Determining the pathogenicity of CFTR missense variants: Multiple comparisons of in silico predictors and variant annotation databases
Abstract Pathogenic variants in the Cystic Fibrosis Transmembrane Conductance Regulator gene (CFTR) are responsible for cystic fibrosis (CF), the commonest monogenic autosomal recessive disease, and CFTR-related disorders in infants and youth. Diagnosis of such diseases relies on clinical, functional, and molecular studies. To date, over 2,000 variants have been described on CFTR (~40% missense). Since few of them have confirmed pathogenicity, in silico analysis could help molecular diagnosis and genetic counseling. Here, the pathogenicity of 779 CFTR missense variants was predicted by consensus predictor PredictSNP and co...
Source: Genetics and Molecular Biology - November 14, 2019 Category: Genetics & Stem Cells Source Type: research
Differential effects of the methylenetetrahydrofolate reductase polymorphisms (C677T and A1298C) on hematological malignancies among Latinos: a meta-analysis
Abstract Our objective was to determine the association between the methylenetetrahydrofolate reductase polymorphisms (C677T and A1298C) and the risk of developing acute lymphoblastic leukemia (ALL), chronic myeloid leukemia (CML), acute myeloid leukemia (AML), and multiple myelomas (MM) in Latinos. PubMed, SCOPUS, EBSCO, LILACS, and other Latin-specific databases were searched for case-control studies that investigated the association between these polymorphisms and hematologic malignancies until November 2017. Genotype distributions were extracted and either fixed-effects or random-effects models were used to calculate t...
Source: Genetics and Molecular Biology - November 14, 2019 Category: Genetics & Stem Cells Source Type: research
Whole exome sequencing identifies a novel variant in an apoptosis-inducing factor gene associated with X-linked recessive hearing loss in a Chinese family
We report on the genetic analysis of a Chinese family in which four male patients presented with postlingual progressive hearing loss, associated with distal muscle wasting and unsteady ataxic gait. Using whole exome sequencing, we identified a new pathogenic variant (c.1463C>T, p.Pro488Leu) in the AIFM1 gene, which encodes the apoptosis-inducing factor mitochondrion-associated 1 precursor. AIFM1 is involved in the mitochondrial respiratory chain and cellular caspase-independent apoptosis pathway and has been reported to cause multiple phenotypes including hearing loss. The p.Pro488Leu missense variant segregated with s...
Source: Genetics and Molecular Biology - November 14, 2019 Category: Genetics & Stem Cells Source Type: research
Mutational landscape of head and neck squamous cell carcinomas in a South Asian population
Abstract Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer type globally and contributes significantly to burden of disease in South Asia. In Pakistan, HNSCC is among the most commonly diagnosed cancer in males and females. The increasing regional burden of HNSCC along with a unique set of risk factors merited a deeper investigation of the disease at the genomic level. Whole exome sequencing of HNSCC samples and matched normal genomic DNA analysis (n=7) was performed. Significant somatic single nucleotide variants (SNVs) were identified and pathway analysis performed to determine frequently affe...
Source: Genetics and Molecular Biology - November 14, 2019 Category: Genetics & Stem Cells Source Type: research
The rs10455872-G allele of the LPA gene is associated with high lipoprotein(a) levels and increased aortic valve calcium in a Mexican adult population
Abstract Polymorphisms in the LPA gene have been associated with aortic valve calcification (AVC). There are wide differences in the allelic frequencies, Lp(a) levels, and the association with AVC among ethnic groups. The aim of this study was to determine the association of the LPA gene polymorphisms with Lp(a) levels and risk of developing AVC, in Mexican-Mestizos population. Six LPA polymorphisms (rs10455872, rs7765803, rs6907156, rs1321195, rs12212807 and rs6919346) were genotyped by TaqMan assays in 1,265 individuals without premature coronary artery disease. The presence of AVC was determined by computed tomography. ...
Source: Genetics and Molecular Biology - November 14, 2019 Category: Genetics & Stem Cells Source Type: research
Association of long non-coding RNA MIAT and MALAT1 expression profiles in peripheral blood of coronary artery disease patients with previous cardiac events
Abstract Long non-coding RNAs (lncRNAs) are implicated in various cellular and pathological processes. Two lncRNAs, myocardial infarction-associated transcript (MIAT) and metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), may be involved in the pathogenesis of coronary artery disease (CAD). Here, we aimed to determine the relative circulating levels of MIAT and MALAT1 in 110 stable CAD patients and 117 controls and to correlate their levels with the clinical and laboratory data. Peripheral blood expression levels were quantified by Real-Time qPCR. The median MIAT expression level in CAD patients was significa...
Source: Genetics and Molecular Biology - November 14, 2019 Category: Genetics & Stem Cells Source Type: research
A systematic scoping review of the genetic ancestry of the Brazilian population
Abstract The genetic background of the Brazilian population is mainly characterized by three parental populations: European, African, and Native American. The aim of this study was to overview the genetic ancestry estimates for different Brazilian geographic regions and analyze factors involved in these estimates. In this systematic scoping review were included 51 studies, comprehending 81 populations of 19 states from five regions of Brazil. To reduce the potential of bias from studies with different sampling methods, we calculated the mean genetic ancestry weighted by the number of individuals. The weighted mean proporti...
Source: Genetics and Molecular Biology - November 14, 2019 Category: Genetics & Stem Cells Source Type: research
Erratum: Decreased serum PON1 arylesterase activity in familial hypercholesterolemia patients with a mutated LDLR gene
Abstract Mosses in conjunction with hornworts and liverworts are collectively referred to as bryophytes. These seedless, nonvascular plants are the closest extant relatives of early terrestrial plants and their study is essential to understand the evolutionary first steps of land plants. Here we report the complete chloroplast (cp) genome sequence of Pseudocrossidium replicatum, a moss belonging to the Pottiaceae family that is common in the central highlands of Mexico, in South America, in southern USA, and in Kenia. The cp genome (plastome) of P. replicatum is 123,512 bp in size, comprising inverted repeats of 9,886 bp a...
