TRICON: Next-Generation Sequencing Can Detect Ebola in Seven Minutes, Raw Data in Under 10

TRICON: Next-Generation Sequencing Can Detect Ebola in Seven Minutes, Raw Data in Under 10
February 17, 2015
By Riley McDermid, BioSpace.com Breaking News Sr. Editor

Metagenomic next-generation sequencing is showing “incredible” promise at rapidly producing clinical diagnoses for virulent diseases such as Ebola and Lyme, Charles Chiu, a medical doctor and associate professor in Laboratory Medicine and Medicine, Infectious Diseases at the University of California, San Francisco, said Tuesday.

“The Oxford Nanopore MinION is able to detect Ebola virus in seven minutes with metagenomic NGS," said Chiu. Chiu said UCSF’s own Sequence-based Ultra-Rapid Pathogen Identification (SURPI) has been similarly as fast. “SURPI optimized detection of pathogens in raw NGS read data down from days to weeks to 10 minutes.”

Chiu made the comments as part of a panel titled “Metagenomic Next-Generation Sequencing for Clinical Diagnosis of Infectious Diseases” at the 2nd International Molecular Medicine Tri-Conference, where over 3,000 attendees from 40 countries have descended upon San Francisco for a week of the latest news and advances in molecular medicine.

SURPI uses a computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data generated from clinical samples.

“SURPIviz is a cloud-based home for program, heat maps shown to help visualize likely pathogens, generate coverage map for genome,” said Chiu. “We developed SURPI to analyze millions of reads in minutes, use rapid filtering, have the tagging of metadata and the tools to visualize.”

"Metagenomic NGS is promising approach but still face regulatory and other hurdles,” said Chiu, who said he was encouraged that they have identified Leptospira using NGS, even when the “Centers for Disease Contol tests were negative on patient because validated on different strains.”

“There is a sensitivity to viruses caused by lack of enrichment, need to deplete host sequences, also limited by multiplexing,” said Chiu.

Nanapore’s MinION device is a small instrument that is compatible with consumable flow cells containing the proprietary sensor chip, Application-Specific Integrated Circuit (ASIC) and nanopores that are needed to perform a complete single-molecule sensing experiment. Users can plug it directly into a laptop or computer for real-time experimental data. It is also adaptable for DNA sequencing, protein sensing and other nanopore sensing techniques.

Regarded as an expert in the emerging field of clinical metagenomics, his research is focused on the development and validation of microarray and NGS for pathogen discovery and clinical diagnosis of infectious diseases, with over 25 patents and peer-reviewed publications.

He said Tuesday he was particularly excited by the speed of all the recent NGS technology.

“Using spike ins, you can see 100 copies/ml of HIV, 1000 copies/mo of CMV, and it can be used for testing viral loads,” said Chiu.”Most samples are body fluids, studied in CLIA lab, turnaround now 12 hours to two days, want to improve to less than eight hours. The coverage maps good for detecting recombination events.”

Hosted by the Cambridge Healthtech Institute this year’s conference will continue for six days and has a focus on Drug Discovery, Genomics, Diagnostics and Information Technology. Tri-Conference, or #TRICON, includes an expanded program with six symposia, over 20 short courses and 17 conference programs.

Over 500 speakers will participate in 400 presentations and panel discussions in programs such as Genomic Technologies for Patient Stratification and Technology-Driven Oncology Clinical Development, and symposia including New Frontiers in Gene Editing and Clinical Cancer Immunotherapy.



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