Project description:The study involves whole exome sequencing of 20 primary tumors obtained from lung squamous carcinoma patients of Indian origin. With this, we aim to describe the mutational profile of this specific subset of lung cancer patients. This knowledge will further allow us to gain an insight into potentially actionable genomic alterations prevalent in Indian lung squamous carcinoma.
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:This study involves characterization of four head and neck cancer cell lines -- NT8e, OT9, AW13516 and AW8507, established from Indian head and neck cancer patients, using SNP arrays, whole exome and whole transcriptome sequencing.
Project description:This study involves characterization of four head and neck cancer cell lines -- NT8e, OT9, AW13516 and AW8507, established from Indian head and neck cancer patients, using SNP arrays, whole exome and whole transcriptome sequencing.
Project description:This study involves characterization of four head and neck cancer cell lines -- NT8e, OT9, AW13516 and AW8507, established from Indian head and neck cancer patients, using SNP arrays, whole exome and whole transcriptome sequencing.
Project description:High-grade neuroendocrine carcinomas (NECs) of the cervix are rare, aggressive cancers accounting for about 1-1.5% of all cervical cancer. The 5-year survival is up to 36% for early-stage disease; however, the advanced-stage disease has <10% survival, with relapse rates exceeding 90%. These cancers are likely to have a vascular invasion and nodal or visceral metastasis. Unfortunately, NEC of the cervix affects young women with a median age of 37. High-grade NECs of other gynecologic origins are even rarer, share similar aggressive behavior and poor outcomes. We performed stranded paired-end RNA-seq of 13 samples, including 12 samples with matched whole exome sequencing (WES) data. Sites of origin for tumors in our cohort were the cervix (69%), ovary (19%), and endometrium (12%). The median number of prior lines of therapy was 1. Median PFS and OS were 1 and 12 months, respectively, indicating their highly lethal nature. Comparing transcriptomic profiles with TCGA cervical and ovarian cancers, chromatin assembly and nucleosome organization were the top GO functions for significantly over-expressed genes in our cohort. Remarkably, under-expressed genes in our cohort were enriched for protein modification and catabolic processes, and neutrophil-mediated immunity. Compared to small cell lung cancer (SCLC), our cohort showed highly distinct transcriptomic patterns, and represented the YAP1 high molecular subtype.
Project description:Homo sapiens fresh whole blood was infected with Candida parapsilosis. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Measurement of Homo sapiens gene expression.
Project description:Homo sapiens fresh whole blood was infected with Candida glabrata. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Measurement of Candida glabrata gene expression.
Project description:Homo sapiens fresh whole blood was infected with Candida tropicalis. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Measurement of Candida tropicalis gene expression.
