Citations

AbstractEpidemiological studies increasingly inform Alzheimer's disease (AD) public health impact, prevention strategies, drug targets, therapeutic interventions, and clinical trial design. For this reason, the Alzheimer's Association Research Roundtable convened an international group of AD experts with experience in conducting both observational and clinical trials for a meeting on October 19 and 20, 2010, in Washington, DC, to discuss the role of epidemiologic studies in AD research and therapeutic advances. Topics included wellness markers and risk factors, with a focus on special populations such as those at elevated risk, super agers, and underserved populations. Discussions also highlighted lessons learned from observational studies of aging, cardiovascular disease, and other disease areas, as well as how new technologies have enabled the gathering of data relevant to drug development and clinical trial conduct.

AbstractThe incidence of chronic lymphocytic leukemia (CLL) is significantly lower in African Americans than whites, but overall survival is inferior. The biologic basis for these observations remains unexplored. We hypothesized that germline genetic predispositions differ between African Americans and whites with CLL and yield inferior clinical outcomes among African Americans. We examined a discovery cohort of 42 African American CLL patients ascertained at Duke University and found that the risk allele frequency of most single nucleotide polymorphisms known to confer risk of development for CLL is significantly lower among African Americans than whites. We then confirmed our results in a distinct cohort of 68 African American patients ascertained by the CLL Research Consortium. These results provide the first evidence supporting differential genetic risk for CLL between African Americans compared with whites. A fuller understanding of differential genetic risk may improve prognostication and therapeutic decision making for all CLL patients.

Abstract The etiology of ovarian cancer is poorly understood but there is clearly a heritable component. Efforts to identify susceptibility alleles rarely consider interactions among alleles or their joint effects because it quickly becomes computationally intractable. In this study, we sought to identify multi-SNP effects jointly with a pathway-based analysis (GSEA-SNP) of 1,952 EOC cases and 2,042 frequency-matched controls genotyped with the Illumina 610K array. All subjects were self-reported non-Hispanic non-Jewish Caucasians, with SNP and sample call rates > 95%. Subjects with ambiguous gender, unresolved identical genotypes and < 80% European ancestry were excluded. SNPs with MAF < 1% were excluded. Missing genotypes were inferred using Mach based on the HapMap CEU population. SNPs not within introns were annotated to genes within 100 bp. We retrieved the following databases of gene sets (GSs) from a compiled database, MsigDB: human chromosome and cytogenetic band, chemical and genetic perturbations, canonical pathways, microRNA binding targets, transcription factor targets (TFT), cancer gene neighborhood (CGN), Cancer modules and Gene Ontology. The GSEA-SNP approach calculates and rank orders the trend statistic for association between each SNP and EOC risk. The Enrichment Score (ES) estimates the overrepresentation of top-ranked SNPs for each GS; the statistical significance was estimated using 10,000 permutations. The ES was normalized according to the size of GS to yield Normalized Enrichment Score (NES). The false discovery (FDR) rate was estimated using NES to adjust for multiple hypothesis testing. A total of 5181 gene-sets were included in the analysis. When controlling the FDR at 15%, 14 of the GSs were highly enriched with association signals, including two chromosomal regions, 8q13 (p = 0.0055, FDR = 0.15) and 6p24 (p = 0.0012, FDR = 0.08). BIOCARTA_LYM_PATHWAY, a pathway related to cell adhesion and diapedesis of lymphocytes, was also significant (p = 0.0002, FDR = 0.12). A TFT GS, composed of genes with promoter regions around transcription start sites containing the motif GGCNRNWCTTYS, was associated with risk (p = 0.0004, FDR = 0.08). Currently, no known transcription factors bind to this computationally predicted motif. Molecular function of double stranded RNA binding was also enriched (p = 0.005, FDR = 0.10). The remaining enriched sets were CGN sets, for which the neighborhoods around the cancer genes were originally defined using correlation of gene expression from 4 large data sets of various cancer types. The enriched CGN included: CD48 (p = 0.011), CD53 (p = 0.009), CD97 (p = 0.011), INPP5D (p = 0.010), PTPN6 (p = 0.008), VAV1 (p = 0.011), ITGAL (p = 0.012), PTPRC (p = 0.012), and STAT6 (p = 0.010). In summary, these analyses detected biologically plausible GSs related to etiology of EOC, highlighting SNPs in core enrichment groups that were not identified using individual SNP tests. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4729. doi:10.1158/1538-7445.AM2011-4729

