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The clinical spectrum of SARS-CoV-2 infection ranges from asymptomatic status to mild infections, to severe disease and death. In this context, the identification of specific susceptibility factors is crucial to detect people at the higher risk of severe disease and improve the outcome of COVID-19 treatment. Several studies identified genetic variants conferring higher risk of SARS-CoV-2 infection and COVID-19 severity. The present study explored their genetic distribution among different populations (AFR, EAS, EUR and SAS). As a result, the obtained data support the existence of a genetic basis for the observed variability among populations, in terms of SARS-CoV-2 infection and disease outcomes. The comparison of ORs distribution for genetic risk of infection as well as for disease outcome shows that each population presents its own characteristics. These data suggest that each country could benefit from a population-wide risk assessment, aimed to personalize the national vaccine programs and the preventative measures as well as the allocation of resources and the access to proper therapeutic interventions. Moreover, the host genetics should be further investigated in order to realize personalized medicine protocols tailored to improve the management of patients suffering from COVID-19.

In the present review, the main features involved in the susceptibility and progression of neurodegenerative disorders (NDDs) have been discussed, with the purpose of highlighting their potential application for promoting the management and treatment of patients with NDDs. In particular, the impact of genetic and epigenetic factors, nutrients, and lifestyle will be presented, with particular emphasis on Alzheimer's disease (AD) and Parkinson's disease (PD). Metabolism, dietary habits, physical exercise and microbiota are part of a complex network that is crucial for brain function and preservation. This complex equilibrium can be disrupted by genetic, epigenetic, and environmental factors causing perturbations in central nervous system homeostasis, contributing thereby to neuroinflammation and neurodegeneration. Diet and physical activity can directly act on epigenetic modifications, which, in turn, alter the expression of specific genes involved in NDDs onset and progression. On this subject, the introduction of nutrigenomics shed light on the main molecular players involved in the modulation of health and disease status. In particular, the review presents data concerning the impact of

A custom plate of OpenArray™ technology was evaluated to test 60 single-nucleotide polymorphisms (SNPs) validated for the prediction of eye color, hair color, and skin pigmentation, and for personal identification. The SNPs were selected from already validated subsets (Hirisplex-s, Precision ID Identity SNP Panel, and ForenSeq DNA Signature Prep Kit). The concordance rate and call rate for every SNP were calculated by analyzing 314 sequenced DNA samples. The sensitivity of the assay was assessed by preparing a dilution series of 10.0, 5.0, 1.0, and 0.5 ng. The OpenArray™ platform obtained an average call rate of 96.9% and a concordance rate near 99.8%. Sensitivity testing performed on serial dilutions demonstrated that a sample with 0.5 ng of total input DNA can be correctly typed. The profiles of the 19 SNPs selected for human identification reached a random match probability (RMP) of, on average, 10−8. An analysis of 21 examples of biological evidence from 8 individuals, that generated single short tandem repeat profiles during the routine workflow, demonstrated the applicability of this technology in real cases. Seventeen samples were correctly typed, revealing a call rate higher than 90%. Accordingly, the phenotype prediction revealed the same accuracy described in the corresponding validation data. Despite the reduced discrimination power of this system compared to STR based kits, the OpenArray™ System can be used to exclude suspects and prioritize samples for downstream analyses, providing well-established information about the prediction of eye color, hair color, and skin pigmentation. More studies will be needed for further validation of this technology and to consider the opportunity to implement this custom array with more SNPs to obtain a lower RMP and to include markers for studies of ancestry and lineage.

Objective The Duchenne/Becker muscular dystrophy (DMD) carrier screening includes the evaluation of mutations in DMD gene, and the most widely used analysis is the multiplex ligation-dependent probe amplification (MLPA) for the DMD deletions/duplications detection. The high frequency of de novo mutations permits to estimate a risk up to 20% of mosaicisms for mothers of sporadic DMD children. The purpose of this study is to evaluate alternative analytical strategy for the detection of mosaics carrier women, in order to improve the recurrence risk estimation. Method Different DNA and RNA analyses were conducted on samples from a woman that conceived a DMD fetus without previous family history of dystrophynopathy. Results Standard MLPA analysis failed to identify mosaicism, even if MLPA doses suggested it. Electrophoresis and direct sequencing conducted on RNA permitted to detect two different amplicons of cDNAs, demonstrating the presence of somatic mosaicism. Subsequent detection of a second affected fetus confirmed the mosaic status on the mother. Conclusion The implementation of RNA analysis in diagnostic algorithm can increase the sensitivity of carrier test for mothers of sporadic affected patients, permitting detection of mosaic status. A revision of analytical guidelines is needed in order to improve the recurrence risk estimation and support prenatal genetic counseling.

