Event:

Nanopore Day, Houston

Date: Thursday 28th March 2019
Location: Houston, TX, USA

Hear from local users about their latest work using nanopore technology and the latest tech updates for Oxford Nanopore.

There is no delegate fee for this event. 

Your place at this event will be confirmed via email from events@nanoporetech.com. Completion of this form does not constitute confirmation. Spaces are limited and will be allocated on a first-come, first-served basis.

Agenda subject to change

Abstracts

Claudia Carvalho, Untangling genomic rearrangements in human diseases using long-read sequencing technology: Genomes show high level of plasticity and undergo structural changes in the form of single-nucleotide variants (SNVs) and rearrangement of DNA sequences with none, subtle or profound consequences to the organism, regardless their size. Therefore, to study human genetic diseases we need to apply molecular tools to identify an individual mutational spectrum and be able to define how the genome architecture changes upon those mutations. In my seminar, I will discuss distinct types of genomic rearrangements that cause genetic diseases with a special focus on triplications, how to detect them and what are the challenges we still face to integrate and interpret those variants in a genomic context. Importantly, we observed that complementary molecular approaches along with difference sequencing technologies can resolve rearrangement structure in complex genomic regions.

Intawat Nookaew, Inferring RNA modification and structure from native RNA sequence: Genome-wide expression analysis has been widely used as a versatile tool for deep characterization and better understanding of cellular processes at transcriptional level. The traditional RNA-seq relies on the DNA sequencing of complementary DNA (cDNA) obtained from reverse transcription and PCR amplification, eliminating the modification events of RNA molecule. With the Oxford Nanopore Technology, direct sequencing of full-length transcript is possible. This enables a quick methodology for genome-wide expression analysis that preserve information of RNA modification events. An approach to decode epitranscriptional landscape from the distinction of errors between the native RNA sequence and cDNA will be presented.

Harsha Vardhan Doddapaneni, Building ‘Super Genomes’: Foundational endeavours such as the Human Genome Project and 1000 Genomes Project paved way for even larger sequencing projects (>10k to >100k samples) focusing on population genomics and disease cohort studies. Short-read sequencing has been predominantly chosen for data generation. However, this approach alone is insufficient for comprehensive discovery of genomic variants and therefore, a framework for improving quality of existing short-read genome data by integrating long/link reads sequencing is needed. We pursued a pilot project with the ultimate aim to generate ‘super genomes’ i.e. whole genome sequences that fully represent all the genome – and all allelic variants. We therefore have the specific goals of extending contiguity, gathering phasing information and gaining resolution into complex alleles.

James Blachly, Real-time Leukemia Diagnostics with Nanopore: Acute Myeloid Leukemia (AML) is the most common leukemia in adults and, unlike almost all other cancers, diagnosis and initiation of treatment often constitute a medical emergency. The mainstay of treatment for 40 years has been very intensive chemotherapy that destroys leukemia and normal bone marrow alike, leading to many weeks of hospitalization, infection risks, and highly variable outcome. In 2017-2019, the US FDA approved 8 new targeted therapies for AML, 4 of which are effective only in the presence of specific genetic mutations. Despite the need for rapid molecular diagnosis and treatment initiation, current sequencing techniques typically require a week or more, even at major academic medical centers. We are developing Nanopore technology and infrastructure to bring real-time, same-day molecular diagnostics to every oncology office.

Sarah Wallace, In Under 32 Orbits: MinION-based Microbial Monitoring of the International Space Station: The MinION has made in situ sequencing feasible in remote locations. Following our 2016 demonstration of its high performance off planet with Earth-prepared samples, we developed and tested an end-to-end, sample-to-sequencer process that could be conducted entirely on the International Space Station. An initial experiment to demonstrate the process was performed with a microbial mock community standard. The DNA from the eight bacterial constituents of the microbial community standard were accurately identified to the species level. Additionally, the species-level percent identifications were similar between flight and ground experiments. To validate the process beyond DNA that was launched, bacterial cells were collected from a NASA Environmental Health Systems Surface Sample Kit contact slide that had been previously collected from and cultured on the ISS. Bacterial colonies for identification were labelled and small portions were introduced to the sequencing process. Return of the contact slide to the ground allowed for standard laboratory processing for bacterial identification. The identifications obtained on the ISS match to those determined on the ground to the species level. This marks the first ever identification of microbes entirely off Earth. Expanding beyond the need to first culture the microbes, a culture-independent, swab-to-sequencer investigation is currently underway to further characterize the microbiome of the ISS. These validated processes could be used for in-flight microbial monitoring, diagnosis of infectious disease in a crewmember, and as a research platform for investigators around the world.

S. Wesley Long, Whole-genome Sequencing of a Human Clinical Isolate of emm28 Streptococcus pyogenes Causing Necrotizing Fasciitis Acquired Contemporaneously with Hurricane Harvey: We discovered an emm28 Streptococcus pyogenes isolate causing necrotizing fasciitis in a patient exposed to the floodwaters of Hurricane Harvey in the Houston, TX, metropolitan area in August 2017. The Oxford Nanopore MinION instrument provided sufficient genome sequence data within 1 h of beginning sequencing to close the genome.

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