Assessing racial, ethnic, and nativity disparities in US cancer mortality using a new integrated platform.

BACKGROUND: Foreign-born populations in the United States have markedly increased, yet cancer trends remain unexplored. Survey-based Population-Adjusted Rate Calculator (SPARC) is a new tool for evaluating nativity differences in cancer mortality. METHODS: Using SPARC, we calculated 3-year (2016-2018) age-adjusted mortality rates and rate ratios for common cancers by sex, age group, race and ethnicity, and nativity. Trends by nativity were examined for the first time for 2006-2018. Traditional cancer statistics draw populations from decennial censuses. However, nativity-stratified populations are from the American Community Surveys, thus involve sampling errors. To rectify this, SPARC employed bias-corrected estimators. Death counts came from the National Vital Statistics System. RESULTS: Age-adjusted mortality rates were higher among US-born populations across nearly all cancer types, with the largest US-born, foreign-born difference observed in lung cancer among Black women (rate ratio = 3.67, 95% confidence interval [CI] = 3.37 to 4.00). The well-documented White-Black differences in breast cancer mortality existed mainly among US-born women. For all cancers combined, descending trends were more accelerated for US-born compared with foreign-born individuals in all race and ethnicity groups with changes ranging from -2.6% per year in US-born Black men to stable (statistically nonsignificant) among foreign-born Black women. Pancreas and liver cancers were exceptions with increasing, stable, or decreasing trends depending on nativity and race and ethnicity. Notably, foreign-born Black men and foreign-born Hispanic men did not show a favorable decline in colorectal cancer mortality. CONCLUSIONS: Although all groups show beneficial cancer mortality trends, those with higher rates in 2006 have experienced sharper declines. Persistent disparities between US-born and foreign-born individuals, especially among Black people, necessitate further investigation.

Healthcare Providers and Parents Highlight Challenges of Pediatric Hand Fracture Care.

Pediatric hand fractures are common, and many are referred to hand surgeons despite less than 10% of referrals requiring surgical intervention. We explored healthcare provider and parent perspectives to inform a new care pathway. Methods: We conducted a qualitative descriptive study using virtual focus groups. Emergency physicians, hand therapists, plastic surgeons, and parents of children treated for hand fractures were asked to discuss their experiences with existing care for pediatric hand fractures, and perceptions surrounding the implementation of a new care pathway. Data were analyzed using directed content analysis with an inductive approach. Results: Four focus groups included 24 participants: 18 healthcare providers and six parents. Four themes were identified: educating parents throughout the hand fracture journey, streamlining the referral process for simple hand fractures, identifying the most appropriate care provider for simple hand fractures, and maintaining strong multidisciplinary connections to facilitate care. Participants described gaps in the current care, including a need to better inform parents, and elucidated the motivations behind emergency medicine physicians' existing referral practices. Participants also generally agreed on the need for more efficient management of simple hand fractures that do not require surgical care. Healthcare providers believed the strong preexisting relationship between surgeons and hand therapists would facilitate the changes brought forward by the new care pathway. Conclusion: These findings highlighted shortcomings of existing care for pediatric hand fractures and will inform the co-development and implementation of a new care pathway to enable more efficient management while preserving good patient outcomes.

Rare germline deleterious variants increase susceptibility for lung cancer.

Although multiple common susceptibility loci for lung cancer (LC) have been identified by genome-wide association studies, they can explain only a small portion of heritability. The etiological contribution of rare deleterious variants (RDVs) to LC risk is not fully characterized and may account for part of the missing heritability. Here, we sequenced the whole exomes of 2777 participants from the Environment and Genetics in Lung cancer Etiology study, a homogenous population including 1461 LC cases and 1316 controls. In single-variant analyses, we identified a new RDV, rs77187983 [EHBP1, odds ratio (OR) = 3.13, 95% confidence interval (CI) = 1.34-7.30, P = 0.008] and replicated two previously reported RDVs, rs11571833 (BRCA2, OR = 2.18; 95% CI = 1.25-3.81, P = 0.006) and rs752672077 (MPZL2, OR = 3.70, 95% CI = 1.04-13.15, P = 0.044). In gene-based analyses, we confirmed BRCA2 (P = 0.007) and ATM (P = 0.014) associations with LC risk and identified TRIB3 (P = 0.009), involved in maintaining genome stability and DNA repair, as a new candidate susceptibility gene. Furthermore, cases were enriched with RDVs in homologous recombination repair [carrier frequency (CF) = 22.9% versus 19.5%, P = 0.017] and Fanconi anemia (CF = 12.5% versus 10.2%, P = 0.036) pathways. Our results were not significant after multiple testing corrections but were enriched in cases versus controls from large scale public biobank resources, including The Cancer Genome Atlas, FinnGen and UK Biobank. Our study identifies novel candidate genes and highlights the importance of RDVs in DNA repair-related genes for LC susceptibility. These findings improve our understanding of LC heritability and may contribute to the development of risk stratification and prevention strategies.

