Body mass index is an overlooked confounding factor in existing clustering studies of 3D facial scans of children with autism spectrum disorder

Cluster analyzes of facial models of autistic patients aim to clarify whether it is possible to diagnose autism on the basis of facial features and further to stratify the autism spectrum disorder. We performed a cluster analysis of sets of 3D scans of ASD patients (116) and controls (157) using Euclidean and geodesic distances in order to recapitulate the published results on the Czech population. In the presented work, we show that the major factor determining the clustering structure and consequently also the correlation of resulting clusters with autism severity degree is body mass index corrected for age (BMIFA). After removing the BMIFA effect from the data in two independent ways, both the cluster structure and autism severity correlations disappeared. Despite the fact that the influence of body mass index (BMI) on facial dimensions was studied many times, this is the first time to our knowledge when BMI was incorporated into the faces clustering study and it thereby casts doubt on previous results. We also performed correlation analysis which showed that the only correction used in the existing clustering studies-dividing the facial distance by the average value within the face-is not eliminating correlation between facial distances and BMIFA within the facial cohort.

Functional studies associate novel DUOX2 gene variants detected in heterozygosity to Crohn's disease

PURPOSE

Crohn's disease is a chronic gastrointestinal inflammatory disease with possible extraintestinal symptoms. There are predisposing genetic factors and even monogenic variants of the disorder. One of the possible genetic factors are variants of the DUOX2 gene. The protein product of the DUOX2 gene is a dual oxidase enzyme producing H2O2 in the bowel. Reduced H2O2 levels impact mucosal homeostasis and contribute to the development of inflammatory bowel disease. Thus far, only 19 patients with IBD with the DUOX2 variants have been described.

METHODS

Here we present a case report of an adolescent female diagnosed at eleven years of age with IBD that was subsequently reclassified as Crohn's disease. She was treated with immunosuppressants and biological therapy but experienced additional complications. Her peripheral blood lymphocyte DNA was studied using massive parallel sequencing. Detected variants were functionally studied.

RESULTS

Whole exome sequencing found two novel DUOX2 gene variants: a de novo variant c.3646C>T; p.R1216W and a maternally inherited variant c.3391G>A; p.A1131T which were initially classified as variants of unknown significance. However, follow-up functional studies demonstrated that both DUOX2 variants led to impaired H2O2 generation, which led to their reclassification to the likely pathogenic class according to the ACMG.net. Therefore, we conclude that these variants are causative for the disease.

CONCLUSIONS

Identifying novel variants in patients with Crohn's disease and their families is important for precision medicine approaches and understanding of the pathogenesis of likely "monogenic" rare forms of inflammatory bowel disease.

Lessons from two series by physicians and caregivers' self-reported data in DDX3X-related disorders

INTRODUCTION AND METHODS

We report two series of individuals with DDX3X variations, one (48 individuals) from physicians and one (44 individuals) from caregivers.

RESULTS

These two series include several symptoms in common, with fairly similar distribution, which suggests that caregivers' data are close to physicians' data. For example, both series identified early childhood symptoms that were not previously described: feeding difficulties, mean walking age, and age at first words.

DISCUSSION

Each of the two datasets provides complementary knowledge. We confirmed that symptoms are similar to those in the literature and provides more details on feeding difficulties. Caregivers considered that the symptom attention-deficit/hyperactivity disorder were most worrisome. Both series also reported sleep disturbance. Recently, anxiety has been reported in individuals with DDX3X variants. We strongly suggest that attention-deficit/hyperactivity disorder, anxiety, and sleep disorders need to be treated.

Co-designing models for the communication of genomic results for rare diseases: a comparative study in the Czech Republic and the United Kingdom

The communication of genomic results to patients and families with rare diseases raise distinctive challenges. However, there is little evidence about optimal methods to communicate results to this group of service users. To address this gap, we worked with rare disease families and health professionals from two genetic/genomic services, one in the United Kingdom and one in the Czech Republic, to co-design that best meet their needs. Using the participatory methodology of Experience-Based Co-Design (EBCD), we conducted observations of clinical appointments (n=49) and interviews with family participants (n=23) and health professionals (n=22) to gather their experience of sharing/receiving results. The findings informed a facilitated co-design process, comprising 3 feedback events at each site and a series of meetings and remote consultations. Participants identified a total of four areas of current service models in need of improvement, and co-designed six prototypes of quality improvement interventions. The main finding was the identification of post-test care as the shared priority for improvement for both health professionals and families at the two sites. Our findings indicate the need to strengthen the link between diagnostics (whether or not a pathogenic variant is found) and post-test care, including psychosocial and community support. This raises implications for the reconfigurations of genomic service models, the redefinition of professional roles and responsibilities and the involvement of rare disease patients and families in health care research.

