SNPMiner Trials by Shray Alag


SNPMiner Trials: Clinical Trial Report


Report for Clinical Trial NCT02089555

Developed by Shray Alag, 2019.
SNP Clinical Trial Gene

Biomarkers for Alzheimer's Disease and Mild Cognitive Impairment in African Americans and Caucasians

African Americans are twice as likely to develop Alzheimer's disease as white Americans, but few African Americans are enrolled in large Alzheimer's biomarker studies. The current proposal aims to determine the influence of Alzheimer's disease and vascular disease on memory and aging in African Americans through modern biomarkers (spinal fluid, MRI, and amyloid imaging), and how these may differ between African Americans and white Americans in preparation for a large multi-center study of aging in African American.

NCT02089555 Mild Cognitive Impairment Alzheimer's Disease
MeSH: Alzheimer Disease Cognitive Dysfunction
HPO: Alzheimer disease Cognitive impairment Mental deterioration

3 Interventions

Name: Lumbar puncture

Description: Cerebrospinal fluid (CSF) will be collected via lumbar puncture. During lumbar puncture, a needle is inserted between two lumbar bones (vertebrae) to remove a sample of cerebrospinal fluid. The procedure involves inserting a thin, hollow needle between the two lower vertebrae (lumbar region), through the spinal membrane (dura) and into the spinal canal and extracting a small amount of fluid. The procedure takes about 45 minutes.

Type: Procedure

African Americans Non-Hispanic Whites

Name: Blood draw

Description: One tube of blood will be collected in an ethylenediaminetetraacetic acid (EDTA)-K2 plasma tube for DNA analysis.

Type: Procedure

African Americans Non-Hispanic Whites

Name: Magnetic Resonance Imaging (MRI)

Description: Each participant will undergo Magnetic Resonance Imaging (MRI) analysis using a modified Alzheimer's Disease Neuroimaging Initiative (ADNI) protocol with a 3 Tesla (3T) MRI Scan. The exam takes approximately 20 minutes.

Type: Procedure

African Americans Non-Hispanic Whites


Primary Outcomes

Measure: CSF endothelial marker levels

Time: one time only

Measure: CSF Alzheimer's biomarker levels

Time: one time only

Secondary Outcomes

Measure: MRI evidence of small vessel disease

Time: one time only

Measure: MRI evidence of brain atrophy

Time: one time only

Time Perspective: Prospective

Case Control


There is one SNP

SNPs


1 K56M

The Lys56Met ICAM1 gene variant associated with low ICAM-1 levels is uniquely found in 16-20% of AA, and these subjects may have impaired downstream activation of neprilysin, an Abeta-degrading enzyme. --- Lys56Met ---

If the hypothesis is true, AA subjects with the Lys56Met gene variant will be more likely to have hippocampal atrophy, temporal-parietal cerebral hypoperfusion, and cerebral amyloid deposition than AA subjects and NHW subjects without the gene variant. --- Lys56Met ---



