a family where the affected DMD patients were not available for study and a molecular strategy was used for female carriers detection and for prenatal diagnosis. Linkage analysis was performed with two markers within the DMD gene, in all family members screened. DMD markers used (pERT87.8/Taq1 and pERT87.15/Xmn1) seemed not to be informative because the propositas mother (II-2) was homozygous for the minor allele at each marker (T2 and X2), however, the proposita and one sister carried only the major allele, which was inherited from the father. These results suggested that a deletion involving both markers could be present, and was inherited from the mother to both daughters. Quantitative multiplex PCR confirmed the deletion in female carriers, involving at least exons 12 to 17. DNA studies of cultured amniotic fluid cells at 14 weeks gestation, by amplification of specific Y-chromosome sequences, followed by multiplex PCR, lead to the diagnosis of a male fetus affected by DMD.

Dystrophinopathy in a young boy with Klinefelter's syndrome

We report the first case of a child with mild dystrophinopathy associated with Klinefelter's syndrome (karyotype 47, XXY). This 3.5-year-old boy was affected by some symptoms suggestive of Becker's muscular dystrophy. Dystrophin immunostaining and immunoblotting procedures confirmed the diagnosis, but polymerase chain reaction-directed gene analysis failed to reveal any macrodeletion. Methylation-based assay did not show preferential X-inactivation. This confirmed the coexistence of the two active X-chromosomes (one of which was of paternal origin), thus accounting for the mild form of dystrophinopathy in this child affected by Klinefelter's syndrome.

DQ microsatellite association studies in three ethnic groups

Polymorphism at the level of three microsatellite markers (DQCAR, DQCARII, G51152) located in the HLA-DQ region was characterized in 78 10th International Histocompatibility Workshop B-cell lines, 718 random Japanese Asians, 99 Norwegian Caucasians and 95 New Guinean Aborigines with established HLA-DRB1, -DQA1 and -DQB1 typing. DQCAR, DQCARII, and G51152 result in 13, 13, and 11 alleles respectively. All three markers were in tight linkage disequilibrium with HLA-DRB1, -DQA1 and -DQB1. DRB1, DQA1, DQCARII, DQCAR, DQB1, and G51152 haplotypes could be defined for all subjects. In fact, DQ microsatellite typing data could predict DQA1 and DQB1 genotypes with high accuracy and may be used as a simple first pass HLA-DQ typing method. The haplotype data was also used to determine recombination in the DRB1-DQA1 (about 80 kb), DQA1-DQCARII (about 4.5 kb), DQCARII-DQCAR (about 7.5 kb), DQCAR-DQB1 (about 1-1.5 kb) and DQB1-G51152 (about 20-25 kb) genomic segments and the relative rate of slippage microsatellite mutations for DQCAR, DQCARII, and G51152. This led us to conclude that recombination is more frequent in the DRB1-DQA1 and DQCAR-DQCARII segments, thus suggesting cross-overs within small genomic segments are not proportional to genetic distance. We also observed that DQCAR had a higher mutation rate than DQCARII or G51152 and that 1 or 2 CA slippage mutations were arising more frequently from large size microsatellite alleles.

Genomic organization and chromosome localization of the human cathepsin K gene (CTSK)

Human cathepsin K is a recently described cysteine protease with high sequence homology to cathepsins S and L, members of the papain superfamily of cysteine proteases. Cathepsin K is abundantly and selectively expressed in osteoclasts and may perform a specialized role in osteoclast-mediated bone resorption. In the present study, the genomic organization and chromosomal localization of human cathepsin K (HGMW-approved symbol CTSK) were determined. Intron-exon boundaries were identified by PCR on human genomic DNA, and subsequently a P1 genomic clone containing the full-length gene was isolated. Cathepsin K spans approximately 12.1 kb of genomic DNA and is composed of eight exons and seven introns. The genomic organization of cathepsin K is similar to that of cathepsins S and L. The gene was mapped to chromosome 1q21 by fluorescence in situ hybridization. Primer walking on the P1 genomic clone identified 1108 bp of 5' flanking sequence and 459 bp of 3' flanking sequence. Ribonuclease protection assay and 5' RACE indicated a single transcriptional start site 49 bp upstream of the initiator Met codon. Analysis of the 5' flanking region indicates that this gene lacks canonical TATA and CAAT boxes and contains multiple potential transcription regulatory sites. The characterization of the cathepsin K gene and its promoter may provide valuable insights not only into its osteoclast-selective expression, but also into the molecular mechanisms responsible for osteoclast activation.