Shray's NLP Project


SNP Report


Report for SNP rs12979860

Developed by Shray Alag, 2019.
SNP Clinical Trial Gene

There are 10 clinical trials

Clinical Trials


1 Cytomegalovirus Reactivation in Non Immunocompromised Patients Undergoing Cardiac Surgery

We hypothesized that the stress of cardiac surgery and cardiopulmonary bypass can cause reactivation of a latent CMV infection and that reactivation might be more prevalent in patients with complicated post-operative course. The study aims are: - To study whether cardiac surgery is a trigger for latent CMV reactivation and to compare reactivation rate between sub groups of patient with complicated post-operative course and non complicated post operative course. - To study the relationship between expression IL28 SNP rs12979860 and the risk of CMV replication in the non immunocompromised patient undergoing cardiac surgery.

NCT02527291 Cardiac Surgery

- To study the relationship between expression IL28 SNP rs12979860 and the risk of CMV replication in the non immunocompromised patient undergoing cardiac surgery.

Primary Outcomes

Secondary Outcomes


2 Efficacy and Safety of Sofosbuvir Plus Daclatasvir in Chinese Treatment-experienced Patients With Chronic Genotype 1b HCV Infection

For those chronic hepatitis C patients, who are interferon-ineligible or intolerant, there is a burning need for the development of pan-oral interferon-free regimen. The investigators examine the efficacy and safety of sofosbuvir, a NS5B nucleotide polymerase inhibitor and daclatasvir, an NS5A replication complex inhibitor in Chinese treatment-experienced cirrhosis patients with chronic G1b infection.

NCT02473211 Chronic Hepatitis C Infection

At baseline, liver stiffness measurement (LSM) using transient elastography (FibroScan®) is used to assess liver fibrosis and the single nucleotide polymorphism ofinterferon-λ 3 (IL-28, rs12979860, C or T) and IFLN4 (ss469415590, TT or ΔG) is determined.

Primary Outcomes

Description: SVR12 is defined as HCV RNA < the lower limit of quantitation (LLOQ) (15 IU/ml) 12 weeks following the last dose of study drug

Measure: Proportion of participants with sustained virologic response 12 weeks after the end of treatment (SVR12)

Time: Post treatment Week 12


3 Impact of Interleukin 28B (rs12979860) Genotype on Virological Responses in Chronic Hepatitis C Treatment

Objective: Pegulated Interferon α2 plus ribavirin is a treatment of choice in patients with chronic hepatitis C infection. This study was conducted to find out the frequency of different IL-28B (rs12979860) genotypes in patients with chronic hepatitis C (HCV genotype type 2 & 3) infection treated with Pegulated Interferon α2 plus ribavirin and to evaluate the role of IL-28B genotypes in achieving Sustained Virological Response (SVR). Methods: In this non-randomized observational study, ninety eight (98) patients with diagnosis of chronic hepatitis C were included. In all patients, Peg-IFN plus Ribavirin were given in standard doses for 24 weeks. End treatment response, sustained virological response, and relapse rate were the primary endpoints of this study. Analysis of IL28B (rs12979860) polymorphism (CC, CT and TT) was performed by PCR-RFLP protocol.

NCT03090035 Hepatitis C Hepatitis C Relapse

Impact of Interleukin 28B (rs12979860) Genotype on Virological Responses in Chronic Hepatitis C Treatment.

Impact of Interleukin 28B (rs12979860) Genotype on Virological Responses Chronic Hepatitis C Treatment Objective: Pegulated Interferon α2 plus ribavirin is a treatment of choice in patients with chronic hepatitis C infection.

This study was conducted to find out the frequency of different IL-28B (rs12979860) genotypes in patients with chronic hepatitis C (HCV genotype type 2 & 3) infection treated with Pegulated Interferon α2 plus ribavirin and to evaluate the role of IL-28B genotypes in achieving Sustained Virological Response (SVR).

Analysis of IL28B (rs12979860) polymorphism (CC, CT and TT) was performed by PCR-RFLP protocol.

