Genetic epidemiologic methods in risk determination in Li-Fraumeni syndrome

Li-Fraumeni syndrome (LFS) is characterized by a variety of neoplasms occurring at a young age with an apparent autosomal dominant transmission. Individuals in pedigrees with LFS have high incidence of second malignancies. Recently LFS has been found to be associated with germline mutations of a tumor-suppressor gene, p53. Because LFS is rare and indeed not a clear-cut disease, it is not known whether all cases of LFS are attributable to p53 germline mutations and how p53 plays in cancer occurrence in such cancer syndrome families. In the present study, DNAs from constitutive cells of two-hundred and thirty-three family members from ten extended pedigrees were screened for p53 mutations. Six out of the ten LFS families had germline mutations at the p53 locus, including point and deletion mutations. In these six families, 55 out of 146 members were carriers of p53 mutations. Except one, all mutations occurred in exons 5 to 8 (i.e., the "hot spot" region) of the p53 gene. The age-specific penetrance of cancer was estimated after the genotype for each family member at risk was determined. The penetrance was 0.15, 0.29, 0.35, 0.77, and 0.91 by 20, 30, 40, 50 and 60 year-old, respectively, in male carriers; 0.19, 0.44, 0.76, and 0.90 by 20, 30, 40, and 50 year-old, respectively, in female carriers. These results indicated that one cannot escape from tumorigenesis if one inherits a p53 mutant allele; at least ninety percent of p53 carriers will develop cancer by the age of 60. To evaluate the possible bias due to the unexamined blood-relatives in LFS families, I performed a simulation analysis in which a p53 genotype was assigned to each unexamined person based on his cancer status and liability to cancer. The results showed that the penetrance estimates were not biased by the unexamined relatives. I also determined the sex, site, and age-specific penetrance of breast cancer in female carriers and lung cancer in male carriers. The penetrance of breast cancer in female carriers was 0.81 by age 45; the penetrance of lung cancer in male carriers was 0.78 by age 60, indicating that p53 play a key role for tumorigenesis in common cancers. ^

