SNPMiner Trials by Shray Alag


SNPMiner Trials: Clinical Trial Report


Report for Clinical Trial NCT03870828

Developed by Shray Alag, 2019.
SNP Clinical Trial Gene

Incidence, Clinical Characteristics and Evaluation of Prognostic and Diagnostic Markers of Interstitial Pneumonia With Autoimmune Features (IPAF) - a Multicenter Prospective Study

Interstitial pneumonia with autoimmune features (IPAF) was defined in 2015 by the Working Group of the European Respiratory Society (ERS) and the American Thoracic Society (ATS) as interstitial pneumonia with some clinical and/or serological features suggesting presence of an underlying autoimmune disorder. However, ofiicial criteria for diagnosis of an autoimmune disease are not met. Aims of the study: 1. Determine the incindence of IPAF in comparison with interstitial lung diseases (ILDs) and classic autoimmune diseases (ADs) in polish pulmonological centers. 2. Clinical, serological, functional and radiological and histopathological characteristics of IPAF patients. 3. Analysis of diagnostic strategies towards specific IPAF subgroups. 4. Characterictics of potencial diagnostic, predictive and prognostic features of IPAF. 5. Prospective assessment of IPAF patients in the courseof 5 years in order to determine stability of the diagnosis and potential progression to other diseases, e.g. ADs.

NCT03870828 Interstitial Lung Disease Interstitial Pneumonia Interstitial Fibrosis Autoimmune Diseases
MeSH: Pneumonia Lung Diseases Lung Diseases, Interstitial Autoimmune Diseases
HPO: Abnormal lung morphology Autoimmunity Interstitial pneumonitis Interstitial pulmonary abnormality Pneumonia

4 Interventions

Name: Bronchoalveolar lavage and taking bronchial mucosa samples

Description: Regional anesthesia and sedation with use of lidocaine and midazolam will be performed, according to anesthesia protocols applied in respective endoscopy units. Intravenous cannula will be inserted prior to BF. During endoscopy, the patient will be monitored according to safety protocols applied in respective endoscopy units. Bronchoalveolar lavage will be performed in the bronchus from the middle robe of right lung or the lingula of left lung (B4, B5). Localization will be chosen based on HRCT results and will be recorded in patient's medical history. Sterile solution of 0, 9% NaCl will be instilled. 200 ml fluid will be applied with a syringe in portions of 25 ml or 50 ml. It is recommended that minimum 60 % of the lavage fluid is retrieved.

Type: Diagnostic Test

Study group IPAF Control group CTD-ILD Control group ILD

Name: 6minute walk test

Description: a submaximal exercise test which entails measurement of distance walked over a span of 6 minutes. Blood pressure, pulse oximetry are measured directly before and after the test. The participant is also periodically asked about their dyspnea sensation

Type: Diagnostic Test

Study group IPAF Control group CTD-ILD Control group ILD

Name: Arterial blood gas

Description: If SpO2 is measured to be < 92%, an artery (radial or femoral) is punctured in order to take a sample of arterial blood. Then, the artery is compressed in order to prevent bleeding/ hematoma.

Type: Diagnostic Test

Study group IPAF Control group CTD-ILD Control group ILD

Name: Blood drawing

Description: A vein will be punctured in order to take a blood sample for further tests

Type: Procedure

Study group IPAF Control group CTD-ILD Control group ILD


Primary Outcomes

Description: It is still unclear whether there are diagnostic markers specific for IPAF or whether there is a significant difference in concentration of fibrosis biomarkers in IPAF, CTD-ILD and ILD groups. Both blood and BAL biomarkers will be taken under consideration, they include chemokine C-C motif ligand 18 (CXCL18), Surfactant Protein A- (SP-A), Surfactant Protein D (SP-D), Krebs von den Lungen-6 protein (KL-6) and chitotrisidase 1 (CHIT1).

