Investigation of the polymorphic AvaII site by a PCR-based assay at the human CD18 gene locus

Multi-locus interactions predict risk for post-PTCA restenosis: an approach to the genetic analysis of common complex disease

The complexity of recognizing the potential contribution of a number of possible predictors of complex disorders is increasingly challenging with the application of large-scale single nucleotide polymorphism (SNP) typing. In the search for putative genetic factors predisposing to coronary artery restenosis following balloon angioplasty, we determined genotypes for 94 SNPs representing 62 candidate genes, in a prospectively assembled cohort of 342 cases and 437 controls. Using a customized coupled-logistic regression procedure accounting for both additive and interactive effects, we identified seven SNPs in seven genes that, together, showed a statistically significant association with restenosis incidence (P <0.0001), accounting for 11.6% of overall variance observed. Among them are candidate genes for cardiovascular pathophysiology (apolipoprotein-species and NOS), inflammatory response (TNF receptor and CD14), and cell-cycle control (p53 and p53-associated protein). Our results emphasize the need to account for complex multi-gene influences and interactions when assessing the molecular pathology of multifactorial medical entities.

Association of a CD18 gene polymorphism with a reduced risk of restenosis after coronary stenting

Inflammatory mechanisms play an important role in the process of restenosis after percutaneous coronary interventions, with cell adhesion molecules, including Mac-1 (CD11b/CD18), as key mediators. A single nucleotide polymorphism, 1323C/T, located in exon 11 of the CD18 gene has been previously described, but its functional and clinical significances have not yet been studied. We assessed whether an association exists between this polymorphism and restenosis after coronary stenting. Clinical and angiographic measures of restenosis were evaluated over 1 year after coronary stent placement in 1,207 consecutive patients. Angiographic restenosis was defined as a > or =50% diameter stenosis at follow-up angiography. Determination of the CD18 1323C/T genotype was based on the polymerase chain reaction technique. The frequency of the T allele was 0.34 and its presence reduced the 1-year risk of a major adverse cardiac event (death, myocardial infarction, target vessel revascularization) by 29% (p = 0.011). Carriers of the T allele had a significantly lower risk of angiographic restenosis compared with noncarriers (odds ratio 0.71, 95% confidence interval 0.55 to 0.92). The incidence of restenosis decreased as a function of the number of T alleles: 38.1% in patients with genotype CC, 31.7% in patients with genotype CT, and 26.0% in patients with genotype TT (p = 0.004). Thus, the 1323T allele of the CD18 gene is associated, in a gene dose-dependent manner, with a lower incidence of angiographic restenosis after coronary stenting. This finding suggests that Mac-1 is involved in the development of restenosis after coronary stent placement.

Complex high-resolution linkage disequilibrium and haplotype patterns of single-nucleotide polymorphisms in 2.5 Mb of sequence on human chromosome 21

One approach to identify potentially important segments of the human genome is to search for DNA regions with nonrandom patterns of human sequence variation. Previous studies have investigated these patterns primarily in and around candidate gene regions. Here, we determined patterns of DNA sequence variation in 2.5 Mb of finished sequence from five regions on human chromosome 21. By sequencing 13 individual chromosomes, we identified 1460 single-nucleotide polymorphisms (SNPs) and obtained unambiguous haplotypes for all chromosomes. For all five chromosomal regions, we observed segments with high linkage disequilibrium (LD), extending from 1.7 to>81 kb (average 21.7 kb), disrupted by segments of similar or larger size with no significant LD between SNPs. At least 25% of the contig sequences consisted of segments with high LD between SNPs. Each of these segments was characterized by a restricted number of observed haplotypes,with the major haplotype found in over 60% of all chromosomes. In contrast, the interspersed segments with low LD showed significantly more haplotype patterns. The position and extent of the segments of high LD with restricted haplotype variability did not coincide with the location of coding sequences. Our results indicate that LD and haplotype patterns need to be investigated with closely spaced SNPs throughout the human genome, independent of the location of coding sequences, to reliably identify regions with significant LD useful for disease association studies.

Two Novel Frame Shift, Recurrent and De Novo Mutations in the ITGB2 (CD18) Gene Causing Leukocyte Adhesion Deficiency in a Highly Inbred North African Population

We have identified four different mutations causing leukocyte adhesion Deficiency (LAD) in the ITGB2 gene of patients from a highly inbred population. Two were novel single-bp deletions (1497delG and 1920delG) causing frame shift and the two others were the missense mutations G284S and R593C. In our study, the G284S was a recurrent mutation while the R593C occurred de novo. We have also characterized a novel Xba1 polymorphic site located at the 5' end of the ITGB2 locus. Family studies showed that the 1497delG mutation segregated with this marker and the intragenic AvaII polymorphic marker, suggesting the presence of a founder effect. The observation of a heterogeneous spectrum including de novo and recurrent mutations causing LAD in a highly inbred population is rather unexpected. In view of the literature published on the molecular genetics of LAD and considering the ethnic origin of the patients studied, our findings confirm the heterogeneity of the mutations causing LAD and point out potential mutational hot spots in the ITGB2 gene.

High level multiplex genotyping by MALDI-TOF mass spectrometry

A primer extension assay is used to perform highly multiplexed genotyping of single nucleotide polymorphisms (SNPs) present in genomic DNA amplified by a multiplex PCR. The assay uses matrix-assisted laser desorption ionization time-of-flight mass spectrometry to accurately measure the masses of short oligonucleotide primers extended by a single dideoxynucleotide. The multiplexed genotyping assays rely on the natural molecular weight differences of DNA bases. By careful analysis of primer composition complementary to the target, or by judicious addition of one or more noncomplementary 5' bases to the genotyping primers, mass spectra of interleaved genotyping products can be generated with no ambiguity in allele assignment. Using a model multiplex PCR system, we demonstrate the ability to perform 12-fold multiplex SNP analysis.