Assessment of Oncology Practice Billing Claims for Supplementing Chemotherapy: A Pilot Study in the Georgia SEER Cancer Registry.

BACKGROUND: Chemotherapy information in the population-based cancer registries is underascertained and lacks detail. We conducted a pilot study in the Georgia SEER Cancer Registry (GCR) to investigate the feasibility of supplementing chemotherapy information using billing claims from six private oncology practices (OP). METHODS: To assess cancer patients' representativeness from OP, we compared individuals with invasive first primary cancers diagnosed during 2013-2015 in the GCR (cohort 1) with those who had at least one OP claim in the 12 months after diagnosis (cohort 2). To assess completeness of OP claims to capture chemotherapy (yes or no), we further restricted cohort 2 to patients ages 65 years and older enrolled in fee-for-service Medicare Part A and B from the diagnosis date through 12 months follow-up or to the date of death. With Medicare data serving as the gold standard, sensitivity, specificity, and kappa statistics for the receipt of chemotherapy per OP claims were calculated by demographic and clinical characteristics. RESULTS: Cancer patients seeking care in the OP included in our analysis were not representative of the underlying patient population in the GCR. The practices underrepresented minorities and uninsured while overrepresenting females, persons with high socioeconomic status, patients residing outside the metropolitan Atlanta area, and persons with advance staged disease. The ability of practice claims to identify chemotherapy receipt was moderate (76.1% sensitivity) but varied by demographic and clinical characteristics (76.1-83.0%). CONCLUSIONS: Given the limited ability of OP claims to identify chemotherapy receipt, we suggest analyzing these data for hypothesis generation, but inference should be limited to this patient cohort.

Confidence intervals for ranks of age-adjusted rates across states or counties.

Health indices provide information to the general public on the health condition of the community. They can also be used to inform the government's policy making, to evaluate the effect of a current policy or healthcare program, or for program planning and priority setting. It is a common practice that the health indices across different geographic units are ranked and the ranks are reported as fixed values. We argue that the ranks should be viewed as random and hence should be accompanied by an indication of precision (i.e., the confidence intervals). A technical difficulty in doing so is how to account for the dependence among the ranks in the construction of confidence intervals. In this paper, we propose a novel Monte Carlo method for constructing the individual and simultaneous confidence intervals of ranks for age-adjusted rates. The proposed method uses as input age-specific counts (of cases of disease or deaths) and their associated populations. We have further extended it to the case in which only the age-adjusted rates and confidence intervals are available. Finally, we demonstrate the proposed method to analyze US age-adjusted cancer incidence rates and mortality rates for cancer and other diseases by states and counties within a state using a website that will be publicly available. The results show that for rare or relatively rare disease (especially at the county level), ranks are essentially meaningless because of their large variability, while for more common disease in larger geographic units, ranks can be effectively utilized.

Impact of emissions from natural gas production facilities on ambient air quality in the Barnett Shale area: a pilot study.

Rapid and extensive development of shale gas resources in the Barnett Shale region of Texas in recent years has created concerns about potential environmental impacts on water and air quality. The purpose of this study was to provide a better understanding of the potential contributions of emissions from gas production operations to population exposure to air toxics in the Barnett Shale region. This goal was approached using a combination of chemical characterization of the volatile organic compound (VOC) emissions from active wells, saturation monitoring for gaseous and particulate pollutants in a residential community located near active gas/oil extraction and processing facilities, source apportionment of VOCs measured in the community using the Chemical Mass Balance (CMB) receptor model, and direct measurements of the pollutant gradient downwind of a gas well with high VOC emissions. Overall, the study results indicate that air quality impacts due to individual gas wells and compressor stations are not likely to be discernible beyond a distance of approximately 100 m in the downwind direction. However, source apportionment results indicate a significant contribution to regional VOCs from gas production sources, particularly for lower-molecular-weight alkanes (< C6). Although measured ambient VOC concentrations were well below health-based safe exposure levels, the existence of urban-level mean concentrations of benzene and other mobile source air toxics combined with soot to total carbon ratios that were high for an area with little residential or commercial development may be indicative of the impact of increased heavy-duty vehicle traffic related to gas production. Implications: Rapid and extensive development of shale gas resources in recent years has created concerns about potential environmental impacts on water and air quality. This study focused on directly measuring the ambient air pollutant levels occurring at residential properties located near natural gas extraction and processing facilities, and estimating the relative contributions from gas production and motor vehicle emissions to ambient VOC concentrations. Although only a small-scale case study, the results may be useful for guidance in planning future ambient air quality studies and human exposure estimates in areas of intensive shale gas production.

