SNPMiner Trials by Shray Alag


SNPMiner SNPMiner Trials (Home Page)


Report for SNP rs429358

Developed by Shray Alag, 2020.
SNP Clinical Trial Gene

There are 4 clinical trials

Clinical Trials


1 Austrian Prospective Cohort Study in Cognitive Function of Elderly Marathon-runners

There is substantial research on the effects of physical exercise on cognitive functions. However, less attention has been paid on the requirements of training intensity and length to enhance cognitive abilities in the elderly. To the investigators knowledge no studies have evaluated the effects of extensive endurance exercise training on cognitive functions by studying elderly marathon runners and bicyclists. On the basis of the scientific literature published so far it is not known whether the beneficial impact of endurance exercise training depends on the intensity of training. The investigators therefore designed a cohort study with adequate power in order to evaluate the effects of intensive endurance exercise training on cognition. This trial, an Austrian prospective cohort study in cognitive function of elderly marathon-runners (APSOEM) is being conducted and will compare neuropsychological performance outcomes of elderly marathon runners or bicyclists with controls matched concerning age, education years, occupation, and verbal intelligence.

NCT01045031 Cognitive Decline
MeSH:Cognitive Dysfunction
HPO:Cognitive impairment Mental deterioration

For this, pre-designed TaqMan SNP-Genotyping assays to distinguish the ApoE ε4 allele from ε2 and ε3 at amino acid position 112 (ApoE rs429358, Assay ID C_3084793_20, Applied Biosystems) and the ApoE ε2 allele from ε3 and ε4 at amino acid position 158 (rs7412, Assay ID C_904973_10, Applied Biosystems) were purchased.

Primary Outcomes

Description: Hypothesis will be tested at the second follow-up examinations.

Measure: the Proportion of Subjects, Who Will Develop Mild Cognitive Impairment

Time: 10 years

Measure: Brain-derived Neurotrophic Factor (BDNF)

Time: Baseline and 5 years

Secondary Outcomes

Description: The following self rating scales were used: WHO-5 Quality of Life Assessment (Braeher, E., Muehlan, H., Albani, C., & Schmidt, S. (2007). Testing and standardization of the German version of the EUROHIS-QOL and WHO-5 quality-of life-indices. Diagnostica, 53(2), 83-96.). Range: 0 - 25, higher scores indicate better quality of life.

Measure: Self Rating by Questionnaires

Time: Baseline and 5 years

Measure: Insulin-like Growth Factor (IGF-1)

Time: Baseline and 5 years

2 Effect of Beta-Glucan Molecular Weight and Viscosity on the Mechanism of Cholesterol Lowering in Humans

The primary aim of this study is to determine whether the cholesterol-lowering efficacy of barley b- glucan varied as function of molecular weight (MW) and the total daily amount consumed. Our second aim is to investigate the mechanism responsible for the action, specifically, whether β-glucan lowers circulating cholesterol concentration via inhibiting cholesterol absorption and synthesis. Thirdly, we aim to determine if any gene-diet interactions are associated with cholesterol lowering by barley β-glucan. In addition, we aim to investigate the alteration of the gut microbiota after β-glucan consumption and the correlation between the altered gut microbiota and cardiovascular disease risk factors.

NCT01408719 Hypercholesterolemia Dietary Supplement: Control Dietary Supplement: 3g LMW beta-glucan Dietary Supplement: 5g LMW beta-glucan Dietary Supplement: 3g HMW beta-glucan
MeSH:Hypercholesterolemia
HPO:Hypercholesterolemia

The Single Nucleotide Polymorphism (SNP) rs3808607 of CYP7A1 gene, rs429358 and rs7412 of APOE gene, and their associations with different blood lipid responses to beta-glucan interventions will be determined.. Changes in Body Weight and Waist Circumference(WC).

Single nucleotide polymorphisms (SNPs), rs3808607 of gene CYP7A1and rs429358 and rs7412 will be determined byTaqMan® SNP Genotyping assay following the manufacturer's protocol.

Primary Outcomes

Description: Fasted total cholesterol concentration will be measured using the automated enzymatic methods.

Measure: Changs in Total Cholesterol

Time: Beginning and end of each phase

Description: Serum LDL cholesterol will be estimated using the Friedewald equation.

Measure: Changes in LDL Cholesterol

Time: Beginning and end of each phase

Secondary Outcomes

Description: The rate of cholesterol absorption and synthesis will be measured in each intervention phase using single stable isotope labelling technique.

