Search results for "ARIA"

2016

AbstractMyopia, currently at epidemic levels in East Asia, is a leading cause of untreatable visual impairment. Genome-wide association studies (GWAS) in adults have identified 39 loci associated with refractive error and myopia. Here, the age-of-onset of association between genetic variants at these 39 loci and refractive error was investigated in 5200 children assessed longitudinally across ages 7–15 years, along with gene-environment interactions involving the major environmental risk-factors, nearwork and time outdoors. Specific variants could be categorized as showing evidence of: (a) early-onset effects remaining stable through childhood, (b) early-onset effects that progressed furthe…

Evaluation of the RYR1 gene genetic diversity in the Latvian White pig breed

2016

The ryanodine receptor 1 (RYR1) is a calcium ion channel in the sarcoplasmic reticulum of skeletal muscle. Multiple polymorphic loci have been identified in the RYR1 gene in human and animals and some of them are associated with certain phenotypes. However, there are still few data on the RYR1 genetic variability in pig and only the missense mutation Arg615Cys, associated with the malignant hyperthermia, porcine stress syndrome and meat quality, has been studied in several commercial and local breeds. Aim. To genotype the rs344435545 (C1972T, Arg615Cys), rs196953058 (T8434C, Phe2769Leu) and rs323041392 (G12484A, Asp4119Asn) in the Latvian local pig breed Latvian White and to evaluate the ev…

Evolutionary impact of copy number variation rates.

2017

[Objective]: Copy number variation is now recognized as one of the major sources of genetic variation among individuals in natural populations of any species. However, the relevance of these unexpected observations goes beyond diagnosing high diversity. [Results]: Here, it is argued that the molecular rates of copy number variation, mainly the deletion rate upon variation, determine the evolutionary road of the genome regarding size. Genetic drift will govern this process only if the efective population size is lower than the inverse of the deletion rate. Otherwise, natural selection will do.

Exome-Wide Association Study on Alanine Aminotransferase Identifies Sequence Variants in the GPAM and APOE Associated With Fatty Liver Disease.

2021

BACKGROUND & AIMS: Fatty liver disease (FLD) is a growing epidemic that is expected to be the leading cause of end-stage liver disease within the next decade. Both environmental and genetic factors contribute to the susceptibility of FLD. Several genetic variants contributing to FLD have been identified in exome-wide association studies. However, there is still a missing hereditability indicating that other genetic variants are yet to be discovered. METHODS: To find genes involved in FLD, we first examined the association of missense and nonsense variants with alanine amino transferase at an exome-wide level in 425,671 participants from the UK Biobank. We then validated genetic variants wit…

CLOVE: classification of genomic fusions into structural variation events

2017

Background A precise understanding of structural variants (SVs) in DNA is important in the study of cancer and population diversity. Many methods have been designed to identify SVs from DNA sequencing data. However, the problem remains challenging because existing approaches suffer from low sensitivity, precision, and positional accuracy. Furthermore, many existing tools only identify breakpoints, and so not collect related breakpoints and classify them as a particular type of SV. Due to the rapidly increasing usage of high throughput sequencing technologies in this area, there is an urgent need for algorithms that can accurately classify complex genomic rearrangements (involving more than …

High prevalence and moderate diversity of Pseudomonas aeruginosa in the U-bends of high-risk units in hospital

2017

The presence of P. aeruginosa in water supply is clearly identified as a risk factor for P. aeruginosa infection in critical care units, even if routes of transmission are often unclear and remain a matter of debate. We determined here the frequency of U-bends contaminated with P. aeruginosa in high-risk units and described the population structure of this opportunistic pathogen in a non-outbreak situation. Eighty-seven U-bends from sinks of rooms in five wards were sampled 3 times and P. aeruginosa was detected in 121 of the 261 (46.4%) U-bend samples. We genotyped 123 P. aeruginosa isolates with pulsed-field gel electrophoresis and multilocus sequence typing and found 41 pulsotypes distri…

Haplotype reference consortium panel: Practical implications of imputations with large reference panels.

2017

Contains fulltext : 177754.pdf (Publisher’s version ) (Open Access) Recently, the Haplotype Reference Consortium (HRC) released a large imputation panel that allows more accurate imputation of genetic variants. In this study, we compared a set of directly assayed common and rare variants from an exome array to imputed genotypes, that is, 1000 genomes project (1000GP) and HRC. We showed that imputation using the HRC panel improved the concordance between assayed and imputed genotypes at common, and especially, low-frequency variants. Furthermore, we performed a genome-wide association meta-analysis of vertical cup-disc ratio, a highly heritable endophenotype of glaucoma, in four cohorts usin…

Identification of miRNAs linked with the drought response of tef [Eragrostis tef (Zucc.) Trotter]

2018

Tef [Eragrostis tef (Zucc.) Trotter], a staple food crop in the Horn of Africa and particularly in Ethiopia, has several beneficial agronomical and nutritional properties, including waterlogging and drought tolerance. In this study, we performed microRNA profiling of tef using the Illumina HiSeq 2500 platform, analyzing both shoots and roots of two tef genotypes, one drought-tolerant (Tsedey) and one drought-susceptible (Alba). We obtained more than 10 million filtered reads for each of the 24 sequenced small cDNA libraries. Reads mapping to known miRNAs were more abundant in the root than shoot tissues. Thirteen and 35 miRNAs were significantly modulated in response to drought, in Alba and…

Viral resistance in HCV infection.

2018

The introduction of new multi-genotypic direct acting antivirals (DAA) in clinical practice has revolutionized HCV treatment, permitting the achievement of >95% rates of sustained virological response in many patients. However, virological failures can occur particularly if the treatments are sub optimal and/or with too short duration. Failure is often associated with development of resistance. The wide genetic variability in terms of different genotypes and subtypes, together with the natural presence and/or easy development of resistance during treatment, are intrinsic characteristics of HCV that may affect the treatment outcome and the chances of achieving a virological cure. This review…

Population Structure in the Model Grass Brachypodium distachyon Is Highly Correlated with Flowering Differences across Broad Geographic Areas

2016

The small, annual grass Brachypodium distachyon (L.) Beauv., a close relative of wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), is a powerful model system for cereals and bioenergy grasses. Genome-wide association studies (GWAS) of natural variation can elucidate the genetic basis of complex traits but have been so far limited in B. distachyon by the lack of large numbers of well-characterized and sufficiently diverse accessions. Here, we report on genotyping-by-sequencing (GBS) of 84 B. distachyon, seven B. hybridum, and three B. stacei accessions with diverse geographic origins including Albania, Armenia, Georgia, Italy, Spain, and Turkey. Over 90,000 high-quality single-nu…