Whole genome mapping: a new paradigm for sequence assembly and genomic characterization

Erin Newburn, Applications Scientist, OpGen, Inc.
Thursday, February 16, 2012, 12:00 PM to 1:00 PM
Location: 240 Physical Sciences Building
Hosted By Nader Pourmand

The Argus™ Whole Genome Mapping System uses large single-molecule reads of 150 Kb to 2.5 Mb to produce de novo (without any reference) high resolution complete whole-genome, ordered restriction maps that can be used for strain typing, comparative genomics, and whole-genome sequence assembly of microorganisms. Whole Genome Mapping was recently used to respond to and analyze the Escherichia coli O104:H4 German outbreak where it was able to identify clonality of the outbreak, differentiate it from prior outbreak isolates, infer genetic content such as virulence genes, and assist in whole-genome sequence assembly by providing a single scaffold for the chromosome. Argus customers are using the technology to investigate the genetic basis of antimicrobial resistance and antigenic variation in parasites such as Plasmodium falciparum, the causative agent of malaria, by looking for genetic events such as insertions, deletions, inversions, and copy-number variants (CNVs). A recently accepted publication by Riley et al. in the Malaria Journal shows how Whole Genome Mapping can be used to identify novel insertions associated with antibiotic resistance and to identify CNVs that sequencing alone is missing. OpGen recently announced joint efforts with large whole-genome sequencing institutions such as BGI and Sanger Wellcome Trust Institute to expand the use of Whole Genome Mapping for sequence finishing of human, plant, and animal genomes using the Argus System. The large genome application, Genome Builder, uses the large single-molecule reads of mapping as well as NextGen sequencing data in a hybrid approach to produce superscaffolds that significantly improve the overall quality of whole-genome sequencing projects by increasing N50 scores and decreasing the total number of scaffolds in the project.  Both the goat and Chinese flowering plum (Prunis muni) DNA sequence assemblies showed significant improvement after utilizing Genome Builder. The large single-molecule reads from Whole Genome Mapping provide a type of data that second- and third-generation sequencing technologies cannot achieve.

Erin Newburn joined OpGen as an application scientist in June 2011. She has over 10 years of research expertise in the areas of molecular biology, genetics, and biotechnology. She has the responsibility for providing technical expertise regarding OpGen technologies internally and externally to OpGen. Newburn did her postdoctoral training at the National Institute of Mental Health in Bethesda, MD, in the Clinical Brain Disorders Branch. She investigated candidate susceptibility genes for major psychiatric illnesses including schizophrenia and bipolar disorder. Newburn received her PhD from the Ohio State University in Integrated Biomedical Science as a Presidential Fellow. At OSU, she investigated the neurotrophic properties of a potential drug therapy for Parkinson’s Disease in the MPTP mouse model. As both a graduate teaching assistant and a Preparing Future Faculty Fellow, she received many training awards including the Society for Neuroscience Women in Neuroscience award. She received her Master’s degree from Wright State University in 2003 working on molecular identification markers of macroinvertebrates for use as ecoindicators of water integrity, and sh received her BS from Muskingum College in Biological and Environmental Science in 1999.