Zimmermann-Laband syndrome in monozygotic twins with a mild neurobehavioral phenotype lacking gingival overgrowth-A case report of a novel KCNN3 gene variant

Zimmermann-Laband syndrome is a rare, heterogeneous disorder characterized by gingival hypertrophy or fibromatosis, aplastic/hypoplastic nails, hypoplasia of the distal phalanges, hypertrichosis, various degrees of intellectual disability, and distinctive facial features. Three genes are considered causative for ZLS: KCNH1, KCNN3, and ATP6V1B2. We report on a pair of female concordant monozygotic twins, both carrying a novel pathogenic variant in the KCNN3 gene, identified using exome sequencing. Only six ZLS patients with the KCNN3 pathogenic variant have been reported so far. The twins show facial dysmorphism, hypoplastic distal phalanges, aplasia or hypoplasia of nails, and hypertrichosis. During infancy, they showed mild developmental delays, mainly speech. They successfully completed secondary school education and are socio-economically independent. Gingival overgrowth is absent in both individuals. Our patients exhibited an unusually mild phenotype compared to published cases, which is an important diagnostic finding for proper genetic counseling for Zimmermann-Laband syndrome patients and their families.

De novo SMARCA2 variants clustered outside the helicase domain cause a new recognizable syndrome with intellectual disability and blepharophimosis distinct from Nicolaides-Baraitser syndrome

PURPOSE

Nontruncating variants in SMARCA2, encoding a catalytic subunit of SWI/SNF chromatin remodeling complex, cause Nicolaides-Baraitser syndrome (NCBRS), a condition with intellectual disability and multiple congenital anomalies. Other disorders due to SMARCA2 are unknown.

METHODS

By next-generation sequencing, we identified candidate variants in SMARCA2 in 20 individuals from 18 families with a syndromic neurodevelopmental disorder not consistent with NCBRS. To stratify variant interpretation, we functionally analyzed SMARCA2 variants in yeasts and performed transcriptomic and genome methylation analyses on blood leukocytes.

RESULTS

Of 20 individuals, 14 showed a recognizable phenotype with recurrent features including epicanthal folds, blepharophimosis, and downturned nasal tip along with variable degree of intellectual disability (or blepharophimosis intellectual disability syndrome [BIS]). In contrast to most NCBRS variants, all SMARCA2 variants associated with BIS are localized outside the helicase domains. Yeast phenotype assays differentiated NCBRS from non-NCBRS SMARCA2 variants. Transcriptomic and DNA methylation signatures differentiated NCBRS from BIS and those with nonspecific phenotype. In the remaining six individuals with nonspecific dysmorphic features, clinical and molecular data did not permit variant reclassification.

CONCLUSION

We identified a novel recognizable syndrome named BIS associated with clustered de novo SMARCA2 variants outside the helicase domains, phenotypically and molecularly distinct from NCBRS.

The clinical significance of A2ML1 variants in Noonan syndrome has to be reconsidered

The RASopathies are a group of clinically and genetically heterogeneous developmental disorders caused by dysregulation of the RAS/MAPK signalling pathway. Variants in several components and regulators of this pathway have been identified as the pathogenetic cause. In 2015, missense variants in A2ML1 were reported in three unrelated families with clinical diagnosis of Noonan syndrome (NS) and a zebrafish model was presented showing heart and craniofacial defects similar to those caused by a NS-associated Shp2 variant. However, a causal role of A2ML1 variants in NS has not been confirmed since. Herein, we report on 15 individuals who underwent screening of RASopathy-associated genes and were found to carry rare variants in A2ML1, including variants previously proposed to be causative for NS. In cases where parental DNA was available, the respective A2ML1 variant was found to be inherited from an unaffected parent. Seven index patients carrying an A2ML1 variant presented with an alternate disease-causing genetic aberration. These findings underscore that current evidence is insufficient to support a causal relation between variants in A2ML1 and NS, questioning the inclusion of A2ML1 screening in diagnostic RASopathy testing.