BAYESIAN STATISTICAL METHODS IN GENE-ENVIRONMENT AND GENE-GENE INTERACTION STUDIES

Complex diseases such as cancer result from multiple genetic changes and environmental exposures. Due to the rapid development of genotyping and sequencing technologies, we are now able to more accurately assess causal effects of many genetic and environmental factors. Genome-wide association studies have been able to localize many causal genetic variants predisposing to certain diseases. However, these studies only explain a small portion of variations in the heritability of diseases. More advanced statistical models are urgently needed to identify and characterize some additional genetic and environmental factors and their interactions, which will enable us to better understand the causes of complex diseases. In the past decade, thanks to the increasing computational capabilities and novel statistical developments, Bayesian methods have been widely applied in the genetics/genomics researches and demonstrating superiority over some regular approaches in certain research areas. Gene-environment and gene-gene interaction studies are among the areas where Bayesian methods may fully exert its functionalities and advantages. This dissertation focuses on developing new Bayesian statistical methods for data analysis with complex gene-environment and gene-gene interactions, as well as extending some existing methods for gene-environment interactions to other related areas. It includes three sections: (1) Deriving the Bayesian variable selection framework for the hierarchical gene-environment and gene-gene interactions; (2) Developing the Bayesian Natural and Orthogonal Interaction (NOIA) models for gene-environment interactions; and (3) extending the applications of two Bayesian statistical methods which were developed for gene-environment interaction studies, to other related types of studies such as adaptive borrowing historical data. We propose a Bayesian hierarchical mixture model framework that allows us to investigate the genetic and environmental effects, gene by gene interactions (epistasis) and gene by environment interactions in the same model. It is well known that, in many practical situations, there exists a natural hierarchical structure between the main effects and interactions in the linear model. Here we propose a model that incorporates this hierarchical structure into the Bayesian mixture model, such that the irrelevant interaction effects can be removed more efficiently, resulting in more robust, parsimonious and powerful models. We evaluate both of the 'strong hierarchical' and 'weak hierarchical' models, which specify that both or one of the main effects between interacting factors must be present for the interactions to be included in the model. The extensive simulation results show that the proposed strong and weak hierarchical mixture models control the proportion of false positive discoveries and yield a powerful approach to identify the predisposing main effects and interactions in the studies with complex gene-environment and gene-gene interactions. We also compare these two models with the 'independent' model that does not impose this hierarchical constraint and observe their superior performances in most of the considered situations. The proposed models are implemented in the real data analysis of gene and environment interactions in the cases of lung cancer and cutaneous melanoma case-control studies. The Bayesian statistical models enjoy the properties of being allowed to incorporate useful prior information in the modeling process. Moreover, the Bayesian mixture model outperforms the multivariate logistic model in terms of the performances on the parameter estimation and variable selection in most cases. Our proposed models hold the hierarchical constraints, that further improve the Bayesian mixture model by reducing the proportion of false positive findings among the identified interactions and successfully identifying the reported associations. This is practically appealing for the study of investigating the causal factors from a moderate number of candidate genetic and environmental factors along with a relatively large number of interactions. The natural and orthogonal interaction (NOIA) models of genetic effects have previously been developed to provide an analysis framework, by which the estimates of effects for a quantitative trait are statistically orthogonal regardless of the existence of Hardy-Weinberg Equilibrium (HWE) within loci. Ma et al. (2012) recently developed a NOIA model for the gene-environment interaction studies and have shown the advantages of using the model for detecting the true main effects and interactions, compared with the usual functional model. In this project, we propose a novel Bayesian statistical model that combines the Bayesian hierarchical mixture model with the NOIA statistical model and the usual functional model. The proposed Bayesian NOIA model demonstrates more power at detecting the non-null effects with higher marginal posterior probabilities. Also, we review two Bayesian statistical models (Bayesian empirical shrinkage-type estimator and Bayesian model averaging), which were developed for the gene-environment interaction studies. Inspired by these Bayesian models, we develop two novel statistical methods that are able to handle the related problems such as borrowing data from historical studies. The proposed methods are analogous to the methods for the gene-environment interactions on behalf of the success on balancing the statistical efficiency and bias in a unified model. By extensive simulation studies, we compare the operating characteristics of the proposed models with the existing models including the hierarchical meta-analysis model. The results show that the proposed approaches adaptively borrow the historical data in a data-driven way. These novel models may have a broad range of statistical applications in both of genetic/genomic and clinical studies.

Complications of misoprostol and other abortion induction methods in the developing world: A systematic review

OBJECTIVE: To systematically review published literature to examine the complications associated with the use of misoprostol and compare these complications to those associated with other forms of abortion induction. ^ DATA SOURCES: Studies were identified through searches of medical literature databases including Medline (Ovid), PubMed (NLM), LILACS, sciELO, and AIM (AFRO), and review of references of relevant articles. ^ STUDY SELECTION AND METHODS: A descriptive systematic review that included studies reported in English and published before December 2012. Eligibility criteria included: misoprostol (with or without other methods) and any other method of abortion in a developing country, as well as quantitative data on the complication of each method. The following is information extracted from each study: author/year, country/city, study design/study sample, age range, setting of data collection, sample size, the method of abortion induction, the number of cases for each method, and the percentage of complications with each method. RESULTS: A total of 4 studies were identified (all in Latin America) describing post-abortion complications of misoprostol and other methods in countries where abortion is generally considered unsafe and/or illegal. The four studies reported on a range of complications including: bleeding, infection, incomplete abortion, intense pelvic pain, uterine perforation, headache, diarrhea, nausea, mechanical lesions, and systemic collapse. The most prevalent complications of misoprostol-induced abortion reported were: bleeding (7-82%), incomplete abortion (33-70%), and infection (0.8-67%). The prevalence of these complications reported from other abortion methods include: bleeding (16-25%), incomplete abortion (15-82%), and infection (13-50%). ^ CONCLUSION: The literature identified by this systematic review is inadequate for determining the complications of misoprostol used in unsafe settings. Abortion is considered an illicit behavior in these countries, therefore making it difficult to investigate the details needed to conduct a study on abortion complications. Given the differences between the reviewed studies as well as a variety of study limitations, it is not possible to draw firm conclusions about the rates of specific-abortion related complications.^

