Prenatal Array-CGH Detection of 3q26.32q26.33 Interstitial Deletion Encompassing the SOX2 Gene: Ultrasound, Pathological, and Cytogenetic Findings.

Background: SOX2 disorders are associated with anophthalmia-esophageal-genital syndrome or microphthalmia, syndromic 3 (MCOPS3- # 206900). Case Report: We describe a third fetal case with a de novo 3q26.32q26.33 deletion extending for 4.31 Mb, detected in a 15-week fetus. After legal interruption of pregnancy, at autopsy, the fetus presented bilateral microphthalmia, right cleft lip and palate, bilateral cerebral ventriculomegaly and dilated third ventricle, microcystic left lung, and intestinal malrotation. Histologically, the left lung showed congenital pulmonary airway malformation (CPAM) type 2. Retinal dysplasia was found in both eyes. Discussion/Conclusion: The human SOX2 gene (OMIM #184429) is located on chromosome 3 at position q26.3-27 and encodes a transcription factor involved in the development of the central and peripheral nervous systems, retina, and lung. In our case, the combination of cerebral, retinal, and pulmonary anomalies, not previously described, are consistent with SOX2 haploinsufficiency due to chromosomal deletion.

Case Report: Sequential postzygotic HRAS mutation and gains of the paternal chromosome 11 carrying the mutated allele in a patient with epidermal nevus and rhabdomyosarcoma: evidence of a multiple-hit mechanism involving HRAS in oncogenic transformation.

We report a 7-year-old boy born with epidermal nevi (EN) arranged according to Blaschko's lines involving the face and head, right upper limb, chest, and left lower limb, who developed a left paratesticular embryonal rhabdomyosarcoma at 18 months of age. Parallel sequencing identified a gain-of-function variant (c.37G>C, p.Gly13Arg) of HRAS in both epidermal nevus and tumor but not in leukocytes or buccal mucosal epithelial cells, indicating its postzygotic origin. The variant accounted for 33% and 92% of the total reads in the nevus and tumor DNA specimens, respectively, supporting additional somatic hits in the latter. DNA methylation (DNAm) profiling of the tumor documented a signature consistent with embryonal rhabdomyosarcoma and CNV array analysis inferred from the DNAm arrays and subsequent MLPA analysis demonstrated copy number gains of the entire paternal chromosome 11 carrying the mutated HRAS allele, likely as the result of paternal unidisomy followed by subsequent gain(s) of the paternal chromosome in the tumor. Other structural rearrangements were observed in the tumours, while no additional pathogenic variants affecting genes with role in the RAS-MAPK and PI3K-AKT-MTOR pathways were identified. Our findings provide further evidence of the contribution of "gene dosage" to the multistep process driving cell transformation associated with hyperactive HRAS function.

Automated quantification of dopaminergic immunostained neurons in substantia nigra using freely available software.

Computerized techniques for image analysis are critical for progress in cell biology. The complexity of the data in current methods eliminates the need for manual image analysis and usually requires the application of multiple algorithms sequentially to the images. Our aim was to develop a software for immunohistochemical analysis of brain dopaminergic neurons combining several computational approaches to automatically analyze and quantify their number in the substantia nigra after a neurotoxic injury. For this purpose, we used a Parkinson's disease animal model to test our application. The dopaminergic neurotoxin, 6-hydroxydopamine, was administered in adult male rats to damage dopaminergic neurons in substantia nigra and to induce hemiparkinsonism. The lesion was corroborated by behavioral evaluation in response to apomorphine and amphetamine. The animals were euthanized and their brains processed for tyrosine hydroxylase immunohistochemistry for dopamine neuron identification. Neurons positive for tyrosine hydroxylase were evaluated in substantia nigra by light microscopy. The images were used to show quantification applicability. To test our software counting accuracy and validity, automatic dopamine neuron number was correlated with the data obtained by three independent observers. Several parameters were used to depict neuronal function in dataset images from control and lesioned brains. In conclusion, we could perform an automated quantification of dopaminergic neurons and corroborate the validity and accuracy of a freely available software.

Mosaic Trisomy 12: Prenatal Diagnosis at Amniocentesis and Molecular Genetic Analysis on Fetal Tissues.