Abstract Background. The hepatocyte growth factor (HGF) signaling pathway regulates key cellular functions related to tumor invasion and metastasis including cell motility, cell proliferation, and morphogenesis. We previously found that minor alleles at a single-nucleotide polymorphism (SNP; rs5745709) in the gene encoding the cytokine HGF was associated with poorer overall survival in women with invasive epithelial ovarian cancer (EOC) enrolled at Mayo Clinic (MAY) and The Cancer Genome Atlas (TCGA) (HR 1.6, 95% CI 1.3-1.9, p=8.9×10−5). In addition, we found that that genotype correlated with HGF expression in ovarian cancer tissue from TCGA women, suggesting that genetically-regulated expression of HGF may play a role in post-diagnosis survival. To further examine this possibility, we evaluated intensity of antibody immunostaining for HGF, MET (HGF's transmembrane tyrosine kinase receptor), and phospho-MET (pMET; MET's activated form) in tumor cells using tissue microarrays (TMAs) created from genotyped primary peritoneal and EOC cases, and correlated these expression levels with overall survival and HGF SNP genotypes. Methods. Participants were 326 white non-Hispanic women over 20 years of age with histologically-confirmed invasive EOC diagnosed between 1998 and 2009. All cases were enrolled at MAY within one year of diagnosis. Five μm sections of TMAs including three 0.6 mm cores per case were immunostained with HGF, MET, and pMET primary antibodies. Staining levels were classified according to combinations of staining extent and intensity as negative (< 10% cells stained), weak, moderate, or strong. The maximal expression value recorded over the multiple cores for each case was used. Cox proportional hazards regression was used to examine associations of overall survival with HGF, MET and pMET expression levels, adjusted for relevant clinical variables. Associations between expression levels and HGF SNP rs5745709 genotypes were examined using linear regression models. Results. HGF and MET expression were not associated with overall survival in our series of EOC cases (p=0.48 and 0.90, respectively). pMET expression was associated with survival, but in the opposite direction of that hypothesized (HR 0.77, 95% CI 0.39-1.52 for moderate expression; HR 0.55, 95% CI 0.27-1.10 for strong expression; each referent to negative/weak, p=0.01). Expression levels were not significantly associated with HGF rs5745709 genotypes (p=0.80 for HGF expression, p=0.89 for MET, p=0.41 for pMET). Conclusion. HGF expression levels were not associated with overall survival or with HGF SNP genotypes that correlated with survival in a previous study. Functional studies such as this one are crucial as a follow-up to discovery-based studies in order to assess biologic plausibility of observed results. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 893. doi:10.1158/1538-7445.AM2011-893

