title: Mutational Profiling Can Establish Clonal or Independent Origin in Synchronous Bilateral Breast and Other Tumors.
abstract: BACKGROUND
  Synchronous tumors can be independent primary tumors or a primary-metastatic (clonal) pair, which may have clinical implications. Mutational profiling of tumor DNA is increasingly common in the clinic. We investigated whether mutational profiling can distinguish independent from clonal tumors in breast and other cancers, using a carefully defined test based on the Clonal Likelihood Score (CLS = 100 x # shared high confidence (HC) mutations/ # total HC mutations).
  
  
  METHODS
  Statistical properties of a formal test using the CLS were investigated. A high CLS is evidence in favor of clonality; the test is implemented as a one-sided binomial test of proportions. Test parameters were empirically determined using 16,422 independent breast tumor pairs and 15 primary-metastatic tumor pairs from 10 cancer types using The Cancer Genome Atlas.
  
  
  RESULTS
  We validated performance of the test with its established parameters, using five published data sets comprising 15,758 known independent tumor pairs (maximum CLS = 4.1%, minimum p-value = 0.48) and 283 known tumor clonal pairs (minimum CLS 13%, maximum p-value <0.01), across renal cell, testicular, and colorectal cancer. The CLS test correctly classified all validation samples but one, which it appears may have been incorrectly classified in the published data. As proof-of-concept we then applied the CLS test to two new cases of invasive synchronous bilateral breast cancer at our institution, each with one hormone receptor positive (ER+/PR+/HER2-) lobular and one triple negative ductal carcinoma. High confidence mutations were identified by exome sequencing and results were validated using deep targeted sequencing. The first tumor pair had CLS of 81% (p-value < 10-15), supporting clonality. In the second pair, no common mutations of 184 variants were validated (p-value >0.99), supporting independence. A plausible molecular mechanism for the shift from hormone receptor positive to triple negative was identified in the clonal pair.
  
  
  CONCLUSIONS
  We have developed the statistical properties of a carefully defined Clonal Likelihood Score test from mutational profiling of tumor DNA. Under identified conditions, the test appears to reliably distinguish between synchronous tumors of clonal and of independent origin in several cancer types. This approach may have scientific and clinical utility.
authors.affiliation: Moores Cancer Center, University of California San Diego, La Jolla, CA, United States of America.
authors.forename: Lei
authors.initials: L
authors.lastname: Bao
authors.affiliation: Moores Cancer Center, University of California San Diego, La Jolla, CA, United States of America.|Division of Biostatistics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, United States of America.
authors.forename: Karen
authors.initials: K
authors.lastname: Messer
authors.affiliation: Department of Medicine, University of California San Diego, La Jolla, CA, United States of America.
authors.forename: Richard
authors.initials: R
authors.lastname: Schwab
authors.affiliation: Department of Pediatrics, University of California San Diego, La Jolla, CA, United States of America.
authors.forename: Olivier
authors.initials: O
authors.lastname: Harismendy
authors.affiliation: Moores Cancer Center, University of California San Diego, La Jolla, CA, United States of America.
authors.forename: Minya
authors.initials: M
authors.lastname: Pu
authors.affiliation: Moores Cancer Center, University of California San Diego, La Jolla, CA, United States of America.
authors.forename: Brian
authors.initials: B
authors.lastname: Crain
authors.affiliation: Moores Cancer Center, University of California San Diego, La Jolla, CA, United States of America.
authors.forename: Shawn
authors.initials: S
authors.lastname: Yost
authors.affiliation: Department of Pediatrics, University of California San Diego, La Jolla, CA, United States of America.
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Frazer
authors.affiliation: Department of Psychiatry, University of California San Diego, La Jolla, CA, United States of America.
authors.forename: Brinda
authors.initials: B
authors.lastname: Rana
authors.affiliation: Department of Pathology, University of California San Diego, La Jolla, CA, United States of America.
authors.forename: Farnaz
authors.initials: F
authors.lastname: Hasteh
authors.affiliation: Department of Surgery, University of California San Diego, La Jolla, CA, United States of America.
authors.forename: Anne
authors.initials: A
authors.lastname: Wallace
authors.affiliation: Department of Medicine, University of California San Diego, La Jolla, CA, United States of America.
authors.forename: Barbara A
authors.initials: BA
authors.lastname: Parker
mesh_terms: D000368:Aged; D001940:Breast / Q000473:pathology*; D001943:Breast Neoplasms / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology; D018270:Carcinoma, Ductal, Breast / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology; D002999:Clone Cells; D004252:DNA Mutational Analysis; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation; D009362:Neoplasm Metastasis / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology; D009378:Neoplasms, Multiple Primary / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology