CASP5 blocking peptide

We conducted a case-control study of renal cancer (987 cases and 1298 controls) in Central and Eastern Europe and analyzed genomic DNA for 319 tagging single-nucleotide polymorphisms (SNPs) in 21 genes involved in cellular growth, differentiation and apoptosis using an Illumina Oligo Pool All (OPA). A haplotype-based method (sliding window analysis of consecutive SNPs) was used to identify chromosome regions of interest that remained significant at a false discovery rate of 10%. Subsequently, risk estimates were generated for regions with a high level of signal and individual SNPs by unconditional logistic regression adjusting for age, gender and study center. Three regions containing genes associated with renal cancer were identified: caspase 1/5/ 4/12(CASP 1/5/ 4/12), epidermal growth factor receptor (EGFR), and insulin-like growth factor binding protein-3 (IGFBP3). We observed that individuals with CASP1/5/4/12 haplotype (spanning area upstream of CASP1 through exon 2 of CASP5) GGGCTCAGT were at higher risk of renal cancer compared to individuals with the most common haplotype (OR: 1.40, 95% CI: 1.10-1.78, p-value = 0.007). Analysis of EGFR revealed three strong signals within intron 1, particularly a region centered around rs759158 with a global p = 0.006 (GGG: OR: 1.26, 95% CI: 1.04-1.53 and ATG: OR: 1.55, 95% CI: 1.14-2.11). A region in IGFBP3 was also associated with increased risk (global p = 0.04). In addition, the number of statistically significant (p-value, 0.05) SNP associations observed within these three genes was higher than would be expected by chance on a gene level. To our knowledge, this is the first study to evaluate these genes in relation to renal cancer and there is need to replicate and extend our findings. The specific regions associated with risk may have particular relevance for gene function and/or carcinogenesis. In conclusion, our evaluation has identified common genetic variants in CASP1, CASP5, EGFR, and IGFBP3 that could be associated with renal cancer risk.

The SAM-T04 method for predicting protein structures uses a single protocol across the entire range of targets, from comparative modeling to new folds. This protocol is similar to the SAM-T02 protocol used in CASP5, but has improvements in the iterative search for similar sequences in finding and aligning templates, in creating fragment libraries, in generating protein conformations, and in scoring the conformations. The automatic procedure made some improvements over simply selecting an alignment to the highest-scoring template, and human intervention made substantial improvements over the automatic procedure. The main improvements made by human intervention were from adding constraints to build (or retain) beta-sheets and from splitting multidomain proteins into separate domains. The uniform protocol was moderately successful across the entire range of target difficulty, but was somewhat less successful than other approaches in CASP6 on the comparative modeling targets.