A resampling-based meta-analysis for detection of differential gene expression in breast cancer

<p>Abstract</p> <p>Background</p> <p>Accuracy in the diagnosis of breast cancer and classification of cancer subtypes has improved over the years with the development of well-established immunohistopathological criteria. More recently, diagnostic gene-sets at the mRNA expression level have been tested as better predictors of disease state. However, breast cancer is heterogeneous in nature; thus extraction of differentially expressed gene-sets that stably distinguish normal tissue from various pathologies poses challenges. Meta-analysis of high-throughput expression data using a collection of statistical methodologies leads to the identification of robust tumor gene expression signatures.</p> <p>Methods</p> <p>A resampling-based meta-analysis strategy, which involves the use of resampling and application of distribution statistics in combination to assess the degree of significance in differential expression between sample classes, was developed. Two independent microarray datasets that contain normal breast, invasive ductal carcinoma (IDC), and invasive lobular carcinoma (ILC) samples were used for the meta-analysis. Expression of the genes, selected from the gene list for classification of normal breast samples and breast tumors encompassing both the ILC and IDC subtypes were tested on 10 independent primary IDC samples and matched non-tumor controls by real-time qRT-PCR. Other existing breast cancer microarray datasets were used in support of the resampling-based meta-analysis.</p> <p>Results</p> <p>The two independent microarray studies were found to be comparable, although differing in their experimental methodologies (Pearson correlation coefficient, R = 0.9389 and R = 0.8465 for ductal and lobular samples, respectively). The resampling-based meta-analysis has led to the identification of a highly stable set of genes for classification of normal breast samples and breast tumors encompassing both the ILC and IDC subtypes. The expression results of the selected genes obtained through real-time qRT-PCR supported the meta-analysis results.</p> <p>Conclusion</p> <p>The proposed meta-analysis approach has the ability to detect a set of differentially expressed genes with the least amount of within-group variability, thus providing highly stable gene lists for class prediction. Increased statistical power and stringent filtering criteria used in the present study also make identification of novel candidate genes possible and may provide further insight to improve our understanding of breast cancer development.</p

A multiplex primer design algorithm for target amplification of continuous genomic regions

Abstract Background Targeted Next Generation Sequencing (NGS) assays are cost-efficient and reliable alternatives to Sanger sequencing. For sequencing of very large set of genes, the target enrichment approach is suitable. However, for smaller genomic regions, the target amplification method is more efficient than both the target enrichment method and Sanger sequencing. The major difficulty of the target amplification method is the preparation of amplicons, regarding required time, equipment, and labor. Multiplex PCR (MPCR) is a good solution for the mentioned problems. Results We propose a novel method to design MPCR primers for a continuous genomic region, following the best practices of clinically reliable PCR design processes. On an experimental setup with 48 different combinations of factors, we have shown that multiple parameters might effect finding the first feasible solution. Increasing the length of the initial primer candidate selection sequence gives better results whereas waiting for a longer time to find the first feasible solution does not have a significant impact. Conclusions We generated MPCR primer designs for the HBB whole gene, MEFV coding regions, and human exons between 2000 bp to 2100 bp-long. Our benchmarking experiments show that the proposed MPCR approach is able produce reliable NGS assay primers for a given sequence in a reasonable amount of time

Analysis of global microRNAome profiles of Caenorhabditis elegans oocytes and early embryos

One of the most complex cell transformations in biology is the remodeling of a fertilized oocyte into a totipotent zygote. There is no transcription during this event, and therefore mRNAs and proteins accumulated in the oocyte during oogenesis are utilized until zygotic genome activation. In order to differentiate into somatic cells, the embryo must erase the totipotency signature coming from the oocyte cytoplasm in the somatic blastomeres. In this study, the microRNAome profiles of oocytes and early embryos before and after zygotic genome activation were identified. By using next-generation high-throughput pyrosequencing and miRNA microarray techniques, miRNAome profiles of Caenorhabditis elegans oocytes (mitotic and meiotic) and early embryos before (2-blastomere stage) and after (8-blastomere stage) zygotic genome activation were generated. Besides observing results similar to those of previous reports, new miRNAs were identified whose expression levels changed during this transformation. After selection and polymerase chain reaction validation of the candidate miRNAs, downstream targets were identified by using bioinformatic tools and they were subjected to pathway analysis. Further analysis of the identified miRNAs in this study may provide a better understanding of the regulation of early embryonic development, germline-soma differentiation, oocyte-embryo transition, and maintenance of totipotency status