Abstract Germline mutations in BRCA2 predispose to breast, ovarian and other cancers. Although most mutations in the gene are known to be pathogenic, there is an increasing number of missense variants for which the contribution to cancer risk is unclear. These missense substitutions are referred to as VUS (variants of uncertain significance). Because loss of BRCA2 HR function leads to defective DNA double-strand break repair and an increased risk of cancer, we evaluated the utility of a cell-based Homologous Recombination (HR) assay for determination of the cancer relevance of BRCA2 VUS. Specifically, we studied VUS localized in the BRCA2 DNA binding domain (DBD) for effects on HR. We transfected full length wild-type and mutant BRCA2 constructs into V-C8 BRCA2 deficient cells along with an I-Sce1-expressing plasmid which induces an unique double strand break in an integrated DR-GFP reporter plasmid. We evaluated the ability of each BRCA2 mutant to repair the induced break by quantifying the GFP positive cells, generated by HR repair of the DNA break, with fluorescent activated cell sorting (FACS). To establish the sensitivity and specificity of the HR assay we evaluated a series of known deleterious and known neutral with the HR assay. These mutations of known effect were identified using a multifactorial likelihood approach, based on available family data, with a prior probability approach based on sequence conservation (A-GVGD) algorithm (http://agvgd.iarc.fr/agvgd_input.php). We calculated the total odds of pathogenicity for co-segregation of variants with the disease in affected carrier families, co-occurrence of VUS (in trans) with deleterious mutations and for family history of cancer of VUS and combined this odds with the A-GVGD based prior probabilities to generate the posterior probability of pathogenicity for each variant. Using this approach we successfully classified 31 VUS as either neutral or deleterious. By comparing these data with results from the HR assay we established that the assay is 100% sensitive (95% CI: 75.3% – 100%) and 100% specific (95% CI: 82.4% – 100%) for deleterious mutations in the BRCA2 DBD domain. In summary we evaluated the sensitivity and specificity of the HR assay for VUS in the DBD relative to a probability model based on family data and A-GVGD algorithm and we showed that the assay was highly sensitive and specific. Based on these results we propose that the HR assay can be used as a classifier of the clinical relevance of the VUS in the absence of direct genetic and family data. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5591. doi:10.1158/1538-7445.AM2011-5591

Abstract Background Aromatase inhibitors (AIs) are standard adjuvant therapy for postmenopausal women with hormone receptor-positive breast cancer. We previously reported that racial/ethnic minority women receiving an AI in NCIC CTG MA.17 experienced fewer hot flashes, fatigue, and arthralgias than Caucasians (Moy B et al. Ann Oncol 2006;17:1637). Here we examined whether race affected clinical outcomes in the MA.27 AI trial comparing exemestane (E) with anastrozole (A). Methods: Fisher's exact test was used to compare observed side effects (0 vs grades 1–5) between minority and Caucasian women. Adverse events (AE), including menopausal symptoms, were assessed according to the Common Terminology Criteria of the National Cancer Institute (version 3.0). ITT univariate test of race effects on overall survival (OS) was determined with a stratified log-rank test, while multivariate testing was with stratified Cox regression. Results: Among 7312 for whom race was known, distribution was: Caucasian (n=6939; 95%); black (n=235; 3%); Asian/Native Hawaiian/Pacific Islander (n=93); 1%; American Indian (n=39; 1%); and mixed race (n=6). Among women treated with E, minorities reported a significantly lower incidence of hot flashes (45% vs. 56%; p=0.003) and fatigue (34% vs. 46%; p=0.001) compared to Caucasians. Similarly with A, minority women reported significantly fewer hot flashes (47% vs. 58%; p=0.002) and lower cholesterol (12% vs. 18%; p=0.01); however, they reported more headaches than Caucasians (16% vs. 10%; p=0.01). Caucasian women were more likely to discontinue therapy due to AE or side effects (32% vs. 24%). There was a significant OS interaction (p=0.02) between race and treatment with minority women on E having fewer deaths than those on A. Caucasian women had HR of E to A of 0.98 (95% CI 0.81−1.20), p=0.85, while minorities had HR of E to A of 0.72 (95% CI 0.33−1.58), p=0.41. Conclusions: Minority women tolerated AIs better and were also more compliant than Caucasians, supporting our previous findings. A significant interaction between race and type of AI therapy for OS was seen, favoring exemestane in minority women. Replication of these findings in larger cohorts is necessary. Since race/ethnicity may serve as a surrogate for genetic differences, our findings suggest pharmacogenomic differences which require further research. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P2-14-02.