Lung cancer is one of the most common malignant tumors. That is why significant efforts of scientists working in the field of molecular Oncology are aimed to find sensitive and specific biomarkers for determining the prognosis of the disease and to monitor patients during treatment. It is needed to optimize the tactics of adjuvant therapy. One of these markers is the circulating tumor DNA (cDNA), namely, the change of its content in the blood plasma after radical surgical treatment. cDNA accounts for 0.01% to 90% of all circulating extracellular DNA, depending on the size of the tumor, its vascularization, and biological properties.
Tumor DNA enters the bloodstream as a consequence of apoptosis, necrosis, phagocytosis of tumor cells as well as in the process of targeted isolation by tumor cells. The half-life of DNA in the bloodstream takes from 16 minutes to 2.5 hours. Thus it can be used as a biomarker that reflects the tumor burden.
The presence of cDNA in the plasma of patients undergone radical treatment (or the absence of a decrease in the level of cDNA compared to its level before surgery) may reflect the presence of minimal residual disease (MRD) phenomenon. MRD stands for the presence of isolated or circulating tumor cells after radical tumor removal. These cells cannot be detected by means of routine diagnostic methods used today.
The presence of MRD markers may indicate a high risk of disease recurrence. Thus, determining the level of cDNA in blood plasma before and after surgery, as well as monitoring its level for a certain time after surgery, can help to identify a group of patients with an increased risk of relapse. All of that will optimize the tactics of monitoring and subsequent treatment of corresponding patients. Another reason to determine the cDNA level after radical treatment is the results of multiple studies showing the following: a boost of cDNA level reflects a disease relapse much earlier than standard imaging methods (CT, MRI). According to global data, an increase of cDNA level in plasma of patients undergone radical surgical treatment can outstrip the relapse detection made by CT for a period of 30 to 180 days.
LUCARD is intended to prove that cDNA can be used not only as a marker for cancer detection, but also as a criterion to evaluate success of treatment after surgery or chemotherapy. While adopting the practice to determine cDNA on 7-8 days after surgery the oncologist will be able to choose the most rational tactics for further treatment and to implement the advanced direction of personalized medicine. All of that will help to prolong the particular person's life and to improve the society health as a whole.
More than 200 patients with operable NSCLC are involved in the study which will help to assess the correlation of changes in the cDNA dynamics after surgery and relapse. The mutations of patients' tumor tissue collected on a panel of 374 genes will be analyzed by NGS (New Generation Sequencing) method. Detected by NGS at least 15 somatic mutations for each patient individually will be selected for the research in pre-and postoperative plasma and during the next four visits. The Nimblegen SeqCap EZ Choice kit (”Roche") is used to enrich targets. Total coverage = 3 MB, average coverage = 500x. In case of absence of sensitizing mutations, other somatic mutations are selected for analysis.
