ACE2-based capacitance sensor for rapid native SARS-CoV-2 detection in biological fluids and its correlation with real-time PCR.

The spread of the SARS-CoV-2 and its increasing threat to human health worldwide have necessitated the development of new technological tools to combat the virus. Particular emphasis is given to the development of diagnostic methods that monitor the spread of the virus rapidly and effectively. In this study, we report the development and testing of an antibody-free biosensor, based on the immobilization of ACE2 protein on the surface of gold interdigitated electrode. When the sensor was used in laboratory conditions for targeting the virus' structural spike protein, it showed a limit of detection [LOD] of 750 pg/µL/mm2. Thereafter, the response of the sensor to swab and saliva samples from hospitalized patients was examined. The virus presence in the samples was confirmed by electrical effective capacitance measurements executed on the biosensor, and correlated with real-time PCR results. We verified that the biosensor can distinguish samples that are positive for the virus from those that are negative in a total of 7 positive and 16 negative samples. In addition, the biosensor can be used for semi-quantitative measurement, since its measurements are divided into 3 areas, the negative samples, the weakly positive and the positive samples. Reproducibility of the experiments was demonstrated with at least 3 replicates and stability was tested by keeping the sensor standby for 7 days at 4 °C before repeating the experiment. This work presents a biosensor that can be used as a fast-screening test at point of care detection of SARS-CoV-2 since it needs less than 2 min to provide results and is of simple operation.

Clinical implementation of preemptive pharmacogenomics in psychiatry: Τhe "PREPARE" study.

PREemptive Pharmacogenomic testing for Preventing Adverse drug REactions (PREPARE) is the first prospective, pre-emptive pharmacogenomic study conducted in Europe, within the frame of the Horizon 2020 program. It aims to determine whether implementing pre-emptive pharmacogenomics (PGx) testing of clinically relevant biomarkers, so as the dose and drug selection to be guided, will result in an overall reduction of both the occurrence and the severity of drug-genotype-associated adverse drug reactions (ADRs). To achieve that, two groups of patients will be recruited; one that will receive treatment according to standard clinical practice and one other that will receive pharmacogenomic-guided treatment. The Laboratory of Pharmacogenomics and Individualized Treatment of the University of Patras, which coordinates and represents Greece in this study, in collaboration with the Department of Psychiatry of the General University Hospital of Patras, the Department of Psychiatry of the Hospital "Attikon" and the Departments of Psychiatry of the Psychiatric Hospital of Athens "Dafni" is going to recruit 1500 psychiatric patients that are going to receive antidepressant or antipsychotic treatment. Our scientific hypothesis is that patients who receive pharmacogenomic guided drug and dose selection will experience 30% less ADRs than patients following standard care. Eligible drugs for inclusion in the PREPARE study, are those for which the clinical decision regarding drug and dose choice can be guided according to the Dutch Pharmacogenomics Working Group Guidelines (DPWG). Overall, 7 antidepressants (citalopram, escitalopram, sertraline, paroxetine, venlafaxine, clomipramine, amitriptyline) and 3 antipsychotics (haloperidol, zuclopenthixol, aripiprazole) related to 17 genetic variations in 2 genes (CYP2D6, CYP2C19) will be examined. Occurrence, severity and causality of adverse drug events (ADEs) will be assessed during monitoring, at month 1 and 3 after starting the index-drug, and at the end of each arm, by using the Common Toxicity Criteria for Adverse Events Scale (CTCAE) and the Liverpool Causality Assessment Tool (LCAT), respectively. The results of our study are expected to significantly contribute to the improvement of psychiatric patients' quality of life, by helping to provide the right drug, to the right dose in terms of efficacy, safety and cost-effectiveness.

Measuring the Value of Pharmacogenomics Evidence.

In recent years, there is a growing need to measure the value of pharmacogenomics testing so that policymakers are well informed to decide about adopting and reimbursing pharmacogenomics testing, prioritizing pharmacogenomics research and development, and encouraging the application of companion diagnostics. Presently, there are limited economic evaluation studies of genome-guided treatment modalities that would allow decision-makers to comparatively assess the value and clinical utility of such interventions.

Implementing Pharmacogenomics in Europe: Design and Implementation Strategy of the Ubiquitous Pharmacogenomics Consortium.

Despite scientific and clinical advances in the field of pharmacogenomics (PGx), application into routine care remains limited. Opportunely, several implementation studies and programs have been initiated over recent years. This article presents an overview of these studies and identifies current research gaps. Importantly, one such gap is the undetermined collective clinical utility of implementing a panel of PGx-markers into routine care, because the evidence base is currently limited to specific, individual drug-gene pairs. The Ubiquitous Pharmacogenomics (U-PGx) Consortium, which has been funded by the European Commission's Horizon-2020 program, aims to address this unmet need. In a prospective, block-randomized, controlled clinical study (PREemptive Pharmacogenomic testing for prevention of Adverse drug REactions [PREPARE]), pre-emptive genotyping of a panel of clinically relevant PGx-markers, for which guidelines are available, will be implemented across healthcare institutions in seven European countries. The impact on patient outcomes and cost-effectiveness will be investigated. The program is unique in its multicenter, multigene, multidrug, multi-ethnic, and multihealthcare system approach.

Agamma-haplotypes: a new group of genetic markers for thalassemic mutations inside the 5' regulatory region of the human Agamma-globin gene.

