Parental origin and somatic mosaicism of PHOX2B mutations in Congenital Central Hypoventilation Syndrome.

Heterozygous polyalanine repeat expansions of PHOX2B have been associated with Congenital Central Hypoventilation Syndrome, a rare neurocristopathy characterized by absence of adequate control of respiration during sleep. Here we report a PHOX2B mutational screening in 63 CCHS patients, 58 of whom presenting with poly-A expansions or frameshift, missense and nonsense mutations. To assess a somatic or germline occurrence of poly-A length variations, the relative amounts of mutant and wild type alleles have been quantified in 20 selected CCHS patients presenting with an expansion, and in their parents. Somatic mosaicism was shown in four parents, while no mosaic was found among CCHS patients. Moreover, while co-segregation analysis of the PHOX2B poly-A expansions with selected marker alleles in the same 20 CCHS trios has not demonstrated any parent-of-origin effect of the mutations, it has provided further clues to clarify the molecular mechanism underlying the expansion occurrence. Finally, the segregation of PHOX2B poly-A anomalous tracts within family members has allowed us to exclude tendency of polymorphic variations towards expansion. This strengthens the notion that expanded polyalanine tracts, identified as frequent disease-causing mutations also in other human diseases, are mitotically and meiotically stable

Incorporating prior biological information in linkage studies increases power and limits multiple testing

We used the Genetic Analysis Workshop 15 Problem 1 data set to search for expression phenotype quantitative trait loci in a highly selected group of genes with a supposedly correlated role in the development of the enteric nervous system. Our strategy was to reduce the level of multiple testing by analyzing at the genome-wide level a limited number of genes considered to be the most promising enteric nervous system candidates on the basis of mouse expression data, and then extend the analysis to a larger number of traits only for a small number of candidate linked regions. Such a study design allowed us to identify a "master regulator" locus for several genes involved in the enteric nervous system, located in 9q31. In particular, one of four traits included in the genome-wide analysis and 2 of 57 from the follow-up single-chromosome analysis showed LOD scores above 2 around position 109 on chromosome 9 by univariate variance-component linkage analysis. Bivariate linkage analysis further supported the presence of a common regulatory locus, with a maximum multipoint LOD score of 5.17 and five additional LOD scores > 3 in the same region. This region is particularly interesting because a susceptibility locus for Hirschsprung disease, a disease characterized by enteric malformation, was previously mapped to 9q31. The proposed strategy of limiting the genome-wide analysis to a small number of well characterized candidate expression phenotypes and following up the most promising results in a larger number of correlated traits may prove successful for other groups of genes involved in a common pathway

Comparative analysis of different approaches for dealing with candidate regions in the context of a genome-wide association study

Genome-wide association studies (GWAS) test hundreds of thousands of single-nucleotide polymorphisms (SNPs) for association to a trait, treating each marker equally and ignoring prior evidence of association to specific regions. Typically, promising regions are selected for further investigation based on p-values obtained from simple tests of association. However, loci that exert only a weak, low-penetrant role on the trait, producing modest evidence of association, are not detectable in the context of a GWAS. Implementing prior knowledge of association in GWAS could increase power, help distinguish between false and true positives, and identify better sets of SNPs for follow-up studies

Beneficial effects of long-term treatment with bosentan on the development of pulmonary arterial hypertension in patients with systemic sclerosis

OBJECTIVE: To investigate the effects of long-term treatment with bosentan on pulmonary arterial hypertension (PAH) in patients with systemic sclerosis. METHODS: Patients with systemic sclerosis were followed between 2003 and 2014; those who developed digital ulcers were treated with standard regimens of bosentan. Patients were assessed at baseline and every 12\u2009months using transthoracic Doppler echocardiography, 6-min walking distance test, Borg dyspnoea index and monitoring of plasma levels of 76-amino-acid N-terminal probrain natriuretic peptide. Patients who developed PAH underwent right heart catheterization to confirm the diagnosis. RESULTS: Sixty-nine patients with systemic sclerosis were enrolled in the study. Of these, 25 developed digital ulcers and received treatment with bosentan; the remaining 44 comprised the control group. None of the patients treated with bosentan developed PAH during the follow-up period. Furthermore, in these patients the mean\u2009\ub1\u2009SD systolic pulmonary arterial pressure significantly decreased from 33.64\u2009\ub1\u20092.91\u2009mmHg at baseline to 26.20\u2009\ub1\u20091.78\u2009mmHg at the end of the follow-up period. In contrast, in the control group, seven patients developed PAH during the follow-up period, with the mean\u2009\ub1\u2009SD systolic pulmonary arterial pressure significantly increasing from 33.57\u2009\ub1\u20092.75\u2009mmHg at baseline to 39.41\u2009\ub1\u20094.11\u2009mmHg at the end of the follow-up period. CONCLUSION: Long-term treatment with bosentan reduces the risk of developing PAH in patients with systemic sclerosis

Custom Array Comparative Genomic Hybridization: the Importance of DNA Quality, an Expert Eye, and Variant Validation.

