Characteristics of The Cancer Genome Atlas cases relative to U.S. general population cancer cases.
Ontology highlight
ABSTRACT: Background
Despite anecdotal reports of differences in clinical and demographic characteristics of The Cancer Genome Atlas (TCGA) relative to general population cancer cases, differences have not been systematically evaluated.Methods
Data from 11,160 cases with 33 cancer types were ascertained from TCGA data portal. Corresponding data from the Surveillance, Epidemiology, and End Results (SEER) 18 and North American Association of Central Cancer Registries databases were obtained. Differences in characteristics were compared using Student's t, Chi-square, and Fisher's exact tests. Differences in mean survival months were assessed using restricted mean survival time analysis and generalised linear model.Results
TCGA cases were 3.9 years (95% CI 1.7-6.2) younger on average than SEER cases, with a significantly younger mean age for 20/33 cancer types. Although most cancer types had a similar sex distribution, race and stage at diagnosis distributions were disproportional for 13/18 and 25/26 assessed cancer types, respectively. Using 12 months as an end point, the observed mean survival months were longer for 27 of 33 TCGA cancer types.Conclusions
Differences exist in the characteristics of TCGA vs. general population cancer cases. Our study highlights population subgroups where increased sample collection is warranted to increase the applicability of cancer genomic research results to all individuals.
SUBMITTER: Wang X
PROVIDER: S-EPMC6189215 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The multi-scale and nonlinear nature of the ocean dynamics dramatically affects the spreading of matter, like pollutants, marine litter, etc., of physical and chemical seawater properties, and the biological connectivity inside and among different basins. Based on the Finite-Scale Lyapunov Exponent analysis of the largest available near-surface Lagrangian data set from the Global Drifter Program, our results show that, despite the large variety of flow features, relative dispersion can ultimately be described by a few parameters common to all ocean sub-basins, at least in terms of order of magnitude. This provides valuable information to undertake Lagrangian dispersion studies by means of models and/or of observational data. Moreover, our results show that the relative dispersion rates measured at submesoscale are significantly higher than for large-scale dynamics. Auxiliary analysis of high resolution GPS-tracked drifter hourly data as well as of the drogued/undrogued status of the buoys is provided in support of our conclusions. A possible application of our study, concerning reverse drifter motion and error growth analysis, is proposed relatively to the case of the missing Malaysia Airlines MH370 aircraft.
| S-EPMC5387742 | biostudies-literature
Project description:Introduction The National Cancer Institute Smoking Cessation at Lung Examination (SCALE) Collaboration includes eight clinical trials testing smoking cessation interventions delivered with lung cancer screening (LCS). This investigation compared pooled participant baseline demographic and smoking characteristics of seven SCALE trials to LCS-eligible smokers in three U.S. nationally representative surveys. Methods Baseline variables (age, sex, race, ethnicity, education, income, cigarettes per day, and time to the first cigarette) from 3614 smokers enrolled in SCALE trials as of September 2020 were compared with pooled data from the Tobacco Use Supplement–Current Population Survey (2018–2019), National Health Interview Survey (2017–2018), and Population Assessment of Tobacco and Health (wave 4, 2016–2017) using the U.S. Preventive Services Task Force 2013 (N = 4803) and 2021 (N = 8604) LCS eligibility criteria. Results SCALE participants have similar average age as the U.S. LCS–eligible smokers using the 2013 criteria but are 2.8 years older using the 2021 criteria (p < 0.001). SCALE has a lower proportion of men, a higher proportion of Blacks, and slightly higher education and income levels than national surveys (p < 0.001). SCALE participants smoke an average of 17.9 cigarettes per day (SD 9.2) compared with 22.4 (SD 9.3) using the 2013 criteria and 19.6 (SD 9.7) using the 2021 criteria (p < 0.001). The distribution of time to the first cigarette differs between SCALE and the national surveys (p < 0.001), but both indicate high levels of nicotine dependence. Conclusions SCALE participants smoke slightly less than the LCS-eligible smokers in the general population, perhaps related to socioeconomic status or race. Other demographic variables reveal small but statistically significant differences, likely of limited clinical relevance with respect to tobacco treatment outcomes. SCALE trial results should be applicable to LCS-eligible smokers from the U.S. population.
