SNPMiner Trials by Shray Alag


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Report for SNP rs1544410

Developed by Shray Alag, 2020.
SNP Clinical Trial Gene

There are 4 clinical trials

Clinical Trials


1 Vitamin D Supplementation Enhances Immune Response to BCG Vaccination in Infants

The purpose of this study is to determine whether a single oral dose of vitamin D given to infants prior to Bacille-Calmette-Guerin (BCG) vaccination will enhance the immune response to BCG vaccination.

NCT01288950 Tuberculosis Dietary Supplement: Vitamin D3 (cholecalciferol)
MeSH: Tuberculosis

The investigators will also determine whether specific host genetic variants including the Fok-I(rs2228570T/C), Bsm-I(rs1544410A/G), GC(rs2282679A/C), DHCR7(rs12785878G/T) and CYP2R1 (rs10741657A/G) polymorphisms affect baseline vitamin D levels and alter the response to vitamin D supplementation.. Bacille-Calmette-Guerin (BCG) vaccine efficacy.

The investigators will determine whether specific host genetic variants including the Fok-I(rs2228570T/C), Bsm-I(rs1544410A/G), GC(rs2282679A/C), DHCR7(rs12785878G/T) and CYP2R1 (rs10741657A/G) polymorphisms affect the response to BCG vaccine in infants receiving either vitamin D or placebo.. Inclusion Criteria: - Healthy mothers > 18 years of age - Term, healthy infants eligible to receive the Bacille-Calmette- Guerin (BCG) vaccine Exclusion Criteria: - Recent maternal history of tuberculosis (within 1 year) or active tuberculosis - Known maternal human immuno-deficiency virus (HIV) infection - Maternal fever or chorio-amnionitis - Maternal use of vitamin D, steroids or immuno-regulatory medications - Household member with active tuberculosis Inclusion Criteria: - Healthy mothers > 18 years of age - Term, healthy infants eligible to receive the Bacille-Calmette- Guerin (BCG) vaccine Exclusion Criteria: - Recent maternal history of tuberculosis (within 1 year) or active tuberculosis - Known maternal human immuno-deficiency virus (HIV) infection - Maternal fever or chorio-amnionitis - Maternal use of vitamin D, steroids or immuno-regulatory medications - Household member with active tuberculosis Tuberculosis Tuberculosis In 2000, there were an estimated 884,000 cases of tuberculosis (TB) in children with many developing severe, disseminated disease.

Primary Outcomes

Description: BCG vaccine efficacy will be assessed by measuring the host immune response against BCG at 2 months, 6 months and one year after BCG immunization. A whole blood assay will be used to measure multiple cytokines and mycobacterial growth suppression.

Measure: Bacille-Calmette-Guerin (BCG) vaccine efficacy

Time: 2 months

Measure: Bacille-Calmette-Guerin (BCG) vaccine efficacy

Time: 6 months

Measure: Bacille-Calmette-Guerin (BCG) vaccine efficacy

Time: 1 year

Secondary Outcomes

Description: Serum 25 hydroxy (OH) vitamin D levels will be measured prior to vitamin D supplementation and at 2 months, 6 months and one year after BCG immunization. The investigators will also determine whether specific host genetic variants including the Fok-I(rs2228570T/C), Bsm-I(rs1544410A/G), GC(rs2282679A/C), DHCR7(rs12785878G/T) and CYP2R1 (rs10741657A/G) polymorphisms affect baseline vitamin D levels and alter the response to vitamin D supplementation.

Measure: Effect of a single dose of 50,000 IU vitamin D3 on serum vitamin D levels

Time: 2 months

Description: The investigators will determine whether specific host genetic variants including the Fok-I(rs2228570T/C), Bsm-I(rs1544410A/G), GC(rs2282679A/C), DHCR7(rs12785878G/T) and CYP2R1 (rs10741657A/G) polymorphisms affect the response to BCG vaccine in infants receiving either vitamin D or placebo.

