SNPMiner Trials by Shray Alag


SNPMiner Trials: Clinical Trial Report


Report for Clinical Trial NCT02284295

Developed by Shray Alag, 2019.
SNP Clinical Trial Gene

Molecular, Cytological Features and Genetic Susceptibility of Occupational Chronic Obstructive Pulmonary Disease Attributable to Different Environmental Exposures 2.

The objective of this study is to investigate molecular, cytological and genetic features of occupational chronic obstructive pulmonary disease (COPD) in conditions of different occupational exposures. In order to achieve this goal serum pro-inflammatory cytokines and standard inflammation markers level, hemostasis, cytological analysis of bronchoalveolar lavage fluid and association of single nucleotide polymorphisms (SNPs) rs1800470 transforming growing factor β1 (TGF β1) gene, rs1828591 hedgehog interacting protein (HHIP) gene, rs4129267 interleukin 6 receptor (IL-6R) gene, rs1051730 nicotinic acetylcholine receptor 3 (CHRNA3) gene with COPD in subjects exposed to silica dust and in those exposed to polycyclic aromatic hydrocarbons exhaust will be investigated. The relationship between genotype and phenotype characteristics, such as an inflammation activity, assessed by C-reactive protein (hsCRP) and tumor necrosis factor alpha (TNF α) serum concentration, in different occupational COPD groups will be studied. The hypothesis is that the mechanisms underlying disease development and progression are different due to environmental risk factor that reflex in differs in disease attributes - molecular biomarkers, cytology results and genetic susceptibility between COPD due to dust, COPD due to chemicals and COPD in smokers therefore COPD can be subdivided into ecological phenotypes according to environmental risk factor.

NCT02284295 Chronic Obstructive Pulmonary Disease
MeSH: Lung Diseases Lung Diseases, Obstructive Pulmonary Disease, Chronic Obstructive Disease Susceptibility Genetic Predisposition to Disease
HPO: Abnormal lung morphology Chronic obstructive pulmonary disease Obstructive lung disease

2 Interventions

Name: exposure to respirable silica dust

Description: History of exposure to respirable silica dust due to job

Type: Other

occupational COPD

Name: exposure to aromatic hydrocarbons

Description: history of exposure to aromatic hydrocarbons due to job

Type: Other

occupational COPD


Primary Outcomes

Description: Comparison of groups

Measure: Difference in serum interleukin 1 beta (IL-1β) level between COPD patients exposed to dust, chemicals and tobacco smoke

Time: 1 day (a single measurement)

Description: Comparison of groups

Measure: Difference in serum tumor necrosis factor alpha (TNFα) level between COPD patients exposed to dust, chemicals and tobacco smoke

Time: 1 day (a single measurement)

Description: Comparison of groups

Measure: Difference in spontaneous thrombocyte aggregation between COPD patients exposed to dust, chemicals and tobacco smoke

Time: 1 day (a single measurement)

Description: Comparison of groups

Measure: Difference in collagen induced thrombocyte aggregation between COPD patients exposed to dust, chemicals and tobacco smoke

Time: 1 day (a single measurement)

Description: Comparison of groups

Measure: Difference in epinephrine induced thrombocyte aggregation between COPD patients exposed to dust, chemicals and tobacco smoke

Time: 1 day (a single measurement)

Description: Comparison of groups

Measure: Difference in adenosine diphosphate induced thrombocyte aggregation between COPD patients exposed to dust, chemicals and tobacco smoke

Time: 1 day (a single measurement)

Description: Comparison of groups

Measure: Difference in fibrinogen level between COPD patients exposed to dust, chemicals and tobacco smoke

Time: 1 day (a single measurement)

Description: Comparison of groups

Measure: Difference in fibrinogen degradation products level between COPD patients exposed to dust, chemicals and tobacco smoke

Time: 1 day (a single measurement)

Description: Comparison of groups

Measure: Difference in D-dimer level between COPD patients exposed to dust, chemicals and tobacco smoke

Time: 1 day (a single measurement)

Description: Comparison of groups

Measure: Difference in serum endothelin1 level between COPD patients exposed to dust, chemicals and tobacco smoke

Time: 1 day (a single measurement)

Description: Comparison of groups

Measure: Difference in serum nitric oxide level between COPD patients exposed to dust, chemicals and tobacco smoke

Time: 1 day (a single measurement)

Description: Comparison of groups

Measure: Differences in cytological analysis of bronchoalveolar lavage fluid results between COPD patients exposed to dust, chemicals and tobacco smoke

Time: 1 day (a single measurement)

Description: Odds ratio and 95% confidence interval will be calculated for each occupational group. Controls - healthy people.

