Trainee Paper Spotlight: April 27, 2016
Trainee Author: Alexis Norris, PhD
Johns Hopkins University
Department of Pathology and Oncology
(Photo courtesy of Alexis Norris, PhD)
Norris, Alexis et al. Nanopore Sequencing Detects Structural Variants in Cancer. Cancer Biology & Therapy, Volume 17, Issue 3, 246-253 (2016).
This article was selected for the April Trainee Paper Spotlight because the authors present promising findings illustrating how nanopore sequencing can be used to identify well-characterized structural variants, which are difficult to detect through second generation sequencing. Nanopore sequencing is a relatively new technology that generates long reads, enabling the identification of structural variation despite its high error rate. In this proof-of-principle article, the authors employ the MinION nanopore sequencing device to assess several common well-characterized structural variants in pancreatic cancer cell lines, including deletions, translocations, inversions, and combinations. By combining dilutions of PCR products containing these structural variants into corresponding wildtype amplicons, the authors elegantly demonstrate that these variants can be identified at 1:100 dilutions with less than 500 reads. The authors also show that the precision of breakpoint identification remains limited with this technology, and comment on the need of bioinformatic optimization to detect breakpoints. Overall, the work illustrates that nanopore sequencing is a sensitive method for the detection of structural variation, which has important implications for not only human genetics research, but also health care in the area of cancer diagnosis and therapeutic monitoring.
Training and Development Committee: Could you describe your research for us?
Dr. Norris: I use computational tools to study the genetic underpinnings of human disease. Specifically, I aim to identify disease-associated genomic and transcriptomic alterations, from cancer to psychiatric disorders. My discovery of a novel structural variant (“TransFlip”) during my thesis work led to my desire to explore long read technologies, like Nanopore.
TDC: What are your career goals?
Dr. Norris: Equally important to my research is my passion for advancing STEM education to students at the K-12 level. I actively volunteer in many organizations to promote this goal, and interacting with students enriches my own scientific pursuits. After my postdoctoral training, I hope to utilize my bioinformatics skills in a genomics education or outreach position.
TDC: Why did you choose genetics as your field of study?
Dr. Norris: The human genome project provided us with a map and the challenge of functionally annotating that map fascinates me. The more we discover about our genome, the more we realize its complexity. The rapid advances in sequencing technologies and ever-expanding array of applications make it an exciting time to be in the bioinformatics field.
TDC: Describe yourself in three words.
Dr. Norris: Enthusiastic, Engaging, and Empowering
The Trainee Paper Spotlight is a monthly feature highlighting outstanding papers written by trainee members of ASHG.