Akshaya Vijaya Annapragada
Repeat elements, which comprise more than half of the human genome, have long been implicated in disease, but have historically been excluded from whole-genome analyses because of incomplete references and computational challenges. I developed a new method (ARTEMIS) to study genome-wide repeats and identified alterations in 820 elements not previously implicated in cancer. I then used ARTEMIS to develop blood tests for early detection of cancer, when tumors can be most effectively treated. Early in my Ph.D. work, I and others developed accessible cancer blood tests using machine learning and whole genome sequencing to analyze tens of millions of cell-free DNA (cfDNA) fragments from less than 1mL of blood (DELFI). Here, I used ARTEMIS to expand the scope of these tests, combining ARTEMIS and DELFI to noninvasively detect lung, liver and other cancers. Finally, I piloted liquid biopsies beyond oncology for detection of fibrotic liver disease. This work has illuminated genome-wide repeat elements in cancer and cfDNA, and provides a proof-of-concept for their use in noninvasive detection of cancer and other diseases. This work was done in the Cancer Genomics Lab, mentored by Victor Velculescu and Rob Scharpf.
Questions & Answers
Why did you choose Johns Hopkins for your work?
As an M.D./Ph.D. student with a background in applied mathematics, it was very important to me to train at a university with outstanding programs in both clinical medicine and quantitative research. The biomedical engineering Ph.D. program and the M.D. program at JHU have provided me with incredible opportunities in these fields.
What does receiving this award mean to you personally and professionally? Do you have any connection with the particular award you received?
I appreciate this validation of the utility and scientific merit of my work. I am grateful for the generosity of Martin and Carol Macht in endowing this award and for the opportunity to present my work as part of the Young Investigators’ Day program. I have been inspired by the work of past recipients, and am honored to join this group myself.
What contributed to your project’s success? (Special skills, interests, opportunities, guidance, etc.)
I have received outstanding mentorship from my Ph.D. advisers, Victor Velculescu and Rob Scharpf, who have helped me design clinically impactful projects and enabled me to explore and grow as a scientist. My amazing colleagues in the Cancer Genomics Lab have also been instrumental to the success of this work.
What thoughts do you have about Young Investigators’ Day itself, as a celebration of the roles students and fellows play in research at Johns Hopkins?
I appreciate that the Young Investigators’ Day program provides significant support and recognition of trainees. Every day, I walk past our lab’s hallway lined with Young Investigators’ Day award posters from former trainees. Knowing those scientists and seeing their work firsthand has been a daily reminder to me of what is possible as a student here. It is personally meaningful to me that I am now part of this lineage.
What has been your best/most memorable experience while at Johns Hopkins?
My best memories are of just being in lab and laughing about random things with friends while brainstorming and troubleshooting exciting science. I am very lucky that my colleagues are all incredible friends who have made each day fun and exciting.
What are your plans over the next year or so? Graduating, looking for faculty positions, etc.?
I recently defended my Ph.D. and am returning to the clinic to complete the final two years of medical school. I’m committed to a career at the intersection of science and medicine, and look forward to completing my clinical training while continuing my research.
Tell me something interesting about yourself that makes you unique. Do you have any special hobbies, interests or life experiences?
I have lived in all four U.S. census bureau regions. I love exploring Baltimore’s coffee shops, taking walks by the harbor and spending time with my family and the lifelong friends I have met here in graduate and medical school.