Measure: Cholesterol Absorption/Synthesis

Time: End of each phase

Description: The Single Nucleotide Polymorphism (SNP) rs3808607 of CYP7A1 gene, rs429358 and rs7412 of APOE gene, and their associations with different blood lipid responses to beta-glucan interventions will be determined.

Measure: Potential Gene-nutrient Interactions: CYP7A1 and APOE

Time: Once for each participant

Description: Body weight will be monitored every day when subject visits the Richardson Centre. Waist circumference will be measured at the beginning and end of each study phase.

Measure: Changes in Body Weight and Waist Circumference(WC)

Time: Every day for body weight; beginning and end of each phase for WC

3 Reading Imperial Surrey Saturated Fat Cholesterol Intervention (RISSCI) Study. RISSCI-1 Blood Cholesterol Response Study

Raised blood cholesterol (also referred to as blood LDL-cholesterol) is a major risk factor for developing heart disease. Dietary saturated fat is recognised as the main dietary component responsible for raising blood LDL-cholesterol, and reducing its intake has been the mainstay of dietary guidelines for the prevention of heart disease for over 30 years. However, there is very little evidence for a direct link between the intake of saturated fat and risk of dying from heart disease. One explanation for this, is that the link between saturated fat intake and heart disease is not a direct one, but relies heavily on the ability of saturated fat to raise blood LDL-cholesterol levels. This LDL cholesterol-raising effect of saturated fat is complex, and highly variable between individuals because of differences in the metabolism of dietary fat and cholesterol between people. The main aim of this study is to measure the amount of variation in blood LDL-cholesterol in 150 healthy volunteers (75 at the University of Surrey and 75 at the University of Reading) in response to lowering the amount of saturated fat in the diet to the level recommended by the government for the prevention of heart disease. This collaborative project between the Universities of Reading, Surrey and Imperial ('RISSCI-1 Blood Cholesterol Response Study') will permit identification of two subgroups of men who show either a high or low LDL-cholesterol response to a reduction in dietary saturated intake. These participants (n=36) will be provided with an opportunity to participate in a similar follow-up study ('RISSCI-2') that will also take place at the University of Surrey and Reading. In this follow-up study, the participants will be asked to repeat a similar study protocol as for RISSCI-1, but undergo more detailed measurements to determine how saturated fat is metabolised in the body.

NCT03270527 Lipids Lipid Metabolism Healthy Other: High SFA diet (Diet 1) Other: Low SFA diet (Diet 2)

rs429358 and rs7412), APOA-I (e.g.

Primary Outcomes

Measure: Changes in fasting total cholesterol (consisting of LDL-cholesterol and HDL) concentrations

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Secondary Outcomes

Measure: Fasting triacylglycerol

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Measure: HDL immune functions

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Measure: HDL anti-inflammatory and anti-oxidant (PON-1) properties

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Measure: HDL capacity to promote cholesterol efflux (ex-vivo)

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Measure: Fasting insulin, glucose

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Measure: Adhesion molecules, markers of vascular function

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Measure: Inflammatory markers & adipokines

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Measure: LDL-R gene expression

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Description: Polymorphic genes with potential influence on the serum LDL response to dietary saturated fat, e.g.: ATP-binding cassette proteins (cholesterol efflux proteins) ABCG5 (e.g. C1950G) ABCG8 (e.g. D19H, C1895T), functional polymorphisms in the farnesoid X receptor (FXR) and bile acid transporters (e.g. solute carrier organics anion 1B1). Fatty acid desaturases (FADS1 and FADS2). The patatin-like phospholipase domain-containing protein (PNPLA3) (e.g. rs738409 C/G), eNOS. Lipid/cholesterol homeostasis: serum apolipoprotein genes: APOE (ε2,ε3,ε4 e.g. rs429358 and rs7412), APOA-I (e.g. -75G/A), APOA4 (e.g. 360-2), APOA5 (e.g. -113/T>:c), APOCIII, APOB (e.g. -516C/T). Lipase genes: (e.g. LPL, HL, MGLL). Lipoprotein receptor genes (e.g. pvu11 in the LDL receptor), lipid transfer proteins (e.g. CETP e.g Taq1B, MTP), and other polymorphic genes related to the absorption and metabolism of dietary fat and regulation of lipid/cholesterol homeostasis.

