Research conducted by the Roychowdhury Laboratory Team includes basic cancer research and translational cancer genomics.

We are a multidisciplinary group with team members who have expertise in diverse fields including cancer genomics, computational biology/computer science, cancer biology, drug development, molecular diagnostics and medical oncology.

Transgenomics Spectrum

Basic cancer research is about the core principles of cancer, while translational cancer research is about using this knowledge to take care of patients through clinical trials. Together, as a multidisciplinary team, we:

  • Evaluate and care for patients through clinical trials
  • Study the genetics of cancer using next generation sequencing
  • Match patients to new smart drugs in trials
  • Evaluate the benefit from such therapies
  • Study how drugs affect the cancer
  • Strive to develop rational combination treatments for patients

Translational Cancer Genomics

LabOverview

Precision Cancer Clinic

We offer a consultation clinic for patients with advanced, metastatic cancers for second opinions regarding their cancer. We provide informed consent, discussing risks and benefits of our clinical study, OSU-13053: Precision Cancer Medicine for Advanced Cancer Through High-throughput Sequencing (NCT02090530). Interested patients must inquire with their hematologist/oncologists first to determine whether they are eligible for such a study.

Precision Tumor Board

We coordinate weekly Precision Tumor Board (PTB), to discuss results and interpretation of genomic testing for patients with advanced, metastatic cancer. This format includes multi-disciplinary expertise with medical oncologists, hematologists, pathologist, genomic scientists, computational biologists, genetic counselors, and cancer biologists.

Genomics-driven Clinical Trials

We participate and develop clinical trials that treat patients with advanced and metastatic cancer based on their molecular features rather than the primary site of disease alone. We develop Investigator-Initiated Trials and also participate in Industry-Sponsored studies through a Genomics-Based Trials Group at OSU’s Comprehensive Cancer Center.

Clinical Grade Genomic Testing: Development

Our lab uses next generation sequencing technologies for both research and clinical sequencing. We develop novel genomic tests that can be migrated and validated in a dedicated clinical grade, CLIA-certified Cancer Genomics Laboratory (CGL). This lab performs testing for clinical trials only and is not a commercial entity or product.


Basic Cancer Research

At Roychowdhury computational biology lab, we are focused on using Next Generation Sequencing (NGS) technologies to sequence cancer-patients’ samples. Through sequencing, we target cancer-specific genes and look for single-nucleotide variants (SNVs), copy-number variants (CNVs), gene expression changes, gene splicing, and chromosomal translocations. We utilize our own custom-designed computational pipelines for exome sequencing and RNA-sequencing analysis. Information gathered from this analysis should help guide proper treatment courses.

Drug Resistance

We study how cancers with genomic alterations become resistant to novel targeted therapies, including but not limited to inhibitors of BRAF, FGFR, PI3K, CDK, RET, and ALK oncogenes. We do this through pre-clinical models of acquired drug resistance and through acquisition of pretreatment and post-progression tumor samples from patients receiving targeted therapies for their cancer treatment.

Discovery

Rare Cancers

We study patients with rare cancers that are so poorly characterized that there are no standard of care treatments for these diseases. We consent them to a clinical study that allows molecular characterization of their cancer using genomic sequencing and other approaches. These studies may lead to novel therapies or applications of existing therapies for patients facing these rare cancers.  

Exceptional Responders

During clinical drug development, some trials are considered failures when 20-40% of patients lack obvious benefit from the novel drug. However, selected patients may have an extraordinary response that could be defined by molecular features of their cancer. We seek to evaluate these patients in order to learn what molecular features could predict who might benefit in the future from that therapy.


Cancer Driver Log

CanDL (Cancer Driver Log) is a project relating to the Roychowdhury bioinformatics team's work. It is a database of potentially actionable driver mutations. The database currently consists of data on:

  • 60 distinct genes
  • 373 distinct variants

The database is a work in progress, so make sure to visit the CanDL website for the most recent information.

Recent advances in next generation sequencing technologies have enabled comprehensive cancer genomic testing by molecular pathologists across multiple tumor types. However, it is often challenging to assign the clinical and biological relevance of specific mutations observed in patients. While there is a multitude of databases that provide in silico assessment, there is no comprehensive database for annotating driver and passenger mutations.