Measure: Bacille-Calmette-Guerin (BCG) vaccine efficacy

Time: 1 year

2 Vitamin D Receptor and Megalin Gene Polymorphisms and Their Association With Obesity, Central Obesity and the Metabolic Syndrome

The link between metabolic disturbances and vitamin D receptor (VDR) and MEGALIN (or LRP2) gene polymorphisms remains unclear, particularly among African-American adults. The associations of single nucleotide polymorphisms (SNPs) for VDR [rs1544410(BsmI:G/A), rs7975232(ApaI:A/C), rs731236(TaqI:G/A)] and MEGALIN [rs3755166:G/A,rs2075252:C/T, rs2228171:C/T] genes with incident and prevalent metabolic disturbances, including obesity, central obesity and metabolic syndrome (MetS) were evaluated. From 1,024 African-Americans participating in the Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS, Baltimore, MD, 2004-2013) study, 539 subjects were selected who had complete genetic data as well as covariates selected for metabolic outcomes at two consecutive examinations (visits 1 and 2) with a mean follow-up time of 4.64±0.93y. Haplotype (HAP) analyses generated polymorphism groups that were linked to incident and prevalent metabolic disturbances.

NCT03279432 Metabolic Syndrome Obesity Central Obesity
MeSH: Obesity Metabolic Syndrome Obesity, Abdominal Syndrome
HPO: Abdominal obesity Obesity Truncal obesity

The associations of single nucleotide polymorphisms (SNPs) for VDR [rs1544410(BsmI:G/A), rs7975232(ApaI:A/C), rs731236(TaqI:G/A)] and MEGALIN [rs3755166:G/A,rs2075252:C/T, rs2228171:C/T] genes with incident and prevalent metabolic disturbances, including obesity, central obesity and metabolic syndrome (MetS) were evaluated.

Primary Outcomes

Description: Obesity was defined as BMI≥30 kg/m2.

Measure: Obesity

Time: 2004-2013

Description: Central obesity was defined based on waist circumference (WC) ≥ 102 cm or 40 inches (men), ≥ 88 cm or 35 inches (women)

Measure: Central Obesity

Time: 2004-2013

Description: Participants who screened positive on at least 3 of 5 conditions ((1) central obesity (see above); (2) dyslipidemia: TAG≥1.695 mmol/L (150 mg/dl); (3) dyslipidemia: HDL-C<40 mg/dL (male), <50 mg/dL (female); (4) blood pressure≥130/85 mmHg; (5) fasting plasma glucose≥6.1 mmol/L (110 mg/dl).(39)) were classified as MetS-positive (2) Similarly, continuous annual rates of change (Δ) in metabolic outcomes were considered, specifically number of metabolic disturbances (MetD), BMI, WC, SBP, DBP, TAG, HDL-C, and Glucose. Binary incident outcomes included obesity, central obesity, MetS and other metabolic disturbance (i.e. hypertension, dyslipidemia-TAG, dyslipidemia-HDL and hyperglycemia).

