Fatigue in taxi drivers and its relationship with traffic accident history and experiences: a cross-sectional study in the north of Iran.

BACKGROUND: The monotonous nature of work, long driving duration, and working overload hours cause frequent fatigue in taxi drivers. A high prevalence of fatigue is associated with traffic accidents. However, the risk factors associated with taxi driver fatigue are unclear. Therefore, the present study aims to determine the rate of fatigue in taxi drivers and its relationship to their traffic accident experience. METHODS: In this descriptive-analytical study, 400 taxi drivers in the city of Rasht were registered in Taxi association selected through random sampling and entered into the study based on inclusion criteria. Data was collected through a researcher-made questionnaire reliable and valid by two medical students. The statistical analysis used ordinal data and a Poisson regression model with SPSS software version 21, with a significance level set at 5%. RESULTS: The driver fatigue self-reported was directly and significantly related to alcohol consumption (OR = 3.43, 95% CI 1.01-11.62) and had a significant and inverse relationship with smoking (OR = 0.50, 95% CI 0.32-0.76), being married (OR = 0.08, 95% CI 0.01-0.40) and driving experience there was (OR = 0.96, 95% CI 0.94-0.98). Drivers' sense of quality of life (QOL) was directly and significantly related to smoking (IRR = 1.43, 95% CI 1.28-1.59), education level under diploma (IRR = 2.41, 95% CI 1.43-4.06) diploma (IRR = 2.06, 95% CI 1.21-3.48) and bachelor (IRR = 2.42, 95% CI 1.36-4.29) and there was a significant and inverse relationship with age (IRR = 0.98, 95%CI 0.98-0.99). There was a significant relationship between the number of traffic accidents in the past year with the level of bachelor's degree (IRR = 3.10, 95% CI 1.43-6.76) and driving experience (IRR = 1.03, 95% CI 1.02-1.04 and inverse relationship between the number of traffic accidents in the past year and the QOL sense (IRR = 0.96, 95% CI 0.93-0.99) and the working hours (IRR = 0.96, 95% CI 0.94-0.99). CONCLUSION: Legislators and policymakers should pay more attention to fatigue in single and inexperienced taxi drivers. Regarding the QOL, pay attention to drivers with high education and older. To reduce the number of crashes, pay more attention to drivers with a bachelor's degree and less driving experience and improve the feeling of QOL.

A deep population reference panel of tandem repeat variation.

Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing from 3550 diverse individuals from the 1000 Genomes Project and H3Africa cohorts. We develop a method, EnsembleTR, to integrate genotypes from four separate methods resulting in high-quality genotypes at more than 1.7 million TR loci. Our catalog reveals novel sequence features influencing TR heterozygosity, identifies population-specific trinucleotide expansions, and finds hundreds of novel eQTL signals. Finally, we generate a phased haplotype panel which can be used to impute most TRs from nearby single nucleotide polymorphisms (SNPs) with high accuracy. Overall, the TR genotypes and reference haplotype panel generated here will serve as valuable resources for future genome-wide and population-wide studies of TRs and their role in human phenotypes.

A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice.

Short tandem repeats (STRs) are a class of rapidly mutating genetic elements typically characterized by repeated units of 1-6 bp. We leveraged whole-genome sequencing data for 152 recombinant inbred (RI) strains from the BXD family of mice to map loci that modulate genome-wide patterns of new mutations arising during parent-to-offspring transmission at STRs. We defined quantitative phenotypes describing the numbers and types of germline STR mutations in each strain and performed quantitative trait locus (QTL) analyses for each of these phenotypes. We identified a locus on Chromosome 13 at which strains inheriting the C57BL/6J (B) haplotype have a higher rate of STR expansions than those inheriting the DBA/2J (D) haplotype. The strongest candidate gene in this locus is Msh3, a known modifier of STR stability in cancer and at pathogenic repeat expansions in mice and humans, as well as a current drug target against Huntington's disease. The D haplotype at this locus harbors a cluster of variants near the 5' end of Msh3, including multiple missense variants near the DNA mismatch recognition domain. In contrast, the B haplotype contains a unique retrotransposon insertion. The rate of expansion covaries positively with Msh3 expression-with higher expression from the B haplotype. Finally, detailed analysis of mutation patterns showed that strains carrying the B allele have higher expansion rates, but slightly lower overall total mutation rates, compared with those with the D allele, particularly at tetranucleotide repeats. Our results suggest an important role for inherited variants in Msh3 in modulating genome-wide patterns of germline mutations at STRs.

A deep population reference panel of tandem repeat variation.

Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing from 3,550 diverse individuals from the 1000 Genomes Project and H3Africa cohorts. We develop a method, EnsembleTR, to integrate genotypes from four separate methods resulting in high-quality genotypes at more than 1.7 million TR loci. Our catalog reveals novel sequence features influencing TR heterozygosity, identifies population-specific trinucleotide expansions, and finds hundreds of novel eQTL signals. Finally, we generate a phased haplotype panel which can be used to impute most TRs from nearby single nucleotide polymorphisms (SNPs) with high accuracy. Overall, the TR genotypes and reference haplotype panel generated here will serve as valuable resources for future genome-wide and population-wide studies of TRs and their role in human phenotypes.

HMOX1 Genetic Polymorphisms Display Ancestral Diversity and May Be Linked to Hypertensive Disorders in Pregnancy.

Racial disparity exists for hypertensive disorders in pregnancy (HDP), which leads to disparate morbidity and mortality worldwide. The enzyme heme oxygenase-1 (HO-1) is encoded by HMOX1, which has genetic polymorphisms in its regulatory region that impact its expression and activity and have been associated with various diseases. However, studies of these genetic variants in HDP have been limited. The objective of this study was to examine HMOX1 as a potential genetic contributor of ancestral disparity seen in HDP. First, the 1000 Genomes Project (1 KG) phase 3 was utilized to compare the frequencies of alleles, genotypes, and estimated haplotypes of guanidine thymidine repeats (GTn; containing rs3074372) and A/T SNP (rs2071746) among females from five ancestral populations (Africa, the Americas, Europe, East Asia, and South Asia, N = 1271). Then, using genomic DNA from women with a history of HDP, we explored the possibility of HMOX1 variants predisposing women to HDP (N = 178) compared with an equivalent ancestral group from 1 KG (N = 263). Both HMOX1 variants were distributed differently across ancestries, with African women having a distinct distribution and an overall higher prevalence of the variants previously associated with lower HO-1 expression. The two HMOX1 variants display linkage disequilibrium in all but the African group, and within EUR cohort, LL and AA individuals have a higher prevalence in HDP. HMOX1 variants demonstrate ancestral differences that may contribute to racial disparity in HDP. Understanding maternal genetic contribution to HDP will help improve prediction and facilitate personalized approaches to care for HDP.

Patterns of de novo tandem repeat mutations and their role in autism.

Autism spectrum disorder (ASD) is an early-onset developmental disorder characterized by deficits in communication and social interaction and restrictive or repetitive behaviours1,2. Family studies demonstrate that ASD has a substantial genetic basis with contributions both from inherited and de novo variants3,4. It has been estimated that de novo mutations may contribute to 30% of all simplex cases, in which only a single child is affected per family5. Tandem repeats (TRs), defined here as sequences of 1 to 20 base pairs in size repeated consecutively, comprise one of the major sources of de novo mutations in humans6. TR expansions are implicated in dozens of neurological and psychiatric disorders7. Yet, de novo TR mutations have not been characterized on a genome-wide scale, and their contribution to ASD remains unexplored. Here we develop new bioinformatics methods for identifying and prioritizing de novo TR mutations from sequencing data and perform a genome-wide characterization of de novo TR mutations in ASD-affected probands and unaffected siblings. We infer specific mutation events and their precise changes in repeat number, and primarily focus on more prevalent stepwise copy number changes rather than large expansions. Our results demonstrate a significant genome-wide excess of TR mutations in ASD probands. Mutations in probands tend to be larger, enriched in fetal brain regulatory regions, and are predicted to be more evolutionarily deleterious. Overall, our results highlight the importance of considering repeat variants in future studies of de novo mutations.

TRTools: a toolkit for genome-wide analysis of tandem repeats.

SUMMARY: A rich set of tools have recently been developed for performing genome-wide genotyping of tandem repeats (TRs). However, standardized tools for downstream analysis of these results are lacking. To facilitate TR analysis applications, we present TRTools, a Python library and suite of command line tools for filtering, merging and quality control of TR genotype files. TRTools utilizes an internal harmonization module, making it compatible with outputs from a wide range of TR genotypers. AVAILABILITY AND IMPLEMENTATION: TRTools is freely available at https://github.com/gymreklab/TRTools. Detailed documentation is available at https://trtools.readthedocs.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Profiling the genome-wide landscape of tandem repeat expansions.