Measure: Other relevant genes involved in the absorption and metabolism of dietary fat

Time: Baseline

Description: Analyses conducted by Imperial College London

Measure: Metabolomic analysis for the determination of the low molecular weight metabolite profiles in the biological fluids

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Measure: Changes in faecal bacterial population

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Description: BMI will also be calculated (kg/ height in m^2)

Measure: Weight

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Measure: Fat mass

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Measure: Fat free mass

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Measure: Waist circumference

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Measure: Hip circumference

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Measure: Blood pressure

Time: Baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Description: Measured via pulse wave assessment using the Mobil-O-graph device.

Measure: Fasting vascular stiffness

Time: baseline, 4 weeks (after diet 1), 8 weeks (after diet 2)

Other Outcomes

Measure: Genotyping for apolipoprotein E to determine the impact of this genotype on changes in the primary and secondary outcome measurements in response to dietary fat intake

Time: Baseline

4 Correlation of Polymorphisms of Lipoprotein Lipase (LpL) and Apolipoprotein E (Apo E) With Lipid Profile of Children With Acute Lymphoblastic Leukaemia During Therapy With L - Asparaginase

Haematological malignancies constitute the most common neoplastic disease in child population, with acute leukemia occupying the number one spot with a percentage of 32.8%. In children, leukaemia is primarily encountered in its acute form (97%) and in the majority of the cases it is presented as Acute Lymphoblastic Leukaemia - ALL (80%). Acute Non-Lymphoblastic Leukemia - ANLL is encountered less frequently (17%) and it includes Acute Myelogenous Leukaemia - AML (15%) and some other rare forms (2%), while the remainder 3% corresponds to chronic leukaemia. L-Asparaginase (L-ASP) is a fundamental component during the loading phase with regards to achieving remission of the disease and, likewise, during the maintenance phase with the intention of establishing that remission in both children and adults suffering from ALL. The cytotoxic effect of the exogenous administration of Asparaginase is caused by the depletion of the reserve of asparagine in the blood. Asparaginase (ASP) acts as a catalyst for the hydrolysis of asparagine to aspartic acid and ammonia. Asparagine is vital for protein and cell synthesis and, therefore, for their survival. The normal cells of the human body have the ability to produce asparagine from aspartic acid, with the assistance of the enzyme asparagine synthetase. However, the neoplastic cells either lack the enzyme completely or contain minute amounts of it resulting in their inability to synthesize asparagine de novo. The survival of these cells and their ability to synthesize proteins depends entirely on receiving asparagine from the blood. Thus, the administration of ASP leads to the inhibition of DNA, RNA and protein synthesis which, in turn, results in the apoptosis of these cells. Despite L-ASP's paramount importance in the chemotherapy treatment of leukaemia, it is responsible for a plethora of toxic adverse effects that sometimes even require the termination of its administration. A critical adverse event of ASP is a disorder in the metabolism of lipids. Specifically, it appears that the activation of the endogenous pathway that produces triglycerides through hepatic synthesis leads to hypertriglyceridaemia. The liver is capable of synthesizing VLDL (Very Low Density Lipoproteins) that are rich in triglycerides. Utilising the effect of the enzyme Lipoprotein Lipase (LpL), located on the vascular endothelium, the triglycerides detach from the VLDL causing the latter to transform into IDL (Intermediate Density Lipoproteins) and afterwards into LDL (Low Density Lipoproteins). The triglycerides are later extracted from the blood circulatory system and stored in the adipose tissue, while the LDL particles connect with tissue receptors or macrophage receptors. The final products of the breakdown (coming from the peripheral hydrolysis of triglycerides with the help of LpL) of chylomicrons, VLDL, the remnants of lipoproteins, will eventually be removed by hepatic receptors. Apolipoprotein E (Apo-E) plays an important role in this procedure, it binds these remnants in the presence of LpL and hepatic lipase. Along the duration of the treatment with ASP, reduced LpL functionality is recorded, resulting in impaired plasma clearance of triglycerides and an increase in their levels, while L-ASP appears to cause disorders in other lipid factors, such as cholesterol, HDL and apolipoprotein A. Disorders of lipid metabolism have been found to be associated with polymorphisms of the LpL and Apo-E genes, sometimes with positive and sometimes with negative effects on the lipid profile and more likely participation in cardiovascular complications. The current study will evaluate, the lipid profile of children with ALL, the effect of L-ASP on the lipid profile of the aforementioned patients, as well as the correlation between the polymorphisms of Lipoprotein Lipase (LpL) and Apolipoprotein E (ApoE) with the values of the lipids during chemotherapy. Both the universal and national bibliography that pertain to the effect of ASP on the potency of LpL and App E and to the values of the lipids in children that suffer from ALL during chemotherapy with L-ASP is limited, while there exists no bibliographic reference correlating the genetic background to LpL and Apo E and the relation of the lipid profile. The current study will examine for the first time gene polymorphisms of LpL and Apo E in children with ALL during treatment with ASP.