The aim of present study was to find out the frequency of different IL28B (rs12979860) genotypes in patients with chronic hepatitis C (genotype type 2 or 3) infection treated with Pegulated Interferon α2 plus ribavirin and to evaluate the role of IL-28B genotypes in achieving Sustained Virological Response (SVR).

Analysis of IL28B (rs12979860) polymorphism (CC, CT and TT) was performed by PCR restriction fragment length polymorphism (RFLP) assay protocol.

Primary Outcomes

Description: Treatment Success rate (End Treatment Response) was noted to check the adequency of treatment

Measure: Treatment Success rate

Time: after 24 weeks of treatment

Secondary Outcomes

Description: Relapse Rate to check re-occurrence of Hepatitis infection

Measure: Relapse Rate

Time: After 48 weeks of treament


4 Phase 2a Study of Boceprevir for the Treatment of Genotype 6 Hepatitis C

The purpose of this study is to evaluate the antiviral efficacy of Boceprevir-based therapy for the treatment of genotype 6 chronic hepatitis C infection. Boceprevir has recently been approved for the treatment of genotype 1 chronic hepatitis C infection. Recent in vitro studies suggest similar efficacy against genotype 6 chronic hepatitis C infection. The investigators therefore hypothesise that: i) Boceprevir is a potent inhibitor of genotype 6 hepatitis C replication in vivo. ii) Boceprevir in combination with pegylated interferon-alpha and ribavirin for 24 weeks will cure a high proportion of patients chronically infected with genotype 6 chronic hepatitis C infection.

NCT01949168 Chronic Hepatitis C

All patients will be of Asian background, will be non-cirrhotic, and will carry a "good response" IL28B genotype (C/C for rs12979860).

Primary Outcomes

Description: Determined by plasma HCV RNA quantification at frequent time points - baseline, day 1, 2, 3, 4 and 5

Measure: Early viral kinetics

Time: Day 5

Secondary Outcomes


5 Security and Efficacy of Triple Therapy Including Direct-Acting Antivirals Against Chronic Hepatitis C Infection In HIV-Coinfected Patients In Real-Life Conditions: The Prospective HEPAVIR Cohort.

The purpose of this study is to evaluate the efficacy and tolerability of DAA-based regimens in the clinical practice in HIV/HCV-coinfected patients. Hypothesis: The efficacy and tolerability of DAA-based regimens in the clinical practice is different to what is observed in clinical trials in HIV/HCV-coinfected patients.

NCT02057003 Hepatitis C, Chronic Human Immunodeficiency Virus

Definition of hepatic fibrosis: - advanced fibrosis: F3 as determined by liver biopsy or 11 kilopascals as determined by transient elastometry - cirrhosis: F4 as determined by liver biopsy or 14.6 kilopascals as determined by transient elastometry Variables collected within in the cohort: - primary outcome variable: SVR (efficacy study) and % of patients who discontinued therapy due to adverse events (safety study) - epidemiological variable: age, sex, interleukin 28B rs12979860 genotype - variables related to hepatitis C virus-infection: infection route, genotype, grade of hepatic fibrosis and method used for its determination, baseline Child-Pough-Index, previous hepatic decompensations - treatment-related variables: previous response to treatment, doses and dose reductions/discontinuations of peg-IFN, RBV and the DAA(s), overall severe adverse events, adverse events that occur in more than 5% of the patients, hepatic decompensations, deaths, HCV viral load at baseline and at each visit - variables related to HIV-infection: Centers for Disease Control and Prevention (CDC) category, HIV viral load, cluster of differentiation 4 (CD4) cell count, antiretroviral regimen - analytical variables: aspartate aminotransferase (AST), alanine aminotransferase (ALT), platelets, leucocytes, low-density lipoprotein cholesterol, bilirubin, gamma-glutamyltransferase (GGT), alkaline phosphatase, - clinical variables: alcohol intake Quality assurance and data checks: Data will be obtained from controlled databases at the participating centers.

Primary Outcomes

Description: Development of severe adverse events related to DAA-based therapy in the clinical practice in patients with chronic hepatitis C and HIV coinfection.