Measure: Metabolic Syndrome

Time: 2004-2013

3 Vitamin D and Skin Pigmentation in Healthy Humans Exposed to UVB

Skin pigmentation (melanin) absorbs ultra violet type B (UVB) radiation found in sunlight and is believed to be responsible for darker-skinned persons' generally low 25(OH)D status. This phenomenon is found in immigrants living in Northern countries and their 25(OH)D responses to UVB-irradiation seem low. We hypothesized that objectively measured skin pigmentation and/or pigment genes influence UVB-induced 25(OH)D increase significantly in combination with other influential parameters. The influence of objectively measured constitutive and facultative skin pigmentation on UVB-induced 25(OH)D increase over time was investigated together with other possible influential parameters. These other influential parameters include sex, age, weight, height, BMI, number of fatty fish meals per week, Fitzpatrick Skin Type and 25(OH)D start level. The genetic parameters include 33 Vitamin D receptor and pigment SNPs. This is a single-centre, open and non-blinded clinical trial. No randomisation was used, as the participants were allocated into two groups based on their Fitzpatrick Skin type and ethnic origin. The light-skinned group included participants with Fitzpatrick Skin type II-IV and were of Northern origin (Denmark, the Faroe Islands and the UK). The darker-skinned included Fitzpatrick Skin Types V-VI originating from countries located at latitudes below 50 degrees N. Thus, it could be ensured that the participants represented a wide range of skin pigmentation. The light-skinned (N = 22) and the darker-skinned subjects (N = 18) were exposed to identical UVB doses on identical body areas over nine weeks with weekly measurements of 25(OH)D. The UVB-induced 25(OH)D synthesis was investigated in summer-pigmented skin with melanin throughout the epidermis and during winter when ambient UVB exposure is negligible. Demographic data (gender, age, weight, height, Fitzpatrick Skin Type, measured constitutive and facultative skin pigmentation (PPF)) was collected/measured and registered in prior to study start. The number of daily consumed fatty fish meals was recorded in a questionnaire. Serum 25(OH)D was analysed weekly.

NCT03409510 Healthy Volunteers Radiation: UVB radiation

The influence of the vitamin D receptor gene was investigated by genotyping the two single nucleotide polymorphisms (SNP), rs1544410 (BsmI) and rs2228570 (FokI), located in the gene (ENSG00000111424, Chromosome 12q13) as previously described.

Primary Outcomes

Description: Serum 25(OH)D is a marker of vitamin D increase induced by UVB

Measure: Change in serum 25(OH)D

Time: Measured at study start and weekly over nine weeks

4 Personalization of AntiTB Treatment: Evaluation of Pharmacological Determinants of Treatment Response

The aim of the study is to investigate the possible correlation of plasma drug concentrations with Time To Positivity (TTP) in liquid culture in patients with active pulmonary multi sensitive TB in the first two weeks of treatment. Secondary aims are: the correlation between plasma drug concentrations and hepato/neuro toxicity; the impact of different allelic variants on PK data, toxicity and TTP in liquid culture; the feasibility of using dried blood/plasma spots to measure plasma concentrations of anti-TB drugs and determine genetic polymorphisms.

NCT03416309 Tuberculosis, Pulmonary
MeSH: Tuberculosis Tuberculosis, Pulmonary

Analyzed SNPs will be: ABCB1 3435C>T (rs1045642), OATP1B1 521T>C (rs4149056) e OATP1B1 85-7793T>C (rs4149032), PXR 63396C>T (rs2472677), BsmI G>A (rs1544410).

Primary Outcomes

Description: Investigate the correlation of plasma drug concentrations (Rifampicin, Isoniazid, Ethambutol and Pyrazinamide, HRZE) with the change in Time To Positivity (TTP) in liquid culture in patients with active pulmonary TB between the baseline and the first week of treatment.

Measure: Correlation between AUC of RHZE and TTP

Time: 1 week from start of treatment

Description: Investigate the correlation of plasma drug concentrations (Rifampicin, Isoniazid, Ethambutol and Pyrazinamide, HRZE) with the change in Time To Positivity (TTP) in liquid culture in patients with active pulmonary TB between the baseline and the second week of treatment.

Measure: Correlation between AUC of RHZE and TTP

Time: 2 weeks from start of treatment

Secondary Outcomes

Description: Investigate the correlation of plasma drug concentrations (Rifampicin, Isoniazid, Ethambutol and Pyrazinamide, HRZE) with hepatotoxicity (increase of AST and/or ALT) and neurotoxicity (peripheral neuropathy)

Measure: Correlation between AUC of RHZE and toxicity

Time: 1 week and 2 weeks from start of treatment

Description: Investigate the impact of different allelic variants of NAT2, SLCO1B1, ABCB1, VDR on AUC of RHZE toxicity and TTP in liquid culture

Measure: Correlation between PG and AUC of RHZE

Time: 1 week and 2 weeks from start of treatment

Description: Assess the consistency of using dried plasma spots to measure plasma concentrations of anti-TB drugs comparing to plasma samples

Measure: Assess the consistency of results using of DPS for measuring the plasma drug concentrations

Time: 1 week and 2 weeks from start of treatment

Description: A pharmacometric model will be develop to correlate pharmacokinetics (AUC of RHZE) with the anti-TB treatment response (clinical and TTP) of the standard first-line anti-TB regimen.

