A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data

<p>Abstract</p> <p>Background</p> <p>Mosaicism for copy number and copy neutral chromosomal rearrangements has been recently identified as a relatively common source of genetic variation in the normal population. However its prevalence is poorly defined since it has been only studied systematically in one large-scale study and by using non optimal <it>ad-hoc </it>SNP array data analysis tools, uncovering rather large alterations (> 1 Mb) and affecting a high proportion of cells. Here we propose a novel methodology, Mosaic Alteration Detection-MAD, by providing a software tool that is effective for capturing previously described alterations as wells as new variants that are smaller in size and/or affecting a low percentage of cells.</p> <p>Results</p> <p>The developed method identified all previously known mosaic abnormalities reported in SNP array data obtained from controls, bladder cancer and HapMap individuals. In addition MAD tool was able to detect new mosaic variants not reported before that were smaller in size and with lower percentage of cells affected. The performance of the tool was analysed by studying simulated data for different scenarios. Our method showed high sensitivity and specificity for all assessed scenarios.</p> <p>Conclusions</p> <p>The tool presented here has the ability to identify mosaic abnormalities with high sensitivity and specificity. Our results confirm the lack of sensitivity of former methods by identifying new mosaic variants not reported in previously utilised datasets. Our work suggests that the prevalence of mosaic alterations could be higher than initially thought. The use of appropriate SNP array data analysis methods would help in defining the human genome mosaic map.</p

Relationship of literacy and heart failure in adults with diabetes

<p>Abstract</p> <p>Background</p> <p>Although reading ability may impact educational strategies and management of heart failure (HF), the prevalence of limited literacy in patients with HF is unknown.</p> <p>Methods</p> <p>Subjects were drawn from the Vermont Diabetes Information System Field Survey, a cross-sectional study of adults with diabetes in primary care. Participants' self-reported characteristics were subjected to logistic regression to estimate the association of heart failure and literacy while controlling for social and economic factors. The Short Test of Functional Health Literacy was used to measure literacy.</p> <p>Results</p> <p>Of 172 subjects with HF and diabetes, 27% had limited literacy compared to 15% of 826 subjects without HF (OR 2.05; 95% CI 1.39, 3.02; <it>P </it>< 0.001). Adjusting for age, sex, race, income, marital status and health insurance, HF continued to be significantly associated with limited literacy (OR 1.55, 95% CI 1.00, 2.41, <it>P </it>= .05).</p> <p>After adjusting for education, however, HF was no longer independently associated with literacy (OR 1.31; 95% CI 0.82 – 2.08; <it>P </it>= 0.26).</p> <p>Conclusion</p> <p>Over one quarter of diabetic adults with HF have limited literacy. Although this association is no longer statistically significant when adjusted for education, clinicians should be aware that many of their patients have important limitations in dealing with written materials.</p

High Expression of Testes-Specific Protease 50 Is Associated with Poor Prognosis in Colorectal Carcinoma

Testes-specific protease 50 (TSP50) is normally expressed in testes and abnormally expressed in breast cancer, but whether TSP50 is expressed in colorectal carcinoma (CRC) and its clinical significance is unclear. We aimed to detect TSP50 expression in CRC, correlate it with clinicopathological factors, and assess its potential diagnostic and prognostic value. = 0.009).Our data demonstrate that TSP50 is a potential effective indicator of poor survival for CRC patients, especially for those with early-stage tumors

Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics

Genomic rearrangements can result in losses, amplifications, translocations and inversions of DNA fragments thereby modifying genome architecture, and potentially having clinical consequences. Many genomic disorders caused by structural variation have initially been uncovered by early cytogenetic methods. The last decade has seen significant progression in molecular cytogenetic techniques, allowing rapid and precise detection of structural rearrangements on a whole-genome scale. The high resolution attainable with these recently developed techniques has also uncovered the role of structural variants in normal genetic variation alongside single-nucleotide polymorphisms (SNPs). We describe how array-based comparative genomic hybridisation, SNP arrays, array painting and next-generation sequencing analytical methods (read depth, read pair and split read) allow the extensive characterisation of chromosome rearrangements in human genomes

Literacy and Health Outcomes: A Systematic Review of the Literature

OBJECTIVE: To review the relationship between literacy and health outcomes. DATA SOURCES: We searched MEDLINE, Cumulative Index to Nursing and Allied Health (CINAHL), Educational Resources Information Center (ERIC), Public Affairs Information Service (PAIS), Industrial and Labor Relations Review (ILLR), PsychInfo, and Ageline from 1980 to 2003. STUDY SELECTION: We included observational studies that reported original data, measured literacy with any valid instrument, and measured one or more health outcomes. Two abstractors reviewed each study for inclusion and resolved disagreements by discussion. DATA EXTRACTION: One reviewer abstracted data from each article into an evidence table; the second reviewer checked each entry. The whole study team reconciled disagreements about information in evidence tables. Both data extractors independently completed an 11-item quality scale for each article; scores were averaged to give a final measure of article quality. DATA SYNTHESIS: We reviewed 3,015 titles and abstracts and pulled 684 articles for full review; 73 articles met inclusion criteria and, of those, 44 addressed the questions of this report. Patients with low literacy had poorer health outcomes, including knowledge, intermediate disease markers, measures of morbidity, general health status, and use of health resources. Patients with low literacy were generally 1.5 to 3 times more likely to experience a given poor outcome. The average quality of the articles was fair to good. Most studies were cross-sectional in design; many failed to address adequately confounding and the use of multiple comparisons. CONCLUSIONS: Low literacy is associated with several adverse health outcomes. Future research, using more rigorous methods, will better define these relationships and guide developers of new interventions

The Prevalence of Limited Health Literacy

OBJECTIVE: To systematically review U.S. studies examining the prevalence of limited health literacy and to synthesize these findings by evaluating demographic associations in pooled analyses. DESIGN: We searched the literature for the period 1963 through January 2004 and identified 2,132 references related to a set of specified search terms. Of the 134 articles and published abstracts retrieved, 85 met inclusion criteria, which were 1) conducted in the United States with ≥25 adults, 2) addressed a hypothesis related to health care, 3) identified a measurement instrument, and 4) presented primary data. The authors extracted data to compare studies by population, methods, and results. MAIN RESULTS: The 85 studies reviewed include data on 31,129 subjects, and report a prevalence of low health literacy between 0% and 68%. Pooled analyses of these data reveal that the weighted prevalence of low health literacy was 26% (95% confidence interval [CI], 22% to 29%) and of marginal health literacy was 20% (95% CI, 16% to 23%). Most studies used either the Rapid Estimate of Adult Literacy in Medicine (REALM) or versions of the Test of Functional Health Literacy in Adults (TOFHLA). The prevalence of low health literacy was not associated with gender (P =.38) or measurement instrument (P =.23) but was associated with level of education (P =.02), ethnicity (P =.0003), and age (P =.004). CONCLUSIONS: A pooled analysis of published reports on health literacy cannot provide a nationally representative prevalence estimate. This systematic review exhibits that limited health literacy, as depicted in the medical literature, is prevalent and is consistently associated with education, ethnicity, and age. It is essential to simplify health services and improve health education. Such changes have the potential to improve the health of Americans and address the health disparities that exist today