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Mol Cell Proteomics. 2016 Mar;15(3):1060-71. doi: 10.1074/mcp.M115.056226. Epub 2015 Dec 2.

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.

Author information

1
From the ‡New York University School of Medicine, New York, NY;
2
§Biomedical Hosting, LLC, Arlington, MA;
3
¶Washington University in St. Louis, St. Louis, MO;
4
‖Broad Institute of Harvard and MIT, Cambridge, MA;
5
**Vanderbilt University School of Medicine, Nashville, TN;
6
‡‡Universtiy of North Carolina School of Medicine, Chapel Hill, NC;
7
§§Pacific Northwest National Laboratory, Richland, WA;
8
¶¶Johns Hopkins University, Baltimore, MD;
9
‖‖Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD.
10
§§Pacific Northwest National Laboratory, Richland, WA; Samuel.Payne@pnnl.gov mellis@dom.wustl.edu david@fenyolab.org.
11
¶Washington University in St. Louis, St. Louis, MO; Samuel.Payne@pnnl.gov mellis@dom.wustl.edu david@fenyolab.org.
12
From the ‡New York University School of Medicine, New York, NY; Samuel.Payne@pnnl.gov mellis@dom.wustl.edu david@fenyolab.org.

Abstract

Improvements in mass spectrometry (MS)-based peptide sequencing provide a new opportunity to determine whether polymorphisms, mutations, and splice variants identified in cancer cells are translated. Herein, we apply a proteogenomic data integration tool (QUILTS) to illustrate protein variant discovery using whole genome, whole transcriptome, and global proteome datasets generated from a pair of luminal and basal-like breast-cancer-patient-derived xenografts (PDX). The sensitivity of proteogenomic analysis for singe nucleotide variant (SNV) expression and novel splice junction (NSJ) detection was probed using multiple MS/MS sample process replicates defined here as an independent tandem MS experiment using identical sample material. Despite analysis of over 30 sample process replicates, only about 10% of SNVs (somatic and germline) detected by both DNA and RNA sequencing were observed as peptides. An even smaller proportion of peptides corresponding to NSJ observed by RNA sequencing were detected (<0.1%). Peptides mapping to DNA-detected SNVs without a detectable mRNA transcript were also observed, suggesting that transcriptome coverage was incomplete (∼80%). In contrast to germline variants, somatic variants were less likely to be detected at the peptide level in the basal-like tumor than in the luminal tumor, raising the possibility of differential translation or protein degradation effects. In conclusion, this large-scale proteogenomic integration allowed us to determine the degree to which mutations are translated and identify gaps in sequence coverage, thereby benchmarking current technology and progress toward whole cancer proteome and transcriptome analysis.

PMID:
26631509
PMCID:
PMC4813688
[Available on 2017-03-01]
DOI:
10.1074/mcp.M115.056226
[Indexed for MEDLINE]
Free PMC Article

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