Expanding the phenotype spectrum associated with pathogenic variants in the COL2A1 and COL11A1 genes

We report the clinical findings of 26 individuals from 16 unrelated families carrying variants in the COL2A1 or COL11A1 genes. Using Sanger and next-generation sequencing, 11 different COL2A1 variants (seven novel), were identified in 13 families (19 affected individuals), all diagnosed with Stickler syndrome (STL) type 1. In nine families, the COL2A1 disease-causing variant arose de novo. Phenotypically, we observed myopia (95%) and retinal detachment (47%), joint hyperflexibility (92%), midface retrusion (84%), cleft palate (53%), and various degrees of hearing impairment (50%). One patient had a splenic artery aneurysm. One affected individual carrying pathogenic variant in COL2A1 showed no ocular signs including no evidence of membranous vitreous anomaly. In three families (seven affected individuals), three novel COL11A1 variants were found. The propositus with a de novo variant showed an ultrarare Marshall/STL overlap. In the second family, the only common clinical sign was postlingual progressive sensorineural hearing impairment (DFNA37). Affected individuals from the third family had typical STL2 signs. The spectrum of disease phenotypes associated with COL2A1 or COL11A1 variants continues to expand and includes typical STL and various bone dysplasias, but also nonsyndromic hearing impairment, isolated myopia with or without retinal detachment, and STL phenotype without clinically detectable ocular pathology.

The Key Role of Purine Metabolism in the Folate-Dependent Phenotype of Autism Spectrum Disorders: An In Silico Analysis

Folate deficiency in the critical developmental period has been repeatedly associated with an increased risk of Autism spectrum disorders (ASD), but the key pathophysiological mechanism has not yet been identified. In this work, we focused on identifying genes whose defect has similar consequences to folate depletion in the metabolic network. Within the Flux Balance Analysis (FBA) framework, we developed a method of blocked metabolites that allowed us to define the metabolic consequences of various gene defects and folate depletion. We identified six genes (GART, PFAS, PPAT, PAICS, ATIC, and ADSL) whose blocking results in nearly the same effect in the metabolic network as folate depletion. All of these genes form the purine biosynthetic pathway. We found that, just like folate depletion, the blockade of any of the six genes mentioned above results in a blockage of purine metabolism. We hypothesize that this can lead to decreased adenosine triphosphate (ATP) and subsequently, an S-adenosyl methionine (SAM) pool in neurons in the case of rapid cell division. Based on our results, we consider the methylation defect to be a potential cause of ASD, due to the depletion of purine, and consequently S-adenosyl methionine (SAM), biosynthesis.

De Novo Heterozygous POLR2A Variants Cause a Neurodevelopmental Syndrome with Profound Infantile-Onset Hypotonia

The RNA polymerase II complex (pol II) is responsible for transcription of all ∼21,000 human protein-encoding genes. Here, we describe sixteen individuals harboring de novo heterozygous variants in POLR2A, encoding RPB1, the largest subunit of pol II. An iterative approach combining structural evaluation and mass spectrometry analyses, the use of S. cerevisiae as a model system, and the assessment of cell viability in HeLa cells allowed us to classify eleven variants as probably disease-causing and four variants as possibly disease-causing. The significance of one variant remains unresolved. By quantification of phenotypic severity, we could distinguish mild and severe phenotypic consequences of the disease-causing variants. Missense variants expected to exert only mild structural effects led to a malfunctioning pol II enzyme, thereby inducing a dominant-negative effect on gene transcription. Intriguingly, individuals carrying these variants presented with a severe phenotype dominated by profound infantile-onset hypotonia and developmental delay. Conversely, individuals carrying variants expected to result in complete loss of function, thus reduced levels of functional pol II from the normal allele, exhibited the mildest phenotypes. We conclude that subtle variants that are central in functionally important domains of POLR2A cause a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia and developmental delay through a dominant-negative effect on pol-II-mediated transcription of DNA.