Therefore, we created an expert-curated database of potentially actionable driver mutations for molecular pathologists and laboratory directors to facilitate literature-based annotation of genomic testing of tumors. We curated the chromosome location, all possible nucleotide positions, for each amino acid change and uploaded them to the CanDL database with associated literature reference.


Collaborations

Non-OSUCCC

  • Arul Chinnaiyan, MD, PhD, University of Michigan
  • Dara Aisner, MD, PhD, University of Colorado

OSUCCC


Funding

We are grateful to the Government and Foundation efforts that strive to end cancer and work tirelessly to fund much needed cancer research. The following are agencies that have supported our team directly:

  • Prostate Cancer Foundation, Young Investigator Award
  • Prostate Cancer Foundation, Special Creativity Award
  • American Cancer Society, Mentored Research Scholar Grant
  • Fore Cancer Research Foundation
  • Pelotonia
  • Pelotonia Idea Award
  • National Cancer Institute, Experimental Therapeutic Network UM1
  • National Human Genome Research Institute

Join our Team

Our team consists of experts in cancer biology, genomics, computational biology, molecular diagnostics, pathology, medical oncology, experimental therapeutics. To accomplish our mission, we promote an environment for teamwork and training for all team members at every stage of training.

We are actively recruiting team members, including graduate students, post-doctoral trainees, and clinical fellows for projects in the following areas:

  • Cancer Genomics
  • Target Discovery
  • Novel NGS assay development
  • Acquired resistance to novel kinase inhibitors, including FGFR pathway and others
  • Evaluation of exceptional responders
  • Computational biology for cancer molecular diagnostics and acquired drug resistance

For applicants with considerable computer science experience, we also offer a specialized translational cancer genomics: computational biology internship (candidates should inquire).

Interested applicants should contact us at Sameek.roychowdhury@osumc.edu and include the following:

  • Area of research interest in our lab
  • Cover letter indicating current and future research interests and expected availability date
  • CV (Curriculum Vitae) or Biosketch, with Names of three references

CCC Members

Sameek Roychowdhury, MD, PhD

Dr. Roychowdhury is a physician scientist in medical oncology focusing on translational cancer genomics and implementing precision cancer medicine. His clinical practice in medical oncology includes patients with advanced, metastatic cancer including prostate, colorectal, and rare cancer subtypes.

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Researchers and Lab Staff

Darshna Bhatt

Darshna Bhatt

Lab Manager. Darshna has 20 years of biomedical laboratory and clinical cancer research experience and is the Lab Manager. She is responsible for lab equipment, staff operations, lab safety, and maintaining lab certifications.

Jharna Datta

Jharna Datta, PhD

Research Scientist. Jharna presently works on research projects directed towards understanding the genetic changes that occur in cancer cells. Her work involves studying acquired drug resistance and exceptional responders. The research is leading to more effective treatment strategies that can be tailored to the genetic profile of individual patients' cancers.

Dorrelyn Martin

Dorrelyn Martin, MS

Research Associate. Dori has several years of experience in cancer genetics and the ENCODE project, she joined the lab to help translate cancer genomic sequencing approaches to patient care. She focuses on the development of novel DNA and RNA sequencing approaches for evaluating patients with advanced cancer, including the analytic and clinical validation of these assays.

Jharna Miya

Jharna Miya, MS

Bioinformatics Specialist. Jharna received her master’s degree in Bioinformatics from NJIT, and currently works in the lab as a biomedical informatics specialist. Her work includes analyzing cancer patient samples, helping develop novel cancer genomic tests in the CLIA-certified Cancer Genomics Laboratory, and is responsible for organizing and ensuring a smooth data flow throughout the lab. She also writes algorithms and uses DNA-sequencing and RNA-sequencing pipelines that the lab uses on the Ohio Supercomputing facility’s cluster to decode valuable information from patient data.

Matthew Reeder

Matthew Reeder, BA

Research Assistant. Matthew is a recent graduate of the College of Wooster. His previous research was focused on plant pathology, and he has enjoyed the transition to clinical applications. His duties involve processing tissue samples, preparing libraries for next generation sequencing, and clinical trial data management. He hopes to use his skills to aid the team in developing improved individualized cancer treatment options.