Measure: Number of patients who develop severe adverse events as measure of safety

Time: 18 months

Secondary Outcomes

Description: The numbers of patients who achieve SVR to DAA-based therapy in absence of interferon will be analyzed.

Measure: Number of patients who achieve SVR to an interferon-free regimen.

Time: 36 weeks


6 A Phase II Multicenter, Parallel-Group, Randomized, Dose-Ranging Study to Investigate the Safety, Tolerability, Pharmacokinetics, and Pharmacodynamics Following 12 Weeks of Oral Administration of GSK2336805 With Pegylated Interferon and Ribavirin in Treatment-Naïve Subjects With Chronic Genotype 1 or 4 Hepatitis C Infection

GSK2336805 is a novel hepatitis C virus (HCV) non-structural 5A (NS5A) inhibitor being developed for the treatment of chronic HCV infection. This Phase II, multicenter, parallel-group, randomized, dose-ranging study will assess the safety and tolerability, antiviral activity, and pharmacokinetics of GSK2336805 at 2 dose levels (40 and 60 mg) in combination with pegylated interferon alfa-2a (PEG) and ribavirin (RIBA) in approximately 100 treatment-naïve subjects with chronic genotype 1 HCV infection. In a separate nonrandomized single-arm cohort, up to 15 treatment-naïve subjects with genotype 4 chronic HCV infection will be enrolled in parallel at the dose level of 60 mg of GSK2336805.

NCT01648140 Hepatitis C, Chronic

Randomization will be stratified by interleukin 28B (IL28B) rs12979860 status (C/C versus carriage of the T allele), HCV genotype (1a vs. 1b), and plasma HCV Ribonucleic Acid (RNA) (<800,000 IU/mL versus ≥800,000 IU/mL).

Primary Outcomes

Description: The ECG parameters including PR interval, QRS duration, uncorrected QT interval, QTcB, QTcF were measured at Baseline, Weeks 1 and 12. Change from Baseline in ECG parameters are summarized for each post-Baseline assessment up to Week 12. Change from Baseline was calculated as the individual post-Baseline value minus the Baseline value. Baseline value is defined as the last Pre-treatment value observed.

Measure: Mean Change From Baseline in PR Interval, QRS Duration, Uncorrected QT Interval and QT Interval Corrected Bazett's Formula (QTcB), QT Interval Corrected Using Fridericia's Formula (QTcF) Values at the Indicated Time Points up to Week 12

Time: Baseline (Week 0) and Weeks 1 and 12

Secondary Outcomes

Description: Correlation GSK2336805 pre-dose plasma concentration (ng/mL) on Day 2 versus reduction in HCV RNA (log IU/mL) on Day 2 was performed. As defined in the RAP for this protocol, correlations between GSK2336805 dose, and selected PK parameters and virological outcomes was analyzed only with graphical presentations to facilitate clinical interpretation and data summarization. These data were also provided in by-participant data listings. Therefore, no statistical summary tables are available.

Measure: Correlation GSK2336805 Pre-dose Plasma Concentration on Day 2 Versus Reduction in HCV RNA on Day 2

Time: Day 2


7 Influence of IL28B Genetic Variation on the Phenotype Infection of HTLV-1

Only 5 to 10% of patients infected with HTLV-1 develop a disease related to infection. The two most serious diseases are adult T-cell leukemia (ATL) and Tropical spastic paraparesis /HTLV-I-associated myelopathy (TSP / HAM). Factors influencing the development of TSP / HAM in the individual HTLV-1 are not yet completely understood. Patients TSP / HAM have a HTLV-1 proviral load (amount of virus) that is 6-10 times higher than seropositive asymptomatic. Various studies have shown that the development of TSP / HAM in the subject HTLV-1 and its rapid evolution is partly attributed to the failure of the immune system that regulates viral replication and expression. It has recently been shown that different versions of Single Nucleotide (human leukocyte antigen) rs12979860, located upstream of the gene for Interleukin 28B (IL28B), influenced the severity of infection with hepatitis C and effectiveness of treatment. By analogy with hepatitis C, a Spanish (Treviño et al., 2012) examined this SNP(single nucleotide polymorphism) in 12 patients TSP / HAM and 29 asymptomatic HIV-positive. CT or TT genotype was statistically more frequent in the group TSP / HAM than in asymptomatic patients (80% versus 20%) and was associated with HTLV-1 proviral load higher. We propose a broader group of patients in our population and Afro-Caribbean, to confirm the results of the latter study was conducted in a predominantly Latin American population.