Schinzel—Giedion Syndrome: First Czech Patients Confirmed by Molecular Genetic Analysis

Schinzel–Giedion syndrome (SGS) is a very rare genetic disorder characterized by distinctive facial features, severe developmental delay, seizures, and skeletal abnormalities. Whole exome sequencing, Sanger sequencing, and correlation with already published variants and cases allowed us to identify two different de novo mutations in the SETBP1 gene: NM_015559.2 (SETBP1): c.2601C > G (p.Ser867Arg) and c. 2608 G > A (p.Gly870Ser) in two Czech patients presenting with SGS features. Both mutations are within exon 4 of SETBP1, supporting the notion that exon 4 represents the mutation hotspot of the gene in patients with SGS.

Unique characteristics of informed consent in clinical genetics and genetic counselling

Rapid development of clinical genetics was enabled by the advances of molecular genetic laboratory diagnostics. Genetic laboratory testing has unique characteristics, and results of germinal genome testing has consequences not only for the patient but also for his relatives. Genetic laboratory testing in the Czech Republic is governed by the act no. 373/2011, which explicitly states that the testing requires the completion of a written informed consent. This article explains in detail the process of obtaining an informed consent within a broader framework of genetic counselling. An informed consent with genetic laboratory testing not only informs the patient (this being its primary purpose), but can also serve as a lead for physicians of other clinical specialties intending to order genetic laboratory tests.

Modeling age-specific facial development in Williams-Beuren-, Noonan-, and 22q11.2 deletion syndromes in cohorts of Czech patients aged 3-18 years: A cross-sectional three-dimensional geometric morphometry analysis of their facial gestalt

Three-dimensional (3D) virtual facial models facilitate genotype-phenotype correlations and diagnostics in clinical dysmorphology. Within cross-sectional analysis of both genders we evaluated facial features in representative cohorts of Czech patients with Williams-Beuren-(WBS; 12 cases), Noonan-(NS; 14), and 22q11.2 deletion syndromes (22q11.2DS; 20) and compared their age-related developmental trajectories to 21 age, sex and ethnically matched controls in 3-18 years of age. Using geometric morphometry statistically significant differences in facial morphology were found in all cases compared to controls. The dysmorphic features observed in WBS were specific and manifested in majority of cases. During ontogenesis, dysmorphic features associated with increased facial convexity become more pronounced whereas other typical features remained relatively stable. Dysmorphic features observed in NS cases were mostly apparent during childhood and gradually diminished with age. Facial development had a similar progress as in controls, while there has been increased growth of patients' nose and chin in adulthood. Facial characteristics observed in 22q11.2DS, except for hypoplastic alae nasi, did not correspond with the standard description of its facial phenotype because of marked facial heterogeneity of this clinical entity. Because of the sensitivity of 3D facial morphometry we were able to reach statistical significance even in smaller retrospective patient cohorts, which proves its clinical utility within the routine setting.

[Hereditary breast cancer: genetic etiology and current possibilities of prevention and surgical treatment]

Cancer is the second most common cause of death in our population just after cardiovascular diseases, since each third individual will become affected by it during their lifetime. Breast cancer is the most common malignancy in women. The lifetime cumulative risk of breast cancer in women under the age of 75 is around 8 % according to Czech statistics. In 70-75 % of all individuals sporadic breast carcinomas are found, with 5-10 % of all women suffer from the hereditary breast and ovarian cancer (HBOC) syndrome. Radical, bilateral, removal of the mammary gland is the most effective prevention of breast cancer in BRCA positive women. We present a summary of 37 BRCA positive Czech patients who underwent prophylactic bilateral mastectomy and whose mean age was 46.5 years. Surgical solution is currently the only effective therapeutic way to prevent breast cancer in BRCA positive women with high genetic risk. The cosmetic consequences of this radical surgery can be solved through many reconstruction tasks.

Odontogenic keratocysts in the Basal Cell Nevus (Gorlin-Goltz) Syndrome associated with paresthesia of the lower jaw: Case report, retrospective analysis of a representative Czech cohort and recommendations for the early diagnosis

OBJECTIVES

Identification of early presenting signs of the Basal Cell Nevus (BCNS; synonyme Gorlin-Goltz) syndrome, which is associated with a principal triad of multiple basal cell nevi, jaw odontogenic keratocysts, and skeletal anomalies, in stomatological and neurological practices. Proposal of multidisciplinary diagnostic algorithm comprising other medical specialists, including pathology, imaging, laboratory and molecular analyses based on the study outcomes.