HPO Nodes


HPO:
Alzheimer disease
Genes 6
PSEN2 CACNA1G APOE APP GATA1 PSEN1
Cognitive impairment
Genes 527
NHLRC1 HEXA HEXB MAG UBA5 CLN8 GDF5 SDHAF1 EPRS TREX1 AARS ERCC2 PNKP ERCC3 ERCC4 ERCC5 ERCC6 CRLF1 ERF MAOA STUB1 HLA-B PDGFB CENPE PDGFRB MAPT HLA-DQB1 SMC1A HLA-DRB1 TRAIP GDF6 ACTB KATNB1 LRRK2 SLC5A7 PEX1 PEX6 PEX10 PEX12 PEX13 DHDDS PEX14 LAGE3 RPS20 TSC1 TSC2 CHD2 TIMMDC1 HNF4A HNRNPA1 TTPA CHRM3 ABCA7 REEP2 MECP2 TTR HNRNPA2B1 TUBA4A KLRC4 MEFV MYORG PGM3 ADD3 TBC1D24 CHRNG SPG21 TNFSF4 MEN1 MEOX1 TTC8 ERCC8 TYROBP HEPACAM TUBB4A UBA1 ADRA2B FBN1 PANK2 SERPINI1 ATRIP MBTPS2 AARS2 ATXN1 ATXN2 FKTN PIK3CA ATXN7 UBTF CLN3 DSTYK CLN5 SCN1A RIN2 SCN2A UCP2 SCN3A CCDC78 CLTC SCN8A ATXN3 FBXO7 PEX16 DCAF17 MLH1 FGD1 KMT2A CYP7B1 RNF216 PLA2G6 CCR1 AKT1 FGF12 FGF14 TOMM40 FGFR3 ATXN10 ABCD1 UQCRC2 TP53RK MTO1 SLC30A9 HSD17B4 POMK ITM2B GMPPB SEC61A1 LTBP4 PLP1 ADAMTSL4 KCNT1 ALG12 ALOX12B SEC23B MOG SDHA SDHB SDHC VCP SDHD COL1A1 COL3A1 ATG5 POMT2 PMS1 KCTD7 COL5A1 COL5A2 FLNA PMS2 VPS37A UBQLN2 FMR1 ARV1 SLC25A4 PLEKHG4 CISD2 CTC1 FKRP WFS1 FA2H RRM2B POLG MPDU1 B3GALNT2 PEX3 LZTFL1 NDUFAF3 DOLK BBIP1 IKBKG POMGNT1 PORCN CP TWNK OPA3 NPC2 SPG11 CNKSR2 LIPN XPA MSH2 XPC POMT1 APOE SIM1 OSGEP XRCC4 APP IDUA FAS GDF3 GBA2 SLC1A2 ZNF365 YWHAG SLC2A1 SLC2A3 ALG2 MMACHC PEX26 CYFIP2 NECAP1 CHMP2B TRAK1 FAN1 MTFMT PRKRA SDR9C7 SLC6A1 UGT1A1 TMEM106B PPP2R2B MLH3 ARSA PPP3CA SNCAIP CSF1R ATP6 TRNC COX1 COX2 COX3 PPT1 CYTB ASAH1 MTOR SLC18A2 SLC20A2 TTC37 TBK1 NUS1 C12ORF65 ND1 VPS35 ND4 ND5 ND6 CST3 CNTNAP2 NUP133 CSTB RNR1 PRKAR1A PRKAR1B GIGYF2 DNAJC5 CYP4F22 SLC13A5 TRNE TRNF PRKCG FTL CEP152 MFSD8 TRNH TRNK TRNL1 ATM CTNS FUS COASY CERS1 TRNP TRNQ SNCB ATP1A2 ATP1A3 TRNS1 SNCA TRNS2 C9ORF72 RNASEH1 TRNV TRNW MAPK10 CTSD CTSH CTSK BBS12 DNAJC3 PLK4 PRNP TMEM240 PINK1 SORL1 GABRB2 GABRB3 IL10 MYD88 IL12A ATP6V1A IFT140 IBA57 ATP6V1E1 CTSF CHCHD10 GALC HTRA1 NKX6-2 SPAST CENPJ ATP7B PSAP KMT2B WWOX PSEN1 SPG7 PSEN2 ATR WDR4 AUH ERAP1 SPR ABCA12 DISC2 VPS13C GJB6 MATR3 SDCCAG8 APTX SPTBN2 CYP27A1 INSR NAGA NAGLU CPLX1 GBA SPART GBE1 NBN PTPN22 GCDH IRF6 GCH1 NDP NDUFA6 PDE10A PEX11B SRCAP ITGA7 PTEN METTL23 DNAJC6 DCTN1 ADA2 NDUFB8 DDB2 GDNF NDUFS2 BDNF NAGS TTC19 STAT4 SNORD118 ITPR1 SYNGAP1 TIMM8A BMPR1A GJB2 PRDM8 CCM2 ARL6IP6 KCNA2 CEP120 PNPLA6 STXBP1 GLA GLB1 BRAF KCNB1 KCNC1 SYNJ1 SULT2B1 TINF2 NFIA KCND3 PTS SQSTM1 SGPL1 ABCC8 SURF1 AP5Z1 DGUOK C19ORF12 SUMF1 KCNJ11 EIF2B4 EIF2B3 AFG3L2 VAMP1 EIF2B2 