Background: Mosaic trisomy 12 is a genetic condition with few cases diagnosed prenatally and postnatally. Phenotypic variability is wide ranging from normal patients to severe congenital anomalies. Case report: A 35-year-old woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Prenatal ultrasound was negative. Cultured amniocytes revealed a karyotype of 47,XX,+12/46,XX. Parents opted for termination of pregnancy at 22 weeks. Postmortem revealed dysmorphic face; hands with broad thumbs and incomplete transverse palmar creases; partial anomalous pulmonary venous return, intestinal malrotation, and bicornuate uterus. Histologically, no anomalies were identified. Cytogenetic analyses on fetal tissues detected mosaic trisomy 12 in thymus, lung, brain, kidney, placenta, and cord blood. Discussion/Conclusion: We report a new case of mosaic trisomy 12 with non-lethal morphological findings not previously described. Although prenatal ultrasound may be negative, genetic counseling should consider minor abnormalities and widespread presence of trisomic cell lines in various internal organs.

Prenatal Diagnosis of Fetal Trisomy 5 Mosaicism with Congenital Pulmonary Airway Malformation Type 3: A Case Report.

Background: Trisomy mosaicism of chromosome 5 is uncommon with few cases described. Case report: A 41-year-old woman underwent ultrasound (US) at 16 weeks, which showed oligohydramnios and intrauterine growth restriction (IUGR). Amniocentesis discovered a karyotype of 47,XX,+5/46,XX. US at 19 weeks disclosed IUGR, enlargement of right side of heart, main pulmonary artery dilatation, and a suspected congenital pulmonary airway malformation (CPAM) in the inferior lobe of the left lung. Due to poor fetal prognosis, the parents opted for legal termination of pregnancy. At postmortem, a wide ventricular septal defect and CPAM type 3 were found. Cytogenetic analyses on fetal tissues detected mosaic trisomy 5 in skin, thymus, kidneys and CPAM. Placenta and fetal peripheral blood revealed normal female karyotype. Discussion/conclusion: These results suggest that if a fetus presents normal phenotypic features, mosaicism may be confined to extraembryonic structures, otherwise, in case of malformations, it may be carried by affected organs.

Whole Exome Sequencing Is the Minimal Technological Approach in Probands Born to Consanguineous Couples.

We report on two siblings suffering from different pathogenic conditions, born to consanguineous parents. A multigene panel for brain malformations and microcephaly identified the homozygous splicing variant NM_005886.3:c.1416+1del in the KATNB1 gene in the older sister. On the other hand, exome sequencing revealed the homozygous frameshift variant NM_005245.4:c.9729del in the FAT1 gene in the younger sister, who had a more complex phenotype: in addition to bilateral anophthalmia and heart defects, she showed a right split foot with 4 toes, 5 metacarpals, second toe duplication and preaxial polydactyly on the right hand. These features have been never reported before in patients with pathogenic FAT1 variants and support the role of this gene in the development of limb buds. Notably, each parent was heterozygous for both of these variants, which were ultra-rare and rare, respectively. This study raises awareness about the value of using whole exome/genome sequencing rather than targeted gene panels when testing affected offspring born to consanguineous couples. In this way, exomic data from the parents are also made available for carrier screening, to identify heterozygous pathogenetic and likely pathogenetic variants in genes responsible for other recessive conditions, which may pose a risk for subsequent pregnancies.

Clinical and Genetic Findings in a Series of Eight Families with Arthrogryposis.

The term "arthrogryposis" is used to indicate multiple congenital contractures affecting two or more areas of the body. Arthrogryposis is the consequence of an impairment of embryofetal neuromuscular function and development. The causes of arthrogryposis are multiple, and in newborns, it is difficult to predict the molecular defect as well as the clinical evolution just based on clinical findings. We studied a consecutive series of 13 participants who had amyoplasia, distal arthrogryposis (DA), or syndromic forms of arthrogryposis with normal intellectual development and other motor abilities. The underlying pathogenic variants were identified in 11 out of 13 participants. Correlating the genotype with the clinical features indicated that prenatal findings were specific for DA; this was helpful to identify familial cases, but features were non-specific for the involved gene. Perinatal clinical findings were similar among the participants, except for amyoplasia. Dilatation of the aortic root led to the diagnosis of Loeys-Dietz syndrome (LDS) in one case. The phenotype of DA type 5D (DA5D) and Escobar syndrome became more characteristic at later ages due to more pronounced pterygia. Follow-up indicated that DA type 1 (DA1)/DA type 2B (DA2B) spectrum and LDS had a more favorable course than the other forms. Hand clenching and talipes equinovarus/rocker bottom foot showed an improvement in all participants, and adducted thumb resolved in all forms except in amyoplasia. The combination of clinical evaluation with Next Generation Sequencing (NGS) analysis in the newborn may allow for an early diagnosis and, particularly in the DAs, suggests a favorable prognosis.