DESIGN

Case report of a male patient reporting paresthesia of their lower jaw, with right facial asymmetry (maxilla and mandible) and radiological detection of large osteolytic lesions in both jaws, including a retrospective analysis of a representative Czech cohort with BCNS from within the last decade.

SETTING

Clinical, imaging and laboratory analyses were carried out at a national tertiary centre.

RESULTS

A multidisciplinary clinical approach followed by surgical management lead to the identification of odontogenic cysts, which were substantiated by histological examination. DNA sequencing of the PTCH1 gene detected a c.2929dupT resulting in p. Tyr977Leufs*16 pathogenic variant. This finding confirmed the clinical and laboraoty diagnosis of BCNS. Parental DNA analysis showed that this causal genetic defect arose de novo. Surgical management and orthodontic therapy were successful.

CONCLUSIONS

Analysis of the reported case and retrospective data analysis provided evidence that paresthesia of the lower jaw should be considered as one of the early presenting signs of this rare disorder in stomatological and neurological practice. Obtained results allowed us to formulate recommendations for diagnostic practice in stomatology and neurology.

Concomitancy of mutation in FRDA gene and FMR1 premutation in 58 year-old woman

DNA testing broadens diagnostic tools available for hereditary ataxias. However, together with current knowledge of genes and their mutations crop up new phenotype figures of diseases already well known. Diagnostic problems in practice can consist in part due to the very similar symptoms of hereditary ataxias and acquaintance in or availability of new techniques such as DNA testing and result in misdiagnosis. We present a case study of a 57 year-old woman with both expansion of the triplet repetitive sequence of FRDA gene and a premutation in FMR1 gene. At present we diagnose her with Very Late Onset Friedreich s ataxia, but we advise of possible combinations or aggravations of her symptoms due to manifestation of Fragile X premutation tremor/ataxia syndrome. In nontypical phenotypes of DNA verifying hereditary ataxias we recommend searching of comorbidity, specifically from a range of hereditary ataxias with very similar spectra of symptoms.

[Case reports of patients with a marker chromosome]

Small, usually supernumerary chromosomes, denoted as marker chromosomes or markers, can be represented by various phenotypic expression, that depends on their origin and extent. Our article presents results of molecular cytogenetic analysis (FISH) of 34 patients with identified marker chromosome. In 21 cases a marker derived from acrocentric chromosome was identified, in 9 cases markers of gonosomal origin [der(X), der(Y)], and in 4 patients markers of some other chromosomes (5, 17, 18) were proved. The most frequent marker was that originating from chromosome 15 (8 cases). Two patients with different phenotype, markedly influenced by the extent of pseudoizodicentric chromosome 15 are described. In accordance with hitherto presented data, presence of supernumerary copies of the critical region PWACR (it is the partial trisomy, resp. tetrasomy 15q11-q13) in majority of cases brings about serious affection described as syndrome of the inverted duplication of chromosome 15. The most typical symptoms are psychomotoric retardation, hypotony, neurological symptoms and autistic features. The article stresses the importance of FISH method in the prenatal examination of marker chromosomes.

[Psychosocial factors associated with genetic testing for certain hereditary types of neoplasms]

Mutations in predisposing genes for some of the hereditary forms of cancer exhibit autosomal dominant mode of inheritance. Introduction of genetic tests for these mutations to the clinical practice initiated studies focused on the psychosocial factors associated with genetic testing. Undergoing the genetic testing is a stressful experience for both the healthy individuals in risk and the patients already affected with cancer. The psychosocial characteristics of the tested individual influence not only the psychological functioning during the testing but also the acceptance of the test, and generally his life style and health practices. Psychological support during the genetic testing process is mostly provided by the genetic counsellor. The findings of psychosocial studies might be therefore helpful for the focusing of the genetic consultation, and fulfilling the client needs and expectations towards testing. Factors of motivation, psychological state, influence of family situation and support, and optionally the involvement of a psychologist into the process of genetic testing are observed.