Towards a Hybrid Method to Categorize Interruptions and Activities in Healthcare

Objective Interruptions are known to have a negative impact on activity performance. Understanding how an interruption contributes to human error is limited because there is not a standard method for analyzing and classifying interruptions. Qualitative data are typically analyzed by either a deductive or an inductive method. Both methods have limitations. In this paper a hybrid method was developed that integrates deductive and inductive methods for the categorization of activities and interruptions recorded during an ethnographic study of physicians and registered nurses in a Level One Trauma Center. Understanding the effects of interruptions is important for designing and evaluating informatics tools in particular and for improving healthcare quality and patient safety in general. Method The hybrid method was developed using a deductive a priori classification framework with the provision of adding new categories discovered inductively in the data. The inductive process utilized line-by-line coding and constant comparison as stated in Grounded Theory. Results The categories of activities and interruptions were organized into a three-tiered hierarchy of activity. Validity and reliability of the categories were tested by categorizing a medical error case external to the study. No new categories of interruptions were identified during analysis of the medical error case. Conclusions Findings from this study provide evidence that the hybrid model of categorization is more complete than either a deductive or an inductive method alone. The hybrid method developed in this study provides the methodical support for understanding, analyzing, and managing interruptions and workflow.

Characteristics and experiences of past participants in the Texas Peer Assistance Program for Nurses

There are nearly 200,000 licensed practicing nurses in the state of Texas, representing one-tenth of the nations' workforce. The prevalence of substance abuse among nurses is estimated to range between six and 20 percent in this professional group.^ Since March 1987, the Texas Peer Assistance Program for Nurses (TPAPN) has offered intervention, education, support and monitoring to nurses in Texas whose practice has become impaired due to substance abuse and/or mental illness. Since then approximately 44 percent of nurses who voluntarily signed participation agreements successfully completed the program; fifty-six percent have not. One determinant of completion for those nurses identified as chemically dependent is abstinence from mood altering substances. Other helping professions report higher rates of abstinence two years following treatment.^ The purpose of this study was to investigate the relationship between relapse, demographics, treatment variables, work setting, "stress" indicators and support factors for nurses who participated in TPAPN. A questionnaire was mailed to 1000 randomly selected nurses who had signed agreements since 1987 and were no longer active in the program. More than 41% of the questionnaires were returned undeliverable.^ Recipients of the questionnaire were known only to TPAPN, never to the investigator. All information was received anonymously except when the participant chose to sign the questionnaire. A cover letter explaining the study and inviting participation was enclosed. Completion and return of the questionnaire was considered consent to participate.^ Findings demonstrated a significant relationship between relapse and opiates as the drug of choice for past participants in the Texas Peer Assistance Program for Nurses. Significant associations were found among factors such as control at work, support, physical complaints, job security, self-esteem and employment in this sample. Respondents shared copious written comments about their experiences in TPAPN. These data were analyzed using qualitative methods and compared with similar studies of recovering nurses. Further research with nurses whose practice has been affected by abuse of chemical and mental illness is warranted. ^

The door of the tomb is open: Participatory action research to assess the impact of strengthened community capacity on maternal health care in rural Mali

