Mendelian Randomization with Incomplete Exposure Data: a Bayesian Approach

We expand Mendelian Randomization (MR) methodology to deal with randomly missing data on either the exposure or the outcome variable, and furthermore with data from nonindependent individuals (eg components of a family). Our method rests on the Bayesian MR framework proposed by Berzuini et al (2018), which we apply in a study of multiplex Multiple Sclerosis (MS) Sardinian families to characterise the role of certain plasma proteins in MS causation. The method is robust to presence of pleiotropic effects in an unknown number of instruments, and is able to incorporate inter-individual kinship information. Introduction of missing data allows us to overcome the bias introduced by the (reverse) effect of treatment (in MS cases) on level of protein. From a substantive point of view, our study results confirm recent suspicion that an increase in circulating IL12A and STAT4 protein levels does not cause an increase in MS risk, as originally believed, suggesting that these two proteins may not be suitable drug targets for MS

Safety and efficacy of direct-acting antivirals in transfusion-dependent thalassemic patients with chronic hepatitis C

Background: Hepatitis C virus (HCV) infection is a major cause of liver-related morbidity and mortality among thalassemic patients. New treatments based on direct-acting antivirals (DAAs) are highly effective and well-tolerated by patients; nonetheless, they have not been studied in thalassemic populations. In this study, we evaluated the safety and efficacy of these treatments in a cohort of Sardinian thalassemic patients with chronic HCV infection. Methods: We consecutively recruited thalassemic patients with HCV infection, who were eligible for DAA therapy at 3 liver units. Different drug combinations, depending on HCV genotype and hepatic disease severity, were used according to the current guidelines. Sustained virological response was assessed at 12 weeks posttreatment. Data regarding the side effects and transfusion requirements were also collected. Results: We recruited 49 patients, including 29 males (59.2%), with the mean age of 43 years (genotype 1, 55.1%). Twenty-one (42.9%) patients had a history of interferon-based treatment. Cirrhosis was detected in 28 (57.1%) patients; only 1 patient had ascites and hypoalbuminemia (Child-Pugh B7). On the other hand, 35 (71.4%) patients received a sofosbuvir-based regimen. Ribavirin treatment was reported in 26 (53.1%) cases. All the patients were followed-up for at least 12 weeks after therapy, and sustained virological response was observed in 98% of the patients. No treatment discontinuation was required due to adverse events. The most common side effects included fatigue (24.5%), headache (10.2%), and anaemia (77%), requiring further blood transfusion in patients receiving ribavirin. Conclusions: This prospective study showed that DAAs are safe and effective agents in thalassemic patients with advanced liver fibrosis, regardless of previous antiviral treatment responses

Association between the ACCN1 Gene and Multiple Sclerosis in Central East Sardinia

Multiple genome screens have been performed to identify regions in linkage or association with Multiple Sclerosis (MS, OMIM 126200), but little overlap has been found among them. This may be, in part, due to a low statistical power to detect small genetic effects and to genetic heterogeneity within and among the studied populations. Motivated by these considerations, we studied a very special population, namely that of Nuoro, Sardinia, Italy. This is an isolated, old, and genetically homogeneous population with high prevalence of MS. Our study sample includes both nuclear families and unrelated cases and controls. A multi-stage study design was adopted. In the first stage, microsatellites were typed in the 17q11.2 region, previously independently found to be in linkage with MS. One significant association was found at microsatellite D17S798. Next, a bioinformatic screening of the region surrounding this marker highlighted an interesting candidate MS susceptibility gene: the Amiloride-sensitive Cation Channel Neuronal 1 (ACCN1) gene. In the second stage of the study, we resequenced the exons and the 3′ untranslated (UTR) region of ACCN1, and investigated the MS association of Single Nucleotide Polymorphisms (SNPs) identified in that region. For this purpose, we developed a method of analysis where complete, phase-solved, posterior-weighted haplotype assignments are imputed for each study individual from incomplete, multi-locus, genotyping data. The imputed assignments provide an input to a number of proposed procedures for testing association at a microsatellite level or of a sequence of SNPs. These include a Mantel-Haenszel type test based on expected frequencies of pseudocase/pseudocontrol haplotypes, as well as permutation based tests, including a combination of permutation and weighted logistic regression analysis. Application of these methods allowed us to find a significant association between MS and the SNP rs28936 located in the 3′ UTR segment of ACCN1 with p = 0.0004 (p = 0.002, after adjusting for multiple testing). This result is in tune with several recent experimental findings which suggest that ACCN1 may play an important role in the pathogenesis of MS

Association between Protective and Deleterious HLA Alleles with Multiple Sclerosis in Central East Sardinia

