63. DETECTION OF COLORECTAL CANCER RELATED ANTIBODY PEPTIDES USING PROTEOGENOMICS

Department: Computer Science & Engineering
Research Institute Affiliation: Graduate Program in Bioinformatics
Faculty Advisor(s): Vineet Bafna

Primary Student
Name: Seong Won Cha
Email: s3cha@ucsd.edu
Phone: 209-890-5652
Grad Year: 2017

Abstract
Tumor antibody peptides environments are known to invoke an immune system response. However, identifying cancer specific antibody using tandem mass spectra remains a challenge because standard protein databases do not include the highly divergent sequences of somatically rearranged immunoglobulin genes. We introduce a novel proteogenomic approach to identify these highly variable antibody peptides. We develop a customized antibody database built solely using tumor RNA-seq data, and analyze MS/MS spectra from 90 distinct colorectal tumor samples. We show that many novel identifications can be found from our customized immunoglobulin gene database, and the identified peptides are from the active immune response to the tumor cell.

Industry Application Area(s)
Life Sciences/Medical Devices & Instruments | Software, Analytics

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