Measure: Correlate AUC of RHZE with antiTB response

Time: 6 months after end of treatment

Description: A pharmacometric model will be develop to correlate PG with the anti-TB treatment response (clinical and TTP) of the standard first-line anti-TB regimen.

Measure: Correlate PG with antiTB response

Time: 6 months after end of treatment


HPO Nodes


Obesity
Genes 465
PDE6A IDH3A ALG13 CANT1 PRKAR1A WDR34 PCARE EIF2S3 RP1 CTSH RAI1 LZTFL1 MTFMT TTC8 PPARG ANOS1 IQSEC2 IQSEC2 C8ORF37 TMEM67 RNPC3 MKRN3 FLRT3 MYT1L SNRNP200 BBS4 IFT172 CEP19 PROKR2 EMD EYS SLC25A4 LEPR KIDINS220 THOC2 PCSK1 PRPF4 ARL6 USP9X RDH12 IGF1 IFT172 ARL3 SOX10 PDE11A FGFR3 NR2E3 CUL4B RAB23 PAX6 ARL2BP DYRK1B GNAS PRPF31 PNPLA6 PRCD RLBP1 FTO KLF11 TBX1 BLK INPP5E HIRA CYP7A1 TMEM43 DHDDS BBS5 MLXIPL LEP CLIP2 WNT4 IFT140 RP2 REEP6 EP300 FHL1 PDE4D SH2B1 CNGA1 CNNM2 PAK3 TNFSF4 IQSEC2 SDCCAG8 MOG TRAPPC9 SDC3 HLA-DQB1 TBL2 POMC ALMS1 PTCHD1 PRPH2 PSMD12 SH3KBP1 SNORD115-1 HSD11B1 ARVCF PRPF8 POMC GUCA1B ATRX SEC24C POMGNT1 ZNF365 SUFU ARMC5 CLCN4 HACE1 RBMX KIAA1549 SLC9A7 SH2B1 IFT27 GNAS EIF2S3 JMJD1C FGF17 COMT MKS1 ZNF81 HERC2 SKI CYP19A1 MKKS SOX2 SLC7A7 GTF2I AKT2 MID2 SIM1 SMARCB1 DNMT3A ENPP1 PRPF6 ZNF408 PRDM16 FGFR1 PROM1 ERMARD BBS10 AIP NPAP1 BEST1 GATA4 BBS1 TUB P4HTM TBX3 KMT2A BBS7 GABRD GP1BB WDR11 RP9 GNAS XRCC4 PAX6 SDCCAG8 RBP3 ADRB3 GNAS PAX4 NSMF NPHP1 RAI1 ATP6AP2 GNAS-AS1 USP8 MAK KCNJ18 CCDC141 IMPDH1 PDSS1 NIPBL ADNP DPYD SETD2 NR0B2 MED12 NDN FAM161A HESX1 NRL BBS10 GHRL DUSP6 LAS1L MKKS P2RY11 BBS5 MEGF8 ZNF711 RREB1 H6PD HESX1 SIN3A CNKSR2 KIDINS220 BBS12 FRMPD4 IFT74 TRIM32 BLK AFF4 POGZ ALB GABRA3 TSPAN7 SLC10A7 SYNE2 CREBBP GNAS RPS6KA3 OFD1 IFT172 APC2 PRKAR1A RPGR BBS9 SNORD116-1 IL1RAPL1 OTX2 NSD1 