NCT01754311 HTLV-I Infections

It has recently been shown that different versions of Single Nucleotide (human leukocyte antigen) rs12979860, located upstream of the gene for Interleukin 28B (IL28B), influenced the severity of infection with hepatitis C and effectiveness of treatment.

Primary Outcomes

Description: The participants will be followed until the end of the study ( with an expected average of 30 days after the inclusion). Explenations : each participant will have a blood sample who will be performed at the recruitement day (for génetics analysis) . After this first visit (recuitement visit) , each participant will have to perform an appointement with the ophtalmologic département ( recuperate datas about the presence or not of an uveitis and a keratoconjunctivitis)

Measure: Presence of CT or TT allele for each participant

Time: 30 days


8 Prevalence of Host and Viral Genotypes in Patients With Chronic Hepatitis B and Hepatitis C Infection in India

This study will define the substantial disease burden associated with viral hepatitis in India, and provide a foundation to understand the host and viral determinants of disease pathogenesis that may ultimately impact treatment decisions and outcome

NCT01772121 Hepatitis B Hepatitis C

Observational Study on Prevalence of Host and Viral Genotypes in Chronic Hepatitis B and Hepatitis C Patients in India This study will define the substantial disease burden associated with viral hepatitis in India, and provide a foundation to understand the host and viral determinants of disease pathogenesis that may ultimately impact treatment decisions and outcome Variation in the IL28B rs12979860 SNP.

Characterize the variation in the IL28B rs12979860 SNP that exists among patients with chronic hepatitis C or chronic hepatitis B infection, in the different geographic regions of India.

Variation in the IL28B rs12979860 SNP.

Primary Outcomes

Description: Characterize the variation in the IL28B rs12979860 SNP that exists among patients with chronic hepatitis C or chronic hepatitis B infection, in the different geographic regions of India

Measure: Variation in the IL28B rs12979860 SNP

Time: One Visit

Secondary Outcomes

Description: Characterize the SNPs present in innate immune factors TLR7 (rs3853839, rs179008); TLR9 (rs41308230, rs5743844 ); RIG-I (rs11795404, rs10813831) and NOD2 (rs2067085, rs2066842), in patients with chronic hepatitis C or chronic hepatitis B in the different geographic regions of India

Measure: Characterize the SNPs present in innate immune factors toll-like receptor 7 (TLR7)

Time: One Visit


9 Efficacy of Pentoxyfylline Addition to a Treatment Scheme Based on Interferon Alpha and Ribavirin on Hepatitis C Virus Coinfected HIV Patients, Considering Interleukin 28B Polymorphism rs12979860