Tandem repeat (TR) expansions have been implicated in dozens of genetic diseases, including Huntington's Disease, Fragile X Syndrome, and hereditary ataxias. Furthermore, TRs have recently been implicated in a range of complex traits, including gene expression and cancer risk. While the human genome harbors hundreds of thousands of TRs, analysis of TR expansions has been mainly limited to known pathogenic loci. A major challenge is that expanded repeats are beyond the read length of most next-generation sequencing (NGS) datasets and are not profiled by existing genome-wide tools. We present GangSTR, a novel algorithm for genome-wide genotyping of both short and expanded TRs. GangSTR extracts information from paired-end reads into a unified model to estimate maximum likelihood TR lengths. We validate GangSTR on real and simulated data and show that GangSTR outperforms alternative methods in both accuracy and speed. We apply GangSTR to a deeply sequenced trio to profile the landscape of TR expansions in a healthy family and validate novel expansions using orthogonal technologies. Our analysis reveals that healthy individuals harbor dozens of long TR alleles not captured by current genome-wide methods. GangSTR will likely enable discovery of novel disease-associated variants not currently accessible from NGS.

Efficacy of gabapentin for the prevention of paclitaxel induced peripheral neuropathy: A randomized placebo controlled clinical trial.

Neuropathy is a dose limiting side effect of taxanes which may impact the quality of life and treatment outcomes. This randomized placebo-controlled double-blinded clinical trial was carried out to assess the efficacy of gabapentin in preventing chemotherapy induced neuropathy. Women with breast cancer were randomized into two groups of paclitaxel chemotherapy with gabapentin 300 mg/three times a day orally or placebo for 2 weeks started at day 1 of each paclitaxel cycle. Two groups were compared based on the relative frequency of neuropathy and change in nerve conducting velocity (NCV). Twenty women were assigned to each study arm. The majority of the neuropathy in gabapentin group was grade 1 in all of the four cycles with no event of ≥grade 3 neuropathy in this group. Compared to the placebo, the rate of 2nd and 3rd grade neuropathy was significantly lower in the gabapentin group (P = 0.000). The change in NCV after four cycles of paclitaxel was significantly lower in the gabapentin group compared to the placebo group (17.7% vs 61.0% decline in NCV for sural and 21.9% vs 62.5% declines in NCV for peroneal nerve). Gabapentin given with paclitaxel is effective in the prevention of intermediate and high grade neuropathies both objectively and subjectively.

Outcomes of Definitive Chemoradiotherapy for Cervical and Upper Thoracic Esophageal Cancers: a Single-Institution Experience of a Rare Cancer.

PURPOSE: Upper esophageal carcinomas are uncommon but confer a poor prognosis. However, there is scarcity of data regarding outcomes of definitive chemoradiotherapy for cervical and upper thoracic esophageal squamous cell carcinoma in Iran. METHODS: In this retrospective cohort study, we analyzed data of patients with squamous cell carcinoma of cervical and upper thoracic esophagus (at 16 to 25 cm from incisors) treated by definitive chemoradiotherapy in our institution between 2007 and 2015. The primary outcome was overall survival and secondary endpoints were predictors of overall survival. RESULTS: From 2007 to 2015, 40 patients were entered to final analysis. The mean age of patients was 59.7 ± 14.3 (range 24-85 years). Sixteen (40%) were node-positive. The median follow-up time was 15.3 months. Twenty-seven patients (67.5%) died during post treatment period. Thirty-five percent and 25% of patients suffered from local and distant recurrences, respectively. The actuarial median overall survival was 19.2 (CI 95% 14.2-24.2) months. The 1- and 2-year overall survival rates were 76 and 38%, respectively. The overall survival was higher among patients who were younger than 50 years, of female gender, had stage II tumor, grades I to II, who received induction chemotherapy, and whom treated with doses < 60 Gy. However, none of the differences was statistically significant. CONCLUSIONS: Cervical and upper thoracic esophageal squamous cell carcinomas are associated with bad outcome. Studies with bigger sample sizes are required to define best treatment strategies.

A reference haplotype panel for genome-wide imputation of short tandem repeats.

Short tandem repeats (STRs) are involved in dozens of Mendelian disorders and have been implicated in complex traits. However, genotyping arrays used in genome-wide association studies focus on single nucleotide polymorphisms (SNPs) and do not readily allow identification of STR associations. We leverage next-generation sequencing (NGS) from 479 families to create a SNP + STR reference haplotype panel. Our panel enables imputing STR genotypes into SNP array data when NGS is not available for directly genotyping STRs. Imputed genotypes achieve mean concordance of 97% with observed genotypes in an external dataset compared to 71% expected under a naive model. Performance varies widely across STRs, with near perfect concordance at bi-allelic STRs vs. 70% at highly polymorphic repeats. Imputation increases power over individual SNPs to detect STR associations with gene expression. Imputing STRs into existing SNP datasets will enable the first large-scale STR association studies across a range of complex traits.