TY - JOUR T1 - Targeted mutation detection in breast cancer using MammaSeqâ„¢ JF - bioRxiv DO - 10.1101/264267 SP - 264267 AU - Nicholas G. Smith AU - Rekha Gyanchandani AU - Grzegorz Gurda AU - Peter C. Lucas AU - Ryan J. Hartmaier AU - Adam M. Brufsky AU - Shannon Puhalla AU - Amir Bahreini AU - Karthik Kota AU - Abigail I. Wald AU - Yuri E. Nikiforov AU - Marina N. Nikiforova AU - Steffi Oesterrich AU - Adrian V. Lee Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/02/13/264267.abstract N2 - Background Breast cancer is the most common invasive cancer among women worldwide. Next-generation sequencing (NGS) has revolutionized the study of cancer across research labs around the globe, however genomic testing in clinical settings remain limited. Advances in sequencing reliability, pipeline analysis, accumulation of relevant data, and the reduction of costs are rapidly increasing the feasibility of NGS-based clinical decision making.Methods We report the development of MammaSeq, a breast cancer specific NGS panel, targeting 79 genes and 1369 mutations, optimized for use in primary and metastatic breast cancer. To validate the panel, 46 solid tumor and 14 plasma circulating-free cfDNA samples were sequenced to a mean depth of 2311X and 1820 X respectively. Variants were called using Ion Torrent Suite 4.0 and annotated with cravat CHASM. CNVKit was used to call copy number variants in the solid tumor cohort. The oncoKB Precision Oncology Database was used to identify clinically actionable variants. ddPCR was used to validate select cfDNA mutations.Results In cohorts of 46 solid tumors and 14 cfDNA samples from patients with advanced breast cancer we identified 592 and 43 protein coding mutations. Mutations per sample in the solid tumor cohort ranged from 1 to 128 (median 3) and the cfDNA cohort ranged from 0 to 26 (median 2.5). Copy number analysis in the solid tumor cohort identified 46 amplifications and 35 deletions. We identified 26 clinically actionable variants (levels 1-3) annotated by OncoKB, distributed across 20 out of 46 cases (40%), in the solid tumor cohort. Allele frequencies of ESR1 and FOXA1 mutations correlated with CA.27.29 levels in patient matched blood draws.Conclusions In solid tumors biopsies and cfDNA, MammaSeq detects clinicaly actionable mutations (oncoKB levels 1-3) in 22/46 (48%) solid tumors and in 4/14 (29%) of cfDNA samples. MammaSeq is a targeted panel suitable for clinically actionable mutation detection in breast cancer.CfDNAcirculating-free cfDNACNVCopy Number VariantsDdPCRDroplet Digital PCRDgIDBDrug-Gene Interaction DatabaseGDNAGenomic DNAGOGene OntologyGWAsGenome Wide Association studiesIDCInvasive Ductal CarcinomaILCInvasive Lobular CarcinomaISPIon Sphere particlesMBCMetastatic Breast CancerNGSNext Generation SequencingPGMIon Torrent Personal Genome MachineSMGSignificantly Mutated GeneSNPSingle Nucleotide PolymorphismSNVSingle Nucleotide VariantTCGAThe Cancer Genome AtlasTMBTumor Mutational Burden ER -