Measure: Identification of IPAF diagnostic markers

Time: 10.2019-10.2020

Time Perspective: Prospective

Cohort


There is one SNP

SNPs


1 S1009A

Samples will be checked for concentration of S1009A protein, chemokine (C-C motif) ligand 2 and chitotrisidase 1 (CHIT 1). --- S1009A ---



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
Autoimmunity
Genes 140
RNASEH2B KRAS TPP2 IL12A RAG1 RAG2 IL12RB1 TREX1 TCF4 GALC ITCH PRTN3 NRAS WAS COMT WIPF1 SPIB TNFSF12 RNASEH2A HLA-DPA1 GPR35 HLA-DPB1 HLA-DQB1 HLA-DRB1 POLG ACP5 KIAA0319L PEPD FADD AIRE TCIRG1 SRP54 OAS1 POU2AF1 CASP10 NBN NLRP1 PTPN22 IRF5 SAMHD1 TRAC CHD7 LMNB2 CAV1 LCK RREB1 SLC7A7 PTEN FAS ADA FASLG CR2 ADAR ADA2 RFX5 RFXAP ANKRD55 JMJD1C ZAP70 GFI1 STAT1 ITK STAT3 STAT4 HIRA TTC7A STIM1 IFNGR1 MST1 RMRP IFIH1 PTPN2 RASGRP1 LIG4 FCGR2C C1GALT1C1 CD3G KMT2D CD247 ICOS MMEL1 CSF2RA CSF2RB SLC12A3 SEC24C CD19 MS4A1 CLCNKB ARVCF CIITA DCLRE1C LACC1 MTHFD1 PIK3R1 RFXANK NFKB1 BTK NFKB2 RNASEH2C UFD1 MIF TNFRSF13C SERPING1 ELANE TNFRSF13B C1QA C1QB C1QC C1R C1S PRKCD C2 C3 CD81 C4A CCN2 CCR6 CTLA4 PLCG2 TNFAIP3 MMP2 C8A LRBA NHEJ1 IL2RA IL2RB IL2RG KDM6A TNFSF15 TNPO3 DNASE1L3 IL6 SEC23B TBX1 IL7R MASP2 GP1BB PNP TBX2 FOXP3
Interstitial pneumonitis
Genes 8
TERC TINF2 STAT3 TERT PLCG2 RAG1 SFTPC FOXP3
Interstitial pulmonary abnormality
Genes 35
GBA UNC119 FARSB RAG1 OAS1 SFTPA1 PARN ATP11A MUC5B ABCA3 TMEM173 PLCG2 ITGA3 RNF168 SFTPA2 ERF DPP9 CSF2RA CSF2RB FAM13A NSMCE3 TERC TINF2 IL1RN RTEL1 SFTPB TERT DSP SFTPC MARS AP3D1 SCARB2 STN1 STAT3 FOXP3
Pneumonia
Genes 117
CYBB NHLRC1 PIGN SLC25A24 CACNA1C RAG1 RAG2 EPM2A COL11A2 FMO3 SAMD9 RNF168 WAS OFD1 USB1 TNFSF12 SFTPC DOCK8 ORC6 SGCG POLA1 SLC35C1 CCDC114 NADK2 ACP5 GNPTAB CFTR NCF1 DDR2 ACTA1 KIAA0586 GAS8 SLC35A1 PEPD BLNK IRF8 CD55 GBA TCIRG1 CASP8 SRP54 NBN NCF2 CHD7 TNFRSF11A NSMCE3 ADA CR2 SELENON SP110 TERT ZAP70 GFI1 LEP ZBTB24 CFB RYR1 STAT3 TBC1D24 RNU4ATAC WDR19 IFNGR1 UNC119 JAK3 RMRP DNAI1 LIG4 TIMM8A KMT2D PANK2 ICOS SFTPA2 RNF125 ALMS1 CD19 MS4A1 EGFR DCLRE1C MTHFD1 TK2 CXCR4 NFIX IGHM KCNJ6 NFKB1 BTK IL21R NFKB2 SETBP1 TNFRSF13C ELANE TNFRSF13B SMARCD2 PRKCD CD79B CD81 CARD11 LTBP3 IGLL1 TAF1 LRBA PLG PLOD1 IL2RG CSPP1 KDM6A NIPBL CFAP410 AFF4 NOTCH3 IL7R MASP2 PNP DNMT3B PMM2 CYBA FOXP3