Sequencing

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11th Annual <strong>Sequencing</strong>, Finishing, and Analysis in the Future Meeting GENEIOUS: A BIOINFORMATICS PLATFORM FOR BIOLOGISTS Thursday, 2nd June 17:05 La Fonda Ballroom Tech Talk (TT‐2.06) Christian Olsen, Helen Shearman, Richard Moir, Matt Kearse, Sidney Markowitz, Jonas Kuhn, Sebastian Dunn, Alex Cooper Biomatters, Inc. Biomatters’ Geneious is a bioinformatics software platform which allows researchers the use of industry leading algorithms for their genomic and protein sequence analyses. Geneious offers a comprehensive suite of functions, including peer‐reviewed tools that enable researchers to be more efficient with their bioinformatic workflows. Geneious is comprised of an extensive tool suite for nextgeneration sequence analysis, molecular cloning, chromatogram assembly, and phylogenetics. This major version release includes tools for RNAseq read mapping and expression analysis, support for scaffolding with de novo assemblies, Golden Gate assembly, and an updated CRISPR tool. Researchers may also choose to extend Geneious with new plugins like Blast2GO (Gene Ontology enrichment), FreeBayes variant finder, Augustus (gene prediction), and BBTools (NGS data QC). Additional features include the 16S Biodiversity tool and Sequence Classifier plugin. The 16S Biodiversity tool identifies high‐throughput 16S rRNA amplicons from environmental samples using the RDP database, and visualizes biodiversity as an interactive chart using a secure web viewer. The Sequence Classifier plugin taxonomically classifies an organic sample by how similar its DNA is to your own database of known sequences using a BLAST‐like algorithm with multiple‐loci and phylogenetic trees to assist with an unknown identification. Geneious easily affords real‐time dynamic interaction with sequence data and empowers biologists to produce stunning publication quality images to increase the visibility of their research. By utilizing Geneious, biologists can quickly streamline their sequence analysis workflows. This tech talk aims to present new features and benefits of the highly‐integrated Geneious sequence analysis platform. 123
11th Annual <strong>Sequencing</strong>, Finishing, and Analysis in the Future Meeting ARTEMISININ DRUG RESISTANCE WORKFLOW FOR PLASMODIUM FALCIPARUM Thursday, 2nd June 17:15 La Fonda Ballroom Tech Talk (TT‐2.07) Christian Olsen 1 , Eldin Talundzic 2 , Helen Shearman 1 1 Biomatters, Inc., 2 Centers for Disease Control and Prevention About 3.2 billion people are at risk of malaria. In 2015, there were ~214 million malaria cases and an estimated 438,000 malaria deaths. Young children, pregnant women and non‐immune travellers from malaria‐free areas are particularly vulnerable to the disease when they become infected. Falciparum malaria is the most lethal human malaria and is transmitted by the Anopheles mosquito. The primary methods for combating malaria are antimalarial treatments like artemisinin and control of the Anopheles mosquito vector. Artemisinin is derived from the sweet wormwood plant Artemisia annua. Artemisinin based compounds are used with other classes of antimalarials to form artemisinin‐based combination therapies (ACTs) which are, currently, the best available treatment for falciparum malaria worldwide. The recent emergence of artemisinin resistance in the Greater Mekong sub‐region poses a major threat to the global effort to control falciparum malaria. Tracking the spread and evolution of artemisininresistant parasites is critical in aiding efforts to contain the spread of drug resistance. This poster describes a workflow, which utilizes a Kelch‐13 (K13) molecular marker, previously identified to be associated with artemisinin resistance. Kelch proteins are a group of proteins that contain multiple Kelch motifs that form a ‐propeller tertiary structure. Kelch‐repeat ‐propellers are generally involved in protein‐protein interactions, though the large diversity of domain architectures and limited sequence identity between kelch motifs make characterization of the kelch superfamily difficult. A total of 417 patient samples from the year 2007, collected during malaria surveillance studies across ten provinces in Thailand, were genotyped for the K13 marker. The targeted gene is amplified with PCR and sequenced using Sanger sequencing. The sequences obtained from samples are compared to a reference sequence and the SNP combinations are examined. This pipeline is implemented in Geneious and was used to identify and track Artemisinin resistance in Thailand. 124
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