A genome-wide tree- and forest-based association analysis of comorbidity of alcoholism and smoking

Genetic mechanisms underlying alcoholism are complex. Understanding the etiology of alcohol dependence and its comorbid conditions such as smoking is important because of the significant health concerns. In this report, we describe a method based on classification trees and deterministic forests for association studies to perform a genome-wide joint association analysis of alcoholism and smoking. This approach is used to analyze the single-nucleotide polymorphism data from the Collaborative Study on the Genetics of Alcoholism in the Genetic Analysis Workshop 14. Our analysis reaffirmed the importance of sex difference in alcoholism. Our analysis also identified genes that were reported in other studies of alcoholism and identified new genes or single-nucleotide polymorphisms that can be useful candidates for future studies

Multivariate linkage analysis using the electrophysiological phenotypes in the COGA alcoholism data

Multivariate linkage analysis using several correlated traits may provide greater statistical power to detect susceptibility genes in loci whose effects are too small to be detected in univariate analysis. In this analysis, we apply a new approach and perform a linkage analysis of several electrophysiological phenotypes of the Collaborative Study on the Genetics of Alcoholism data of the Genetic Analysis Workshop 14. Our approach is based on a variance-component model to map candidate genes using repeated or longitudinal measurements. It can take into account covariate effects and time-dependent genetic effects in general pedigree data. We compare our results with the ones obtained by SOLAR using single measurement data. Our multivariate linkage analysis found linkage evidence on two regions on chromosome 4: around marker GABRB1 at 51.4 cM and marker FABP2 at 116.8 cM (unadjusted p-value = 0.00006)

Socio-demographic, Clinical, and Genetic Determinants of Quality of Life in Lung Cancer Patients.

Patient reported health-related quality of life (QOL) is a major component of the overall well-being of cancer patients, with links to prognosis. In 6,420 lung cancer patients, we identified patient characteristics and genetic determinants of QOL. Patient responses from the SF-12 questionnaire was used to calculate normalized Physical Component Summary (PCS) and Mental Component Summary (MCS) scores. Further, we analyzed 218 single nucleotide polymorphisms (SNPs) in the p38 MAPK signaling pathway, a key mediator of response to cellular and environmental stress, as genetic determinants of QOL in a subset of the study population (N = 641). Trends among demographic factors for mean PCS and MCS included smoking status (PCS Ptrend < 0.001, MCS Ptrend < 0.001) and education (PCS Ptrend < 0.001, MCS Ptrend < 0.001). Similar relationships were seen for MCS. The homozygous rare genotype of MEF2B: rs2040562 showed an increased risk of a poor MCS (OR: 3.06, 95% CI: 1.05-8.92, P = 0.041). Finally, survival analysis showed that a low PCS or a MCS was associated with increased risks of five-year mortality (HR = 1.63, 95% CI: 1.51-1.77, HR = 1.23, 95% CI: 1.16-1.32, respectively) and there was a significant reduction in median survival time (Plog-rank < 0.001). These findings suggest that multiple factors contribute to QOL in lung cancer patients, and baseline QOL can impact survival

Personalized Risk Assessment in Never, Light, and Heavy Smokers in a prospective cohort in Taiwan.

The objective of this study was to develop markedly improved risk prediction models for lung cancer using a prospective cohort of 395,875 participants in Taiwan. Discriminatory accuracy was measured by generation of receiver operator curves and estimation of area under the curve (AUC). In multivariate Cox regression analysis, age, gender, smoking pack-years, family history of lung cancer, personal cancer history, BMI, lung function test, and serum biomarkers such as carcinoembryonic antigen (CEA), bilirubin, alpha fetoprotein (AFP), and c-reactive protein (CRP) were identified and included in an integrative risk prediction model. The AUC in overall population was 0.851 (95% CI = 0.840-0.862), with never smokers 0.806 (95% CI = 0.790-0.819), light smokers 0.847 (95% CI = 0.824-0.871), and heavy smokers 0.732 (95% CI = 0.708-0.752). By integrating risk factors such as family history of lung cancer, CEA and AFP for light smokers, and lung function test (Maximum Mid-Expiratory Flow, MMEF25-75%), AFP and CEA for never smokers, light and never smokers with cancer risks as high as those within heavy smokers could be identified. The risk model for heavy smokers can allow us to stratify heavy smokers into subgroups with distinct risks, which, if applied to low-dose computed tomography (LDCT) screening, may greatly reduce false positives

Pediatric Myopia Progression During the COVID-19 Pandemic Home Quarantine and the Risk Factors: A Systematic Review and Meta-Analysis

