Decomposition of $\rm R\times C$ contingency table chi -square: Application to binned DNA fragment size data and population structure analysis

The purpose of this research is to develop a new statistical method to determine the minimum set of rows (R) in a R x C contingency table of discrete data that explains the dependence of observations. The statistical power of the method will be empirically determined by computer simulation to judge its efficiency over the presently existing methods. The method will be applied to data on DNA fragment length variation at six VNTR loci in over 72 populations from five major racial groups of human (total sample size is over 15,000 individuals; each sample having at least 50 individuals). DNA fragment lengths grouped in bins will form the basis of studying inter-population DNA variation within the racial groups are significant, will provide a rigorous re-binning procedure for forensic computation of DNA profile frequencies that takes into account intra-racial DNA variation among populations. ^

Genetic variation in genes for the xenobiotic-metabolizing enzymes CYP1A1, EPHX1, GSTM1, GSTT1, and GSTP1 and susceptibility to colorectal cancer in Lynch syndrome.

Individuals with Lynch syndrome are predisposed to cancer due to an inherited DNA mismatch repair gene mutation. However, there is significant variability observed in disease expression likely due to the influence of other environmental, lifestyle, or genetic factors. Polymorphisms in genes encoding xenobiotic-metabolizing enzymes may modify cancer risk by influencing the metabolism and clearance of potential carcinogens from the body. In this retrospective analysis, we examined key candidate gene polymorphisms in CYP1A1, EPHX1, GSTT1, GSTM1, and GSTP1 as modifiers of age at onset of colorectal cancer among 257 individuals with Lynch syndrome. We found that subjects heterozygous for CYP1A1 I462V (c.1384A>G) developed colorectal cancer 4 years earlier than those with the homozygous wild-type genotype (median ages, 39 and 43 years, respectively; log-rank test P = 0.018). Furthermore, being heterozygous for the CYP1A1 polymorphisms, I462V and Msp1 (g.6235T>C), was associated with an increased risk for developing colorectal cancer [adjusted hazard ratio for AG relative to AA, 1.78; 95% confidence interval, 1.16-2.74; P = 0.008; hazard ratio for TC relative to TT, 1.53; 95% confidence interval, 1.06-2.22; P = 0.02]. Because homozygous variants for both CYP1A1 polymorphisms were rare, risk estimates were imprecise. None of the other gene polymorphisms examined were associated with an earlier onset age for colorectal cancer. Our results suggest that the I462V and Msp1 polymorphisms in CYP1A1 may be an additional susceptibility factor for disease expression in Lynch syndrome because they modify the age of colorectal cancer onset by up to 4 years.

Investigating the effects of the 2007 Texas tobacco tax increase on the smoking behavior of adults

Smoking is major cause of premature mortality and morbidity in the United States. The health consequences of tobacco usage are increasingly concentrated in minority and lower socioeconomic groups. One of the most effective means of deterring tobacco consumption and generating revenue to fund prevention activities is the levying of excise taxes. In 2007 the state of Texas increased the excise tax on cigarettes by $1.00 per pack. This study sought to determine if there was a significant effect on smoking prevalence in the state by examining Behavioral Risk Factor Surveillance System (BRFSS) data for two years leading up to the tax increase-2005 and 2006- and two years post tax increase -2007 and 2008. Results were compared against a chi square distribution and three multiple logistic regression models were created to adjust for race/ethnicity, age, education and income. Results from this study show that there was not a significant decrease in smoking prevalence for most of the groups stratified by age, income and ethnicity. There was not a significant decrease in the younger adults aged 18-34 by income, ethnicity, or education. Smoking prevalence increased for some groups, e.g., Hispanic females. In the regression models, the tax effect was not significant. While overall prevalence decreased by 9%, there were not significant reductions among non-White or Hispanic survey participants. Taxed sales dropped by approximately 17% according to the Texas Comptroller. Without BRFSS data measuring daily cigarette consumption among current smokers, now not assessed, it is impossible to determine whether the discrepancy in reported prevalence and taxes sales is attributable to consumption of fewer cigarettes among smokers or tax avoidance.^

Detection of nonrandom association of alleles from the distribution of the number of heterozygous loci in a sample.