| S-EPMC9257405 | biostudies-literature
Project description:Lead is a ubiquitous pollutant that constitutes an environmental hazard worldwide. Although lead has been known as a carcinogenic factor in animal models, its role in human carcinogenesis is still a topic of debate with limited epidemiological evidence. Moreover, the association between urinary lead, as the most non-invasive and accessible way for lead measurement in human, and cancer mortality in general population has never been explored. We addressed this subject using continuous National Health and Nutrition Examination Survey 1999-2010 data and its Mortality Follow-Up Study. Of 5,316 subjects in study population, 161 participants died due to cancer. Cancer-specific mortality was associated with urinary lead levels after multivariable adjustment. Kaplan-Meier survival curve and cubic regression spline analyses indicated that high concentration of urinary lead exhibited significant association with raised death rate of cancer. Despite the marked decrease in environmental lead levels over the past three decades, lead exposure is still the significant determinant of cancer mortality in general population in U.S., and quantification of urinary lead may serve as a non-invasive approach to facilitate biomarker discovery and clinical translational research.
| S-EPMC6036403 | biostudies-literature
Project description:The COVID-19 pandemic is taking a significant global toll on emotional well-being, but evidence of mental health impacts in the United States remains limited. In April 2020, we conducted an exploratory survey of U.S. residents to understand prevalence of and factors associated with psychological distress during the pandemic. Data collection was conducted using Qualtrics, an online survey platform, and U.S. adult respondents were recruited via Amazon's Mechanical Turk platform. Among 1,366 respondents, 42% (n = 571) reported clinically significant anxiety and 38% (n = 519) reported clinically significant depression. Factors associated with anxiety and depressive symptoms included Hispanic/Latino ethnicity; younger age; lower income; employment as or living with a health care worker-first responder; caregiver status; SARS-CoV-2 infection status; decreased frequency of engagement in healthy behaviors; and changed frequency of engagement in unhealthy behaviors. That some of these factors are associated with elevated distress during the pandemic is not yet widely appreciated and might be useful in informing management of mental health care resources.
| S-EPMC8258251 | biostudies-literature
Project description:Invasive pneumococcal disease (IPD) has greatly decreased since implementation in the U.S. of the 7 valent conjugate vaccine (PCV7) in 2000 and 13 valent conjugate vaccine (PCV13) in 2010. We used whole genome sequencing (WGS) to predict phenotypic traits (serotypes, antimicrobial phenotypes, and pilus determinants) and determine multilocus genotypes from 5334 isolates (~90% of cases) recovered during 2015-2016 through Active Bacterial Core surveillance. We identified 44 serotypes; 26 accounted for 98% of the isolates. PCV13 serotypes (inclusive of serotype 6C) accounted for 1503 (28.2%) isolates, with serotype 3 most common (657/5334, 12.3%), while serotypes 1 and 5 were undetected. Of 305 isolates from children <5 yrs, 60 (19.7%) were of PCV13 serotypes 19A, 19F, 3, 6B, and 23F (58/60 were 19A, 19F, or 3). We quantitated MLST-based lineages first detected during the post-PCV era (since 2002) that potentially arose through serotype-switching. The 7 predominant emergent post-PCV strain complexes included 23B/CC338, 15BC/CC3280, 19A/CC244, 4/CC439, 15A/CC156, 35B/CC156, and 15BC/CC156. These strains accounted for 332 isolates (6.2% of total) and were more frequently observed in children <5 yrs (17.7%; 54/305). Fifty-seven categories of recently emerged (in the post PCV7 period) putative serotype-switch variants were identified, accounting for 402 isolates. Many of these putative switch variants represented newly emerged resistant strains. Penicillin-nonsusceptibility (MICs > 0.12 ?g/ml) was found among 22.4% (1193/5334) isolates, with higher penicillin MICs (2-8 ?g/ml) found in 8.0% (425/5334) of isolates that were primarily (372/425, 87.5%) serotypes 35B and 19A. Most (792/1193, 66.4%) penicillin-nonsusceptible isolates were macrolide-resistant, 410 (34.4%) of which were erm gene positive and clindamycin-resistant. The proportion of macrolide-resistant isolates increased with increasing penicillin MICs; even isolates with reduced penicillin susceptibility (MIC = 0.06 ?g/ml) were much more likely to be macrolide-resistant than basally penicillin-susceptible isolates (MIC < 0.03 ?g/ml). The contribution of recombination to strain diversification was assessed through quantitating 35B/CC558-specific bioinformatic pipeline features among non-CC558 CCs and determining the sizes of gene replacements. Although IPD has decreased greatly and stabilized in the post-PCV13 era, the species continually generates recombinants that adapt to selective pressures exerted by vaccines and antimicrobials. These data serve as a baseline for monitoring future changes within each invasive serotype.
