Different regression equations relate age to the incidence of Lauren types 1 and 2 stomach cancer in the SEER database: these equations are unaffected by sex or race

BACKGROUND: Although impacts upon gastric cancer incidence of race, age, sex, and Lauren type have been individually explored, neither their importance when evaluated together nor the presence or absence of interactions among them have not been fully described. METHODS: This study, derived from SEER (Surveillance, Epidemiology, and End Results (SEER) Program of the National Cancer Institute) data, analyzed the incidences of gastric cancer between the years 1992–2001. There were 7882 patients who had developed gastric cancer. The total denominator population was 145,155, 669 persons (68,395,787 for 1992–1996, 78,759,882 for 1997–2001). Patients with multiple tumors were evaluated as per the default of the SEER*Stat program. 160 age-, five year period (1992–1996 vs 1997–2001)-, sex-, race (Asian vs non-Asian)-, Lauren type- specific incidences were derived to form the stratified sample evaluated by linear regression. (160 groups = 2 five year periods × 2 race groups × 2 sexes × 2 Lauren types × 10 age groups.) Linear regression was used to analyze the importance of each of these explanatory variables and to see if there were interactions among the explanatory variables. RESULTS: Race, sex, age group, and Lauren type were found to be important explanatory variables, as were interactions between Lauren type and each of the other important explanatory variables. In the final model, the contribution of each explanatory variable was highly statistically significant (t > 5, d.f. 151, P < 0.00001). The regression equation for Lauren type 1 had different coefficients for the explanatory variables Race, Sex, and Age, than did the regression equation for Lauren type 2. CONCLUSION: The change of the incidence of stomach cancer with respect to age for Lauren type 1 stomach cancer differs from that for Lauren type 2 stomach cancers. The relationships between age and Lauren type do not differ across gender or race. The results support the notion that Lauren type 1 and Lauren type 2 gastric cancers have different etiologies and different patterns of progression from pre-cancer to cancer. The results should be validated by evaluation of other databases

Consent codes: upholding standard data use conditions

A systematic way of recording data use conditions that are based on consent permissions as found in the datasets of the main public genome archives (NCBI dbGaP and EMBL-EBI/CRG EGA).SOMD is supported by the Canadian Institutes of Health Research (grants EP1-120608; EP2-120609), the Canada Research Chair in Law and Medicine, and the Public Population Project in Genomics and Society (P3G). DNP and ESL are supported, in part, by the Intramural Research Program of the NIH, Office of the Director, Office of Science Policy. BMK is supported by the Canada Research Chairs Program. MT and MR are sponsored by ODEX4all (NWO 650.002.002) and funding from the European Commission (FP-7 project RD-Connect, grant agreement No. 305444

'You want the right amount of oversight' : interviews with data access committee members and experts on genomic data access

Purpose: Genomic data sharing is vital for optimizing the use of public-funded research data. Data access committees (DACs) have been introduced as a core component of governance in controlled access models. However, the tasks, structure, and functionality of DACs often remain unstudied. This article investigates the role and adequacy of DACs in access reviews from the perspective of DAC members and experts. Methods: Twenty semi-structured interviews were conducted with both DAC members engaged in genomic data sharing via controlled-access databases and experts in the field. Results: The respondents indicated that protecting the privacy of data subjects along with recognition of data producers' efforts are the main underlying reasons of access review and the controlled-access model. In reviewing the ethical basis and the scientific aspects of access requests, tools and mechanisms such as consent forms, data access agreements, and guidelines have been used. Nevertheless, DAC members and experts identified shortcomings associated with current approaches that may adversely impact the effectiveness and efficiency of access review. Conclusion: The identified shortcomings of current approaches to access review could be addressed via complementary mechanisms and alternative models of data sharing to facilitate access to data sets in a responsible fashion

Who should have access to genomic data and how should they be held accountable? Perspectives of Data Access Committee members and experts

Facilitating the responsible access to genomic research data is an emerging ethical and scientific imperative. Data Access Committees (DACs) assess the ethical footing and scientific feasibility of the data access requests and evaluate the qualification of applicants to ensure they are bona fide researchers. Through semi-structured interviews, we explored the opinions and experiences of 20 DAC members and experts concerning the users' qualification criteria and mechanisms to hold users accountable. According to our respondents, such evaluation is necessary to ensure applicants are trustworthy, meet a certain level of expertise or experience and are aware of the rules and the associated concerns with genomic data sharing. The respondents noted, however, that the qualification criteria are fragmented or are poorly delineated at times. Thus, developing qualification criteria seems vital for an objective, fair and responsible access procedure. Similarly, the access review will benefit from using common ways of verifying the users' affiliations. Furthermore, some DAC members expressed concern over the uncertain oversight of downstream data use, in particular where data are shared across borders. DAC members and experts did not consider current sanctions and enforcement procedures to be crystal clear. Therefore, data sharing policies should address this gap by establishing proportionate sanctions both against data producers and data users' non-compliance. Users' home institutes will need to have an active role in keeping oversight on the downstream data uses, considering their ultimate responsibility if wrongdoings happen

Genetics of coronary artery calcification among African Americans, a meta-analysis

Background: Coronary heart disease (CHD) is the major cause of death in the United States. Coronary artery calcification (CAC) scores are independent predictors of CHD. African Americans (AA) have higher rates of CHD but are less well-studied in genomic studies. We assembled the largest AA data resource currently available with measured CAC to identify associated genetic variants.Methods: We analyzed log transformed CAC quantity (ln(CAC + 1)), for association with ~2.5 million single nucleotide polymorphisms (SNPs) and performed an inverse-variance weighted meta-analysis on results for 5,823 AA from 8 studies. Heritability was calculated using family studies. The most significant SNPs among AAs were evaluated in European Ancestry (EA) CAC data; conversely, the significance of published SNPs for CAC/CHD in EA was queried within our AA meta-analysis.Results: Heritability of CAC was lower in AA (~30%) than previously reported for EA (~50%). No SNP reached genome wide significance (p &lt; 5E-08). Of 67 SNPs with p &lt; 1E-05 in AA there was no evidence of association in EA CAC data. Four SNPs in regions previously implicated in CAC/CHD (at 9p21 and PHACTR1) in EA reached nominal significance for CAC in AA, with concordant direction. Among AA, rs16905644 (p = 4.08E-05) had the strongest association in the 9p21 region.Conclusions: While we observed substantial heritability for CAC in AA, we failed to identify loci for CAC at genome-wide significant levels despite having adequate power to detect alleles with moderate to large effects. Although suggestive signals in AA were apparent at 9p21 and additional CAC and CAD EA loci, overall the data suggest that even larger samples and an ethnic specific focus will be required for GWAS discoveries for CAC in AA populations. © 2013 Wojczynski et al.; licensee BioMed Central Ltd