Background: The variant rs34983651 (UGT1A1*28) and its genotyping are used to prevent irinotecan-induced toxicity. Several variants are in close linkage disequilibrium. Our objective was to evaluate the potential correlation of genotyping UGT1A1*80 i...
Genotyping-by-sequencing (GBS) has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model s...
The advent of next-generation DNA sequencing (NGS) technologies has led to the development of rapid genome-wide Single Nucleotide Polymorphism (SNP) detection applications in various plant species. Recent improvements in sequencing throughput combine...
Targeted genome editing is a powerful tool in reverse genetic studies of gene function in many aspects of biological and pathological processes. The CRISPR/Cas system or engineered endonucleases such as ZFNs and TALENs are the most widely used genome...
The results of the genital human papillomavirus (HPV) detection in 439 cervical samples by cervical cytology were compared with sequencing analysis and a newly developed HPV genotyping 9G membrane test. The excellent sensitivity and specificity of th...
Evidence that Hepatitis D virus (HDV) genotype is involved in HDV infection pathogenesis is increasing. Indeed, HDV genotypes have been shown to be linked to different outcomes in terms of liver fibrosis and treatment response. Herein, we show that t...
Masson pine (Pinus massoniana Lamb.) is an important tree species in China, but its genomic research has been hindered due to a large genome size. Genotyping-by-sequencing (GBS) has been a powerful approach to revolutionize the field of genomic resea...
The Acanthamoeba genus comprises the free-living amoebae that are ubiquitously present as opportunistic pathogens. They cause serious human diseases—for instance, Acanthamoeba keratitis (AK), granulomatous amoebic encephalitis (GAE), cutaneous...
Hepatitis B virus (HBV) is divided into nine genotypes, A to I. Currently, it remains unclear how the individual genotypes contribute to the estimated 250 million chronic HBV infections. We performed a literature search on HBV genotyping data through...
According to the World Health Organization (WHO), 71 million people were living with Hepatitis C virus (HCV) infection worldwide in 2015. Each year, about 399,000 HCV-infected people succumb to cirrhosis, hepatocellular carcinoma, and liver failure....
Echinococcus granulosus sensu lato (s.l.) is the causative agent of cystic echinococcosis in animals and humans. Different E. granulosuss.l. genotypes exhibit great diversity in their life cycle, host selectivity and pathogenicity. For this reason, t...
Single nucleotide polymorphisms (SNPs) have been widely used for gene identification. Allelic discrimination for an individual SNP with high reliability and flexibility is critical for the accurate detection of beneficial genes linked to specific SNP...
Easy-to-perform, fast, and inexpensive methods of differentiation of Escherichia coli strains beyond the species level are highly required. Herein two new, original tools for genotyping of E. coli isolates are proposed. The first of the developed met...
In dairy cattle, identifying polymorphisms that contribute to complex economical traits such as residual feed intake (RFI) is challenging and demands accurate genotyping. In this study, we compared imputed genotypes (n = 192 cows) to those obtained u...
Fusarium is among the top 10 most economically important plant pathogens in the world. Trichothecenes are the principal mycotoxins produced as secondary metabolites by select species of Fusarium and cause acute and chronic toxicity in animals and hum...
Background: The enhanced sensitivity of next-generation sequencing (NGS) for assessing hepatitis B virus (HBV) quasispecies heterogeneity over clone-based sequencing (CBS) is well documented. However, its comparative reliability for genotype determin...
In recent years, plant genotyping has been shifting from the accumulation of whole-genome data toward their effective use in breeding programs This review examines key genotyping platforms, including single-nucleotide polymorphism (SNP) arrays, reduc...
Mycobacterium bovis is the main pathogen of bovine, zoonotic, and wildlife tuberculosis. Despite the existence of programs for bovine tuberculosis (bTB) control in many regions, the disease remains a challenge for the veterinary and public health sec...
Coxiella burnetii is a zoonotic pathogen that resides in wild and domesticated animals across the globe and causes a febrile illness, Q fever, in humans. Several distinct genetic lineages or genomic groups have been shown to exist, with evidence for...
Introduction: There are very few reported cases of Whipple disease (WD), a rare chronic disease in Greece. In this report, we present a classic WD case in a Greek firefighter and the detection of an autochthonous Tropheryma whipplei genotype in this...
Objective: To develop a convenient; sensitive; accurate; and economical technique for genotyping of hepatitis B viruses (HBVs). Methods: The mercapto-modified B1; B2; C1; and C2-specific genotyping probes consisted of two probes for each HBV genotype...
The results of HPV detection in 550 cervical samples by cervical cytology were compared with the sequencing analysis and HPV genotyping 9G membrane test. The HPV genotyping 9G membrane test can efficiently identify and discriminate five HR-HPV geno...
Non-albicans Candida infections have recently gained worldwide attention due to their intrinsic resistance to different antifungal agents and the limited therapeutic options for treating them. Although the Candida parapsilosis complex is reporte...
Tamoxifen remains a cornerstone of treatment for patients with oestrogen-receptor-positive breast cancer. Tamoxifen efficacy depends on the biotransformation, predominantly via the cytochrome P450 2D6 (CYP2D6) isoform, to the active metabolite endoxi...