The COVID-19 pandemic caused by SARS-CoV-2 represents a public health emergency, which became even more challenging since the detection of highly transmissible variants and strategies against COVID-19 were indistinctly established. We characterized the temporal viral load kinetics in individuals infected by original and variant strains. Naso-oropharyngeal swabs from 33,000 individuals (admitted to the IRCCS Santa Lucia Foundation Drive-in, healthcare professionals and hospitalized patients who underwent routinary screening) from November 2020 to June 2021 were analyzed. Of them, 1735 subjects were selected and grouped according to the viral strain. Diagnostic analyses were performed by CE-IVD RT-PCR-based kits. The subgenomic-RNA component was assessed in 36 subjects using digital PCR. Infection duration, viral load decay speed, effects of age and sex were assessed and compared by extensive statistical analyses. Overall, infection duration and viral load differed between the groups (p &lt, 0.05). Male sex was more present among both original and variant carriers affected with high viral load and showing fast decay speed, whereas original strain carriers with slow decay speed resulted in older (p &lt, 0.05). Subgenomic-RNA was detected in the positive samples, including those with low viral load. This study provides a picture of the viral load kinetics, identifying individuals with similar patterns and showing differential effects of age and sex, thus providing potentially useful information for personalized management of infected subjects.

This work describes the application of NGS for molecular diagnosis of RP in a family with a history of severe hypovision. In particular, the proband received a clinical diagnosis of RP on the basis of medical, instrumental examinations and his family history. The proband was subjected to NGS, utilizing a customized panel including 24 genes associated with RP and other retinal dystrophies. The NGS analysis revealed a novel missense variant (c.668T &gt, A, I223N) in PRPH2 gene, which was investigated by segregation and bioinformatic analysis. The variant is located in the D2 loop domain of PRPH2, which is critical for protein activity. Bioinformatic analysis described the c.668T &gt, A as a likely pathogenic variant. Moreover, a 3D model prediction was performed to better characterize the impact of the variant on the protein, reporting a disruption of the &alpha, helical structures. As a result, the variant protein showed a substantially different conformation with respect to the wild-type PRPH2. The identified variant may therefore affect the oligomerization ability of the D2 loop and, ultimately, hamper PRPH2 proper functioning and localization. In conclusion, PRPH2_c.668T &gt, A provided a molecular explanation of RP symptomatology, highlighting the clinical utility of NGS panels to facilitate genotype&ndash, phenotype correlations.

Facioscapulohumeral muscular dystrophy (FSHD) is a genetic neuromuscular disorder which mainly affects the muscles of the face, shoulder, and upper arms. FSHD is generally associated with the contraction of D4Z4 macrosatellite repeats on 4q35 chromosome or mutations in SMCHD1, which are responsible of the toxic expression of DUX4 in muscle tissue. Despite the recent application of NGS techniques in the clinical practice, the molecular diagnosis of FSHD is still performed with dated techniques such as Southern blotting. The diagnosis of FSHD requires therefore specific skills on both modern and less modern analytical protocols. Considering that clinical and molecular diagnosis of FSHD is challenging, it is not surprising that only few laboratories offer a comprehensive characterization of FSHD, which requires the education of professionals on traditional techniques even in the era of NGS. In conclusion, the study of FSHD provides an excellent example of using classical and modern molecular technologies which are equally necessary for the analysis of DNA repetitive traits associated with specific disorders.

Psoriatic arthritis (PsA) is a chronic inflammatory arthropathy characterized by the association of arthritis and psoriasis (Ps). The precise etiology of PsA is unknown, but epidemiological studies supported the existence of a genetic component for the disease. Here we report an association study on a large PsA Italian cohort for DNA variants recently reported as associated alleles at PSORS2 (17q25) in Ps cohorts from the US. We focused on discovering a possible involvement of PSORS2 associated SNPs in pathogenesis of PsA. We selected two SNPs (rs7420, rs734232) within the proximal peak and two SNPs (rs869190 and rs1561946) within distal peak of PSORS2. Our results ruled out PSORS2 alleles as susceptibility factors in arthritis psoriatic patients of Italian origin and suggested that previous linkage signal reported for chromosome 17q25 should be independent on the presence of PsA.

This study reports a comparative analysis between results of transabdominal coelocentesis and traditional invasive procedure in order to assess the usefulness of coelocentesis as a source of fetal DNA for molecular and chromosomal analysis. A number of 28 women were included in the study. A successful sampling of coelomic fluid was obtained in 25 women by transabdominal procedure. A positive amplification of DNA with QF-PCR techniques was obtained in 90% of cases, while 10% of cases failed to reveal interpretable results. Although all samples were cultured, the growth rate was not sufficient to determine karyotypes within 2 weeks. Five samples were selected to be analyzed by array-based comparative genomic hybridization (a-CGH) but the interpretation of these results was difficult and ambiguous. Our results suggest that transabdominal coelocentesis is suitable for the detection of single DNA variation and for QF-PCR analysis, while further experiments are needed to develop optimized protocols for traditional karyotyping and array-analysis.