The distribution of the number of heterozygous loci in two randomly chosen gametes or in a random diploid zygote provides information regarding the nonrandom association of alleles among different genetic loci. Two alternative statistics may be employed for detection of nonrandom association of genes of different loci when observations are made on these distributions: observed variance of the number of heterozygous loci (s2k) and a goodness-of-fit criterion (X2) to contrast the observed distribution with that expected under the hypothesis of random association of genes. It is shown, by simulation, that s2k is statistically more efficient than X2 to detect a given extent of nonrandom association. Asymptotic normality of s2k is justified, and X2 is shown to follow a chi-square (chi 2) distribution with partial loss of degrees of freedom arising because of estimation of parameters from the marginal gene frequency data. Whenever direct evaluations of linkage disequilibrium values are possible, tests based on maximum likelihood estimators of linkage disequilibria require a smaller sample size (number of zygotes or gametes) to detect a given level of nonrandom association in comparison with that required if such tests are conducted on the basis of s2k. Summarization of multilocus genotype (or haplotype) data, into the different number of heterozygous loci classes, thus, amounts to appreciable loss of information.

Racial and ethnic disparities in diabetes mellitus and hypertension: Influence of income and insurance status in a cross-sectional study of the United States

Racial/ethnic disparities in diabetes mellitus (DM) and hypertension (HTN) have been observed and explained by socioeconomic status (education level, income level, etc.), screening, early diagnosis, treatment, prognostic factors, and adherence to treatment regimens. To the author's knowledge, there are no studies addressing disparities in hypertension and diabetes mellitus utilizing Hispanics as the reference racial/ethnic group and adjusting for sociodemographics and prognostic factors. This present study examined racial/ethnic disparities in HTN and DM and assessed whether this disparity is explained by sociodemographics. To assess these associations, the study utilized a cross-sectional design and examined the distribution of the covariates for racial/ethnic group differences, using the Pearson Chi Square statistic. The study focused on Non-Hispanic Blacks since this ethnic group is associated with the worst health outcomes. Logistic regression was used to estimate the prevalence odds ratio (POR) and to adjust for the confounding effects of the covariates. Results indicated that except for insurance coverage, there were statistically significant differences between Non-Hispanic Blacks and Non-Hispanic Whites, as well as Hispanics with respect to study covariates. In the unadjusted logistic regression model, there was a statistically significant increased prevalence of hypertension among Non-Hispanic Blacks compared to Hispanics, POR 1.36, 95% CI 1.02-1.80. Low income was statistically significantly associated with increased prevalence of hypertension, POR 0.38, 95% CI 0.32-0.46. Insurance coverage, though not statistically significant, was associated with an increase in the prevalence of hypertension, p>0.05. Concerning DM, Non-Hispanic Blacks were more likely to be diabetic, POR 1.10, 95% CI 0.85-1.47. High income was statistically significantly associated with decreased prevalence of DM, POR 0.47, 95% CI 0.39-0.57. After adjustment for the relevant covariates, the racial disparities between Hispanics and Non-Hispanic Blacks in HTN was removed, adjusted prevalence odds (APOR) 1.21, 95% CI 0.88-1.67. In this sample, there was racial/ethnic disparity in hypertension but not in diabetes mellitus between Hispanics and Non-Hispanic Blacks, with disparities in hypertension associated with socioeconomic status (family income, education, marital status) and also by alcohol, physical activity and age. However, race, education and BMI as class variables were statistically significantly associated with hypertension and diabetes mellitus p<0.0001. ^

Colorectal cancer screening: Racial/ethnic and gender disparities in a population-based cross-sectional analysis of the United States

Gender and racial/ethnic disparities in colorectal cancer screening (CRC) has been observed and associated with income status, education level, treatment and late diagnosis. According to the American Cancer Society, among both males and females, CRC is the third most frequently diagnosed type of cancer and accounts for 10% of cancer deaths in the United States. Differences in CRC test use have been documented and limited to access to health care, demographics and health behaviors, but few studies have examined the correlates of CRC screening test use by gender. This present study examined the prevalence of CRC screening test use and assessed whether disparities are explained by gender and racial/ethnic differences. To assess these associations, the study utilized a cross-sectional design and examined the distribution of the covariates for gender and racial/ethnic group differences using the chi square statistic. Logistic regression was used to estimate the prevalence odds ratio and to adjust for the confounding effects of the covariates. ^ Results indicated there are disparities in the use of CRC screening test use and there were statistically significant difference in the prevalence for both FOBT and endoscopy screening between gender, χ2, p≤0.003. Females had a lower prevalence of endoscopy colorectal cancer screening than males when adjusting for age and education (OR 0.88, 95% CI 0.82–0.95). However, no statistically significant difference was reported between racial/ethnic groups, χ 2 p≤0.179 after adjusting for age, education and gender. For both FOBT and endoscopy screening Non-Hispanic Blacks and Hispanics had a lower prevalence of screening compared with Non-Hispanic Whites. In the multivariable regression model, the gender disparities could largely be explained by age, income status, education level, and marital status. Overall, individuals between the age "70–79" years old, were married, with some college education and income greater than $20,000 were associated with a higher prevalence of colorectal cancer screening test use within gender and racial/ethnic groups. ^

