Road to the Biomarker discovery via NGS-based transcriptomics: a case study
ABSTRACT: One of the key reasons for a slower rate of discovery of new diagnostic or therapeutic molecules, in recent years, is lack of attention to thorough screening and identification of target molecules. If researchers do not identify the right target molecule it can result in failure at later stages of R & D or during clinical trials.
Exploring gene expression profiles is key to biomarker discovery, which in turn is crucial for diagnostics, prognostics, and therapeutics. With the advent of modern techniques such as the microarrays, NGS, and mass spectrophotometry, and parallel bio-IT approaches, there is a higher potential to generate more data and a more meaningful short-listing of potential target molecules. RNA-sequencing particularly offers hope to identify key transcript- and/or protein-isoforms associated with diseases. But the data need to be carefully analyzed and interpreted. This has been a non-obvious challenge. There seems to be a tremendous gap between general biologists, health professionals, molecular biologists, pharmacologists and computational biologists/bioinformaticians. My team has been doing some research in meeting such challenges, at IBAB (www.ibab.ac.in).We earlier developed a simple yet effective computational meta-analysis method. We also carefully compiled public transcriptomic data and developed a few software and databases for better analysis and interpretation of the data. Using the newly developed methods, we identified a list of genes and specific alternatively spliced forms of transcripts, which may be important for a type of male infertility (non-obstructive azoospermia – which we think is a good model to work towards better male contraceptives as well).Then they performed their own RNA-sequencing using clinical samples and validated the observations. are currently performing more data analysis, particularly in terms of network analysis, and pick crucial biomarker-candidates for non-obstructive azoospermia as well as a few other disease conditions, such as lung and breast cancer, as well.
Meet Dr. Kshitish Acharya, Scientist, IBAB at Emerging Role of Next Generation Sequencing in Clinical Genomics on November 01 in Mumbai.#NGSCG#GENOMICS2017