Identification of Differentially Expressed Genes in Human Bladder Cancer using Oligonucleotide Microarray

Bladder cancer is one of the most common malignancies in developed countries while transitional cell carcinomas (Tee) are the origin of more than 90% of diagnosed bladder cancers. Patients diagnosed with bladder cancer basically belong to two clinically distinct groups, namely non-muscle invasive (which are papillary pattern) and muscle invasive (which are solid). These carcinomas pose the greatest clinical problems due to the high recurrence of non-muscle invasive tumors even after transurethral resection of the tumors. At present, there are no clinically useful markers available for identifying bladder cancer patients with a high risk of disease recurrence or progressIon. Multiple molecular events take place when normal epithelial cells are transformed into tumor tissues. These can now be monitored simultaneously, by using oligonucleotide rnicroarrays and the expression patterns of three different grades of Tee namely Tee WHO Grade I, Tee WHO Grade II and Tee WHO Grade III (according to WHO classification) can be established. In this study, individual cell suspensions were prepared from bladder tumor biopsies. Pools of cells were also prepared from noncancerous tissues. Total RNA was isolated and reverse transcribed into eDNA. In vitro transcription into cRNA was carried out with the incorporation of Cy3 and Cy5 dyes. Labeled cRNA probes were co-hybridized to the microarray slide containing 1,853 cancer related genes. Following hybridization procedure, scanning of the array slides was carried out to identify the gene expression levels in each of the sample investigated. To determine the co-expression patterns displayed between different stages of the bladder cancer, hierarchical clustering analysis that group tumors according to similarity in their expression profile was used. Hierarchical clustering demonstrated an unambiguous separation of TCC WHO Grade I from Grades II and III of these urothelial tumors. In addition, based on the gene function, nine clusters of genes were identified. These genes are associated with cell adhesion molecules, protein synthesis, oncogenes, apoptosis markers, growth factors, immunology, cell cycle regulators, transcription factors and angiogenesis. Fold-change analysis of gene expression revealed 106, 49 and 51 genes that are over-expressed and 13, 186 and 132 that are suppressed in TCC Grades I, II and III, respectively. A gene is considered differentially expressed if its relative expression is two-fold or greater. Because of the inherent limitations in the reliability of microarray, genes identified as differentially expressed were validated with a PCR-based method. Real-Time peR was able to confirmed 75% of the microarray data. These results were in concordance to that previously reported. This study indicates that gene expression patterns can be identified in bladder cancer by combining oligonucleotide arrays and Real-Time PCR analysis. These data combined with other data from similar research, could provide insights into the extent of expression differences underlying malignancy of the bladder cancer and reveal genes that may prove useful as diagnostic or prognostic markers

The first Malay database toward the ethnic-specific target molecular variation

BACKGROUND:The Malaysian Node of the Human Variome Project (MyHVP) is one of the eighteen official Human Variome Project (HVP) country-specific nodes. Since its inception in 9(th) October 2010, MyHVP has attracted the significant number of Malaysian clinicians and researchers to participate and contribute their data to this project. MyHVP also act as the center of coordination for genotypic and phenotypic variation studies of the Malaysian population. A specialized database was developed to store and manage the data based on genetic variations which also associated with health and disease of Malaysian ethnic groups. This ethnic-specific database is called the Malaysian Node of the Human Variome Project database (MyHVPDb). FINDINGS:Currently, MyHVPDb provides only information about the genetic variations and mutations found in the Malays. In the near future, it will expand for the other Malaysian ethnics as well. The data sets are specified based on diseases or genetic mutation types which have three main subcategories: Single Nucleotide Polymorphism (SNP), Copy Number Variation (CNV) followed by the mutations which code for the common diseases among Malaysians. MyHVPDb has been open to the local researchers, academicians and students through the registration at the portal of MyHVP ( http://hvpmalaysia.kk.usm.my/mhgvc/index.php?id=register ). CONCLUSIONS:This database would be useful for clinicians and researchers who are interested in doing a study on genomics population and genetic diseases in order to obtain up-to-date and accurate information regarding the population-specific variations and also useful for those in countries with similar ethnic background

Global Globin Network Consensus Paper: Classification and Stratified Roadmaps for Improved Thalassaemia Care and Prevention in 32 Countries

The Global Globin Network (GGN) is a project-wide initiative of the Human Variome/Global Variome Project (HVP) focusing on haemoglobinopathies to build the capacity for genomic diagnosis, clinical services, and research in low- and middle-income countries. At present, there is no framework to evaluate the improvement of care, treatment, and prevention of thalassaemia and other haemoglobinopathies globally, despite thalassaemia being one of the most common monogenic diseases worldwide. Here, we propose a universally applicable system for evaluating and grouping countries based on qualitative indicators according to the quality of care, treatment, and prevention of haemoglobinopathies. We also apply this system to GGN countries as proof of principle. To this end, qualitative indicators were extracted from the IthaMaps database of the ITHANET portal, which allowed four groups of countries (A, B, C, and D) to be defined based on major qualitative indicators, supported by minor qualitative indicators for countries with limited resource settings and by the overall haemoglobinopathy carrier frequency for the target countries of immigration. The proposed rubrics and accumulative scores will help analyse the performance and improvement of care, treatment, and prevention of haemoglobinopathies in the GGN and beyond. Our proposed criteria complement future data collection from GGN countries to help monitor the quality of services for haemoglobinopathies, provide ongoing estimates for services and epidemiology in GGN countries, and note the contribution of the GGN to a local and global reduction of disease burden