This participatory action-research project addressed the hypothesis that strengthened community and women's capacity for self-development will lead to action to address maternal health problems and the prevention of maternal morbidity and mortality in Mali. Research objectives were: (1) to undertake a comparative cross-sectional study of the association of community capacity with improved maternal health in rural areas of Sanando, Mali, where capacity building interventions have taken place in some villages but not in others. (2) to describe women's maternal health status, access to and use of maternal health services given their residence in program or comparison communities.^ The participatory action research project was an integrated qualitative and quantitative study using participatory rural appraisal exercises, semi-structured group interviews and a cross-sectional survey.^ Factors related to community capacity for self-development were identified: community harmony; an understanding of the benefits of self-development; dynamic leadership; and a structure to implement collective activities.^ A distinct difference between the program and comparison villages was the commitment to train and support traditional birth attendants (TBAs). The TBAs in the program villages work in the context of the wider, integrated self-development program and, 10 years after their initial training, the TBAs continue to practice.^ Many women experience labor and childbirth alone or are attended by an untrained relative in both program and comparison villages. Nevertheless a significant change is apparent, with more women in program villages than in comparison villages being assisted by the TBAs. The delivery practices of the TBAs reveal the positive impact of their training in the "three cleans" (clean hands of the assistant, clean delivery surface and clean cord-cutting). The findings of this study indicate a significant level of unmet need for child spacing methods in all villages.^ The training and support of TBAs in the program villages yielded significant improvements in their delivery practices, and resulting outcomes for women and infants. However, potential exists for further community action. Capacities for self-development have not yet been directed toward an action plan encompassing other Safe Motherhood interventions, including access to family planning services and emergency obstetric care services. ^

Perspective transformation: Women in long-term recovery from alcohol abuse

Objective. The purpose of this study was to determine the meaning of personal transformation for twenty women in long term, stable recovery from alcohol abuse; to identify themes or patterns of this recovery, and; to determine the extent to which they experienced the phenomenon of perspective transformation. ^ Method. Volunteers were recruited by advertisement, word of mouth, and through a closed circuit web based broadcast. A descriptive, exploratory study, which analyzed perspective transformation from the standpoint of five action phases, was conducted. Data was collected using in-depth personal interviews and questionnaires. Subjects' responses were analyzed by qualitative methods. Triangulation was performed on the grouped data comparing the interviews to the data produced by the questionnaires. Quantitative analysis of questionnaire items explored behavioral changes experienced before and after alcoholism recovery. ^ Results. Five phases of recovery were identified. Phase I which involved recognition that alcohol was a problem and change might be possible took several years during which 3 major transitions occurred: (1) from often being alienated to having relationships with family and friends; (2) from daily upheavals to eventually a more peaceful existence, and; (3) from denial that alcohol was a problem to acceptance and willingness to change. Recovery was often seen in a spiritual context, which also required ongoing support. During Phase II there was an assessment of self, others, and the environment which revealed a pattern of intense unhappiness and negative feelings toward self and others with a disregard for cultural norms. Phase III revealed a period of desperation as life became unmanageable, but gradual willingness to accept support and guidance and a desire to improve self and help others. This led to improvement of existing role performance and the willingness to try out new roles. In Phase IV there was a pattern of personal growth which included: the establishment of boundaries, setting priorities, a willingness to place others' needs above their own, acceptance of responsibility, and learning to cope without alcohol, often with the use of tools learned in AA. During Phase V, many experienced knowledge of frailties but growing respect for self and others, with an improved ability to function in giving relationships. Implications for Prevention and Recovery: Early education concerning addiction and recovery may play a crucial role in prevention and early recovery, as it did for children of women in this study. Recovery requires persistent effort and organized support. ^

Health, education and community: Assets and needs of a small urban community in north east Tamaulipas, Mexico: A community based participatory research assessment