Measure: Association of SNPs rs1800470 TGF β1 gene, rs1828591 HHIP gene, rs4129267 IL-6R gene, rs1051730 CHRNA3 gene with COPD in subjects exposed to dust and in those exposed to chemicals. (Odds ratio and 95% confidence interval)

Time: 1 day (a single measurement)

Secondary Outcomes

Description: For SNPs that will occur associated with occupational COPD differences in hsCRP and TNFα serum concentration between subjects with different genotypes will be established separately for exposed to dust COPD group and for exposed to chemicals COPD group.

Measure: Relationship between genotype and phenotype characteristics, such as an inflammation activity, assessed by hsCRP and TNF α serum concentration, in different occupational COPD groups.

Time: 1 day (a single measurement)

Time Perspective: Cross-Sectional

Case Control


There are 4 SNPs

SNPs


1 rs1051730

In order to achieve this goal serum pro-inflammatory cytokines and standard inflammation markers level, hemostasis, cytological analysis of bronchoalveolar lavage fluid and association of single nucleotide polymorphisms (SNPs) rs1800470 transforming growing factor β1 (TGF β1) gene, rs1828591 hedgehog interacting protein (HHIP) gene, rs4129267 interleukin 6 receptor (IL-6R) gene, rs1051730 nicotinic acetylcholine receptor 3 (CHRNA3) gene with COPD in subjects exposed to silica dust and in those exposed to polycyclic aromatic hydrocarbons exhaust will be investigated.

Association of SNPs rs1800470 TGF β1 gene, rs1828591 HHIP gene, rs4129267 IL-6R gene, rs1051730 CHRNA3 gene with COPD in subjects exposed to dust and in those exposed to chemicals.


2 rs1800470

In order to achieve this goal serum pro-inflammatory cytokines and standard inflammation markers level, hemostasis, cytological analysis of bronchoalveolar lavage fluid and association of single nucleotide polymorphisms (SNPs) rs1800470 transforming growing factor β1 (TGF β1) gene, rs1828591 hedgehog interacting protein (HHIP) gene, rs4129267 interleukin 6 receptor (IL-6R) gene, rs1051730 nicotinic acetylcholine receptor 3 (CHRNA3) gene with COPD in subjects exposed to silica dust and in those exposed to polycyclic aromatic hydrocarbons exhaust will be investigated.

Association of SNPs rs1800470 TGF β1 gene, rs1828591 HHIP gene, rs4129267 IL-6R gene, rs1051730 CHRNA3 gene with COPD in subjects exposed to dust and in those exposed to chemicals.


3 rs1828591

In order to achieve this goal serum pro-inflammatory cytokines and standard inflammation markers level, hemostasis, cytological analysis of bronchoalveolar lavage fluid and association of single nucleotide polymorphisms (SNPs) rs1800470 transforming growing factor β1 (TGF β1) gene, rs1828591 hedgehog interacting protein (HHIP) gene, rs4129267 interleukin 6 receptor (IL-6R) gene, rs1051730 nicotinic acetylcholine receptor 3 (CHRNA3) gene with COPD in subjects exposed to silica dust and in those exposed to polycyclic aromatic hydrocarbons exhaust will be investigated.

Association of SNPs rs1800470 TGF β1 gene, rs1828591 HHIP gene, rs4129267 IL-6R gene, rs1051730 CHRNA3 gene with COPD in subjects exposed to dust and in those exposed to chemicals.