[Genetic study of 20 patients with autism disorders]

BACKGROUND

Many observations indicate that genetic factors play an important role in the aetiology of autism. Up to now, however, no genetic markers have been convincingly identified which influence the predisposition to this disorder. Complex genetic analysis of autistic patients and their families may therefore lead to the identification of features which could help to direct further search for the predisposing genes.

METHODS AND RESULTS

We have analysed a sample of 20 patients with autism spectrum disorders. The patients have been subjected to clinical genetic examination, cytogenetic analysis and DNA analysis of the FMR1 gene. In the sample studied we have observed more boys (15/20), various degree of mental retardation (18/20), high frequency of complications during pregnancy (10/20) and delivery (10/20), increased incidence of psychiatric disorders, behavioural abnormalities and suicides among the relatives, and increased head circumference and unusually formed ears in the probands. Three patients had different chromosomal aberrations or variants (t(21;22), inv(9) and inv(10)). One patient harboured expansion of the trinucleotide repeat sequence in the FMR1 gene on the full mutation level which is characteristic for the fragile X syndrome, and one patient is suspected to suffer from the Rett syndrome.

CONCLUSIONS

Our observations confirm and extend the results reported in the literature. Most interesting are mainly the macrocephaly which may be associated with the recently described increased neonatal levels of neural growth factors in autistic individuals, ear malformations which may indicate aberrations in the HOXA1 gene pathway, the occurrence of chromosomal inversions recurrent in autism, and peculiarities in the pedigrees of the patients.

[Genetics of autism]

Autism is a severe psychiatric disorder characterised by deficits in social interaction, disturbed communication and adherence to stereotype routines and interests. Nowadays it is completely clear that this disorder has a biological basis and many observations show strong genetic determination of autism. The importance of genetic factors is supported by frequent association of this disorder with known hereditary diseases or with various chromosomal aberrations, by high concordance of the disorder in monozygotic twins, higher risk for the siblings of autistic patients and also by the frequent occurrence of milder symptoms of the autistic spectrum in more distant relatives. All these findings show that the autistic phenotype results from unfavourable combination of alleles of several genes in interplay with factors of the environment. This model of multifactorial inheritance of autism serves at present as the starting point for the search for predisposing genes in the human genome. The association is tested between autism and alleles of candidate genes selected based on known biochemical and physiological role of their protein products, or based on their location close to recurrent chromosomal rearrangements or in regions identified by whole-genome linkage analyses. Studies of most of these genes have not yielded clear-cut results yet, but the participation of some of them in the aetiology of autism is possible.

[Specialized genetic counseling in pediatric and adult oncology patients]

Five to ten percent of oncological diseases exhibit monogenic mode of inheritance. They occur as a consequence of the germline mutations of tumor suppressor genes and of the genes engaged in reparative processes. Most common monogenically determined oncological diseases are: AD form of breast and ovarian cancer, hereditary nonpolyposis colorectal cancer (HNPCC, Lynch sy.) and familiar adenomatous polyposis (FAP). The aim of the genetic investigation is to evaluate whether the index family deals with the hereditary form of tumor predisposition, than, if possible, to perform DNA analysis in the family and to propose preventive screening program (methods) for the probands in risk.

[DNA diagnosis of the fragile X chromosome syndrome--FRAXA using PCR]

BACKGROUND

Fragile X syndrome is gonosomal recessive mental retardation with the frequency 1:1000 in male population. Fragile X syndrome is caused by amplification of CGG repeat in 1. exon of FMT-1 gene. The aim of this study was to set up and validate a rapid and efficient PCR diagnosis to select FRAXA negative patients in population of mental retarded patients.

METHODS AND RESULTS

In the set up phase of the method, 196 patients were diagnosed. We were using modified radioactive PCR of CGG. Obtained PCR fragments were separated on 6% denaturing PAGE. Results were correlated with Southern blot analysis using pE5.1 probe. STR-PCR was verified on a large set of patients and shows validity and efficiency of results in the case of pre- and full mutations in male hemizygous patients too. For estimation of carriers with pre- and full mutation by females modified diagnostic approach was developed. There was no difference found between results from PCR and Southern blot analysis.

CONCLUSIONS

The PCR method is convenient not only for selection of FRAXA negative patients, but for diagnosis of full mutation and premutation of affected probands.