title: The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine.
abstract: The diversity of clinical tumor profiling approaches (small panels to whole exomes with matched or unmatched germline analysis) may engender uncertainty about their benefits and liabilities, particularly in light of reported germline false positives in tumor-only profiling and use of global mutational and/or neoantigen data. The goal of this study was to determine the impact of genomic analysis strategies on error rates and data interpretation across contexts and ancestries.
  
  
  
  We modeled common tumor profiling modalities-large (n = 300 genes), medium (n = 48 genes), and small (n = 15 genes) panels-using clinical whole exomes (WES) from 157 patients with lung or colon adenocarcinoma. We created a tumor-only analysis algorithm to assess germline false positive rates, the impact of patient ancestry on tumor-only results, and neoantigen detection.
  
  
  
  After optimizing a germline filtering strategy, the germline false positive rate with tumor-only large panel sequencing was 14 % (144/1012 variants). For patients whose tumor-only results underwent molecular pathologist review (n = 91), 50/54 (93 %) false positives were correctly interpreted as uncertain variants. Increased germline false positives were observed in tumor-only sequencing of non-European compared with European ancestry patients (p < 0.001; Fisher's exact) when basic germline filtering approaches were used; however, the ExAC database (60,706 germline exomes) mitigated this disparity (p = 0.53). Matched and unmatched large panel mutational load correlated with WES mutational load (r(2) = 0.99 and 0.93, respectively; p < 0.001). Neoantigen load also correlated (r(2) = 0.80; p < 0.001), though WES identified a broader spectrum of neoantigens. Small panels did not predict mutational or neoantigen load.
  
  
  
  Large tumor-only targeted panels are sufficient for most somatic variant identification and mutational load prediction if paired with expanded germline analysis strategies and molecular pathologist review. Paired germline sequencing reduced overall false positive mutation calls and WES provided the most neoantigens. Without patient-matched germline data, large germline databases are needed to minimize false positive mutation calling and mitigate ethnic disparities.
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02115, USA.|Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.
authors.forename: Andrea
authors.initials: A
authors.lastname: Garofalo
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
authors.forename: Lynette
authors.initials: L
authors.lastname: Sholl
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02115, USA.|Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.
authors.forename: Brendan
authors.initials: B
authors.lastname: Reardon
authors.affiliation: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.
authors.forename: Amaro
authors.initials: A
authors.lastname: Taylor-Weiner
authors.affiliation: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.
authors.forename: Ali
authors.initials: A
authors.lastname: Amin-Mansour
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02115, USA.|Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.
authors.forename: Diana
authors.initials: D
authors.lastname: Miao
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02115, USA.|Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.
authors.forename: David
authors.initials: D
authors.lastname: Liu
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02115, USA.
authors.forename: Nelly
authors.initials: N
authors.lastname: Oliver
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02115, USA.|Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
authors.forename: Laura
authors.initials: L
authors.lastname: MacConaill
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Ducar
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
authors.forename: Vanesa
authors.initials: V
authors.lastname: Rojas-Rudilla
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02115, USA.|Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.
authors.forename: Marios
authors.initials: M
authors.lastname: Giannakis
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02115, USA.
authors.forename: Arezou
authors.initials: A
authors.lastname: Ghazani
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02115, USA.
authors.forename: Stacy
authors.initials: S
authors.lastname: Gray
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02115, USA.
authors.forename: Pasi
authors.initials: P
authors.lastname: Janne
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02115, USA.
authors.forename: Judy
authors.initials: J
authors.lastname: Garber
authors.affiliation: Department of Medical Ethics and Health Policy, University of Pennsylvania, Philadelphia, PA, USA.
authors.forename: Steve
authors.initials: S
authors.lastname: Joffe
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
authors.forename: Neal
authors.initials: N
authors.lastname: Lindeman
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02115, USA.|Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.|Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02115, USA.
authors.forename: Nikhil
authors.initials: N
authors.lastname: Wagle
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02115, USA. Levi_Garraway@dfci.harvard.edu.|Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA. Levi_Garraway@dfci.harvard.edu.|Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02115, USA. Levi_Garraway@dfci.harvard.edu.
authors.forename: Levi A
authors.initials: LA
authors.lastname: Garraway
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02115, USA. Eliezerm_vanallen@dfci.harvard.edu.|Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA. Eliezerm_vanallen@dfci.harvard.edu.|Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02115, USA. Eliezerm_vanallen@dfci.harvard.edu.
authors.forename: Eliezer M
authors.initials: EM
authors.lastname: Van Allen
mesh_terms: D000230:Adenocarcinoma / Q000175:diagnosis / Q000235:genetics* / Q000473:pathology; D000077192:Adenocarcinoma of Lung; D000951:Antigens, Neoplasm / Q000235:genetics*; D003110:Colonic Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000473:pathology; D030541:Databases, Genetic; D059472:Exome; D005189:False Positive Reactions; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D023281:Genomics / Q000379:methods; D018095:Germ-Line Mutation; D006801:Humans; D008175:Lung Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000473:pathology; D059645:Mutation Rate; D010375:Pedigree; D057285:Precision Medicine; D017422:Sequence Analysis, DNA
chemical_list: D000951:Antigens, Neoplasm
keywords: Disparities; Genomics; Immuno-oncology; Neoantigens; Panel testing; Precision medicine