Stephanie Renzullo Research

Stephanie Renzullo’s Conference Presentations Related to MinION Access Program (MAP)

2015 Beta Beta Beta NE-1 Regional Conference; Hosted by the Rho Zeta Chapter

April 25, 2015

stephanie-renzullo

Student Oral Presentation

Optimization of the MinION DNA Sequencing Device for Future Applications in Understanding the Role of Human Endogenous Retroviruses in Human Disease

*Stephanie Renzullo and Derek Dube, Ph.D., Rho Zeta, University of Saint Joseph

DNA sequencing has revolutionized the biological sciences, however current methods are time consuming, require large equipment, and have limitations in read length and/or throughput. The MinION is a new, miniaturized platform for DNA sequencing that has the power to sequence DNA molecules of any length in a single read, in near real-time. While requiring optimization, this platform has the potential to overcome the obstacles of read assembly and differentiation of extremely similar genomes. Here, we present our attempts to examine and improve the MinION’s base calling accuracy as part of the MinION Access Program. To achieve this, we prepared viral plasmids with known DNA sequences, ran these samples on the MinION device altering specific parameters and utilizing different generations of the technology, and compared the MinION output to the known sequence. Our initial studies show promising improvements in the base calling accuracy compared to early versions of the technology, but indicate certain obstacles that still need to be overcome.  If the MinION platform can be further optimized, we will utilize it to examine the endogenous retroviral sequences in individuals with lymphoma, to determine if these viruses have an active role in the development or exacerbation of the disease.

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2015 USJ Symposium Day Oral Presentation

April 2015

Analyzing the Constituent Members of the Human Endogenous Retrovirus Type K (HML-2) Family Activated in Lymphoma Patients through the Optimization and Development of the MinION Sequencing Platform

*Stephanie Renzullo and Derek Dube, Ph.D., Rho Zeta, University of Saint Joseph

DNA sequencing can provide invaluable information in the fields of biology and human health. Previous methods of DNA sequencing such as Sanger sequencing and deep sequencing have revolutionized the field, however these methods are time consuming and require large, expensive equipment. The MinION is a newly developed, miniaturized method for DNA sequencing that has the power to sequence DNA molecules of any length in a single read. While still requiring optimization, this has the potential to overcome the obstacles of read assembly and allow for extremely similar organisms to be confidently sequenced for the first time. Viral elements including Human Endogenous Retroviruses (HERVs) comprise at least 8% of the human genome, but are now mostly inert due to mutations and deletions. The HERV-K family of viruses is the most recent family to enter the human genome, can be upwards of 90% similar in their genomic sequences, and HERV-K activation has been associated with certain cancers. Here, we hypothesize that the HERV-K family of viruses may play a role in causing, sustaining, or perpetuating human lymphoma. Knowing the genomic sequence of these viruses may improve our understanding of the mechanisms of cancer, leading to better treatments and better preventions. To test our hypothesis, our study will occur in two aims. First, we will attempt to optimize the MinION sequencing platform. Secondly, we will use this technology to directly sequence and analyze the HERV-K family members present in the plasma of human lymphoma patients.  Here, we present work focused on Aim 1.

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USJ Symposium Day Poster Presentation

April 14, 2016

Optimization and Development of the MinION Sequencing Platform to Analyze and Sequence Viruses Present in the Local Environment

Stephanie Renzullo and Derek Dube, Ph.D., Rho Zeta, University of Saint Joseph

DNA sequencing methods can provide invaluable information for the fields of biology and human health. However, most sequencing methods are time consuming and require large, expensive equipment. The MinION is a new method for DNA sequencing that has the power to sequence DNA molecules of any length in a single read. While still requiring optimization, this technology has the potential to be revolutionary, overcoming the obstacles of read assembly, and allowing for organisms with extremely similar genomes to be confidently sequenced for the first time.  The goals of this study are to aid in the optimization of this new technology and then assess its efficacy in an examination of the viruses present within local environmental waters. Knowing which viruses humans may be being exposed to in environments, like our drinking waters and streams, can serve to inform policy decisions and create a healthier community. We hypothesize that after optimization, the MinION will be an ideal technology for assessing viral presence in environmental samples due to its ability to sequence an entire genome in a single read, and numerous genomes essentially simultaneously. The sequenced viral genomes will then be compared to known viral sequences to determine the viral identity and assess the health risk associated with populations being exposed to those viruses. Our work over the past year and a half, in collaboration with bioinformaticians at the University of Michigan, shows promising improvements to the MinION’s base-calling accuracy, and we are currently conducting further experiments using newly designed algorithms to improve accuracy further and assess the viral communities.

Stephanie Renzullo’s Symposium Day Poster (Optimization and Development of the MinION Sequencing Platform to Analyze and Sequence Viruses Present in the Local Environment) was an “award winner.”

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