NCT04364451 Acute Lymphoblastic Leukemia Other: Correlation of Polymorphisms of Lipoprotein Lipase (LpL) and Apolipoprotein E (Apo E) With Lipid Profile of Children With Acute Lymphoblastic Leukaemia During Therapy With L - Asparaginase
MeSH:Leukemia Precursor Cell Lymphoblastic Leukemia-Lymphoma Leukemia, Lymphoid
HPO:Leukemia Lymphoid leukemia

Moreover, an examination of LpL polymorphisms (the three most common polymorphisms p.N291S, p.D9N, p.S447X) and of Apo E polymorphisms [ε2(rs7412-T,rs429358-T), ε3(rs7412-C, rs429358-T) and ε4 (rs7412-C, rs429358-C)] will be performed after isolating the DNA from the peripheral blood and analyzing it with molecular techniques.

Primary Outcomes

Description: The genotypes of children with ALL will be recorded and it might constitute an early indicative factor concerning the treatment's outcome. Thusly, essential information will be extracted about the possible contribution of genotype of children under treatment with L-ASP to the lipid disorder as shown in the lab results, to better monitoring of each unique phase of the therapy for clinical occurrences and complication and to faster therapeutic intervention.

Measure: The correlation of lipoprotein lipase (LpL) and apolipoprotein E (apoE) polymorphisms with lipid values during the chemotherapy protocol.

Time: Baseline

Description: During the disease's diagnosis, the lipid profile of the patients' will be determined by measuring the changes of the following parameters compared to the baseline measures: cholesterol (mg/dl), triglycerides(mg/dl), HDL-cholesterol(mg/dl), LDL-cholesterol(mg/dl), apolipoprotein A1(mg/dl), apolipoprotein B100(g/L), lipoprotein α [Lp(α)](nmol/l), glucose (mg/dl), SGOT (U/I), SGPT (U/I), TSH (mU/l) FT4 (pmol/l) amylase (U/I) and lipase (U/I).

Measure: Assessment of the effect of asparaginase by measuring the changes induced in the lipid profile of children with acute lymphoblastic leukaemia.

Time: Baseline and days 11, 15, 24, 33 in loading phase and days 8, 16, 21 in maintenance phase