Childhood cancer survivor satisfaction with characteristics of clinical care

This study investigated the characteristics of a clinic that affect how satisfied survivors of childhood cancer are with their medical care. Questionnaire and interview data from the Passport for Care: Texas Implementation project collected between January 2011 to April 2012 were analyzed. Eleven clinics in Texas participated. Questionnaire respondents were childhood cancer survivor patients who had been off therapy for at least 2 years, or their parents. Interview respondents were clinical providers or research staff at the participating clinics. The outcomes evaluated were answers to a single question on satisfaction with care and a composite Percent Satisfaction Score created from seven other questionnaire items that were correlated (Spearman Rho >0.3) with the question on satisfaction. The following characteristics were also evaluated: sex, age, race, education, and type of cancer. The following clinic indicators were evaluated: type of clinic (general vs. dedicated cancer survivor clinics), number of providers, number of survivors, ratio of survivors/providers, distribution of handouts, distribution of treatment summaries, and use of Children's Oncology Group (COG) guidelines. ^ The only demographic characteristic that affected satisfaction was race. A Kruskal-Wallis test showed a statistically significant difference (Chi-square 6.129, 2 d.f., p = 0.0467). To analyze this further, Wilcoxon Rank Sum test of pairings of the three groups were performed. A Bonferroni correction for multiple testing was applied, with p = 0.017 indicating significance at alpha = 0.05. There was no significant difference between the White and Hispanic groups or between the Hispanic and "Other" groups. For the White and "Other" groups there was a significant difference for the satisfaction item (p = 0.0123) but not for the Percent Satisfaction Score (p = 0.0289). These results suggest that race may influence satisfaction and should be evaluated further in future studies. ^ None of the clinic indicators affected the Percent Satisfaction Score. Going to a clinic that distributed patient information handouts (Wilcoxon Rank Sum p = 0.048) and going to a clinic with >=100 survivors (Wilcoxon Rank Sum p = 0.021) were associated with increased satisfaction. The population of childhood cancer survivors is a growing group of individuals with special health needs. In the future survivors will likely seek medical care in a variety of clinical settings, so it is important to investigate features to improve patient satisfaction with clinical care.^

Survival analysis of circulating tumor cells in triple-negative breast cancer

Background. Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer death among females, accounting for 23% (1.38 million) of the total new cancer cases and 14% (458,400) of the total cancer deaths in 2008. [1] Triple-negative breast cancer (TNBC) is an aggressive phenotype comprising 10–20% of all breast cancers (BCs). [2-4] TNBCs show absence of estrogen, progesterone and HER2/neu receptors on the tumor cells. Because of the absence of these receptors, TNBCs are not candidates for targeted therapies. Circulating tumor cells (CTCs) are observed in blood of breast cancer patients even at early stages (Stage I & II) of the disease. Immunological and molecular analysis can be used to detect the presence of tumor cells in the blood (Circulating tumor cells; CTCs) of many breast cancer patients. These cells may explain relapses in early stage breast cancer patients even after adequate local control. CTC detection may be useful in identifying patients at risk for disease progression, and therapies targeting CTCs may improve outcome in patients harboring them. Methods . In this study we evaluated 80 patients with TNBC who are enrolled in a larger prospective study conducted at M D Anderson Cancer Center in order to determine whether the presence of circulating tumor cells is a significant prognostic factor in relapse free and overall survival . Patients with metastatic disease at the time of presentation were excluded from the study. CTCs were assessed using CellSearch System™ (Veridex, Raritan, NJ). CTCs were defined as nucleated cells lacking the presence of CD45 but expressing cytokeratins 8, 18 or 19. The distribution of patient and tumor characteristics was analyzed using chi square test and Fisher's exact test. Log rank test and Cox regression analysis was applied to establish the association of circulating tumor cells with relapse free and overall survival. Results. The median age of the study participants was 53years. The median duration of follow-up was 40 months. Eighty-eight percent (88%) of patients were newly diagnosed (without a previous history of breast cancer), and (60%) of patients were chemo naïve (had not received chemotherapy at the time of their blood draw for CTC analysis). Tumor characteristics such as stage (P=0.40), tumor size (P=69), sentinel nodal involvement (P=0.87), axillary lymph node involvement (P=0.13), adjuvant therapy (P=0.83), and high histological grade of tumor (P=0.26) did not predict the presence of CTCs. However, CTCs predicted worse relapse free survival (1 or more CTCs log rank P value = 0.04, at 2 or more CTCs P = 0.02 and at 3 or more CTCs P < 0.0001) and overall survival (at 1 or more CTCs log rank P value = 0.08, at 2 or more CTCs P = 0.01 and at 3 or more CTCs P = 0.0001. Conclusions. The number of circulating tumor cells predicted worse relapse free survival and overall survival in TNBC patients.^