Landscape service flow dynamics in the metropolitan area of Córdoba (Argentina).

Human decisions, policies, and management strategies play an important role in structuring landscape patterns in a metropolitan area. Land-use/land-cover (LULC) changes can be considered probably the most important factor affecting the environment and the maintenance of landscape service flow. In particular, processes such as agricultural intensification, deforestation, urbanization and industrialization affect landscape heterogeneity in terms of composition and configuration. However, the multifunctional aspect of LULC as well as traditional agricultural practices can contribute to the maintenance of landscape service flow. This research aims to analyze and assess: (1) LULC dynamics and change from 1988 to 2019 within the metropolitan area of Córdoba (Argentina); (2) the effect of this change on landscape composition and configuration; (3) the flow of landscape services from 1988 to 2019, with the identification of hot-spots of landscape service provision. To analyze LULC dynamics and change within the study area, three Landsat images were utilized, while change detection analysis has been performed to identify the areas most affected by changes, the spatial distribution of change and the change trajectories of LULC classes in terms of landscape composition and configuration. Finally, the valuation of landscape service flow has been carried out by placing an economic value on the LULC classes, through the use of proxies. LULC pattern change has resulted in the expansion of extensive agriculture. The total variation from 1988 to 2019 has highlighted a significant reduction of Horticulture, Forests, and Grasslands, which have been converted into other classes (Urban and Extensive Agriculture). This conversion of LULC classes has had profound effects on landscape service flow, which guarantees the well-being of local communities. This research has contributed to the knowledge of where the hot-spots of landscape service' provision are located by helping landscape managers to identify suitable local policies able to preserve them, thus avoiding their loss, and enhancing landscape integrity, functionality, and resilience.

Expanding the phenotype of Wiedemann-Steiner syndrome: Craniovertebral junction anomalies.

Wiedemann-Steiner syndrome (WDSTS) is a rare autosomal dominant condition caused by heterozygous loss of function variants in the KMT2A (MLL) gene, encoding a lysine N-methyltransferase that mediates a histone methylation pattern specific for epigenetic transcriptional activation. WDSTS is characterized by a distinctive facial phenotype, hypertrichosis, short stature, developmental delay, intellectual disability, congenital malformations, and skeletal anomalies. Recently, a few patients have been reported having abnormal skeletal development of the cervical spine. Here we describe 11 such individuals, all with KMT2A de novo loss-of-function variants: 10 showed craniovertebral junction anomalies, while an 11th patient had a cervical abnormality in C7. By evaluating clinical and diagnostic imaging data we characterized these anomalies, which consist primarily of fused cervical vertebrae, C1 and C2 abnormalities, small foramen magnum and Chiari malformation type I. Craniovertebral anomalies in WDSTS patients have been largely disregarded so far, but the increasing number of reports suggests that they may be an intrinsic feature of this syndrome. Specific investigation strategies should be considered for early identification and prevention of craniovertebral junction complications in WDSTS patients.

Workload measurement for molecular genetics laboratory: A survey study.

Genetic testing availability in the health care system is rapidly increasing, along with the diffusion of next-generation sequencing (NGS) into diagnostics. These issues make imperative the knowledge-drive optimization of testing in the clinical setting. Time estimations of wet laboratory procedure in Italian molecular laboratories offering genetic diagnosis were evaluated to provide data suitable to adjust efficiency and optimize health policies and costs. A survey was undertaken by the Italian Society of Human Genetics (SIGU). Forty-two laboratories participated. For most molecular techniques, the most time-consuming steps are those requiring an intensive manual intervention or in which the human bias can affect the global process time-performances. For NGS, for which the study surveyed also the interpretation time, the latter represented the step that requiring longer times. We report the first survey describing the hands-on times requested for different molecular diagnostics procedures, including NGS. The analysis of this survey suggests the need of some improvements to optimize some analytical processes, such as the implementation of laboratory information management systems to minimize manual procedures in pre-analytical steps which may affect accuracy that represents the major challenge to be faced in the future setting of molecular genetics laboratory.