4 rs4129267

In order to achieve this goal serum pro-inflammatory cytokines and standard inflammation markers level, hemostasis, cytological analysis of bronchoalveolar lavage fluid and association of single nucleotide polymorphisms (SNPs) rs1800470 transforming growing factor β1 (TGF β1) gene, rs1828591 hedgehog interacting protein (HHIP) gene, rs4129267 interleukin 6 receptor (IL-6R) gene, rs1051730 nicotinic acetylcholine receptor 3 (CHRNA3) gene with COPD in subjects exposed to silica dust and in those exposed to polycyclic aromatic hydrocarbons exhaust will be investigated.

Association of SNPs rs1800470 TGF β1 gene, rs1828591 HHIP gene, rs4129267 IL-6R gene, rs1051730 CHRNA3 gene with COPD in subjects exposed to dust and in those exposed to chemicals.



HPO Nodes


HPO:
Abnormal lung morphology
Genes 786
NHLRC1 EPHB4 MKKS ERBB2 SLC29A3 ERCC2 ABCA3 DGCR6 GLDN ERCC3 LZTR1 ABL1 ESS2 RNF168 ERF ZMPSTE24 MANBA AICDA PYROXD1 MARS USP9X SLC35C1 MAT2A TRAIP ACP5 NCF1 ACTA1 ACTA2 ETFA ETFB KIAA0319L ETFDH NAA10 CCNO TCIRG1 EVC MMP21 MCM4 IKZF1 EWSR1 CD46 KLHL41 TMEM173 RRAS ACVRL1 RREB1 ARID1A ADA COLQ IL17F MECP2 KLRC4 IFT43 MYSM1 NME8 MEFV RYR1 STN1 TBC1D24 BAP1 CDC45 GREB1L CITED2 FANCB ARID1B SAMD9L FBN1 PANK2 SFTPA2 KITLG MBTPS2 MGP AARS2 ZMYND10 CIITA FCGR3A ARHGAP31 AGA JAG1 AGT AGTR1 MIF MITF GPC4 SCN9A SCN10A SCNN1A SCNN1B WDR35 EMG1 SCNN1G CC2D2A AK2 SFTPA1 AKT1 NOP10 FGFR1 FGFR3 IFT80 PWAR1 PRKAG2 DOCK6 LTBP4 RSPH9 ALOX12B FOXF1 ALPL CRTAP FOXE3 FOXC2 FOXE1 FLI1 FLNA FLNB FRAS1 CLCA4 FBLN5 FMO3 CCDC22 LAMTOR2 OFD1 SFTPB SFTPC CTC1 PUF60 SGCG SGSH KLHL40 IFT81 SLC35A1 ITGA8 IKBKG ELP1 FUZ SLC34A2 BIRC3 XIAP LIPN CHD7 APOE AP3B1 FAS FCN3 NHP2 FASLG EPG5 MSN SDR9C7 WDR19 MST1 DNAI1 NPHP3 PIEZO2 TNFSF11 ARSB SLC11A1 G6PC3 ARVCF DYNC2LI1 MTHFD1 ASAH1 SLC18A3 SLC25A1 RFXANK SLCO2A1 DLL3 FSHR SNAI2 SMARCA4 RSPO2 SMARCB1 FLCN SMARCC2 SMARCD2 SMARCE1 FOXP1 SMN1 C11ORF95 CARD11 SMPD1 MESP2 NR5A1 FUCA1 ATM NGLY1 SNAP25 TBC1D23 MCTP2 SNRPN MUSK ATP5F1A GAA H19 AFF4 INVS MASP2 SON