The cost of insuring the uninsured in the U.S.

Objectives: This study included two overarching objectives. Through a systematic review of the literature published between 1990 and 2012, the first objective aimed to assess whether insuring the uninsured would result in higher costs compared to insuring the currently insured. Studies that quantified the actual costs associated with insuring the uninsured in the U.S. were included. Based upon 2009 data from the Medical Expenditure Panel Survey (MEPS), the second objective aimed to assess and compare the self-reported health of populations with four different insurance statuses. The second part of this study involved a secondary data analysis of both currently insured and currently uninsured individuals who participated in the MEPS in 2009. The null hypothesis was that there were no differences across the four categories of health insurance status for self-reported health status and healthcare service use. The alternative hypothesis was that were differences across the four categories of health insurance status for self-reported health status and healthcare service use. Methods: For the systematic review, three databases were searched using search terms to identify studies that actually quantified the cost of insuring the uninsured. Thirteen studies were selected, discussed, and summarized in tables. For the secondary data analysis of MEPS data, this study compared four categories of health insurance status: (1) currently uninsured persons who will become eligible for Medicaid under the Patient Protection and Affordable Care Act (PPACA) healthcare reforms in 2014; (2) currently uninsured persons who will be required to buy private insurance through the PPACA health insurance exchanges in 2014; (3) persons currently insured under Medicaid or SCHIP; and (4) persons currently insured with private insurance. The four categories were compared on the basis of demographic information, health status information, and health conditions with relatively high prevalence. Chi-square tests were run to determine if there were differences between the four groups in regard to health insurance status and health status. With some exceptions, the two currently insured groups had worse self-reported health status compared to the two currently uninsured groups. Results: The thirteen studies that met the inclusion criteria for the systematic review included: (1) three cost studies from 1993, 1995, and 1997; (2) four cost studies from 2001, 2003, and 2004; (3) one study of disabilities and one study of immigrants; (4) two state specific studies of uninsured status; and (5) two current studies of healthcare reform. Of the thirteen studies reviewed, four directly addressed the study question about whether insuring the uninsured was more or less expensive than insuring the currently insured. All four of the studies provided support for the study finding that the cost of insuring the uninsured would generally not be higher than insuring those already insured. One study indicated that the cost of insuring the uninsured would be less expensive than insuring the population currently covered by Medicaid, but more expensive to insure than the populations of those covered by employer-sponsored insurance and non-group private insurance. While the nine other studies included in the systematic review discussed the costs associated with insuring the uninsured population, they did not directly compare the costs of insuring the uninsured population with the costs associated with insuring the currently insured population. For the MEPS secondary data analysis, the results of the chi-square tests indicated that there were differences in the distribution of disease status by health insurance status. As anticipated, with some exceptions, the uninsured reported lower rates of disease and healthcare service use. However, for the variable attention deficit disorder, the uninsured reported higher disease rates than the two insured groups. Additionally, for the variables high blood pressure, high cholesterol, and joint pain, the currently insured under Medicaid or SCHIP group reported a lower rate of disease than the two currently insured groups. This result may be due to the lower mean age of the currently insured under Medicaid or SCHIP group. Conclusion: Based on this study, with some exceptions, the costs for insuring the uninsured should not exceed healthcare-related costs for insuring the currently uninsured. The results of the systematic review indicated that the U.S. is already paying some of the costs associated with insuring the uninsured. PPACA will expand health insurance coverage to millions of Americans who are currently uninsured, as the individual mandate and insurance market reforms will require. Because many of the currently uninsured are relatively healthy young persons, the costs associated with expanding insurance coverage to the uninsured are anticipated to be relatively modest. However, for the purposes of construing these results, it is important to note that once individuals obtain insurance, it is anticipated that they will use more healthcare services, which will increase costs. (Abstract shortened by UMI.)^