title: An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.
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.
authors.affiliation: From the ‡New York University School of Medicine, New York, NY;
authors.forename: Kelly V
authors.initials: KV
authors.lastname: Ruggles
authors.affiliation: From the ‡New York University School of Medicine, New York, NY;
authors.forename: Zuojian
authors.initials: Z
authors.lastname: Tang
authors.affiliation: From the ‡New York University School of Medicine, New York, NY;
authors.forename: Xuya
authors.initials: X
authors.lastname: Wang
authors.affiliation: From the ‡New York University School of Medicine, New York, NY;
authors.forename: Himanshu
authors.initials: H
authors.lastname: Grover
authors.affiliation: §Biomedical Hosting, LLC, Arlington, MA;
authors.forename: Manor
authors.initials: M
authors.lastname: Askenazi
authors.affiliation: From the ‡New York University School of Medicine, New York, NY;
authors.forename: Jennifer
authors.initials: J
authors.lastname: Teubl
authors.affiliation: ¶Washington University in St. Louis, St. Louis, MO;
authors.forename: Song
authors.initials: S
authors.lastname: Cao
authors.affiliation: ¶Washington University in St. Louis, St. Louis, MO;
authors.forename: Michael D
authors.initials: MD
authors.lastname: McLellan
authors.affiliation: ‖Broad Institute of Harvard and MIT, Cambridge, MA;
authors.forename: Karl R
authors.initials: KR
authors.lastname: Clauser
authors.affiliation: **Vanderbilt University School of Medicine, Nashville, TN;
authors.forename: David L
authors.initials: DL
authors.lastname: Tabb
authors.affiliation: ‖Broad Institute of Harvard and MIT, Cambridge, MA;
authors.forename: Philipp
authors.initials: P
authors.lastname: Mertins
authors.affiliation: **Vanderbilt University School of Medicine, Nashville, TN;
authors.forename: Robbert
authors.initials: R
authors.lastname: Slebos
authors.affiliation: ¶Washington University in St. Louis, St. Louis, MO;
authors.forename: Petra
authors.initials: P
authors.lastname: Erdmann-Gilmore
authors.affiliation: ¶Washington University in St. Louis, St. Louis, MO;
authors.forename: Shunqiang
authors.initials: S
authors.lastname: Li
authors.affiliation: ‡‡Universtiy of North Carolina School of Medicine, Chapel Hill, NC;
authors.forename: Harsha P
authors.initials: HP
authors.lastname: Gunawardena
authors.affiliation: ‡‡Universtiy of North Carolina School of Medicine, Chapel Hill, NC;
authors.forename: Ling
authors.initials: L
authors.lastname: Xie
authors.affiliation: §§Pacific Northwest National Laboratory, Richland, WA;
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.affiliation: ¶¶Johns Hopkins University, Baltimore, MD;
authors.forename: Jian-Ying
authors.initials: JY
authors.lastname: Zhou
authors.affiliation: ¶¶Johns Hopkins University, Baltimore, MD;
authors.forename: Shisheng
authors.initials: S
authors.lastname: Sun
authors.affiliation: ‡‡Universtiy of North Carolina School of Medicine, Chapel Hill, NC;
authors.forename: Katherine A
authors.initials: KA
authors.lastname: Hoadley
authors.affiliation: ‡‡Universtiy of North Carolina School of Medicine, Chapel Hill, NC;
authors.forename: Charles M
authors.initials: CM
authors.lastname: Perou
authors.affiliation: ‡‡Universtiy of North Carolina School of Medicine, Chapel Hill, NC;
authors.forename: Xian
authors.initials: X
authors.lastname: Chen
authors.affiliation: ¶Washington University in St. Louis, St. Louis, MO;
authors.forename: Sherri R
authors.initials: SR
authors.lastname: Davies
authors.affiliation: ¶Washington University in St. Louis, St. Louis, MO;
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Maher
authors.affiliation: ‖‖Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD.
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Kinsinger
authors.affiliation: §§Pacific Northwest National Laboratory, Richland, WA;
authors.forename: Karen D
authors.initials: KD
authors.lastname: Rodland
authors.affiliation: ¶¶Johns Hopkins University, Baltimore, MD;
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.affiliation: ¶¶Johns Hopkins University, Baltimore, MD;
authors.forename: Zhen
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: ¶Washington University in St. Louis, St. Louis, MO;
authors.forename: Li
authors.initials: L
authors.lastname: Ding
authors.affiliation: ¶Washington University in St. Louis, St. Louis, MO;
authors.forename: R Reid
authors.initials: RR
authors.lastname: Townsend
authors.affiliation: ‖‖Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD.
authors.forename: Henry
authors.initials: H
authors.lastname: Rodriguez
authors.affiliation: ¶¶Johns Hopkins University, Baltimore, MD;
authors.forename: Daniel
authors.initials: D
authors.lastname: Chan
authors.affiliation: §§Pacific Northwest National Laboratory, Richland, WA;
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.affiliation: **Vanderbilt University School of Medicine, Nashville, TN;
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Liebler
authors.affiliation: ‖Broad Institute of Harvard and MIT, Cambridge, MA;
authors.forename: Steven A
authors.initials: SA
authors.lastname: Carr
authors.affiliation: §§Pacific Northwest National Laboratory, Richland, WA; Samuel.Payne@pnnl.gov mellis@dom.wustl.edu david@fenyolab.org.
authors.forename: Samuel
authors.initials: S
authors.lastname: Payne
authors.affiliation: ¶Washington University in St. Louis, St. Louis, MO; Samuel.Payne@pnnl.gov mellis@dom.wustl.edu david@fenyolab.org.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Ellis
authors.affiliation: From the ‡New York University School of Medicine, New York, NY; Samuel.Payne@pnnl.gov mellis@dom.wustl.edu david@fenyolab.org.
authors.forename: David
authors.initials: D
authors.lastname: Fenyő
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D005260:Female; D016678:Genome; D006801:Humans; D008325:Mammary Neoplasms, Experimental / Q000235:genetics* / Q000378:metabolism; D051379:Mice; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D040901:Proteomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D053719:Tandem Mass Spectrometry; D059467:Transcriptome