High frequency of pathogenic ACAN variants including an intragenic deletion in selected individuals with short stature.

CONTEXT: Defining the underlying etiology of idiopathic short stature (ISS) improves the overall management of an individual. OBJECTIVE: To assess the frequency of pathogenic ACAN variants in selected individuals. DESIGN: The single-center cohort study was conducted at a tertiary university children's hospital. From 51 unrelated patients with ISS, the 16 probands aged between 3 and 18 years (12 females) with advanced bone age and/or autosomal dominant inheritance pattern of short stature were selected for the study. Fifteen family members of ACAN-positive probands were included. Exome sequencing was performed in all probands, and additional copy number variation (CNV) detection was applied in selected probands with a distinct ACAN-associated phenotype. RESULTS: Systematic phenotyping of the study cohort yielded 37.5% (6/16) ACAN-positive probands, with all novel pathogenic variants, including a 6.082 kb large intragenic deletion, detected by array comparative genomic hybridization (array CGH) and exome data analysis. All variants were co-segregated with short stature phenotype, except in one family member with the intragenic deletion who had an unexpected growth pattern within the normal range (-0.5 SDS). One patient presented with otosclerosis, a sign not previously associated with aggrecanopathy. CONCLUSIONS: ACAN pathogenic variants presented a common cause of familial ISS. The selection criteria used in our study were suggested for a personalized approach to genetic testing of the ACAN gene in clinical practice. Our results expanded the number of pathogenic ACAN variants, including the first intragenic deletion, and suggested CNV evaluation in patients with typical clinical features of aggrecanopathy as reasonable. Intra-familial phenotypic variability in growth patterns should be considered.

A Systematic Clinical Review of Prenatally Diagnosed Tetrasomy 9p.

Tetrasomy 9p was first described in 1973 and approximately 68 cases with a variable phenotype have been reported to date with 22 of them being detected prenatally. The objective of this study was to review prenatally-reported cases of tetrasomy 9p thus far and to identify ultrasound phenotypes that may be suggestive of this specific syndrome. A PubMed database search was done in February 2018 without any restriction of publication date orjournals, with the use of the following keywords: tetrasomy 9p, tetrasomy 9p prenatal, mosaic tetrasomy 9p, mosaic tetrasomy 9p prenatal, isochromosome 9p, duplication 9p prenatal, trisomy 9p prenatal. Reported cases were included if the clinical presentation and diagnostic approach of each case was clearly described. The most common characteristics of prenatally-detected tetrasomy 9p are intrauterine growth retardation (IUGR, 57.0%), central nervous system (CNS) abnormalities (59.0%), skeletal anomalies (29.0%), genitourinary and renal anomalies (29.0%) and cardiac defects (29.0%). The phenotypic spectrum of tetrasomy 9p is rather unspecific as these findings are commonly associated with other chromosome anomalies, as well as microdeletion/microduplication or monogenic syndromes. The combination of early fetal morphology and diagnostic genetic testing enables a definite tetrasomy 9p diagnosis and effective further pregnancy management.

Points to consider for laboratories reporting results from diagnostic genomic sequencing.

Although NGS technologies are well-embedded in the clinical setting for identification of genetic causes of disease, guidelines issued by professional bodies are inconsistent regarding some aspects of reporting results. Most recommendations do not give detailed guidance about whether variants of uncertain significance (VUS) should be reported by laboratory personnel to clinicians, and give conflicting messages regarding whether unsolicited findings (UF) should be reported. There are also differences both in their recommendations regarding whether actively searching for secondary findings (SF) is appropriate, and in the extent to which they address the duty (or lack thereof) to reanalyse variants when new information arises. An interdisciplinary working group considered the current guidelines, their own experiences, and data from a recent qualitative study to develop a set of points to consider for laboratories reporting results from diagnostic NGS. These points to consider fall under six categories: (i) Testing approaches and technologies used, (ii) Approaches for VUS; (iii) Approaches for reporting UF, (iv) Approaches regarding SF; (v) Reanalysis of data & re-contact; and vi) Minors. While it is unclear whether uniformity in reporting across all laboratories is desirable, we hope these points to consider will be useful to diagnostic laboratories as they develop their processes for making decisions about reporting VUS and UF from NGS in the diagnostic context.

Legislation of direct-to-consumer genetic testing in Europe: a fragmented regulatory landscape.

Despite the increasing availability of direct-to-consumer (DTC) genetic testing, it is currently unclear how such services are regulated in Europe, due to the lack of EU or national legislation specifically addressing this issue. In this article, we provide an overview of laws that could potentially impact the regulation of DTC genetic testing in 26 European countries, namely Austria, Belgium, Cyprus, the Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Ireland, Italy, Latvia, Lithuania, Luxembourg, Norway, Poland, Portugal, Romania, Slovakia, Slovenia, Spain, Sweden, the Netherlands and the United Kingdom. Emphasis is placed on provisions relating to medical supervision, genetic counselling and informed consent. Our results indicate that currently there is a wide spectrum of laws regarding genetic testing in Europe. There are countries (e.g. France and Germany) which essentially ban DTC genetic testing, while in others (e.g. Luxembourg and Poland) DTC genetic testing may only be restricted by general laws, usually regarding health care services and patients' rights.

Therapeutic perspectives of epigenetically active nutrients.

Many nutrients are known for a wide range of activities in prevention and alleviation of various diseases. Recently, their potential role in regulating human health through effects on epigenetics has become evident, although specific mechanisms are still unclear. Thus, nutriepigenetics/nutriepigenomics has emerged as a new and promising field in current epigenetics research in the past few years. In particular, polyphenols, as part of the central dynamic interaction between the genome and the environment with specificity at physiological concentrations, are well known to affect mechanisms underlying human health. This review summarizes the effects of dietary compounds on epigenetic mechanisms in the regulation of gene expression including expression of enzymes and other molecules responsible for drug absorption, distribution, metabolism and excretion in cancer, metabolic syndrome, neurodegenerative disorders and hormonal dysfunction.