Source: Genetics and Molecular Biology - August 30, 2019 Category: Genetics & Stem Cells Source Type: research
The chloroplast genome of the desiccation-tolerant moss Pseudocrossidium replicatum (Taylor) R.H. Zander
Abstract Mosses in conjunction with hornworts and liverworts are collectively referred to as bryophytes. These seedless, nonvascular plants are the closest extant relatives of early terrestrial plants and their study is essential to understand the evolutionary first steps of land plants. Here we report the complete chloroplast (cp) genome sequence of Pseudocrossidium replicatum, a moss belonging to the Pottiaceae family that is common in the central highlands of Mexico, in South America, in southern USA, and in Kenia. The cp genome (plastome) of P. replicatum is 123,512 bp in size, comprising inverted repeats of 9,886 bp a...
Source: Genetics and Molecular Biology - August 30, 2019 Category: Genetics & Stem Cells Source Type: research
De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana
Abstract Dysphania schraderiana is widely distributed in Lhasa (Tibet, China) and used as a traditional medicine. However, the lack of genetic information hinders the understanding of its physiological processes, such as the biosynthesis of secondary metabolites. Herein, we used Illumina Hiseq4000 platform to sequence the transcriptome of flower and leaf tissues from D. schraderiana for the first time. Totally, 40,142 unigenes were assembled from approximately 5.2 million clean reads. All unigenes underwent gene prediction and were subsequently annotated in a NR (NCBI non-redundant protein) database, COG (Clusters of Ortho...
Source: Genetics and Molecular Biology - August 30, 2019 Category: Genetics & Stem Cells Source Type: research
Impact of co-blocking the costimulatory signals on immune-related genes after high-risk rabbit corneal allograft using 2nd-generation DNA sequencing technology
In conclusion, the co-blocking of costimulatory signals can significantly reduce genes that promote corneal allograft rejection. The inhibition of corneal allograft rejection gene expression was significantly enhanced. These gene expression results can explain the conclusion of previous work at the genetic level. (Source: Genetics and Molecular Biology)
Source: Genetics and Molecular Biology - August 30, 2019 Category: Genetics & Stem Cells Source Type: research
MicroRNA-21 over expression in umbilical cord blood hematopoietic stem progenitor cells by leukemia microvesicles
In this study, we examine the ability of leukemia microvesicles to induce proliferation in hematopoietic stem progenitor cells (HSPCs) via microRNA-21 dysregulation. Herein, leukemia microvesicles were isolated from HL-60 and NB-4 cell lines by ultracentrifugation, and then their protein content was measured. Normal HSPCs were isolated from umbilical cord blood samples by a CD-34 antibody. These cells were treated with 20 and 40 μ g/mL leukemia microvesicles for 5 and 10 days, respectively. Cell count, CD-34 analysis, and a microRNA-21 gene expression assay were done at days 5 and 10. HSPCs showed a significant increase i...
Source: Genetics and Molecular Biology - August 30, 2019 Category: Genetics & Stem Cells Source Type: research
NFAT5 is differentially expressed in Sprague-Dawley rat tissues in response to high salt and high fructose diets
This study aimed to test the hypothesis that consumption of high salt and fructose diets would increase tissue-specific expression of two critical osmotically-regulated genes, nuclear factor of activated T-cells 5 (NFAT5) and aldose reductase (AR). Fifty Sprague-Dawley rats were placed on a control, 4% NaCl, 8% NaCl, or 64% fructose diet for eight weeks. Fourteen different tissue samples were harvested and snap-frozen, followed by RNA purification, cDNA synthesis, and NFAT5 and AR gene expression quantification by real-time PCR.Our findings demonstrate that NFAT5 and AR expression are up-regulated in the kidney medulla, li...
Source: Genetics and Molecular Biology - August 30, 2019 Category: Genetics & Stem Cells Source Type: research
Comparative cytogenetics of nine populations of the Rhinella genus (Anura, Bufonidae) with a highlight on their conservative karyotype
Abstract The genus Rhinella is one of the most diverse groups of bufonid toads, currently composed by 93 valid species and naturally distributed throughout different Neotropical ecoregions. Here, we analyze nine Brazilian populations of toads representing species of the Rhinella margaritifera and Rhinella marina groups. These new data include the first description of the R. hoogmoedi and R. proboscidae karyotypes, as well as other taxonomically unresolved forms. Chromosomal analysis of the populations revealed pronounced chromosomal uniformity (2n=22), including the diploid number and chromosomal morphology. Three differen...
Source: Genetics and Molecular Biology - August 30, 2019 Category: Genetics & Stem Cells Source Type: research
Whole-genome duplication and hemoglobin differentiation traits between allopatric populations of Brazilian Odontophrynus americanus species complex (Amphibia, Anura)
Abstract Two allopatric populations of Brazilian diploid and tetraploid Odontophrynus americanus species complex, both from S ão Paulo state, had their blood hemoglobin biochemically analyzed. In addition, these specimens were cytogenetically characterized. Biochemical characterization of hemoglobin expression showed a distinct banding pattern between the allopatric specimens. Besides this, two distinct phenotypes, not li nked to ploidy, sex, or age, were observed in adult animals of both populations. Phenotype A exhibits dark-colored body with small papillae, ogival-shaped jaw with reduced interpupillary distance and sho...
Source: Genetics and Molecular Biology - August 30, 2019 Category: Genetics & Stem Cells Source Type: research