DNAH11 SOS1 SOS2 SNORD115-1 TRAF3IP2 MYD88 SOX10 SOX11 STK36 MYH3 INTU MYH7 SPAG1 MYH11 EOGT MYL2 DIS3L2 GALNS MYLK RIPK1 SPINK1 KIF1A MYO5A CHST14 TNFSF12 RTEL1 ERAP1 MYO9A JAGN1 MYOD1 NADK2 SDCCAG8 B2M PKD1L1 NAGLU GAS8 MAP3K20 GATA2 GATA4 GATA6 FADD GBA PWRN1 SRP54 NBN DRC1 SIK1 NCF2 NCF4 SLC46A1 CCND1 BCL2 NDN TNFRSF11A BCL6 NEB GDF1 BCR GPKOW GFI1 STAT1 CFB STAT3 STAT4 BGN STAT5B SLC52A3 BLM IFIH1 DNAAF3 STK11 MALT1 NEK1 BMPR2 STX1A GLA GPC3 GLB1 BRAF BRCA2 SULT2B1 NFE2L2 GLE1 GLI1 NFIX GLI3 NFKB1 BTK NFKB2 NFKBIA HES7 BUB1 VAMP1 BUB1B VPS13A LRRC56 HYLS1 KIAA0556 C4A TRPV3 ATP11A BCL10 TAF1 BMPER HERC2 STRA6 MYRF TAP1 TAP2 TAPBP AP3D1 GNS CFAP410 NOTCH1 TBX1 NOTCH2 NOTCH3 TBCE GP1BB PNP SPINK5 TBX5 TBX6 NPM1 CACNA1C TCF4 NIPAL4 TCF3 CARMIL2 NRAS GPR35 DOK7 ROR2 DDR2 NUMA1 NUP88 HGSNAT BAZ1B CASP8 OAS1 CASP10 MUC5B IL17RC RIPK4 OCRL SYT2 SPECC1L CAV1 RUNX2 SLC7A7 NSMCE3 CBL TERC CHAMP1 SERPINH1 TERT NXN DICER1 NR2F2 POLR3A TFRC TGFB1 GRIP1 TGFB2 TGFB3 UNC119 TGFBR1 TGFBR2 SLC22A18 LMOD3 TGM1 CORO1A GTF2E2 CD3D CD3E CD3G GTF2I CD8A DPP9 CD19 MS4A1 DCLRE1C ZNF341 NKX2-1 IL12A-AS1 CD28 TK2 GUSB BTNL2 SCARB2 TLR4 DNAI2 TNFRSF13C LRRC8A TNFRSF13B CD79A CD79B CD81 PRKN PARN HABP2 PAX3 PAX6 SPIDR LRBA TNFRSF1A TNFRSF1B BUB3 DNAAF1 KAT6B AGRN HACD1 TP53 ATP6V0A2 BMP15 PCNT HELLS TPM2 TPM3 CFH PIGN HFE TPP2 SCN11A POU6F2 CFAP300 HLA-B PDGFRA PDGFRB HLA-DPA1 ORC6 HLA-DPB1 CCDC114 CTSC HLA-DRB1 CFTR TRPS1 PEPD BLNK SLC5A7 PEX1 CLEC7A SOX18 PEX13 CHAT TSC1 TSC2 LRRC6 WNT4 TRIP13 TRIP11 LYST CHRM3 TRIP4 ZNHIT3 CHRNA1 PGM3 CHRND CHRNG HIRA RNU4ATAC TYK2 SLC2A10 CRELD1 SERPINA1 ICOS CLCN7 HOXD13 PIK3CA PIK3CD PIK3R1 HPGD EDARADD RAB3GAP2 HPS1 UFD1 A2ML1 NPAP1 SNX10 HRAS PKHD1 PSMC3IP GTF2H5 UMPS CCR1 UNG CCR6 IL17RA DGCR8 PLCG2 PLEC PLG SERPINF2 PLOD1 PLP1 KDM6A NIPBL CCDC151 ALG12 COG4 PML COL1A1 PMM2 COL2A1 COL3A1 VHL SLC25A24 COL5A1 COL5A2 COL6A1 HSPG2 COL6A2 COL6A3 PIGL PSAT1 EXOSC9 COL11A2 MAGEL2 COL13A1 DONSON WAS COMT CCDC103 WIPF1 TAPT1 ADAMTS3 ADAMTS2 CLIP2 DLL4 NSD2 NELFA MAP3K8 