title: Chromosomal Instability Estimation Based on Next Generation Sequencing and Single Cell Genome Wide Copy Number Variation Analysis.
abstract: Genomic instability is a hallmark of cancer often associated with poor patient outcome and resistance to targeted therapy. Assessment of genomic instability in bulk tumor or biopsy can be complicated due to sample availability, surrounding tissue contamination, or tumor heterogeneity. The Epic Sciences circulating tumor cell (CTC) platform utilizes a non-enrichment based approach for the detection and characterization of rare tumor cells in clinical blood samples. Genomic profiling of individual CTCs could provide a portrait of cancer heterogeneity, identify clonal and sub-clonal drivers, and monitor disease progression. To that end, we developed a single cell Copy Number Variation (CNV) Assay to evaluate genomic instability and CNVs in patient CTCs. For proof of concept, prostate cancer cell lines, LNCaP, PC3 and VCaP, were spiked into healthy donor blood to create mock patient-like samples for downstream single cell genomic analysis. In addition, samples from seven metastatic castration resistant prostate cancer (mCRPC) patients were included to evaluate clinical feasibility. CTCs were enumerated and characterized using the Epic Sciences CTC Platform. Identified single CTCs were recovered, whole genome amplified, and sequenced using an Illumina NextSeq 500. CTCs were then analyzed for genome-wide copy number variations, followed by genomic instability analyses. Large-scale state transitions (LSTs) were measured as surrogates of genomic instability. Genomic instability scores were determined reproducibly for LNCaP, PC3, and VCaP, and were higher than white blood cell (WBC) controls from healthy donors. A wide range of LST scores were observed within and among the seven mCRPC patient samples. On the gene level, loss of the PTEN tumor suppressor was observed in PC3 and 5/7 (71%) patients. Amplification of the androgen receptor (AR) gene was observed in VCaP cells and 5/7 (71%) mCRPC patients. Using an in silico down-sampling approach, we determined that DNA copy number and genomic instability can be detected with as few as 350K sequencing reads. The data shown here demonstrate the feasibility of detecting genomic instabilities at the single cell level using the Epic Sciences CTC Platform. Understanding CTC heterogeneity has great potential for patient stratification prior to treatment with targeted therapies and for monitoring disease evolution during treatment.
authors.affiliation: Epic Sciences, Inc., San Diego, CA, United States of America.
authors.forename: Stephanie B
authors.identifier: http://orcid.org/0000-0002-7432-5639
authors.initials: SB
authors.lastname: Greene
authors.affiliation: Epic Sciences, Inc., San Diego, CA, United States of America.
authors.forename: Angel E
authors.initials: AE
authors.lastname: Dago
authors.affiliation: Epic Sciences, Inc., San Diego, CA, United States of America.
authors.forename: Laura J
authors.initials: LJ
authors.lastname: Leitz
authors.affiliation: Epic Sciences, Inc., San Diego, CA, United States of America.
authors.forename: Yipeng
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Epic Sciences, Inc., San Diego, CA, United States of America.
authors.forename: Jerry
authors.initials: J
authors.lastname: Lee
authors.affiliation: Epic Sciences, Inc., San Diego, CA, United States of America.
authors.forename: Shannon L
authors.initials: SL
authors.lastname: Werner
authors.affiliation: Genentech, Inc./ Roche, San Francisco, CA, United States of America.
authors.forename: Steven
authors.initials: S
authors.lastname: Gendreau
authors.affiliation: Genentech, Inc./ Roche, San Francisco, CA, United States of America.
authors.forename: Premal
authors.initials: P
authors.lastname: Patel
authors.affiliation: Genentech, Inc./ Roche, San Francisco, CA, United States of America.
authors.forename: Shidong
authors.initials: S
authors.lastname: Jia
authors.affiliation: Genentech, Inc./ Roche, San Francisco, CA, United States of America.
authors.forename: Liangxuan
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Epic Sciences, Inc., San Diego, CA, United States of America.
authors.forename: Eric K
authors.initials: EK
authors.lastname: Tucker
authors.affiliation: Epic Sciences, Inc., San Diego, CA, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: Malchiodi
authors.affiliation: Epic Sciences, Inc., San Diego, CA, United States of America.
authors.forename: Ryon P
authors.initials: RP
authors.lastname: Graf
authors.affiliation: Epic Sciences, Inc., San Diego, CA, United States of America.
authors.forename: Ryan
authors.initials: R
authors.lastname: Dittamore
authors.affiliation: Epic Sciences, Inc., San Diego, CA, United States of America.
authors.forename: Dena
authors.initials: D
authors.lastname: Marrinucci
authors.affiliation: Epic Sciences, Inc., San Diego, CA, United States of America.
authors.forename: Mark
authors.initials: M
authors.lastname: Landers
mesh_terms: D045744:Cell Line, Tumor; D043171:Chromosomal Instability / Q000235:genetics*; D056915:DNA Copy Number Variations / Q000235:genetics*; D015723:Gene Library; D015894:Genome, Human; D042822:Genomic Instability; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D009360:Neoplastic Cells, Circulating / Q000473:pathology; D051059:PTEN Phosphohydrolase / Q000235:genetics; D011944:Receptors, Androgen / Q000235:genetics; D015203:Reproducibility of Results; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: C410798:AR protein, human; D011944:Receptors, Androgen; D051059:PTEN Phosphohydrolase; C494929:PTEN protein, human