Julie Reeser

Julie Reeser, PhD

Clinical Research Coordinator. Julie is a recent PhD graduate from The Ohio State University who now works as the Clinical Research Coordinator and Technical Director for a CLIA-certified Cancer Genomics Laboratory. She is involved in enrolling patients in the OSU-13053 trial and coordinates clinical tumor sequencing. She is also involved in the Precision Tumor Board, which serves as a platform for discussion of genomics in the treatment of cancer.

Amy Smith

Amy Smith

Lead Clinical Lab Technologist. Amy is a Medical Laboratory Scientist certified by the American Society for Clinical Pathology. She has been working in clinical laboratories for over 10 years, with the last five years focused on molecular techniques. Her current duties involve processing blood and tissue samples, extracting nucleic acids, and preparing libraries for next generation sequencing. Her goal is to utilize her skills to help the team improve treatment options for cancer patients.

Eliot Zhu

Eliot Zhu, MS

Bioinformatics Specialist. Eliot obtained his BS and MS in Systems Biology and Bioinformatics from Case Western Reserve University in 2014. His work includes development and implementation of algorithms to analyze targeted DNA and RNA sequencing of patient tumors.

Students

Senthilkumar Damodaran, MD, PhD

Medical Oncology Fellow (2012-Current)

Mikayla Dantuono

Mikayla Dantuono

Mikayla is a second year student at the Ohio State University working towards an honors degree in biology. Her goal is to go to medical school and be able to lead her own research lab one day.

Eli Gardner

High School Student (2013-Current)

Raffi Hagopian

Medical Student, Bioinformatics (2012-Current)

Yang Liu

Medical Student (2013-Current)

Ezra Lyon

Ezra Lyon

Medical Student. Ezra joined the lab team shortly after starting medical school at The Ohio State University. Prior to starting the M.D. program, he worked in industry for 6 years as a computational biologist involved in the design and analysis of microarray and sequencing assays. He currently works on next generation sequencing assays to detect gene fusions in clinical cancer samples.

Karan Naik

Karan Naik

Karan is a second year honors student at Ohio State University pursuing a major in Biomedical Science with a minor in Spanish. He has been with the lab since the fall of his freshman year. Following graduation, he wishes to attain a dual MD/PhD degree.

Cristina Ocrainiciuc

Undergraduate Student, Third Year (2012-Current)

Hannah Parks

Undergraduate Student, Fourth Year (2012-Current)

Sounak Roy

Undergraduate Student, First Year (2012-Current)

Eric Samorodnitsky

Eric Samorodnitsky, PhD

Post-Doctoral Fellow, Computational Biology (2013-Current). Eric is a post-doctoral fellow in computational biology, and is involved in clinical cancer sequencing utilizing integrative DNA and RNA sequencing approaches. Eric’s future work will entail making software to model all the different cancer pathways in order to assist physicians in choosing courses for treatment when a patient’s cancer becomes resistant to a particular targeted therapy.

Lillian Spetrino

Undergraduate Student, Third Year (Summer 2013, 2014)

Michele Wing

Michele Wing, PhD

Graduate Student Assistant (2013-Current). Michele completed her PhD at the University of North Carolina, and completed her ACMG fellowship at Nationwide Children’s. She joined the lab team to help translate cancer genomics for patient care through helping to develop and implement our CLIA-certified Cancer Genomics Laboratory. She is involved in data analysis, data management, and novel assay development. Because of her interest in clinical applications of genetics, she is also studying to be Nurse Practitioner at The Ohio State University.


Publications

Roychowdhury Laboratory

Biomedical Research Tower, Room 508

460 West 12th Ave

Columbus, OH 43210

Telephone: 614-685-5842

sameek.roychowdhury@osumc.edu

Sameek Roychowdhury, MD, PhD

Roychowdhury Sameek5082

 

Dr. Roychowdhury is a physician scientist in medical oncology focusing on translational cancer genomics and implementing precision cancer medicine. His clinical practice in medical oncology includes patients with advanced, metastatic cancer including prostate, colorectal, and rare cancer subtypes.

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