The human leukocyte antigen (HLA) complex on chromosome 6p21 has been unambiguously associated with multiple sclerosis (MS). The complex features of the HLA region, especially its high genic content, extreme polymorphism, and extensive linkage disequilibrium, has prevented to resolve the nature of HLA association in MS. We performed a family based association study on the isolated population of the Nuoro province (Sardinia) to clarify the role of HLA genes in MS. The main stage of our study involved an analysis of the ancestral haplotypes A2Cw7B58DR2DQ1 and A30Cw5B18DR3DQ2. On the basis of a multiplicative model, the effect of the first haplotype is protective with an odds ratio (OR) = 0.27 (95% confidence interval CI 0.13–0.57), while that of the second is deleterious, OR 1.78 (95% CI 1.26–2.50). We found both class I (A, Cw, B) and class II (DR, DQ) loci to have an effect on MS susceptibility, but we saw that they act independently from each other. We also performed an exploratory analysis on a set of 796 SNPs in the same HLA region. Our study supports the claim that Class I and Class II loci act independently on MS susceptibility and this has a biological explanation. Also, the analysis of SNPs suggests that there are other HLA genes involved in MS, but replication is needed. This opens up new perspective on the study of MS

Fat-Corrected Pancreatic <i>R</i>2* Relaxometry from Multi-Echo Gradient-Recalled Echo Sequence Using Convolutional Neural Network

Fat-corrected R2* relaxometry from multi-echo gradient-recalled echo sequences (mGRE) could represent an efficient approach for iron overload evaluation, but its use is limited by computational constraints. A new method for the fast generation of R2* and fat fractions (FF) maps from mGRE using a convolutional neural network (U-Net) and deep learning (DL) is presented. A U-Net for the calculation of pancreatic R2* and FF maps was trained with 576 mGRE abdominal images and compared to conventional fat-corrected relaxometry. The U-Net was effectively trained and provided R2* and FF maps visually comparable to conventional methods. Predicted pancreatic R2* and FF values were well correlated with the conventional model. Estimated and ground truth mean R2* values were not significantly different (43.65 ± 21.89 vs. 43.77 ± 19.81 ms, p = 0.692, intraclass correlation coefficient-ICC = 0.9938, coefficient of variation-CoV = 5.3%), while estimated FF values were slightly higher in respect to ground truth values (27.8 ± 16.87 vs. 25.67 ± 15.43 %, p < 0.0001, ICC = 0.986, CoV = 10.1%). Deep learning utilizing the U-Net is a feasible method for pancreatic MR fat-corrected relaxometry. A trained U-Net can be efficiently used for MR fat-corrected relaxometry, providing results comparable to conventional model-based methods

Fast generation of <i>T2</i>* maps in the entire range of clinical interest: application to thalassemia major patients

T2* maps obtained by the processing of multiecho MR sequences can be useful in several clinical applications. T2* map generation procedures should join a processing time compatible with on-line image analysis with a good precision in the entire T2* range of clinical interest. Fast generation of T2* maps can be achieved by the estimation of the T2* values by the weighted linear fitting of the logarithm of the signal (WLSL) method. This approach fails if the signal decay diverges from a pure exponential decay, as happens at low T2* values where the rapid decay in the signal intensity leads to a plateau in the later echo times (TE). The proposed method implements the automatic truncation of the signal decay curves to be fitted in order to compensate for the signal collapse at low T2* values, allowing the extension of the WLSL method through the entire clinical range of T2* values. Validation was performed on synthetic images and on 60 thalassemia major patients with different levels of myocardial iron overload. Phantom experiments showed that a 5% fitting error threshold represented the best compromise between T2* value measurement precision and processing time. A good agreement was found between T2* map pixel-wise measurements and ROI-based measurements performed by expert readers (CoV=1.84% in global heart T2*, CoV=5.8% in segmental analysis). In conclusion, the developed procedure was effective in generating correct T2* maps for the entire T2* clinical range.</br

Gender Differences in Knowledge and Perception of Cardiovascular Disease among Italian Thalassemia Major Patients

We evaluated gender differences in knowledge and perception of cardiovascular disease (CVD) among Italian thalassemia major (TM) patients. An anonymous questionnaire was completed by 139 &beta;-TM patients (87 (62.7%) females, 40.90 &plusmn; 8.03 years). Compared to females, males showed a significantly higher frequency of CVDs, and they less frequently selected tumors in general as the greatest health problem for people of the same age and gender (48.1% vs. 66.7%; p = 0.031) and as the greatest danger to their future health (26.9% vs. 43.7%; p = 0.048). CVDs were designated as the greatest danger to their future health by a significantly higher percentage of males than females (53.8% vs. 36.8%; p = 0.048). Both males and females showed a good knowledge of cardiovascular risk factors and preventive measures for CVDs. No gender differences were detected in the subjective well-being and the perceived cardiovascular risk. The perceived risk was not influenced by age, presence of cardiovascular risk factors, or disease, but no patient with a low perceived CVD risk had myocardial iron overload. Our findings highlight the need to implement future educational programs aimed at increasing the awareness of CVD as the greatest health issue, especially among the female TM population, and at informing TM patients of the different actors, besides iron, that play a role in the development of cardiovascular complications