| S-EPMC6262371 | biostudies-literature
Project description:Although population genetics studies have significantly accelerated the evolutionary and functional interrogations of genes and regulations, limited polymorphism data are available for rhesus macaque, the model animal closely related to human. Here, we report the first genome-wide effort to identify and visualize the population genetics profile in rhesus macaque. On the basis of the whole-genome sequencing of 31 independent macaque animals, we profiled a comprehensive polymorphism map with 46,146,548 sites. The allele frequency for each polymorphism site, the haplotype structure, as well as multiple population genetics parameters were then calculated on a genome-wide scale. We further developed a specific interface, the RhesusBase PopGateway, to facilitate the visualization of these annotations, and highlighted the applications of this highly integrative platform in clarifying the selection signatures of genes and regulations in the context of the primate evolution. Overall, the updated RhesusBase provides a comprehensive monkey population genetics framework for in-depth evolutionary studies of human biology.
| S-EPMC4839223 | biostudies-literature
Project description:Few studies have examined the broad health effects of occupational exposures in flight attendants apart from disease-specific morbidity and mortality studies. We describe the health status of flight attendants and compare it to the U.S. population. In addition, we explore whether the prevalence of major health conditions in flight attendants is associated with length of exposure to the aircraft environment using job tenure as a proxy.We surveyed flight attendants from two domestic U.S. airlines in 2007 and compared the prevalence of their health conditions to contemporaneous cohorts in the National Health and Nutrition Survey (NHANES), 2005-2006 and 2007-2008. We weighted the prevalence of flight attendant conditions to match the age distribution in the NHANES and compared the two populations stratified by gender using the Standardized Prevalence Ratio (SPR). For leading health conditions in flight attendants, we analyzed the association between job tenure and health outcomes in logistic regression models.Compared to the NHANES population (n =5,713), flight attendants (n?=?4,011) had about a 3-fold increase in the age-adjusted prevalence of chronic bronchitis despite considerably lower levels of smoking. In addition, the prevalence of cardiac disease in female flight attendants was 3.5 times greater than the general population while their prevalence of hypertension and being overweight was significantly lower. Flight attendants reported 2 to 5.7 times more sleep disorders, depression, and fatigue, than the general population. Female flight attendants reported 34% more reproductive cancers. Health conditions that increased with longer job tenure as a flight attendant were chronic bronchitis, heart disease in females, skin cancer, hearing loss, depression and anxiety, even after adjusting for age, gender, body mass index (BMI), education, and smoking.This study found higher rates of specific diseases in flight attendants than the general population. Longer tenure appears to explain some of the higher disease prevalence. Conclusions are limited by the cross-sectional design and recall bias. Further study is needed to determine the source of risk and to elucidate specific exposure-disease relationships over time.
