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.
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
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.
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.
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.
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.
- Arul Chinnaiyan, MD, PhD, University of Michigan
- Dara Aisner, MD, PhD, University of Colorado
- John Hays, MD, PhD (Medical Oncology)
- Heather Hampel, MS, CGC (Genetics)
- Robert Pilarski, MS, CG (Genetics)
- Kristin Dittmar, MD (Radiology)
- Xiao-Ping Zhou, MD (Pathology)
- Aharon Freud, MD (Pathology)
- Michael Wells, MD (Eye)
- Barb Kleiber, CRC
- Joe Benner, CRC
- Jennifer Sexton, CRC
- Susan Ottman, CRC
- OCDC Team
- JARO Team
- cIRB Team
- IDS Team
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 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.firstname.lastname@example.org 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