Assessment of the relationship between Contegra conduit size and early valvar insufficiency.

BACKGROUND: Contegra bovine jugular vein (BJV) conduit results vary widely, and little attention has been directed at assessment of early conduit insufficiency. Conduit insufficiency is graded subjectively, and criteria vary. Several studies have used branch pulmonary artery flow reversal (BPAFR) to define severe conduit insufficiency. BJV valves are larger than human pulmonary valves of similar diameter. We hypothesize that anatomic differences between BJV and human pulmonary valves limit the use of BPAFR in the evaluation of BJV competence. Our purposes were to (1) assess the prevalence of early and 6-month BJV conduit insufficiency in our patients, (2) determine if conduit size affects BJV competence, and (3) determine if BPAFR is a specific discriminator of severe conduit insufficiency. METHODS: We reviewed 135 BJV conduits. One cardiologist blinded to original reports reviewed postoperative and 6-month echocardiograms. Conduits were grouped by size: group 1, 12 to 14 mm (n=51), and group 2, 16 to 22 mm (n=84). Moderate or greater insufficiency was considered clinically significant. RESULTS: Early conduit insufficiency was common in group 1 (37%) and rare in group 2 (5%, p<0.0001). After excluding conduits with significant insufficiency, BPAFR occurred in 18% (group 1, 27%; group 2, 13%; p=0.02). At follow-up, insufficiency worsened in group 1 but was stable in group 2. CONCLUSIONS: Early conduit insufficiency is common and worsens with follow-up in small BJVs. Conduit insufficiency is limited in larger sizes and remains stable. BJV exhibits BPAFR commonly in the absence of significant conduit insufficiency. BPAFR should not be used as a primary criterion for grading insufficiency in BJV conduits.

An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures.

LC-MS/MS has emerged as the method of choice for the identification and quantification of protein sample mixtures. For very complex samples such as complete proteomes, the most commonly used LC-MS/MS method, data-dependent acquisition (DDA) precursor selection, is of limited utility. The limited scan speed of current mass spectrometers along with the highly redundant selection of the most intense precursor ions generates a bias in the pool of identified proteins toward those of higher abundance. A directed LC-MS/MS approach that alleviates the limitations of DDA precursor ion selection by decoupling peak detection and sequencing of selected precursor ions is presented. In the first stage of the strategy, all detectable peptide ion signals are extracted from high resolution LC-MS feature maps or aligned sets of feature maps. The selected features or a subset thereof are subsequently sequenced in sequential, non-redundant directed LC-MS/MS experiments, and the MS/MS data are mapped back to the original LC-MS feature map in a fully automated manner. The strategy, implemented on an LTQ-FT MS platform, allowed the specific sequencing of 2,000 features per analysis and enabled the identification of more than 1,600 phosphorylation sites using a single reversed phase separation dimension without the need for time-consuming prefractionation steps. Compared with conventional DDA LC-MS/MS experiments, a substantially higher number of peptides could be identified from a sample, and this increase was more pronounced for low intensity precursor ions.

Transcriptomes of human prostate cells.

BACKGROUND: The gene expression profiles of most human tissues have been studied by determining the transcriptome of whole tissue homogenates. Due to the solid composition of tissues it is difficult to study the transcriptomes of individual cell types that compose a tissue. To overcome the problem of heterogeneity we have developed a method to isolate individual cell types from whole tissue that are a source of RNA suitable for transcriptome profiling. RESULTS: Using monoclonal antibodies specific for basal (integrin beta4), luminal secretory (dipeptidyl peptidase IV), stromal fibromuscular (integrin alpha 1), and endothelial (PECAM-1) cells, respectively, we separated the cell types of the prostate with magnetic cell sorting (MACS). Gene expression of MACS-sorted cell populations was assessed with Affymetrix GeneChips. Analysis of the data provided insight into gene expression patterns at the level of individual cell populations in the prostate. CONCLUSION: In this study, we have determined the transcriptome profile of a solid tissue at the level of individual cell types. Our data will be useful for studying prostate development and cancer progression in the context of single cell populations within the organ.