POLA1 WNT3 POLE GNPTAB EFEMP2 WRN IRF8 WT1 PORCN MINPP1 NABP1 GTF2IRD1 IDUA CFI CR2 LGI4 SP110 CREBBP CFAP298 ZAP70 CRKL PPP1CB DNAH1 IFNGR1 PPP2R1B BCL11B CSF2RA CSF2RB SEC24C IGH LACC1 NEK8 IGHM IL21R SETBP1 RBPJ LPIN2 MPLKIP PRKAR1A NKX2-5 CYP4F22 PRKCD CCN2 CTLA4 IGLL1 PRKDC PRKG1 MAPK1 IKBKB IL1RN CEP57 CCDC65 IL2RA IL2RG HYDIN IL6 IL7R CYBA PRPS1 CYBB MKRN3 IL10 IL12A TCTN3 PRSS1 IFT140 ZBTB16 SAMD9 PRTN3 PLVAP PSAP INHBA ABCA12 TMEM94 MCIDAS RIPPLY2 IFT172 PIEZO1 INPPL1 CYBC1 RNF113A KIAA0586 VPS33A INSR CD55 IPW IRF1 PTPN22 IRF5 TTC25 NHLRC2 DNAL1 KEAP1 ITGA3 ITGA7 PTEN BCOR ACE NEK9 ZEB2 ZBTB24 PTH1R MRPS22 PHGDH SNORD116-1 MKS1 HELLPAR ITPR1 FAM111B NSDHL DNAJB13 TMEM260 JAK3 DNAAF5 FREM2 TIMM8A FAM20C PTPN11 CEP120 RNF125 ALMS1 CLPB RSPH1 TINF2 TECPR2 WASHC5 FGF20 CXCR4 KCNJ6 HPS4 DHCR7 DHCR24 NECTIN1 IL21 DKC1 ALDH18A1 FIP1L1 CDT1 DNAH5 DNASE1L3 RAB27A IL23R KIF11 CCDC40 DNMT3B FOXP3 KRAS SLC12A6 RAF1 RAG1 DGCR2 RAG2 FAT4 EPM2A EVC2 B3GLCT ITCH RAPSN RARA RARB RSPH4A RASA2 WDR34 NUP107 USB1 DSG1 RB1 DSP DOCK8 DYNC2H1 SLC26A2 DNAAF4 ASCC1 DVL3 LAMA2 AGGF1 FARSB WDR60 LAMB2 RELA RELB REN DPF2 LBR ARMC4 REST RET LCK RFC2 WRAP53 GPC6 CCNQ ECM1 SELENON TBL1XR1 RFX5 RFXAP GMNN JMJD1C LEP CCDC39 LEPR LETM1 LFNG EDNRB ADGRG6 MKRN3-AS1 CEP55 RIT1 TTC7A DNAAF2 SLC25A22 RMRP LIFR MFAP5 RASGRP1 MLXIPL LIG4 LIMK1 RSPH3 KMT2D FAM13A LMNA EGFR CDCA7 TRIM28 RCBTB1 VANGL1 CCBE1 LOX ARID2 IER3IP1 ALG9 HPS6 RLIM IRAK4 TTC21B EHMT1 ELANE TRPV4 UBAC2 PIH1D3 ALOXE3 EIF2AK4 ELN LTBP3 RPGR DCTN4 SH2D1A ENG CSPP1 TBL2 EP300 COQ7 RPL10 SMAD3 SMAD4
Chronic obstructive pulmonary disease
Genes 28
CYBB PTPN22 NCF2 MYH7 NCF4 SERPINA1 CTLA4 MMP1 PRTN3 GLA WAS RREB1 COMT SEC24C WIPF1 ARVCF HLA-DPA1 HLA-DPB1 DNAAF4 JMJD1C TBX1 NFKB1 CYBC1 NCF1 UFD1 HIRA GP1BB CYBA
Obstructive lung disease
Genes 35
CYBB SCNN1A SCNN1B APC SCNN1G PTPN22 NCF2 MYH7 NCF4 SERPINA1 CTLA4 MMP1 PRTN3 GLA WAS RREB1 COMT SEC24C MGP WIPF1 ARVCF HLA-DPA1 HLA-DPB1 DNAAF4 JMJD1C DNASE1L3 TBX1 NFKB1 CYBC1 CFTR NCF1 UFD1 HIRA GP1BB CYBA