title: A Plasma-Based Protein Marker Panel for Colorectal Cancer Detection Identified by Multiplex Targeted Mass Spectrometry.
abstract: Colorectal cancer (CRC) testing programs reduce mortality; however, approximately 40% of the recommended population who should undergo CRC testing does not. Early colon cancer detection in patient populations ineligible for testing, such as the elderly or those with significant comorbidities, could have clinical benefit. Despite many attempts to identify individual protein markers of this disease, little progress has been made. Targeted mass spectrometry, using multiple reaction monitoring (MRM) technology, enables the simultaneous assessment of groups of candidates for improved detection performance.
  
  
  
  A multiplex assay was developed for 187 candidate marker proteins, using 337 peptides monitored through 674 simultaneously measured MRM transitions in a 30-minute liquid chromatography-mass spectrometry analysis of immunodepleted blood plasma. To evaluate the combined candidate marker performance, the present study used 274 individual patient blood plasma samples, 137 with biopsy-confirmed colorectal cancer and 137 age- and gender-matched controls. Using 2 well-matched platforms running 5 days each week, all 274 samples were analyzed in 52 days.
  
  
  
  Using one half of the data as a discovery set (69 disease cases and 69 control cases), the elastic net feature selection and random forest classifier assembly were used in cross-validation to identify a 15-transition classifier. The mean training receiver operating characteristic area under the curve was 0.82. After final classifier assembly using the entire discovery set, the 136-sample (68 disease cases and 68 control cases) validation set was evaluated. The validation area under the curve was 0.91. At the point of maximum accuracy (84%), the sensitivity was 87% and the specificity was 81%.
  
  
  
  These results have demonstrated the ability of simultaneous assessment of candidate marker proteins using high-multiplex, targeted-mass spectrometry to identify a subset group of CRC markers with significant and meaningful performance.
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Jones
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Bruce E
authors.initials: BE
authors.lastname: Wilcox
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Ryan W
authors.initials: RW
authors.lastname: Benz
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Naveen
authors.initials: N
authors.lastname: Babbar
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Genna
authors.initials: G
authors.lastname: Boragine
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Ted
authors.initials: T
authors.lastname: Burrell
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Ellen B
authors.initials: EB
authors.lastname: Christie
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Lisa J
authors.initials: LJ
authors.lastname: Croner
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Phong
authors.initials: P
authors.lastname: Cun
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Roslyn
authors.initials: R
authors.lastname: Dillon
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Stefanie N
authors.initials: SN
authors.lastname: Kairs
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Athit
authors.initials: A
authors.lastname: Kao
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Ryan
authors.initials: R
authors.lastname: Preston
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Scott R
authors.initials: SR
authors.lastname: Schreckengaust
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Heather
authors.initials: H
authors.lastname: Skor
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: William F
authors.initials: WF
authors.lastname: Smith
authors.affiliation: Applied Proteomics, Inc., San Diego, CA.
authors.forename: Jia
authors.initials: J
authors.lastname: You
authors.affiliation: Applied Minds, Glendale, CA.
authors.forename: W Daniel
authors.initials: WD
authors.lastname: Hillis
authors.affiliation: USC Norris Westside Cancer Center and USC Center for Applied Molecular Medicine, Beverly Hills, CA.
authors.forename: David B
authors.initials: DB
authors.lastname: Agus
authors.affiliation: Applied Proteomics, Inc., San Diego, CA. Electronic address: john@appliedproteomics.com.
authors.forename: John E
authors.initials: JE
authors.lastname: Blume
mesh_terms: D000328:Adult; D000368:Aged; D019540:Area Under Curve; D014408:Biomarkers, Tumor / Q000097:blood*; D015179:Colorectal Neoplasms / Q000097:blood / Q000175:diagnosis*; D055088:Early Detection of Cancer / Q000379:methods*; D005260:Female; D006801:Humans; D008297:Male; D013058:Mass Spectrometry / Q000379:methods*; D008875:Middle Aged; D012372:ROC Curve; D012680:Sensitivity and Specificity
chemical_list: D014408:Biomarkers, Tumor
keywords: Classification; Colorectal cancer; Machine learning; Mass spectrometry, Multiple reaction monitoring