This study illustrates the relationship between a group of nucleotide variations within the 5' regulatory region of the Agamma-globin gene [Agamma-588 A-->G, Agamma-499 T-->A and the 4-bp deletion (Agamma-225 to -222 AGCA)] and the spectrum of delta- and beta-thalassemia mutations in the Hellenic population. These sequence variations, screened by means of denaturing gradient gel electrophoresis, form four separate frameworks (Agamma-haplotypes), each one of which was found to be linked in cis with certain delta- and beta-thalassemia mutations found in the Hellenic population. In addition, two novel base substitutions inside the 5' regulatory region of the Agamma-globin gene (Agamma-521 C-->A and Ay-500 C-->T) were identified during this study, which together with Agamma-haplotypes seem to be silent polymorphisms during adult life, as indicated by transient expression assays. Our data show that Agamma-haplotypes represent genetic markers for the spectrum of thalassemic mutations, found in the Hellenic population and can constitute an important genetic repository upon which mutations leading to thalassemia and hemoglobinopathies occurred.

Modification of human beta-globin locus PAC clones by homologous recombination in Escherichia coli.

We report here modifications of human beta-globin PAC clones by homologous recombination in Escherichia coli DH10B, utilising a plasmid temperature sensitive for replication, the recA gene and a wild-type copy of the rpsL gene which allows for an efficient selection for plasmid loss in this host. High frequencies of recombination are observed even with very small lengths of homology and the method has general utility for introducing insertions, deletions and point mutations. No rearrangements were detected with the exception of one highly repetitive genomic sequence when either the E.COLI: RecA- or the lambdoid phage encoded RecT and RecE-dependent recombination systems were used.

Molecular heterogeneity of the glucose-6-phosphate dehydrogenase deficiency in the Hellenic population.

We report results from a systematic study to identify the molecular basis of glucose-6-phosphate dehydrogenase (G6PD) deficiency on a sample of 299 male subjects from the Hellenic population. Our stepwise approach involved partial biochemical characterization and quantitation of the enzyme's activity, MboII restriction endonuclease digestion to identify the G6PD Mediterranean variant, which represents the most frequent G6PD variant in our population and a nonradioactive polymerase chain reaction-single-strand conformation polymorphism methodology for the detection of the underlying molecular defect(s) in the rest of the non-Mediterranean G6PD-deficient individuals. Through this approach, six different G6PD variants were identified (G6PD Mediterranean, G6PD Hermoupolis, G6PD Cassano, G6PD Seattle, G6PD Ierapetra and G6PD Acrokorinthos), two of which were new (G6PD Hermoupolis, G6PD Acrokorinthos). In essence, this study underlines the remarkable genetic heterogeneity of the G6PD deficiency in the Hellenic population, while the finding of the double mutant, G6PD Hermoupolis, may help to outline the relationship and evolution of mutations in the human G6PD locus.

A novel 23-bp deletion in exon 5 of the p53 tumor suppressor gene.

We report a novel p53 deletion in a 63-year-old female with breast cancer. Mutation screening of DNA samples, obtained from tumor specimens from 98 individuals with breast cancer, by a combined polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis showed that the index case had a somatic mutation identified to be a 23-bp deletion in exon 5 of the p53 gene. This deletion would be expected to yield a truncated and functionally inactive p53 protein molecule, probably resulting in cell transformation. The existence of 6-bp palindromic-like sequences encompassing the deleted fragment suggests that the slipped mispairing mechanism is not involved in producing the deletion, which probably resulted from palindromic pairing during replication.

Contribution of gene conversion in the evolution of the human beta-like globin gene family.

Gene conversion is referred to as one of two types of mechanisms known to act on gene families, mainly to maintain their sequence homogeneity or, in certain cases, to produce sequence diversity. The concept of gene conversion was established 20 years ago by researchers working with fungi. A few years later, gene conversion was also observed in the human genome, i.e. the gamma-globin locus. The aim of this article is to emphasize the role of genetic recombination, particularly of gene conversion, in the evolution of the human beta-like globin genes and further to summarize its contribution to the convergent evolution of the fetal globin genes. Finally, this article attempts to re-examine the origin and spread of specific mutations of the beta-globin cluster, such as the sickle cell or beta-thalassemia mutations, on the basis of repeated gene conversion events.

The Cretan type of non-deletional hereditary persistence of fetal hemoglobin [A gamma-158C-->T] results from two independent gene conversion events.

We report a new type of non-deletional hereditary persistence of fetal hemoglobin that is due to a C-->T transition at position -158, relative to the Cap site of the human Agamma-globin gene. This mutation was identified in three unrelated adult cases presenting slightly elevated levels of fetal hemoglobin (Hb F), i.e. 2.9-5.1%, and normal hematological indices. Our sequencing results, from both polymerase chain reaction-amplified and subcloned DNA fragments, indicate that the A gamma -158C-->T mutation occurred by two independent gene conversion events in the three cases studied. In addition, hematological and molecular data, including restriction fragment length polymorphism haplotyping in the beta-globin gene cluster, extended haplotype analysis inside the gamma-globin gene region and routine analysis of three tandem repeat loci (D1S80, 3'HVR/apoB and F8vWf), led us to conclude that the A gamma -158C-->T mutation in one of the three cases occurred recently in the parental germ line (P=99.47%), representing the first example of a de novo gene conversion event identified in humans.

A new base substitution in the 5' regulatory region of the human Agamma globin gene is linked with the betaS gene.

A new T --> A base substitution, identified inside the 5' regulatory region of the human Agamma globin gene (Agamma-499 T -->A), is reported. This nucleotide change was found to be linked in cis with the mutation producing sickle cell anemia (CD6 GAG-->GTG: betaS gene).

HbF-Lesvos: an HbF variant due to a novel G gamma mutation (:G gamma 75 ATA-->ACA) detected in a Greek family.

A T-->C substitution at position 402 of the G gamma globin gene results in an isoleucine to threonine substitution at codon 75 of the G gamma globin chain and the formation of HbF-Lesvos [alpha2 G gamma2 75 (E19) Ile-->Thr].