Demographics of patients with heart failure who were over 80 years old and were admitted to the cardiology clinics in Turkey

WOS: 000468584300005PubMed ID: 30930455Objective: Heart failure (HF) has a high prevalence and mortality rate in elderly patients; however, there are few studies that have focused on patients older than 80 years. The aim of this study is to describe and compare the age-specific demographics and clinical features of Turkish elderly patients with HF who were admitted to cardiology clinics. Methods: The Epidemiology of Cardiovascular Disease in Elderly Turkish population (ELDER-TURK) study was conducted in 73 centers in Turkey, and it recruited a total of 5694 patients aged 65 years or older. In this study, the clinical profile of the patients who were aged 80 years or older and those between 65 and 79 years with HF were described and compared based on the ejection fraction (EF)-related classification: HFrEF and HFpEF (is considered as EF: >= 50%). Results: A total of 1098 patients (male, 47.5%; mean age, 83.5 +/- 3.1 years) aged 80 years and 4596 patients (male, 50.2 %; mean age, 71.1 +/- 4.31 years) aged 65-79 years were enrolled in this study. The prevalence of HF was 39.8% for patients who were >= 80 years and 27.1% for patients 65-79 years old. For patients aged >= 80 years with HF, the prevalence rate was 67% for hypertension (HT), 25.6% for diabetes mellitus (DM), 54.3% for coronary artery disease (CAD), and 42.3% for atrial fibrilation. Female proportion was lower in the HFrEF group (p=0.019). The prevalence of HT and DM was higher in the HFpEF group (p= 80 years with HFrEF (p<0.01). Conclusion: HF is common in elderly Turkish population, and its frequency increases significantly with age. Females, diabetics, and hypertensives are more likely to have HFpEF, whereas CAD patients are more likely to have HFrEF.Turkish Society of CardiologyThis study was supported by Turkish Society of Cardiology

Demographics of patients with heart failure who were over 80 years old and were admitted to the cardiology clinics in Turkey

Objective: Heart failure (HF) has a high prevalence and mortality rate in elderly patients; however, there are few studies that have focused on patients older than 80 years. The aim of this study is to describe and compare the age-specific demographics and clinical features of Turkish elderly patients with HF who were admitted to cardiology clinics. Methods: The Epidemiology of Cardiovascular Disease in Elderly Turkish population (ELDER-TURK) study was conducted in 73 centers in Turkey, and it recruited a total of 5694 patients aged 65 years or older. In this study, the clinical profile of the patients who were aged 80 years or older and those between 65 and 79 years with HF were described and compared based on the ejection fraction (EF)-related classification: HFrEF and HFpEF (is considered as EF: >= 50\%). Results: A total of 1098 patients (male, 47.5\%; mean age, 83.5 +/- 3.1 years) aged 80 years and 4596 patients (male, 50.2 \%; mean age, 71.1 +/- 4.31 years) aged 65-79 years were enrolled in this study. The prevalence of HF was 39.8\% for patients who were >= 80 years and 27.1\% for patients 65-79 years old. For patients aged >= 80 years with HF, the prevalence rate was 67\% for hypertension (HT), 25.6\% for diabetes mellitus (DM), 54.3\% for coronary artery disease (CAD), and 42.3\% for atrial fibrilation. Female proportion was lower in the HFrEF group (p=0.019). The prevalence of HT and DM was higher in the HFpEF group (p<0.01), whereas CAD had a higher prevalence in the HFrEF group (p=0.02). Among patients aged 65-79 years, 43.9\% (548) had HFpEF, and 56.1\% (700) had HFrEF. In this group of patients aged 65-79 years with HFrEF, the prevalence of DM was significantly higher than in patients aged >= 80 years with HFrEF (p<0.01). Conclusion: HF is common in elderly Turkish population, and its frequency increases significantly with age. Females, diabetics, and hypertensives are more likely to have HFpEF, whereas CAD patients are more likely to have HFrEF