Project description:Cancer is predominantly a somatic disease. A mutant allele found in cancer cell genome is considered somatic when it is absent in paired normal genome and dbSNP, the most comprehensive public SNP database. However, dbSNP inadequately represents several non-Caucasian populations including that from the Indian subcontinent, posing a limitation in cancer genomic analyses of data from these populations. We present TMC-SNPdb, as the first open source freely accessible (through ANNOVAR), flexible and upgradable SNP database from whole exome data of 62 normal samples derived from cancer patients of Indian origin, representing 114,309 unique germline variants. TMC-SNPdb is presented with a companion subtraction tool that can be executed with command line option or an easy-to-use graphical user interface (GUI) with the ability to deplete additional Indian population specific SNPs over and above that possible with dbSNP and 1000 Genomes databases. Using an institutional generated whole exome data set of 132 samples of Indian origin, we demonstrate that TMC-SNPdb reduced 42%, 33% and 28% false positive somatic events post dbSNP depletion in Indian origin tongue, gallbladder, and cervical cancer samples, respectively. Beyond cancer somatic analyses, we anticipate utility of TMC-SNPdb in several Mendelian germline diseases.
Project description:We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3’ and/or 5’ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5’ differences and in support of this we report that a 5’ isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5’ isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes
Project description:Gene expression profiling of immortalized human mesenchymal stem cells with hTERT/E6/E7 transfected MSCs. hTERT may change gene expression in MSCs. Goal was to determine the gene expressions of immortalized MSCs.