EIF2B5 VPS13A PEX19 PEX2 PEX5 CLN6 MFN2 GM2A ALDH18A1 KCNQ2 KCNQ3 C4A CACNA1G KIF5A GNAS SEMA4A RAB39B DMD CAMTA1 ROBO3 DNM1 PHOX2B QDPR RAB27A IL23R NOTCH3 DNMT1 PDE11A TBP NPC1 NPHP1 CACNA1A KRAS MARS2 SCO2 KRT6A KRT6B NIPAL4 HNF1A SOST CUX2 DNAJC13 EPM2A ROGDI KRT16 AMN NRAS ATN1 KRT17 NUP107 GNE SZT2 PRICKLE1 RBBP8 KRT81 KRT83 HCN1 MYO1H NTRK2 KRT86 TPRKB HGSNAT NR4A2 LAMA2 DNM1L GJC2 GRID2 GRN LAMP2 OCRL BBS5 GRIN2D RBM28 PRRT2 CUBN SLC7A7 TYMP ECM1 ATP13A2 MCOLN1 OPA1 EDN3 DARS2 TSFM KRIT1 BBS10 EEF1A2 RMRP TGFBR2 TARDBP TGM1 MSH6 COL18A1 WDR45 KLLN LMNB1 ABCA5 SMC3 P2RY11 AIFM1 IL12A-AS1 TK2 AASS EIF2B1 ALG9 SCARB2 SLC25A15 AP3B2 TLR4 PRDX1 EIF4G1 PAH CTDP1 TREM2 CYP2U1 UBAC2 WDR73 ZFYVE26 ALOXE3 CLMP DSG4 BSCL2 HSD17B10 POLG2 PDCD10 EPCAM CLCF1 HCRT TP53 HTT ATP6V0A2 JPH3 PCNT XPR1 ALG13 LARGE1
Mental deterioration
Genes 266
NHLRC1 GABRB2 HEXA GABRB3 HEXB UBA5 CLN8 SDHAF1 ATP6V1A TREX1 AARS ATP6V1E1 CTSF CHCHD10 ERCC2 GALC HTRA1 ERCC4 ERCC6 SPAST ATP7B PSAP WWOX PSEN1 PSEN2 PDGFB PDGFRB MAPT DISC2 VPS13C SMC1A MATR3 APTX CYP27A1 ACTB NAGLU LRRK2 CPLX1 GBA GBE1 DHDDS NBN IRF6 CHD2 GCH1 NDP NDUFA6 PDE10A TIMMDC1 HNF4A DCTN1 ADA2 HNRNPA1 NDUFB8 TTPA ABCA7 MECP2 TTR HNRNPA2B1 TUBA4A NDUFS2 MYORG SNORD118 TBC1D24 SPG21 SYNGAP1 ERCC8 TYROBP HEPACAM TIMM8A TUBB4A PRDM8 PANK2 KCNA2 SERPINI1 PNPLA6 STXBP1 MBTPS2 GLB1 AARS2 KCNB1 KCNC1 SYNJ1 TINF2 ATXN2 ATXN7 PTS SQSTM1 SGPL1 UBTF CLN3 ABCC8 SURF1 CLN5 AP5Z1 SCN1A DGUOK C19ORF12 SUMF1 KCNJ11 UCP2 SCN3A CLTC SCN8A VPS13A ATXN3 FBXO7 DCAF17 CLN6 MFN2 GM2A ALDH18A1 KMT2A RNF216 PLA2G6 FGF12 TOMM40 ATXN10 ABCD1 GNAS RAB39B DNM1 QDPR ITM2B PLP1 RAB27A SDHA NOTCH3 SDHB VCP SDHD DNMT1 PDE11A TBP NPC1 KCTD7 CACNA1A SCO2 HNF1A CUX2 DNAJC13 EPM2A ROGDI UBQLN2 FMR1 AMN NRAS ATN1 ARV1 PLEKHG4 SZT2 CISD2 PRICKLE1 CTC1 WFS1 HCN1 FA2H NTRK2 RRM2B POLG NDUFAF3 HGSNAT NR4A2 DNM1L CP TWNK GRN NPC2 SPG11 CNKSR2 XPA GRIN2D RBM28 APOE CUBN APP IDUA TYMP GBA2 ATP13A2 MCOLN1 SLC1A2 YWHAG OPA1 SLC2A3 MMACHC CYFIP2 NECAP1 CHMP2B TRAK1 EEF1A2 SLC6A1 TMEM106B TARDBP COL18A1 WDR45 PPP2R2B ARSA PPP3CA SNCAIP CSF1R ATP6 TRNC COX1 LMNB1 COX2 COX3 PPT1 CYTB ASAH1 TK2 SLC20A2 SCARB2 TBK1 NUS1 ND1 AP3B2 VPS35 ND5 PRDX1 EIF4G1 ND6 PAH CST3 CNTNAP2 TREM2 CSTB PRKAR1A PRKAR1B GIGYF2 DNAJC5 SLC13A5 TRNE TRNF PRKCG ZFYVE26 FTL BSCL2 MFSD8 HSD17B10 TRNK TRNL1 CTNS FUS COASY CERS1 TRNQ SNCB ATP1A2 ATP1A3 TRNS1 SNCA TRNS2 C9ORF72 RNASEH1 TRNV TRNW MAPK10 CTSD PRNP HTT ATP6V0A2 PINK1 JPH3 XPR1 SORL1