HACE1 PCSK1 FGFR1 SETD2 BAZ1B EHMT1 ZNF41 INS PROK2 POU3F4 IFT88 PDE6B GNAS ABCC8 RGR ARL13B KMT2D GHR GNAS NEK2 RFC2 CA4 LIPE RERE MAPK8IP3 RHO SCAPER BPTF RAP1A DLG3 BBS9 PCNT LEP IGFALS CRB1 RPS6KA3 TBX1 NEUROD1 CEP164 GTF2IRD1 SIM1 MECP2 ARX SMC3 PHIP TRIP12 CARTPT NTRK2 HDAC8 AGTR2 SEMA3A BRAF AHR PWRN1 OFD1 SETD5 ADNP LZTFL1 PROK2 KISS1R CEP290 HS6ST1 CDHR1 DEAF1 MAN1B1 RAP1B CTNNB1 USP8 BBS2 GCK UPF3B ELN MAN1B1 PTEN TRIM32 MKS1 ROM1 BBS2 LEPR KCNJ11 MRAP2 PRPF3 PDGFB LRAT TRAF3IP1 HDAC8 SPRY4 ELN SRY FEZF1 VPS13B TACR3 KIF7 TAF1 RAB23 FOXP1 HDAC8 CERKL CLRN1 AGRP BBS2 MOG TOPORS ARNT2 ARHGEF6 FMR1 USP27X SHANK3 XYLT1 VPS13B SMAD4 UFD1 EGF UCP3 BBS12 IFT172 SNRPN CACNA1S USH2A HNF1A ACADVL ADRB2 MEGF8 C8ORF37 APOE WDPCP IGF1R CCDC141 NIN IPW MAGEL2 GDI1 NF2 HGSNAT ARL6 HUWE1 SEMA4A EHMT1 SYP IDH3B PRMT7 CEP290 PCNT SH2B1 HDAC4 ADCY3 TTC8 CHD7 AKT2 ABCA4 LMNA HCRT MC4R DMD ZNF513 CRX SYNE1 XYLT1 BDNF TBX3 MC3R KLHL7 DCC SPG11 TTC8 POMC ALMS1 FTSJ1 PDX1 KDM6A LIMK1 BBIP1 BBS7 RPE65 CCDC28B EXOC6B BBIP1 AHI1 ARMC5 AGBL5 PDE4D TULP1 SMC1A DHX38 CEL ARL6 MAGEL2 PROKR2 HLA-DRB1 MKRN3-AS1 SHOX RAD21 IMPG2 ZNF711 C8ORF37 IFT27 PWAR1 PNKP FGF8 HNF4A CDH23 BBS1 WT1 GNAS MTTP ZBTB20 KIZ APPL1 FLII IL17RD SPATA7 MERTK TCF20 MECP2 CXORF56 LMNA BBS4 SLC7A14 SOX3 MC4R LAS1L KCNAB2 CUL4B PDE6G ARHGEF18 SAG RAB39B STX16 UBE3A ACSL4 TBX1 MCM3AP TUB ATRX FSCN2 PHF6 TRAPPC9 PHF6 WT1 CNGB1 HCFC1
Truncal obesity
Genes 51
SLC7A7 AKT2 INPP5E PRKAR1A MAN1B1 IGF1R RAD21 LAS1L EP300 GHR GNAS RNPC3 CDH23 PCNT BPTF PCNT KMT2A ZBTB20 IGFALS AKT2 ALMS1 THOC2 PCSK1 PSMD12 HDAC8 XRCC4 IGF1 XYLT1 VPS13B SMC3 PDE11A HDAC8 POMC ALMS1 MC4R LAS1L HDAC8 SLC10A7 DYRK1B CREBBP GNAS FMR1 USP8 XYLT1 SETD5 ARMC5 PHF6 TRAPPC9 NIPBL ADNP SMC1A