Panel of Genes
AKT1, BRAF, DDR2, EGFR, HER2, KRAS, MEK1, NRAS, PIK3, PTEN, NTRK1, NTRK2, NTRK3, TP53, CDKN2A, ALK( Rearrangement), MET (Amplification), RET (Rearrangement), ROS1 (Rearrangement), FGFR3 (Fusions), RICTOR (Amplification), SOX2 (Amplification), FGFR1-2 (+Amplification), XPC, WT1, NF1, KIT, TSC1, MSH2, GPC3, BRCA1, BRCA2 (+Amplification), ERBB2, MAP2K1, CD79A, EPHB1, EPHB4, GRM8, LIFR, LPHN3, LPP, MYH9, NCOA1, NCOA2, PMS1, POT1, POU5F1, SOX2, CD79B, SSX1, STK36, WAS, WHSC1, WRN, GNAS, HRAS, ATRX, EPHB6, HCAR1, HFN1A, BAP1, CDC73, CDK12, CDH1, ERCC1, HIF1A, ERCC3, HLF, LRP18, LTF, NCOA4, NFK81, PPARG, PPP2R1, ASUFU, CDH11, SYK, XPA, IDH1, CDKN, LTK, NFK82, PRDM1, SYNE1, XPC, XP01, IDH2, JAK2, CDKN2, BCDH2, ERCC4, HOOK3, ERCC5, HSP90AA1, PRKAR1A, TAF1, XRCC2, KOR, CEBPA, CDH20, CHEK1, CDH5, CDK8, ERGETS1, HSP90A81, ICK, MAF8, MAGEA1, NKX2-1, NLRP1, PRKDC, PSIP1, TAF1L, TAL1, ZNF384, ZNF521, KIT, KRAS, CHEK2, CREBBP, CDKN2C, ETV1, IGF1R, MAGl1, CRBNEXT1, FANCC, IGF2R, IKZF1, IL2, MAML2, MARK1, MARK4, M8D1, NOTCH4, NSD1, NUMA1, PAK3, PARP1, PAX3, PTGS2, PTPRD, RECQL4, REL, RHOH, T8X22, TCF12, TCL1A, TET1, TFE3, ABL1, AKT1, AR, AXL, BRAF, MAP2K1, MAP2K2, MET, MTOT, MTC, DNMT3A, CIC, ETV4, IGF2, MALT1, FANCA, CKS1B, MAP3K7, NUP214, PTPRT, RALGDS, TCF3, TCF7L1, AKT2, AKT3, MAP2K4, MAPK1, FANCD2, CMPK1, EXT2, IKBKB, FAM123B, IKBKE, MAPK8, NUP98, RARA, TCF7L2, ALK, FBXW7, COL1A1, MLH1, CREB1, FANCF, MPL, MSH2, MSH6, CRKL, FANCG, IL21R, FANCJ, IL6ST, MCL1, PAXS, NBN, CRTC1, FAS, IL7R, MDM2, PAX, RNASEL, RNF2, TGF8R2, TGM7, CBL, MYCNNF1, CSMD3, CYP2D6, DEK, DST, FLCN, FLT4, FOXP1, G6PD, ING4, IRF4, ITGA9, JUN, KAT6A, MDM4, MEN1, MLL2, MRE11, AMTR, MTRR, PAX8, P8RM1, PDGF8, PIK3CD, PIK3CG, PIK3R2, RNF213, RPS6KA2, SAMD9, SOHO, SEPT9, SGK1, TH8S1, TIMP3, TNFAIP3, TRIM24, TRIM33, TRIP11, CCND1, CDK4, CDK6, EGFR, ESR1, EZH2, FGFR1, NFE2L2, NRAS, PDGFRB, RAF1, SF3B1, NF2, CTNNA1, FH, NOTCH1, CTNNB1, NOTCH2, CYLD, FLl1, FLT1, IRS2, ITGA10, MITF, MLL, P8X1, PDE4DIP, RRM1, RUNX1T1, TLR4, TLX1, CSF1R, DDR2, NTRK3, CYP2C19, PDGFRA, NPM1, PALB2, FN1, ITGB2, MLL3, PER1, PIK3R1, DAXX, FOXL2, ITGB3, MLLT10, PGAP3, SBDS, SDHA, TNFRSF14, TNK2, ERBB2, PIK3CA, PMS2, DCC, JAK1, MMP2, PHOX28, SDHB, TOP1, ERBB3, ERBB4, PIK3CB, PTCH1, FOX01, FOX03, JAK3, MN1, PIK3C28, SDHD, TPR, ERCC2, PTPN11, PTEN, DDIT3, RADSO, DICER1, FOXP4, RET, RB1, RUNX1, DPYD, FZR1, KAT6B, SETD2, GATA1, KDM5C, KDM6A, MUC1, MUTYH, PIM1, PKHD1, SH2D1A, SMAD2, TRRAP, TSHR, FGFR2, SMO, SMARCA4, EML4, KEAP1, MY8, PLAG1, SMAD4, UBR5, FGFR3, FGFR4, SRC, SMARCB1, EP300, GATA2, GATA3, KLF6, MYCL1, PLCG1, SMUG1, UGT1A1, FLT3, ARID1A, STK11, EP400, GPR124, LCK, MYD88, MYH11, PLEKHGS, PML, SOCS1, SOX11, USP9X, VHL, GNA11, GNAQ, ASXL1, ATM, ATR, TET2, EPHA3, GDNF, LAMP1, TP53, EPHA7, TSC1, A8L2, ACVR2A, ADAMTS2, AFF1, AFF3, AKAP9, APC, ARID2, ARNT, ATF1, AURKA, AURK8, AURKC, BAI3, BCL10, BCL11A, BCL118, BCL2, BCL2L1, BCL2L2, BCL3, BCL6, BCL9, BCR, B1RC2, B1RC3, B1RC5, BLM, BLNK, BMPR1A, BRD3, BTK, BUB1B, CARD11, CASCS, CCND2, CCNE1, TSC2, BAT26, BAT25, BAT34C4, BAT40, D10S196, D13S153, D13S175, D17S250, D17S588, D17S787, D18S55, D18S61, D18S64, D18S69, D20S100, D2S123, D3S1029, D5S107, D5S346, D7S519, D8S87, NR21, NR22, NR24, MONO-27.