Fulminant hepatitis is a severe clinical disease characterized by a marked decline in liver function and encephalopathy. In a previous survey, using metagenomics in a group of 27 patients with this clinical condition, we observed an expressive quanti...
Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multi...
Human papillomavirus (HPV) is a common sexually transmitted infection worldwide, which spreads via contact with infected genital, anal, and oral/pharyngeal areas (oral sex) owing to diverse manners of sexual intercourse. In this study, we devised an...
Notwithstanding the substantial clinical impact of Helicobacter pylori, its convinced routes of transmission and sources have not been reported. Based on the quarrelsome hypothesis, foods and especially dairy products play an authoritative role in th...
Germplasm collections are a treasure trove of humanity. The accessions constituting those collections (wild crop relatives, landraces, cultivars, etc.) contain genes and allelic variants, which evolved prior to or post domestication, in the course of...
The discovery of a globally distributed porcine circovirus (Porcine circovirus 3; PCV-3) has led to intense research activity and the production of a large amount of molecular data. Different research groups have proposed several, not always concorda...
African swine fever virus (ASFV) has been spreading through Europe, Asia, and the Caribbean after its introduction in Georgia in 2007 and, due to its particularly high mortality rate, poses a continuous threat to the pig industry. The golden standard...
Twitcher (Twi) is a neurological Krabbe disease (KD, or globoid cell leukodystrophy) spontaneous mutant line in mice. The genome of the Twi mouse presents a single nucleotide polymorphism (SNP), leading to an enzymatically inactive galactosylceramida...
Human adenoviruses (HAdV) are a prevalent cause of diarrhea in children all over the world. Adenoviral infections are responsible for 2% to 10% of diarrheic cases. A long-term investigation was required to gain better knowledge about the incidence of...
Cyclospora cayetanensis is an emerging foodborne parasite that causes cyclosporiasis, an enteric disease of humans. Domestically acquired outbreaks have been reported in Canada every spring or summer since 2013. To date, investigations into the poten...
Xanthomonas euroxanthea is a bacterial species encompassing both pathogenic and non-pathogenic strains and is frequently found colonizing the same host plants as X. arboricola. This presents the need to develop a detection and genotyping assay able t...
Enterocytozoon bieneusi is a fungus-like protist that can cause malabsorption and diarrhea in sheep, other animals, and humans, threatening the development of animal husbandry and public health. To date, there are no data about the prevalence and gen...
The maintenance of plant germplasm and its genetic diversity is critical to preserving and making it available for food security, so this invaluable diversity is not permanently lost due to population growth and development, climate change, or changi...
Microsporidia are considered to be highly diverged and specialized parasites, and can infect a wide variety of vertebrate and invertebrate hosts. Enterocytozoon bieneusi is the most prevalent species in humans and various livestock, wildlife, and com...
In traditional bee breeding, the honeybee queen is chosen for breeding based on the performance of the colony produced by its mother. However, we cannot be entirely certain that a specific queen will produce offspring with desirable traits until we o...
The main challenge associated with genotyping based on conventional length polymorphisms is the cross-laboratory standardization of allele sizes. This step requires the inclusion of standards and manual sizing to avoid false results. Capillary electr...
The development of efficient, robust, and high-throughput SNP genotyping platforms is pivotal for crop genetics and breeding. Recently, SNP genotyping platforms based on target capture sequencing, which is very flexible in terms of the number of SNP...
Probabilistic genotyping has become widespread. EuroForMix and DNAStatistX are both based upon maximum likelihood estimation using a γ model, whereas STRmix™ is a Bayesian approach that specifies prior distributions on the unknown model parameters. A...
This study investigated the genetic diversity of Mycobacterium avium subsp. paratuberculosis (Map)—the causative agent of paratuberculosis—isolated from different host species in Germany. A total of 500 isolates from 243 cattle herds and...
Pneumocystis jirovecii pneumonia (PJP) is an opportunistic infection affecting immunocompromised patients. Patients with acute myeloid leukemia (AML) are not considered at high risk of PJP, thus, prophylaxis is not recommended. Between 2010 and...
Enterocytozoon bieneusi is an important zoonotic intestinal protozoon causing diarrhea in humans and animals, threatening public health and livestock farming. This study aimed to investigate the infection and genotype distribution of E. bieneusi in b...
Porcine rotavirus (PoRV), a primary etiological agent of viral diarrhea in piglets, frequently co-infects with other enteric pathogens, exacerbating disease severity and causing substantial economic losses. Its genetic recombination capability enable...
Chlamydia psittaci is a bacterium that infects several species of birds and mammals. It is the causal agent of avian chlamydiosis and psittacosis in humans and it is globally distributed. Chlamydia psittaci is one of the main zoonotic pathogens trans...
Francisella tularensis is the causative agent of the zoonotic disease tularemia. In Germany, most human infections are caused by contact with infected hares. The aim of this study was to characterize Francisella tularensis subsp. holarctica strains i...
Enterocytozoon bieneusi is an intracellular pathogen that can parasitize humans and a variety of animals. The infection of E. bieneusi in most hosts is asymptomatic, but in immunocompromised individuals, it can lead to serious complications such as a...
Background and objectives: The human respiratory syncytial virus (hRSV) is among the important respiratory pathogens affecting children. Genotype-specific attachment (G) gene sequencing is usually used to determine the virus genotype. The reliability...
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