| S-EPMC4007523 | biostudies-literature
Project description:BackgroundUrine cadmium concentrations were associated with all-cause and cardiovascular mortality in men in the 1988-1994 U.S. National Health and Nutrition Examination Survey (NHANES) population. Since 1988, cadmium exposure has decreased substantially in the United States. The associations between blood and urine cadmium and cardiovascular disease (CVD) mortality at more recent levels of exposure are unknown.ObjectivesWe evaluated the prospective association of blood and urine cadmium concentrations with all-cause and CVD mortality in the 1999-2004 U.S. population.MethodsWe followed 8,989 participants who were ? 20 years of age for an average of 4.8 years. Hazard ratios for mortality end points comparing the 80th to the 20th percentiles of cadmium distributions were estimated using Cox regression.ResultsThe multivariable adjusted hazard ratios [95% confidence intervals (CIs)] for blood and urine cadmium were 1.50 (95% CI: 1.07, 2.10) and 1.52 (95% CI: 1.00, 2.29), respectively, for all-cause mortality, 1.69 (95% CI: 1.03, 2.77) and 1.74 (95% CI: 1.07, 2.83) for CVD mortality, 1.98 (95% CI: 1.11, 3.54) and 2.53 (95% CI: 1.54, 4.16) for heart disease mortality, and 1.73 (95% CI: 0.88, 3.40) and 2.09 (95% CI: 1.06, 4.13) for coronary heart disease mortality. The population attributable risks associated with the 80th percentile of the blood (0.80 ?g/L) and urine (0.57 ?g/g) cadmium distributions were 7.0 and 8.8%, respectively, for all-cause mortality and 7.5 and 9.2%, respectively, for CVD mortality.ConclusionsWe found strongly suggestive evidence that cadmium, at substantially low levels of exposure, remains an important determinant of all-cause and CVD mortality in a representative sample of U.S. adults. Efforts to further reduce cadmium exposure in the population could contribute to a substantial decrease in CVD disease burden.
| S-EPMC3404657 | biostudies-literature
Project description:BackgroundUntil very recently, preconception genetic testing was only conducted in particular communities, ethnic groups or families for which an increased risk of genetic disease was identified. To detect in general population a risk for a couple to have a child affected by a rare, recessive or X-linked, genetic disease, carrier screening is proposed in several countries. We aimed to determine the current public opinion relative to this approach in France, using either a printed or web-based questionnaire.ResultsAmong the 1568 participants, 91% are favorable to preconception genetic tests and 57% declare to be willing to have the screening if the latter is available. A medical prescription by a family doctor or a gynecologist would be the best way to propose the test for 73%, with a reimbursement from the social security insurance. However, 19% declare not to be willing to use the test because of their ethic or moral convictions, and the fear that the outcome would question the pregnancy. Otherwise, most participants consider that the test is a medical progress despite the risk of an increased medicalization of the pregnancy.ConclusionThis first study in France highlights a global favorable opinion for the preconception genetic carrier testing under a medical prescription and a reimbursement by social security insurance. Our results emphasize as well the complex concerns underpinned by the use of this screening strategy. Therefore, the ethical issues related to these tests include the risk of eugenic drift mentioned by more than half of the participants.
| S-EPMC7955630 | biostudies-literature
Project description:Age-related olfactory loss (presbyosmia) is a prevalent sensory impairment with a large public health impact. In cross-sectional analyses, we found striking health disparities in olfactory function among older U.S. adults. Here, we report a 5-year follow-up to determine the magnitude of within-person olfactory decline.The National Social Life, Health, and Aging Project (NSHAP) interviewed a probability sample of home-dwelling older U.S. adults (57-85 years) in 2005-2006 (Wave 1) and reinterviewed them in 2010-2011 (Wave 2), assessing demographics, social life, and health, including olfaction. Odor identification was measured with a 5-item version of the Sniffin' Sticks (0-5 correct). Fourteen hundred and thirty-six respondents provided olfaction data in both waves. Multivariate linear and logistic regression were used to model the association between change in olfactory performance and demographic, health, and psychosocial factors.Odor identification declined most rapidly among older individuals (0.25 additional errors per 5 years for each decade of age, p < .001) and in men (0.17 additional errors per 5 years compared to women, p = .005). Among those with perfect scores in Wave 1, African Americans declined more rapidly than Whites (p = .04). Neither socioeconomic status, health conditions, cognition, mental health, alcohol use nor smoking was associated with change in olfaction (p > .05, all).The rate of olfactory decline increases with age and is greater among men than women despite adjusting for differences in psychosocial and health conditions, indicating physiologic factors as drivers. African Americans are more likely to experience initial olfactory decline, consistent with an earlier onset of aging among this subgroup.
| S-EPMC4715242 | biostudies-other