BackgroundThe COVID-19 pandemic has made many countries adopt restrictive measures like home quarantine. Children were required to study at home, which made parents worried about the rapid myopic progression of their children. To compare myopia progression during the COVID-19 pandemic home quarantine with the time before it and risk factors of myopia progression, we conducted this study.MethodsWe searched PubMed, Embase, the Cochrane Library, and Web of Science to find literature from December 2019 to March 2022 related to COVID-19 pandemic home quarantine and children's myopia progression. Outcomes of myopia progression included axial length and spherical equivalent refraction. Factors of digital screen device time and outdoor activity time were analyzed.ResultsTen studies were included in this meta-analysis. Compared to the same period before the COVID-19 pandemic, spherical equivalent refraction decreased (OR = −0.27; 95% CI = [−0.33, −0.21]; Z = 8.42; P < 0.00001). However, the subgroup analysis showed that there were no significant differences in spherical equivalent refraction between the two groups in higher-grade school-aged children (grades 4 and above, 11 to 18 years old) (OR = 0.01; 95% CI = [−0.05, 0.07]; Z =0.4; P = 0.69). The outcome of axial length showed no significant difference (OR = 0.06; 95% CI = [−0.31, 0.44]; Z = 0.34; P = 0.74). As for risk factors, the forest plots showed that digital screen device time (OR = 4.56; 95% CI = [4.45, 4.66]; Z = 85.57; P < 0.00001) and outdoor activity time (OR = −1.82; 95% CI = [−2.87, −0.76]; Z = 3.37; P = 0.0008) were risk factors of myopia progression.ConclusionCompared with the time before the COVID-19 pandemic, myopia progression in children during COVID-19 pandemic home quarantine was accelerated, especially in younger children. Increased digital screen device and decreased outdoor activity times were risk factors. When home quarantine eases, more time on outdoor activities and less time on digital screen devices are needed for children.Systematic Review Registrationhttps://www.crd.york.ac.uk/prospero/logout.php

Phase I study of nab-paclitaxel, gemcitabine, and bevacizumab in patients with advanced cancers.

BackgroundWe performed a phase I modified 3 + 3 dose escalation study to evaluate the safety and activity of bevacizumab plus gemcitabine and nab-paclitaxel in patients with advanced solid tumours.MethodsPatients were given fixed dose gemcitabine plus increasing doses of nab-paclitaxel and bevacizumab. Toxicity, response, and association with VEGF polymorphism was analysed.ResultsThe study enrolled 110 patients who had undergone a median of 3 prior lines of therapy. The median age was 60 years (range, 17-85 years), and 55 patients (50%) had gemcitabine-refractory disease. We observed 3 dose-limiting toxicities during dose escalation and 3 DLTs in expansion cohorts. Dose escalation to 150 mg/m2 nab-paclitaxel and 15 mg/kg bevacizumab with 1000 mg/m2 of gemcitabine was well tolerated with no MTD. One patient with gemcitabine-refractory peritoneal papillary carcinoma had a complete response, 13 patients (13%) had partial responses, and 54 patients (52%) had stable disease ≥12 weeks. Exploratory VEGF single nucleotide polymorphism (SNP) analysis was performed on 13 patients.ConclusionsThe combination of gemcitabine, nab-paclitaxel, and bevacizumab is safe, well-tolerated, and has activity in advanced malignancies, including gemcitabine-refractory tumours. Based on this study, the recommended phase 2 dose is gemcitabine 1000 mg/m2, nab-paclitaxel 125 mg/m2, and bevacizumab 15 mg/kg. VEGF polymorphism data should be evaluated in future bevacizumab-based trials

Prevalence of Aflatoxin-Associated TP53R249S Mutation in Hepatocellular Carcinoma in Hispanics in South Texas

We aimed to determine whether aflatoxin dietary exposure plays a role in the high incidence of hepatocellular carcinoma (HCC) observed among Hispanics in South Texas. We measured TP53R249S somatic mutation, hallmark of aflatoxin etiology in HCC, using droplet digital PCR and RFLP. TP53R249S mutation was detected in 3 of 41 HCC tumors from Hispanics in South Texas (7.3%). We also measured TP53R249S mutation in plasma cell-free DNA (cfDNA) from 218 HCC patients and 96 Hispanic subjects with advanced fibrosis or cirrhosis, from South Texas. The mutation was detected only in Hispanic and Asian HCC patients, and patients harboring TP53R249S mutation were significantly younger and had a shorter overall survival. The mutation was not detected in any Hispanic subject with advanced fibrosis or cirrhosis. Genes involved in cell-cycle control of chromosomal replication and in BRCA1-dependent DNA damage response were enriched in HCCs with TP53R249S mutation. The E2F1 family members, E2F1 and E2F4, were identified as upstream regulators. TP53R249S mutation was detected in 5.7% to 7.3% of Hispanics with HCC in South Texas. This mutation was associated with a younger age and worse prognosis. TP53R249S was however not detected in Hispanics in South Texas with cirrhosis or advanced fibrosis. Aflatoxin exposure may contribute to a small number of HCCs in Hispanics in South Texas, but the detection of TP53R249S mutation in plasma cfDNA is not a promising biomarker of risk assessment for HCC in subjects with cirrhosis or advanced fibrosis in this population. Cancer Prev Res; 11(2); 103-12. ©2017 AACR