HPO Nodes


HP:0001268: Mental deterioration
Genes 461
SMC1A FUS PDE11A PLEKHG4 CTC1 SPG11 FA2H PLA2G6 SYNJ1 C9ORF72 HTT UBAP1 ND5 HEXB PTS MAPT TRNS2 PDGFB APOL2 TWNK GBA FGF12 JPH3 KCNB1 NOTCH3 APOE PAH MAPK10 CNTNAP2 APP COL4A1 ABCC8 MCOLN1 RAB27A CLN6 ERCC6 COX3 GRN APOE ADH1C BSCL2 FMR1 TRNS1 UCP2 PRNP VPS13C GLUD2 TBK1 GBA KCNA2 DISC2 CSTB WFS1 ATP6 HSD17B10 MAPT FTL VCP CSF1R C9ORF72 CYTB NDUFA6 PDGFRB PRKCG ZFYVE26 CSTB HTR2A JPH3 PSEN2 GDAP2 MAPT EPM2A C9ORF72 APP PODXL LRRK2 C19ORF12 HNRNPA2B1 CACNA1A SERPINI1 CP CFAP43 PRNP HLA-DQB1 SNCA ND1 SGPL1 DNM1 CPLX1 VPS35 NDUFB8 C9ORF72 ATXN3 SNCA GABRA5 CHMP2B TIMM8A ATN1 LRRK2 PARK7 DNMT1 TTR ASAH1 SCN1A GIGYF2 APP CHD2 ATP13A2 COX2 UBQLN2 HNRNPA1 ATN1 VPS13A CHMP2B TYROBP SLC2A3 ACTB SQSTM1 CST3 HCN1 ERCC2 SDHB ATP13A2 CHCHD10 SPG21 GRN MAPT GCH1 PSEN1 PNPLA6 SPG21 IDUA TRNL1 SYN2 ITM2B GBA C9ORF72 CHI3L1 MAPT PSAP GBA SZT2 CLN8 ATXN2 TREM2 TREM2 MMACHC NPC1 CTNS PDGFRB PLAU AP2M1 DNM1 TRPM7 HFE SNORD118 SNCA NDUFS2 TBK1 NDP SQSTM1 DAOA SLC6A1 YWHAG SUMF1 TREX1 GLB1 FTL DNAJC6 TRNQ UBA5 CNKSR2 HGSNAT UBTF NUS1 MFN2 PSAP ALDH18A1 COX1 TMEM106B ARV1 ASAH1 TARDBP TLR3 SYNJ1 MAPT STXBP1 EIF4G1 HNRNPA2B1 HNF1A MAPT VCP PSEN1 PANK2 ATP13A2 CYFIP2 AARS1 PSEN1 HNF4A PRDM8 COMT ND6 PSEN1 GRN NOTCH3 ALDH18A1 ATP7B DNMT1 GRN ATP13A2 PPT1 RAB39B CYP27A1 TRNC CUX2 GABRA2 SDHD PRDM8 ACTL6B PSEN2 APOL4 MBTPS2 CTSD TRAK1 HEXA CLTC ATXN10 SNCAIP ATXN7 RTN4R POLG SUMF1 SQSTM1 TMEM106B GM2A PSEN1 NDUFAF3 MECP2 PRKN TK2 CLN8 DNMT1 POLG PRDX1 CISD2 GRN TREM2 LMNB1 NRAS SNCA SCO2 PSAP CHMP2B APP TUBA4A SLC1A2 RBM28 UCHL1 ATXN2 TBP TRNF MAPT GABRB3 PPP2R2B PRNP XPR1 CHD2 MAPT NOS3 COL18A1 DNM1L HEPACAM XPA TYROBP SNCA SLC20A2 CSF1R PRNP TRNW PRNP SDHA WFS1 SNCB SCN9A RRM2B ARSA SURF1 MAPT C19ORF12 CHMP2B APP RBM28 SNCA ADA2 GABRB2 AP5Z1 TBC1D24 ATP1A2 TREM2 DGUOK ATXN2 MAPT ERCC8 HTRA2 QDPR DCTN1 TMEM106B HTRA1 GBA2 NBN PLA2G6 PLA2G6 DARS2 CP APP AARS2 VCP WDR45 MATR3 HTRA1 MAPT MATR3 HTT PDE10A PANK2 TUBB4A GBA2 PRICKLE1 NR4A2 GALC ADA2 WDR45 NHLRC1 ST3GAL5 RNASEH1 SQSTM1 VCP ERCC4 KCNA2 DNAJC13 TRNK AMN EEF1A2 TIMMDC1 HTT TOMM40 PRNP ATP6V1A CLN3 KCNJ11 CACNA1B SDHAF1 PRNP GRIN2D ROGDI FBXO7 APP PLP1 TRNV TINF2 NPC2 BSCL2 ABCD1 ATP6V1A GBA FA2H COASY CERS1 APTX TREM2 RNF216 CLN6 VPS13C GBA CLN5 TBK1 PPP3CA MYORG PDGFB PRKAR1A GBE1 DNAJC5 MAPT TTPA TRNE GBA RRM2B EPM2A FA2H SYNGAP1 TYMP PPP2R2B TREX1 MPO KMT2A OPA1 MFSD8 ATXN7 PINK1 PSEN1 CFAP43 LRRK2 CTSF AP3B2 DHDDS ARSA NAGLU SPAST RNF216 FMR1 ITM2B IRF6 TIMM8A TBP HIBCH RRM2B KCNC1 GABRG2 ATXN8OS PSEN1 SLC13A5 WWOX SCN8A PINK1 PRNP SLC13A5 ATP6 PDGFRB SCARB2 SORL1 DRD3 CUBN ATP6V0A2 GNAS PARS2 ROGDI NOTCH2NLC NTRK2 KCTD7 DCAF17 SPG11 SCN3A ABCA7 VCP VCP ARSA SYNJ1 NHLRC1 SCN1A CHCHD10 A2M PRKAR1B TBP NECAP1 ATP1A3 MTHFR CHMP2B ATP6V1E1 TRNK DCTN1 TARDBP
Protein Mutations 3
K56M V158M V66M