Endocrinological Abnormalities Are a Main Feature of 17p13.1 Microduplication Syndrome: A New Case and Literature Review.

To date, 5 cases of 17p13.1 microduplications have been described in the literature. Intellectual disability was reported as the core feature, together with minor facial dysmorphisms and obesity, but a characteristic phenotype for 17p13.1 microduplication has not been delineated. Here, we describe a patient with a 1.56-Mb de novo duplication in 17p13.1, affected by mild intellectual disability, facial dysmorphisms, obesity, and diabetes. By comparing the different phenotypes of currently described cases, we delineated the main clinical features of 17p13.1 microduplication syndrome. All patients described to date had variable facial dysmorphisms; therefore, it was difficult to define a common facial gestalt. Furthermore, we stress endocrinological abnormalities as important features and the need to monitor these over time.

Unexpected results in the constitution of small supernumerary marker chromosomes.

Traditional approaches for the classification of Small Supernumerary Marker Chromosomes (sSMC), mostly based on FISH techniques, are time-consuming and not always sufficient to fully understand the true complexity of this class of rearrangements. We describe four supernumerary marker chromosomes that, after array-CGH, were interpreted rather differently in respect to the early classification made by conventional cytogenetics and FISH investigations, reporting two types of complex markers which DNA content was overlooked by conventional approaches: 1. the sSMC contains non-contiguous regions of the same chromosome and, 2. the sSMC, initially interpreted as a supernumerary del(15), turns out to be a derivative 15 to which the portion of another chromosome was attached. All are likely derived from partial trisomy rescue events, bringing further demonstration that germline chromosomal imbalances are submitted to intense reshuffling during the embryogenesis, leading to unexpected complexity and changing the present ideas on the composition of supernumerary marker chromosomes.

Early detection (9+6 weeks) of cardiac failure in a fetus diagnosed as Turner syndrome by 2D transvaginal ultrasound-guided coelocentesis.

A 28-year-old woman was diagnosed by transvaginal ultrasound at 9+6 weeks with early fetal cardiac failure (hydrothorax and bradycardia). Doppler analysis of ductus venosus showed a negative A-wave pattern. The follow-up sonogram obtained at 11+6 weeks documented a missed abortion. A transvaginal ultrasound-guided coelocentesis was performed under local cervical anesthesia before uterine suction and 8 mL of clear extracoelomic fluid were successfully aspirated. Cytogenetic analysis demonstrated a 45,X karyotype. Ultrasound and Doppler waveform analysis of ductus venosus allowed early diagnosis of fetal cardiac failure. Coelocentesis may be the method of choice for early fetal karyotyping and may be used in the future to induce immunologic tolerance.

Reversible immobilization of asiatic black bear (Ursus thibetanus) with detomidine-tiletamine-zolazepam and atipamezole.

Chemical immobilization of free-ranging and captive wildlife is often required in many clinical situations. In this trial, tiletamine-zolazepam was combined with the alpha2-agonist, detomidine, in order to use the least amount of anesthetic drug possible to achieve a rapid immobilization; to ensure safety for animals and operators; and to be easily reversible with specific antagonists for a fast recovery. Twelve captive Asiatic black bears were anesthetized for clinical procedures, including clinical examination and blood sample collection, and for electrocardiographic and echocardiographic procedures. The combination detomidine-tiletamine-zolazepam, at the dosages of 0.03 mg/kg for detomidine and 1.5 mg/kg for tiletamine-zolazepam, proved to be reliable and effective in immobilizing Asiatic black bears for a 1-hr handling period for routine clinical procedures. Minimal or no respiratory and/or cardiopulmonary adverse side effects were observed, even with dosages calculated on the basis of an estimated body weight. The respiratory rate, pulse rate, and hemoglobin-oxygen saturation remained stable for the entire duration of anesthesia. Cardiac rhythm was always sinusal in all animals. Small injection volumes and darts for blowpipe use were utilized to minimize tissue damage at the site of injection. Induction and recovery were smooth and predictable, and provided for the safety of operators who could observe the bears' activities from a safe distance. Furthermore, the availability of the alpha2-antagonist atipamezole to counteract the effects of detomidine made this anesthetic regimen easily controllable and reversible. Moreover, the recovery time can be shortened by intravenous administration of this antagonist drug.