This study explored the health, education, social assets, needs, attitudes, and behaviors of residents of Ferrocarril #4, a small urban community in Tamaulipas, Mexico. A collaborative Participatory Action Research approach was used to emphasize community involvement. Using Triangulation to ensure validity, qualitative methods included key informant in depth interviews, participant observation and participatory discussion groups with women and men. A personal interview with a probability sample of women was done. The median age of interviewees was 37 years. The majority was married or had a partner. Over half of respondents completed grades 6-9. Employed women (25%) earned a median weekly salary equivalent to ∼56 USD. Women with health insurance (67.7%) were covered mainly through Social Security and Seguro Popular. One in 5 reported bad health. Barriers to care were primarily money and transportation. To improve health care, women wanted a full service clinic in or close to the community and affordable health care. Socially, 28% of respondents had no close friends in the community and most did not participate in beneficial community activities. Many women did not socialize with others and help from neighbors was situational. Primary school teachers lacked parental support and it interfered with classroom efforts. Healthy community discussion groups focused on personal and environmental hygiene and safety. Valuable assets exist in the community. To date, collaborative efforts resulted in a school First Aid station, a school nurse visit weekly, posting of emergency contact phone numbers in the school and community center, and development of a student health information form. ^

Latino perceptions of and barriers to preventive healthcare maintenance in the southwest United States

Between the 1990 and 2000 Censuses, the Latino population accounted for 40% of the increase in the nation’s total population. The growing population of Latinos underscores the importance for understanding factors that influence whether and how Latinos take care of their health. According to the U.S. Department of Human Health Service’s Office of Minority Health (OMH), Latinos are at greater risk for health disparities (2003). Factors such as lack of health insurance and access to preventive care play a major role in limiting Latino use of primary health care (Institute of Medicine, 2005). Other significant barriers to preventive health care maintenance behaviors have been identified in current literature such as primary care physician interaction, self-perceived health status, and socio-cultural beliefs and traditions (Rojas-Guyler, King, Montieth and 2008; Meir, Medina, and Ory, 2007; Black, 1999). Despite these studies, there remains less information regarding interpersonal perceptions, environmental dynamics and individual and cultural attitudes relevant to utilization of healthcare (Rojas-Guyler, King, Montieth and 2008; Aguirre-Molina, Molina and Zambrana, 2001). Understanding the perceptions of Latinos and the barriers to health care could directly affect healthcare delivery. Improved healthcare utilization among Latinos could reduce the long term health consequences of many preventable and manageable diseases. The purpose of this study was to explore Latino perceptions of U.S. health care and desired changes by Latinos in the U.S. healthcare system. The study had several objectives, including to explore perceived barriers to healthcare utilization and the resulting effects on health among Latinos, to describe culturally influenced attitudes about health care and use of health care services among Latinos, and to make recommendations for reducing disparities by improving healthcare and its utilization. The current study utilized data that were collected as part of a larger study to examine multidimensional, cross-cultural issues relevant to interactions between healthcare consumers and providers. Qualitative methods were used to analyze four Spanish-language focus group transcripts to interpret cultural influences on perceptions and beliefs among Latinos. Direct coding of transcript content was carried out by two reviewers, who conducted independent reviews of each transcript. Team members developed and refined thematic categories, positive and negative cases, and example text segments for each theme and sub-theme. Incongruities of interpretations were resolved through extensive discussion. Study participants included 44 self-identified Latino adults (16 male, 28 female) between age 18 and 64 years. Thirty seven (84.1%) of the participants were immigrants. The study population comprised eight ethnic subgroups. While 31% of the participants reported being employed on a full-time basis, only 18.4% had medical insurance that was private or employee sponsored. Five major themes regarding the perceptions and healthcare utilization behaviors of Latinos were consistent across all focus groups and were identified during the analysis. These were: (1) healthcare utilization, experience, and access; (2) organizational and institutional systems; (3) communication and interpersonal interactions between healthcare provider, staff, and patient; (4) Latinos’ perception of their own health status; (5) cultural influences on healthcare utilization, which included an innovation termed culturally-bound locus of control. Healthcare utilization was directly influenced by healthcare experience, access, current health status, and cultural factors and indirectly influenced by organizational systems. There was a strong interdependence among the main themes. The ability to communicate and interact effectively with healthcare providers and navigate healthcare systems (organizational and institutional access) significantly influenced the participant’s health care experience, most often (indirectly) impacting utilization negatively. ^ Research such as this can help to identify those perceptions and attitudes held by Latinos concerning utilization or underutilization of healthcare systems. These data suggest that for healthcare utilization to improve among Latinos, healthcare systems must create more culturally competent environments by providing better language services at the organizational level and more culturally sensitive providers at the interpersonal level. Better understanding of the complex interactions between these impediments can aid intervention developments, and help health providers and researchers in determining appropriate, adequate, and effective measurers of care to better increase overall health of Latinos.^