ADP-ribosylation factor guanine nucleotide-exchange factor 2 (ARFGEF2): a new potential biomarker in Huntington's disease.

Microarray searches have revealed potential genetic biomarkers in a wide variety of human diseases. Identification of biomarkers for disease status is particularly important in chronic neurodegenerative diseases where brain tissue cannot be sampled. A previous study identified 12 genes from microarray analysis as associated with Huntington's disease, although the relationships had not been validated. We used new machine learning approaches to reanalyse those microarray data and to rank the identified potential genetic biomarkers. We then performed quantitative reverse transcription-polymerase chain reaction analysis on a subset of the candidate genes in blood samples from an independent cohort of 23 Huntington's disease patients and 23 healthy controls. Our highest ranked genes did not overlap with the 12 previously identified, but two were significantly up-regulated in the Huntington's disease group: ARFGEF2 and GOLGA8G. Little is known about the latter, but the former warrants further analysis as it is known to be associated with intracellular vesicular trafficking, disturbances of which characterize Huntington's disease.

Epidemiology of Huntington's disease in Slovenia.

OBJECTIVES: The objective of this study was to estimate the prevalence of Huntington's disease (HD) in Slovenia using direct mutation analysis. MATERIALS AND METHODS: Symptomatic patients and presymptomatic individuals at risk for HD referred to the Institute of Medical Genetics between 1997 and 2007 were included in the study. The patients were ascertained through multiple sources. The prevalence was estimated on 31 December 2006. RESULTS: A total of 116 and 68 individuals with CAG repeat number >36 were symptomatic and presymptomatic, respectively. The prevalence of HD in Slovenia was estimated at 5.16/10(5) (95% confidence interval 4.16-6.16). CONCLUSIONS: This is the first report on the epidemiology and prevalence of HD in Slovenia. The prevalence of HD is comparable with previously reported data in other European countries. In Slovenia, a higher proportion of individuals at risk for HD decide on predictive mutational testing as compared with the estimated numbers for Europe, United States, Canada and Australia.

Angiotensin-converting enzyme I/D gene polymorphism and risk of multiple sclerosis.

OBJECTIVES: Angiotensin-converting enzyme (ACE) activity is increased in blood and cerebrospinal fluid of patients with multiple sclerosis (MS). In addition, in experimental autoimmune encephalomyelitis (EAE), an animal model of MS, the blockade of ACE suppresses the disease itself. To analyze the genetic association of the ACE gene with MS, we examined ACE gene insertion/deletion (I/D) polymorphism in MS patients. MATERIALS AND METHODS: A total of 313 MS patients from Slovenia and Croatia and 376 healthy controls were genotyped by polymerase chain reaction method. RESULTS: We found statistically significant differences in the distribution of ACE I/D allele frequencies (P < 0.01) and genotypes (P < 0.04) in male patients. ACE DD genotype was associated with MS in men at an odds ratio of 1.86 (95% CI 1.09-3.19, P = 0.02). CONCLUSIONS: DD genotype of ACE gene might contribute to a higher risk of developing MS in men.

Heterogeneity of the triple A syndrome and assessment of a case.

Allgrove syndrome (triple A syndrome) is a rare autosomal recessive disorder characterized by achalasia, alacrima, adrenal insufficiency, and--occasionally--autonomic instability. Disease causing mutations have been found in the AAAS gene on 12q13, but no strong phenotype-genotype correlation could be found. We present a 28 year-old woman with classical systemic features of triple A syndrome with prominent neurological dysfunctions/deficits, including distal muscular atrophy, progressive muscle weakness and wasting of both legs, sensibility dysfunction, hyperreflexia and autonomic dysfunction presented with excessive sweating. DNA sequencing of the AAAS gene revealed compound heterozygosity for previously reported mutations. A similar genotype was previously reported, but with a remarkably different phenotype.

Genome-wide expression profiling of human blood reveals biomarkers for Huntington's disease.

Huntington's disease (HD) is an autosomal dominant disorder caused by an expansion of glutamine repeats in ubiquitously distributed huntingtin protein. Recent studies have shown that mutant huntingtin interferes with the function of widely expressed transcription factors, suggesting that gene expression may be altered in a variety of tissues in HD, including peripheral blood. Affymetrix and Amersham Biosciences oligonucleotide microarrays were used to analyze global gene expression in blood samples of HD patients and matched controls. We identified 322 mRNAs that showed significantly altered expression in HD blood samples, compared with controls (P < 0.0005), on two different microarray platforms. A subset of up-regulated mRNAs selected from this group was able to distinguish controls, presymptomatic individuals carrying the HD mutation, and symptomatic HD patients. In addition, early presymptomatic subjects showed gene expression profiles similar to those of controls, whereas late presymptomatic subjects showed altered expression that resembled that of symptomatic HD patients. These elevated mRNAs were significantly reduced in HD patients involved in a dose-finding study of the histone deacetylase inhibitor sodium phenylbutyrate. Furthermore, expression of the marker genes was significantly up-regulated in postmortem HD caudate, suggesting that alterations in blood mRNAs may reflect disease mechanisms observed in HD brain. In conclusion, we identified changes in blood mRNAs that clearly distinguish HD patients from controls. These alterations in mRNA expression correlate with disease progression and response to experimental treatment. Such markers may provide clues to the state of HD and may be of predictive value in clinical trials.