Carlos Sosa, Ph.D., is currently working with the Clinical Genome Sequencing Laboratory in the Department of Laboratory Medicine and Pathology at Mayo Clinic. He is also an adjunct assistant professor at the University of Minnesota Rochester in the Bioinformatics and Computational Biology graduate program.
Dr. Sosa's research interests are in RNA sequencing (RNA-seq) to study different types of cancer using solid and liquid biopsies, in particular, to determine gene and transcript expression. His research involves the application of RNA-seq to help develop prognostic and screening models based on gene expression to study cancers such as kidney cancer, prostate cancer and rare cancers.
- Whole blood mRNA expression-based cancer prognosis. Work in this area includes developing prognostic models using whole-blood mRNA gene profiling in diseases such as metastatic renal cell carcinoma. This work relies on performing whole-transcriptome RNA-seq identify genes that can be associated with overall survival.
- Identification of novel fusions in rare cancers. Rhabdomyosarcomas are examples of rare cancers in the prostate, kidney and urinary bladder. The use of multiple methodologies to identify fusion events provides consensus to validate novel fusions. This requires RNA-seq and mapping reads to a genome reference.
- Developing next-generation pipelines to analyze data with clinical applicability. This work includes the design of multiple steps from primary analysis to visualizing results. Clinical pipelines require stringent regulations. Software quality control is a key component in all the steps of data flow and software development.
- Identification of new procedures for quality control in the clinic. The Clinical Genome Sequencing Lab is certified by the Clinical Laboratory Improvement Amendments and College of American Pathologists' Laboratory Accreditation Program for the testing of many germline and somatic diseases. The accuracy of analyzing patient data is of paramount importance as it is used in the diagnosis and the development of a treatment regime. The informatic process needs to follow stringent guidelines to ensure precision and reproducibility.
Significance to patient care
Dr. Sosa's research goal is to provide clinicians and practitioners with models, information and workflows that can be used in the clinic. This requires that tools and pipelines must be properly tested and comply with methodologies highlighted by federal, state and institutional (Mayo Clinic) regulatory requirements for patient use.
- Recipient, Certificate of Appreciation, Massachusetts Institute of Technology, 2016
- Recipient, Technical Authorship Award, IBM Bravo! Author Olympics, Bronze, IBM, 2011
- Member, Bioinformatics and Computational Biology Curriculum Committee, University of Minnesota, 2007
- Member, Bioinformatics and Computational Biology Planning Committee, University of Minnesota, 2007
- Member, Minnesota's Tekne Award: The Established Innovation Award is IBM, Minnesota High Tech Association, 2006
- Recipient, Technical Authorship Award, IBM Bravo! Author Olympics, Bronze, IBM, 2005
- Recipient, Technical Authorship Award, IBM Bravo! IBM, 2005
- Recipient, Certificate of Achievement, Applications a la Carte(e), Cray Research, Inc., 1993
- Recipient, Dan Trivich Memorial Award for Research in Physical Chemistry, Wayne State University, 1986