Uniparental disomy (UPD) describes the inheritance of both homologues of a pair of chromosomes from only one parent. This condition is often caused by nondisjunction events during meiosis. UPD has been reported as a rare cause of the autosomal recessive disorder and aberrant expression of imprinted genes that are expressed from only one parental allele, either maternal or paternal. Maternal and/or paternal UPD for chromosome 7 is the most frequently observed UPD after UPD15. Here we developed and validated, for the first time, an effective, CE-based method for a rapid and economic detection based on two-fluorescent STR multiplexes.

Uniparental disomy (UPD) describes the inheritance of both homologues of a pair of chromosomes from only one parent. During the last two decades, the clinical impact of UPD and associated imprinting disorders, such as Prader-Willi syndrome (PWS) and Angelman syndrome (AS) increasingly have come to our attention. About 25% of PWS and 3%-5% of AS are a consequence of UPD with the resulting phenotype generated from the parent of origin of the disomic pair of chromosomes 15. Chromosome 15 UPD testing is relevant in various prenatal diagnostic conditions including apparent confined placental mosaicism, homologous and nonhomologous Robertsonian translocations involving chromosome 15 and 14, and as genomic biomarker for detecting chromosome origin. In this work we developed and validated a two fluorescent STRs multiplex assay for a rapid, economic and fully informative detection of UPD 15 by capillary electrophoresis.

Tutte le malattie, ad eccezione dei traumi (forse), hanno una componente genetica. La dermatite atopica (DA) non sfugge a questa regola. Da un punto di vista genetico la DA si definisce una malattia complessa, determinata dall’ interazione tra fattori genetici e fattori ambientali. Al contrario delle malattie mendeliane,per le malattie complesse non esistono geni in grado di determinare per se lo sviluppo della patologia, bensi esistono geni che predispongono l’individuo allo sviluppo delle malattie. Non si sviluppera dermatite atopica solo per effetto dei geni di suscettibilita o solo per effetto dei fattori ambientali scatenanti, ma soltanto da una loro interazione.

Background Single nucleotide polymorphisms (SNPs) within the LOXL1 gene are associated with pseudoesfoliation syndrome and pseudoesfoliation glaucoma. The aim of our study is to investigate a potential involvement of LOXL1 gene in the pathogenesis of pigment dispersion syndrome (PDS) and pigmentary glaucoma (PG). Methods A cohort of Caucasian origin of 84 unrelated and clinically well-characterised patients with PDS/PG and 200 control subjects were included in the study. Genomic DNA from whole blood was extracted and the coding and regulatory regions of LOXL1 gene were risequenced in both patients and controls to identify unknown sequence variations. Genotype and haplotype analysis were performed with UNPHASED software. The expression levels of LOXL1 were determined on c-DNA from peripheral blood lymphocytes by quantitative real-time RT-PCR. Results A significant allele association was detected for SNP rs2304722 within the fifth intron of LOXL1 (Odds ratio (OR = 2.43, p-value = 3,05e-2). Haplotype analysis revealed the existence of risk and protective haplotypes associated with PG-PDS (OR = 3.35; p-value = 1.00e-5 and OR = 3.35; p-value = 1.00e-4, respectively). Expression analysis suggests that associated haplotypes can regulate the expression level LOXL1. Conclusions Haplotypes of LOXL1 are associated with PG-PDS independently from rs1048661, leading to a differential expression of the transcript.

Objectives To determine the effects of the polymorphismsCFHTyr402His andARMS2del443ins54 on susceptibility to age-related macular degeneration (AMD) and to find the frequencies of these single-nucleotide polymorphisms in an Italian population that was not examined clinically. Methods A total of 286 control subjects (126 men and 160 women) and 159 white patients (73 men and 86 women) harboring exudative AMD in 1 eye were recruited. A third group of 182 DNA samples from blood donors of the same geographical areas were also typed to assess the frequency ofCFHTyr402His andARMS2del443ins54 polymorphisms in the general population. The data were analyzed statistically by a standard 2 × 2 table, Fisher exact tests, and odds ratios. Results The deletion-insertion at chromosome 10q26 (del443ins54) showed the strongest association with AMD in terms of bothPvalue and odds ratio (P = 2.7 × 10−15; odds ratio = 3.25), and a highly significant association was also confirmed for Tyr402His at theCFHlocus (P = 9.9 × 10−13; odds ratio = 2.86). We found no differences in allele and genotype association between classic and occult choroidal neovascularization. We also observed that 39% of the samples in the general Italian population were at least 5.4 times more likely than control subjects to develop AMD. Conclusions To our knowledge, this is the first confirmation of the association of del443ins54 in Italian patients with AMD, and we also confirmed the association of Tyr402His withCFH. Genetic analysis of the general population suggested that analysis of theARMS2andCFHrisk alleles alone may be helpful in differentiating high-risk individuals (odds ratio > 5.00) from low-risk individuals (odds ratio Clinical Relevance Individuals at high risk for developing AMD could be identified and selected for specific prevention programs. In this context, the development of prevention programs based on dietary antioxidants or on close monitoring of at-risk individuals should be considered or suggested.