SCGPM Seminar: Chandra Pedamallu, Sanofi

SCGPM Seminar: Chandra Pedamallu, Sanofi

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James H. Clark Center

318 Campus Dr

Seminar Room S360

Stanford, CA 94305

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Patho-genomics : Computational methods for pathogen identification in human diseases

Chandra Sekhar Pedamallu, Sanofi

Monday, August 14th
12:00N - 1:00PM
Clark S360
Lunch provided - please register

ABSTRACT: An estimated 15-20% of all malignancies are caused by infectious agents, such as human papillomavirus (HPV), Epstein-Barr virus, or Helicobacter pylori. The development of massively parallel next generation sequencing technologies affords unique opportunities for pathogen discovery (e.g. Merkel cell polyomavirus). In this talk, I will describe our methods for novel pathogen identification in human diseases using a computational subtraction approach called PathSeq. I will also describe how PathSeq is evolved over years. This method has been successfully used to identify significant enrichment of Fusobacterium species in colorectal carcinomas compared to non-neoplastic colon tissue from the same patients. We have also discovered a novel bacterium, Bradyrhizobium enterica, associated with cord transplant related colitis syndrome. In addition, our methods have been applied for investigating novel genomic relationships between HPV and squamous cell carcinomas of the cervix. Future work will focus on improving the efficiency and scalability of our methods as well as their potential applications for point-of-care diagnostics.

BIO: Chandra Sekhar Pedamallu obtained his B.Tech (Mechnical Engineering) at Nagarjuna University, India, M.Tech (Industrial Management) at Indian Institute of Technology Madras, India his Ph.D (System Engineering) from Nanyang Technological University, Singapore. Chandra did his Postdoctoral Fellowship from Bioinformatics Department, New England Biolabs, USA. He worked at Dr. Matthew Meyerson’s lab at Dana-Farber Cancer Institute / The Broad Institute/ Harvard Medical School as Sr. Computational Biologist for 6 years. During his tenure at Meyerson Lab, he worked /led on several pathogen discovery projects in various disease areas which includes Cancer, Autoimmune diseases, Crohns, and etc. He is also involved in several cancer genome analysis projects (calling somatic mutation, quantification of expression data, etc). He is an expert in developing large scale analysis pipeline, and analysis of large scale data. Chandra also involved in analysis of TCGA, SIGMA and other large scale studies. Currently, Chandra is working as Next Generation Sequencing (NGS) Pipelline Lead at Oncology, Sanfoi. At Sanofi, he leads a group meant for developing NGS analysis and infrastructure for large scale sequencing project. In addition, Chandra co-authored 75 manuscripts in various prestigious journals includes Cell, Nature, NEJM, and etc.

ABOUT THE SCGPM: The Stanford Center for Genomics and Personalized Medicine (SCGPM) seeks to advance genomic technology so that someday both genetic and molecular profiling will become powerful and routine tools for predicting disease risk and monitoring and treating a wide range of pathologies. Towards this mission, the SCGPM serves to centralize and develop collaborative intellectual and technological resources that promote genomic research and analysis, predict drug response, educate physicians, and examine the ethics of personalized medicine. This includes large basic science projects such as ENCODE that decipher the human genome as well as clinical research projects such as the sequencing of cancer genomes and individuals with inherited diseases. Through these efforts, the Center aims to bring genomics to the clinic.

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The SCGPM supports the Genetics Bioinformatics Service Center, a SoM core facility for genomics research that provides a secure on-premise computing infrastructure, Google Cloud gateway, and bioinformatics consulting. The facilities are available to all faculty members at Stanford University.

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