Current Hepatitis C virus (HCV) treatment consists of the combination of interferon alpha 2a (IFN-alpha 2a) plus ribavirin (RBV) and it provides sustained virologic responses (SVR) on 54 to 56% on HCV monoinfected patients and this response is even lower on HIV-HCV coinfected patients. A previous study on HCV monoinfected patients showed that the addition of pentoxyfylline (PTX) to a treatment scheme based on interferon-alfa and ribavirin increased SVR on 25%, although it is not known if the same effect is to be obtained in HCV-HIV coinfected patients. On the other hand, other factors such as host genetics, have proved to influence treatment response on HCV infected patients. The best described genetic factor so far is the interleukin 28B (IL28B) polymorphism rs12979860, where a cytosine-cytosine (CC) genotype provides an almost twice increase on SVR than the rest of the genotypes. Therefore, this is a randomized, double blind study to assess the efficacy of pentoxyfylline addition to a treatment scheme based on interferon-alfa and ribavirin in chronic HCV genotype 1, co-infected HIV-1 positive subjects, considering the IL28B polymorphism rs12979860. HIV-HCV coinfected subjects currently receiving Highly active antiretroviral therapy (HAART), with at least 8 months on undetectable HIV viral load and T helper cells count of 200 or higher will be included. Patients will be randomized on one of two groups: - Group A: IFN alpha 2a + RBV + PTX - Group B: IFN alpha 2a + RBV + placebo Patients will be followed for primary outcome during 72 (for rapid responders) or 96 weeks (for non rapid responses). Outcome measures will be the following: - SVR rate 24 weeks after the end of treatment - Grade of Hepatic fibrosis from baseline to the end of treatment, measured by transient elastography and the AST to platelet ratio index (APRI index) - IL28B rs12979860 genotype The study hypothesis is that the addition of PTX to a treatment scheme based on IFN-alfa2a and RBV in chronic HCV genotype 1, co-infected HIV-1 positive subjects will improve SVR rate and fibrosis progression irrespectively of IL28B rs12979860 genotype.

NCT02008214 Hepacivirus HIV Infections

Efficacy of Pentoxyfylline Addition to a Treatment Scheme Based on Interferon Alpha and Ribavirin on Hepatitis C Virus Coinfected HIV Patients, Considering Interleukin 28B Polymorphism rs12979860.

The best described genetic factor so far is the interleukin 28B (IL28B) polymorphism rs12979860, where a cytosine-cytosine (CC) genotype provides an almost twice increase on SVR than the rest of the genotypes.

Therefore, this is a randomized, double blind study to assess the efficacy of pentoxyfylline addition to a treatment scheme based on interferon-alfa and ribavirin in chronic HCV genotype 1, co-infected HIV-1 positive subjects, considering the IL28B polymorphism rs12979860.

Outcome measures will be the following: - SVR rate 24 weeks after the end of treatment - Grade of Hepatic fibrosis from baseline to the end of treatment, measured by transient elastography and the AST to platelet ratio index (APRI index) - IL28B rs12979860 genotype The study hypothesis is that the addition of PTX to a treatment scheme based on IFN-alfa2a and RBV in chronic HCV genotype 1, co-infected HIV-1 positive subjects will improve SVR rate and fibrosis progression irrespectively of IL28B rs12979860 genotype.

Primary Outcomes

Description: Primary objective: is to evaluate sustained virologic response at post treatment week 24 following treatment with IFNalpha 2a/RBV/PTX with genotype 1 chronic HCV infection + HIV infection

Measure: sustained virologic rate 24 weeks post treatment with IFNalpha 2a/RBV/PTX with genotype 1 chronic HCV infection + HIV infection

Time: SVR rate at 24 weeks after the end of therapy

Secondary Outcomes

Description: secondary objective (2): Evaluate rapid virologic response (RVR) and extended rapid virologic response (eRVR)

Measure: rapid virologic response (RVR) and extended rapid virologic response (eRVR) rates

Time: RVR at week 4 and eRVR at week 48 post treatment



HPO Nodes


Recurrent skin infections
Genes 36
XIAP BTD USP8 CD79A CD79B COL7A1 GINS1 FERMT3 DSG1 ELANE FOXC2 GATA1 TMC6 CFI SHANK3 IGHM IGLL1 ITGA6 ITGB4 KRT1 KRT5 KRT14 LAMA3 LAMB3 LAMC2 NFKB1 BLNK PIK3R1 FERMT1 CHST14 CDH23 TCF3 LRRC8A UROS TMC8 GJC2
Chronic hepatitis due to cryptosporidium infection
Genes 1
IL21R
Severe Epstein Barr virus infection
Prolonged bleeding after surgery
Genes 5
F7 F13B P2RX1 VWF P2RY12
Chronic active hepatitis
Genes 5
AIRE C4B KRT8 KRT18 ALMS1
Hyperpepsinogenemia I
Genes 1
NPPA
Enteroviral hepatitis
Genes 1
BTK