The presence of false positive and false negative results in the Array Comparative Genomic Hybridization (aCGH) design is poorly addressed in literature reports. We took advantage of a custom aCGH recently carried out to analyze its design performance, the use of several Agilent aberrations detection algorithms, and the presence of false results. Our study provides a confirmation that the high density design does not generate more noise than standard designs and, might reach a good resolution. We noticed a not negligible presence of false negative and false positive results in the imbalances call performed by the Agilent software. The Aberration Detection Method 2 (ADM-2) algorithm with a threshold of 6 performed quite well, and the array design proved to be reliable, provided that some additional filters are applied, such as considering only intervals with average absolute log2ratio above 0.3. We also propose an additional filter that takes into account the proportion of probes with log2ratio exceeding suggestive values for gain or loss. In addition, the quality of samples was confirmed to be a crucial parameter. Finally, this work raises the importance of evaluating the samples profiles by eye and the necessity of validating the imbalances detected

Custom Array Comparative Genomic Hybridization: the Importance of DNA Quality, an Expert Eye, and Variant Validation

The presence of false positive and false negative results in the Array Comparative Genomic Hybridization (aCGH) design is poorly addressed in literature reports. We took advantage of a custom aCGH recently carried out to analyze its design performance, the use of several Agilent aberrations detection algorithms, and the presence of false results. Our study provides a confirmation that the high density design does not generate more noise than standard designs and, might reach a good resolution. We noticed a not negligible presence of false negative and false positive results in the imbalances call performed by the Agilent software. The Aberration Detection Method 2 (ADM-2) algorithm with a threshold of 6 performed quite well, and the array design proved to be reliable, provided that some additional filters are applied, such as considering only intervals with average absolute log2ratio above 0.3. We also propose an additional filter that takes into account the proportion of probes with log2ratio exceeding suggestive values for gain or loss. In addition, the quality of samples was confirmed to be a crucial parameter. Finally, this work raises the importance of evaluating the samples profiles by eye and the necessity of validating the imbalances detected

OSM/OSMR and Interleukin 6 Family Cytokines in Physiological and Pathological Condition

Oncostatin M (OSM) is a member of the interleukin-6 (IL-6) family of cytokines and can bind two different receptors, Leukemia inhibitory factor receptor (LIFR) and Oncostatin M receptor (OSMR), through a complex containing the common glycoprotein 130 (gp130) subunit [...

Patients’ preferences, feelings, and benefits on Music-Based Intervention: A Pilot Study in COVID-19 Hospitalization

Introduction: COVID-19 patients survive in isolation with stringent measures of infection containment, leading to anxiety, fear, stress, loneliness, and depression. Music is recognized as useful to promote multiple health outcomes, including anxiolytic effects, pain-relieving, and relaxing effects that favour well-being and social interaction in healthcare settings. Objective: This study aimed to determine the impact of a pre-recorded music-based intervention on the music perception in hospitalized COVID-19 patients. Music appreciation, evoked emotions, and self-reported effects were explored and compared before and after music-based intervention, also considering the gender of the patients. Methods: This prospective study consisted of a pre-recorded music-based intervention administered to 272 patients hospitalized for COVID-19 by piping the music into rooms of inpatient medical area. Pre-recorded musical pieces of were selected by a music therapist considering specific formal and parametric characteristics, with the purposes of distraction, entertainment, relaxation, and emotional support. The patients’ opinions were collected using an ad hoc self-report questionnaire and a short data survey that followed the Consolidated Framework for Implementation Research (CFIR) guidelines. Results: Music resulted to be the preferred entertainment activity during hospitalization by 84.6% of patients, with 96.6% of them expecting a positive effect and a very high grade of usefulness attributed to music before hospitalization and even higher afterwards. The music intervention significantly changed the patients’ perception of music from everyday life to hospitalization (p<0.0001). It proved successful in evoking pleasure and fun, which raised from 18.4% of everyday life to 41.1% during hospitalization. The usefulness of listening music to alleviate unpleasant feelings including anxiety, fear, loneliness, and low mood in COVID-19 disease, had a significant increase from 22.5% to 60.0% after the music intervention. Conclusion: Music-based intervention, directed according to reference frameworks, provides self-reported social and emotional support in hospitalized patients for COVID-19

Integration of Linkage Analysis and Next-Generation Sequencing Data

Genetic mapping by linkage analysis has been for many years the first step in the identification of genes responsible for rare Mendelian disorders. When the focus of genetic research shifted toward the study of the more complex common disorders, alternative approaches such as association studies were shown to be more successful in identifying common variants of small effect that are in part responsible for susceptibility to such conditions. Recent advances in technologies that make feasible the sequencing of whole exomes or genomes have renewed interest in the identification of rare variants, which are in principle amenable to being detected by linkage analysis. As a result, linkage analysis and family based studies in general are being reexamined as an aid to filter and validate results of whole exome and whole genome sequencing experiments. This chapter will describe a few representative papers that have incorporated linkage analysis and its results in the design, execution, and interpretation of whole genome or whole exome sequencing studies