Proteogenomic Analysis of Single Amino Acid Polymorphisms in Cancer Research.
The integration of genomics and proteomics has led to the emergence of proteogenomics, a field of research successfully applied to the characterization of cancer samples. The diagnosis, prognosis and response to therapy of cancer patients will largely benefit from the identification of mutations present in their genome. The current state of the art of high throughput experiments for genome-wide detection of somatic mutations in cancer samples has allowed the development of projects such as the TCGA, in which hundreds of cancer genomes have been sequenced. This huge amount of data can be used to generate protein sequence databases in which each entry corresponds to a mutated peptide associated with certain cancer types. In this chapter, we describe a bioinformatics workflow for creating these databases and detecting mutated peptides in cancer samples from proteomic shotgun experiments. The performance of the proposed method has been evaluated using publicly available datasets from four cancer cell lines.
Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra, Pamplona, Spain.
Alba
A
Garin-Muga
Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra, Pamplona, Spain.|Division of Hepatology and Gene Therapy, Center for Applied Medical Research, University of Navarra, Pamplona, Spain.|IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.
Fernando J
FJ
Corrales
Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra, Pamplona, Spain. vsegura@unav.es.|IdiSNA, Navarra Institute for Health Research, Pamplona, Spain. vsegura@unav.es.
Victor
V
Segura
D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D045744:Cell Line, Tumor; D030562:Databases, Protein; D015870:Gene Expression; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D058977:Molecular Sequence Annotation; D050505:Mutant Proteins / Q000235:genetics* / Q000378:metabolism; D009154:Mutation; D009363:Neoplasm Proteins / Q000235:genetics* / Q000378:metabolism; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D000071696:Proteogenomics / Q000379:methods*
D050505:Mutant Proteins; D009363:Neoplasm Proteins
Cancer research; Proteogenomics; SAP detection; TCGA project