Multi-locus genetic risk score predicts risk for Crohn’s disease in Slovenian population

Zupančič, Katarina; Skok, Kristijan; Repnik, Katja; Weersma, Rinse K.; Potočnik, Uroš; Skok, Pavel

doi:10.3748/wjg.v22.i14.3777

Cited by 13 publications

(9 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…MAF is a frequency which is the second most common allele exsiting in the given population. It plays a surprising part in heritability since MAF variants which occurs only once, known as “singletons”, drive a huge amount of the selection 25 . MAF is very widely used in the population genetics research.…”

Section: Discussionmentioning

confidence: 99%

“…The EV-GRS was a method that considered both the effects of Minor Allele Frequency (MAF) and SNP 21 . According to the definition, EV-GRS thought SNP and MAF both have a very important impact on the outcome in each SNP locus 25 . The calculation formula and the model are as follows: where n was the number of SNPs, ln (OR i) was the weight of the ith SNP locus, MAF i was the MAF of the ith SNP locus, G i was the ith risk allele of SNP locus.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Combining genetic risk score with artificial neural network to predict the efficacy of folic acid therapy to hyperhomocysteinemia

Chen

Huang

Diao

et al. 2021

Sci Rep

View full text Add to dashboard Cite

Artificial neural network (ANN) is the main tool to dig data and was inspired by the human brain and nervous system. Several studies clarified its application in medicine. However, none has applied ANN to predict the efficacy of folic acid treatment to Hyperhomocysteinemia (HHcy). The efficacy has been proved to associate with both genetic and environmental factors while previous studies just focused on the latter one. The explained variance genetic risk score (EV-GRS) had better power and could represent the effect of genetic architectures. Our aim was to add EV-GRS into environmental factors to establish ANN to predict the efficacy of folic acid therapy to HHcy. We performed the prospective cohort research enrolling 638 HHcy patients. The multilayer perception algorithm was applied to construct ANN. To evaluate the effect of ANN, we also established logistic regression (LR) model to compare with ANN. According to our results, EV-GRS was statistically associated with the efficacy no matter analyzed as a continuous variable (OR = 3.301, 95%CI 1.954–5.576, P < 0.001) or category variable (OR = 3.870, 95%CI 2.092–7.159, P < 0.001). In our ANN model, the accuracy was 84.78%, the Youden’s index was 0.7073 and the AUC was 0.938. These indexes above indicated higher power. When compared with LR, the AUC, accuracy, and Youden’s index of the ANN model (84.78%, 0.938, 0.7073) were all slightly higher than the LR model (83.33% 0.910, 0.6687). Therefore, clinical application of the ANN model may be able to better predict the folic acid efficacy to HHcy than the traditional LR model. When testing two models in the validation set, we got the same conclusion. This study appears to be the first one to establish the ANN model which added EV-GRS into environmental factors to predict the efficacy of folic acid to HHcy. This model would be able to offer clinicians a new method to make decisions and individual therapeutic plans.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Combining genetic risk score with artificial neural network to predict the efficacy of folic acid therapy to hyperhomocysteinemia

Chen

Huang

Diao

et al. 2021

Sci Rep

View full text Add to dashboard Cite

show abstract

“…In our female patient, after the introduction of methylprednisolone in IV form, significant improvement in the clinical picture and skin changes was achieved. Even the problems of the affected large intestine were alleviated in the following weeks because steroids are one of the key drugs in IBD (3). During the follow-up period, due to the unfavorable course of CD, we introduced biological drugs, TNF-alfa inhibitors (infliximab), and immunomodulators (azathioprine), which are still being used.…”

Section: Discussionmentioning

confidence: 99%

“…In western Europe the incidence is 10 per 100,000 and the prevalence 100 per 100,000. In Slovenia, the incidence is 5 per 100,000; unfortunately, there are no precise data on the prevalence (3,4). Epidemiological, genetic, and immunological data show that CD is a heterogeneous disorder with a multifactorial etiology in which genetics and environmental factors trigger the disease.…”

Section: Introductionmentioning

confidence: 99%

Acute febrile neutrophilic dermatosis in a patient with Crohn’s disease: case report and review of the literature

Skok

2018

Acta Dermatovenerologica Alpina Pannonica Et Adriatica

Self Cite

View full text Add to dashboard Cite

“…So far, studies on the efficacy of folic acid therapy have only explored the impacts of single nucleotide polymorphism (SNP), and there is a certain one-sidedness. Individual SNP have small effect on risk and have poor predictive ability (19) . To combine the relatively small effects of individual SNP and to better capture the complex relationship between genetics and the folic acid efficacy, the use of genetic risk score (GRS) has been proposed.…”

mentioning

confidence: 99%

Prediction model for the efficacy of folic acid therapy on hyperhomocysteinaemia based on genetic risk score methods

Zhang

Liu

et al. 2019

Br J Nutr

View full text Add to dashboard Cite

No risk assessment tools for the efficacy of folic acid treatment for hyperhomocysteinaemia (HHcy) have been developed. We aimed to use two common genetic risk score (GRS) methods to construct prediction models for the efficacy of folic acid therapy on HHcy, and the best gene–environment prediction model was screened out. A prospective cohort study enrolling 638 HHcy patients was performed. We used a logistic regression model to estimate the associations of two GRS methods with the efficacy. Performances were compared using area under the receiver operating characteristic curve (AUC). The simple count genetic risk score (SC-GRS) and weighted genetic risk score (wGRS) were found to be independently associated with the efficacy of folic acid treatment for HHcy. Using the SC-GRS, per risk allele increased with a 1·46-fold increased failure risk (P < 0·001) after adjustment for traditional risk factors, including age, sex, BMI, smoking, alcohol consumption, history of diabetes, history of hypertension, history of hyperlipidaemia, history of stroke and history of CHD. When used the wGRS, the association was strengthened (OR = 2·08, P < 0·001). Addition of the SC-GRS and wGRS to the traditional risk model significantly improved the predictive ability by AUC (0·859). A precise gene–environment predictive model with good performance was developed for predicting the treatment failure rate of folic acid therapy for HHcy.

show abstract

Multi-locus genetic risk score predicts risk for Crohn’s disease in Slovenian population

Abstract: The authors proved the possibility of building accurate genetic risk score based on 33 risk variants on Slovenian CD patients which may serve as a screening tool in the targeted population.

Cited by 13 publications

References 29 publications

Combining genetic risk score with artificial neural network to predict the efficacy of folic acid therapy to hyperhomocysteinemia

Combining genetic risk score with artificial neural network to predict the efficacy of folic acid therapy to hyperhomocysteinemia

Acute febrile neutrophilic dermatosis in a patient with Crohn’s disease: case report and review of the literature

Prediction model for the efficacy of folic acid therapy on hyperhomocysteinaemia based on genetic risk score methods

Contact Info

Product

Resources

About