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. 2020 Feb;15(2):216–230. doi: 10.1016/j.jtho.2019.10.007

Figure 3.

Figure 3

Somatic mutations in SCLC circulating free DNA (cfDNA) and comparison of detection frequencies between cfDNA and circulating tumor cell (CTC) readouts. (A) The 62 patient cfDNA samples (29 patients with ES SCLC and 33 patients with LS SCLC) are arranged from left to right with each column representing mutation profile of an individual patient cfDNA sample. The genes are arranged from top to bottom according to the incidence of mutation of the gene in this cohort of patients and are displayed on the left y axis of the heatmap. The incidence of mutations occurring on a specific gene is annotated on the right y axis of the heatmap. (B) Detection frequencies were determined for the 62 patients whose samples passed the targeted next-generation sequencing quality control steps. Positive CNA samples were scored on the basis of any of the three copy number alteration (CNA) metric values rising above predetermined control thresholds, and for cfDNA targeted mutation analysis (MUT), the sample was scored positive if at least one mutation was detected. (C) Comparison of cfDNA analysis and CellSearch CTC enumeration. For 51 of the 69 cfDNA samples from the cohort of patients with SCLC, a parallel blood sample was collected at the same time point and CellSearch CTC enumeration was carried out. For cfDNA, samples were scored as positive samples if any of the CNA metric values were above predetermined control thresholds or if at least one mutation was present. Positive CTC samples were defined as any sample having at least one CellSearch CTC. Abbreviations: ES, extensive-stage; LS, limited-stage; MUT, Mutation; M+C, MUT and CNA; D+C, cfDNA and CTC; TP53, tumor protein p53 gene; RB1, retinoblastoma gene; MUC16, mucin 16, cell surface associated gene; COL22A1, collagen type XXII alpha 1 chain gene; NOTCH1, notch 1 gene; KMT2D, lysine methyltransferase 2D gene; PDE4DIP, phosphodiesterase 4D interacting protein gene; TP73, tumor protein p73 gene; FGFR1, fibroblast growth factor receptor 1 gene; NTRK1, neurotrophic receptor tyrosine kinase 1 gene; SLIT2, slit guidance ligand 2 gene; EPHA5, EPH receptor A5 gene; ZNF521, zinc finger protein 521 gene; CREBBP, CREB binding protein gene; EP300, E1A binding protein p300 gene; FLT4, fms related tyrosine kinase 4 gene; GNAS, GNAS complex locus gene; KEAP1, kelch like ECH associated protein 1 gene; KMT2A, lysine methyltransferase 2A gene; MSH6, mutS homolog 6 gene; MTOR, mechanistic target of rapamycin kinase gene; NFE2L2, nuclear factor, erythroid 2 like 2 gene; NOTCH2, notch gene; NOTCH3, notch gene; PIK3CA, phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha gene; ALK, ALK receptor tyrosine kinase gene; APC, APC, WNT signaling pathway regulator gene; ATM, ATM serine/threonine kinase gene; EPHA3, EPH receptor A3 gene; ERBB2, erb-b2 receptor tyrosine kinase 2 gene; FANCG, FA complementation group G gene; KIT, KIT proto-oncogene receptor tyrosine kinase gene; LIFR, LIF receptor subunit alpha gene; MET, MNNG HOS Transforming gene; NTRK3, neurotrophic receptor tyrosine kinase 3 gene; PARP4, poly(ADP-ribose) polymerase family member 4 gene; PDGFRA, platelet derived growth factor receptor alpha gene; PTEN, phosphatase and tensin homolog gene; RAD51C, RAD51 paralog C gene; SETBP1, SET binding protein 1 gene; TSC2, tuberous sclerosis 2 gene; AR, androgen receptor gene; ATR, ATR serine/threonine kinase gene; BRCA1, BRCA1, DNA repair associated gene; BRCA2, BRCA2, DNA repair associated gene; BRIP1, BRCA1 interacting protein C-terminal helicase 1 gene; CHEK2, checkpoint kinase 2 gene; FANCD2, Fanconi anemia complementation group D2 gene; FANCE, FA complementation group E gene; FANCL, FA complementation group L gene; GATA3, GATA binding protein 3 gene; GRIN2A, glutamate ionotropic receptor NMDA type subunit 2A gene; HRAS, Harvey rat sarcoma viral oncogene homolog gene; IDH2, isocitrate dehydrogenase (NADP(+)) 2, mitochondrial gene; NF1, neurofibromin 1 gene; NFATC2, nuclear factor of activated T cells 2 gene; PRKDC, protein kinase, DNA-activated, catalytic polypeptide gene; RAD50, RAD52 homolog, DNA repair protein gene; RBL2, retinoblastoma-like 2 gene; RET, ret proto-oncogene gene; RUNX1T1, RUNX1 translocation partner 1 gene; STK11, serine/threonine kinase 11 gene; TSC1, tuberous sclerosis 1 gene; WT1, Wilms tumor 1 gene.