"I understood what she meant when she said '21st century medicine'": A qualitative analysis of patient responses for plans for colorectal cancer screening following a recommendation from their physician

Although physician recommendation has been significantly associated with colorectal cancer screening (CRCS), it still does not motivate all patients to get CRCS. Although improved physician recommendation for CRCS has been shown to increase patient CRCS screening, questions remain about what elements of that discussion may lead to screening. The objective of this study is to describe patients' perceptions and interpretations about their physician's recommendation for CRCS during their annual wellness exam. A subset of patients (n=51) participating in a supplement study of a behavioral intervention trial designed to increase CRCS completed a follow-up, open-ended interview two to four weeks after their annual wellness visit. Using qualitative methods, transcripts of these interviews were analyzed. Findings suggest that most patients would follow their physician's recommendation for CRCS despite not engaging in much discussion. Patients may refrain from CRCS discussion because of a commitment to CRCS, awareness of screening guidelines, and trust in physician's honesty and beneficence. Yet many patients left their wellness exams with questions, refraining because of future plans to consult with their physicians, perceived time constraints or a lack of a patient-physician relationship. If patients are leaving their wellness exams with unanswered questions, interventions should prepare physicians for patient reticence, teaching physicians how to assure patients that CRCS is a primary care activity where all questions and concerns, including cost and scheduling, may be resolved.^

Social and economically influenced factors associated with breast cancer treatment among blacks and whites. A qualitative study

Background: Despite the fact breast cancer mortality has declined in recent years, the mortality gap between African-American and white women continues to grow. A part of these disparities may be due to either inadequately following guideline recommended treatment or treatment delays. Although racial/ethnic disparities in breast cancer treatment and mortality have been extensively documented, the mechanisms by which these disparities occur remain largely unknown. Social and economically influenced factors such as choice of providers, distance of treatment facility, transportation, health insurance, and job related factors may also contribute to racial differences in breast cancer treatment; however, these have not been explored sufficiently in previous research. ^ Aim: The purpose of this study was to evaluate the role of social and economically influenced factors that may contribute to racial disparities in the receipt of guideline recommended treatment using the Health Disparities Model. ^ Methods: In this qualitative comparative case study, data from medical records, structured telephone interviews, and in-depth patient interviews explored the relationship between social and economically influenced factors and breast cancer treatment. Transcripts were analyzed using standard iterative process followed by immersion/crystallization approach. Participants were identified through rapid ascertainment from the New Jersey Cancer Registry and this study included 8 African-American and 8 white women aged 20-85 years old diagnosed with early stage breast cancer between 2003-2007, matched on age, race, and physician recommended treatment. ^ Results: We did not identify differences by race in factors that influenced the receipt of breast cancer treatment among the individual matched pairs. Four prominent themes emerged among women from both groups who experienced similar difficulties influenced by socioeconomic factors. Choice of providers, distance of facility, health insurance, and job related factors all contributed to breast cancer treatment experience among these women. Conclusions: We identified common issues influenced by socioeconomic factors and its relation with the receipt of breast cancer treatment, regardless of race. However, more research is needed to study the additional factors conveying racial differences affecting breast cancer treatment. ^