Answering fundamental questions through the use of genome sequencing: an
example each from medicine and agriculture
Dr. Binay Panda
Ganit Labs, Bio-IT Centre, Inst. of Bioinformatics & Applied Biotechnology, Bangalore, INDIA
Room 333 WERC (Fishbowl)*
The field of DNA sequencing has attracted much attention from all corners, starting from innovators, investors and scientists working in multiple fields. The development in the field holds tremendous potential to change the way we live, to revolutionize medicine, agriculture and finding solutions in the alternate energy space. With the advent of newgeneration sequencing technologies, biology has changed forever. With the chemistry to generate sequence data using high-throughput assays largely taken care of, the challenge is shifted from ‘data generation’ phase to ‘data management, analysis and interpretation’ phase. I shall talk about our work using genome sequencing and how we are beginning to unravel fundamental questions in both medicine and agriculture.
Head and neck squamous cell carcinoma is the sixth most common cancer in the world, with a mortality rate of nearly 50%. Oral cancer is the most common subtype of head and neck cancers in human, with a worldwide incidence in greater than 300,000 cases. India has one of the highest incidence and mortality of oral cancers in the world. By using newgeneration genome sequencing, we have analyzed genomes, exomes and transcriptomes of oral tongue tumors and their associated potentially malignant lesions from the same patients. Pipeline tools were optimized to attain significant sensitivity in detecting SNVs, copy number alterations and other structural variations. I plan to discuss about our findings on novel somatic SNVs, indels, structural variations, novel transcripts and epigenetic changes in oral tongue tumor.
India is home to plenty of ethno-botanical knowledge base derived from many plant species. Despite this, modern scientific know-how on many of these wonder species is lacking. Azadirachta indica, neem, is one such species that is a unique, versatile and important. Neem oil and its derivatives support multiple cottage industries in India and is one of the important contributors to the country’s bio-economy. The neem tree is also one of the most intensively studied sources for natural products. Due to its wide array of applications, azadirachtin, a terpenoid derived from neem seed kernel, has been the subject of intense research for decades. Although, efforts have been successful in the past towards synthesizing azadirachtin in the lab, the commercial viability of the labsynthesized azadirachtin remains low. Despite the wealth of information, there is no sequence information available on its genome and/or transcriptomes. I shall discuss our work on neem genome sequencing and study of the plant’s transcriptomes that is the first step towards understanding of the diverse pathways and enzymes involved in the synthesis of terpenoids. Our work may pave way(s) for mass-production of these useful terpenoids and other chemicals that could support sustainable agriculture in resource-poor settings.
BIO: Binay Panda: Binay read biochemistry at the University of Oxford, UK where he got his doctoral degree in virus biology. He subsequently joined the Scripps Research Institute, La Jolla, California as American Cancer Society postdoctoral fellow. Before returning to India to set up Ganit Labs, he co-founded a molecular diagnostics startup company in the San Francisco bay area with focus on early detection of cancer using genetic markers. Prior to that, he worked at the genomics firm Affymetrix both at Santa Clara, California and Tokyo, Japan where he built the firm’s scientific operations. Binay was also a visiting researcher of genome science at the University of Tokyo, Japan. Binay is a visiting Professor at the Mazumdar Shaw Cancer Centre, Narayana Hrudayalaya Health City, Bangalore. Binay is primarily interested in studying genes and genomes.
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