Expanding the Phenotypic Spectrum of Alazami Syndrome: Two Unrelated Spanish Families.

Alazami syndrome is a rare disorder with an autosomal recessive inheritance caused by pathogenic biallelic variants in the LARP7 gene. Clinically, it is mainly characterized by short stature, intellectual disability, and dysmorphic facial features. However, the phenotype is not yet well-defined because less than 50 cases have been described to date. Here, we report three new patients from two unrelated Spanish families who, in addition to the defined features of Alazami syndrome, also exhibit unique features that broaden the phenotypic spectrum of the syndrome. Moreover, we describe the novel frameshift variant c.690_699delins27 in the LARP7 gene, in which loss of function is a known mechanism of Alazami syndrome.

Heterozygous and Homozygous Variants in SORL1 Gene in Alzheimer's Disease Patients: Clinical, Neuroimaging and Neuropathological Findings.

In the last few years, the SORL1 gene has been strongly implicated in the development of Alzheimer's disease (AD). We performed whole-exome sequencing on 37 patients with early-onset dementia or family history suggestive of autosomal dominant dementia. Data analysis was based on a custom panel that included 46 genes related to AD and dementia. SORL1 variants were present in a high proportion of patients with candidate variants (15%, 3/20). We expand the clinical manifestations associated with the SORL1 gene by reporting detailed clinical and neuroimaging findings of six unrelated patients with AD and SORL1 mutations. We also present for the first time a patient with the homozygous truncating variant c.364C>T (p.R122*) in SORL1, who also had severe cerebral amyloid angiopathy. Furthermore, we report neuropathological findings and immunochemistry assays from one patient with the splicing variant c.4519+5G>A in the SORL1 gene, in which AD was confirmed by neuropathological examination. Our results highlight the heterogeneity of clinical presentation and familial dementia background of SORL1-associated AD and suggest that SORL1 might be contributing to AD development as a risk factor gene rather than as a major autosomal dominant gene.

First female with Allan-Herndon-Dudley syndrome and partial deletion of X-inactivation center.

Allan-Herndon-Dudley is an X-linked recessive syndrome caused by pathogenic variants in the SLC16A2 gene. Clinical manifestations are a consequence of impaired thyroid metabolism and aberrant transport of thyroid hormones to the brain. Carrier females are generally asymptomatic and may show subtle symptoms of the disease. We describe a female with a complete Allan-Herndon-Dudley phenotype, carrying a de novo 543-kb deletion of the X chromosome. The deletion encompasses exon 1 of the SLC16A2 gene and JPX and FTX genes; it is known that the latter two genes participate in the X-inactivation process upregulating XIST gene expression. Subsequent studies in the patient demonstrated the preferential expression of the X chromosome with the JPX and FTX deletion.

First patient with mosaic NOTCH3 gene pathogenic variant. Unrevealed mosaicisms and importance of their detection.

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is an inherited small vessel disease caused predominantly by pathogenic variants in NOTCH3 gene. Neither germline nor somatic mosaicism has been previously published in NOTCH3 gene. CADASIL is inherited in an autosomal dominant manner; only rare cases have been associated with de novo pathogenic variants. Mosaicism is more common than previously thought because mosaic variants often stay unrevealed. An apparently de novo variant might actually be a consequence of a parental mosaicism undetectable with Sanger sequencing, especially in the case of low grade mosaicism. Parental testing by sensitive tools like deep targeted next-generation sequencing (NGS) analysis could detect cases of unrevealed medium or low level mosaicism in patients tested by Sanger sequencing. Here, we report the first patient with mosaic NOTCH3 gene pathogenic variant to our knowledge; the allelic fraction in the leucocyte DNA was low (13%); the pathogenic variant was inhered by his two daughters. The patient was diagnosed by deep targeted NGS analysis after studying his two affected daughters. This report highlights the importance of parental testing by sensitive tools like deep targeted NGS analysis. Detection of mosaicism is of great importance for diagnosis and adequate family genetic counseling.

A Novel Pathogenic Variant in the MN1 Gene in a Patient Presenting with Rhombencephalosynapsis and Craniofacial Anomalies, Expanding MN1 C-terminal Truncation Syndrome.

Meningioma-1 is a transcription activator that regulates mammalian palate development and is required for appropriate osteoblast proliferation, motility, differentiation, and function. Microdeletions involving the MN1 gene have been linked to syndromes including craniofacial anomalies, such as Toriello-Carey syndrome. Recently, truncating variants in the C-terminal portion of the MN1 transcriptional factor have been linked to a characteristic and distinct phenotype presenting with craniofacial anomalies and partial rhombencephalosynapsis, a rare brain malformation characterized by midline fusion of the cerebellar hemispheres with partial or complete loss of the cerebellar vermis. It has been called MN1 C-terminal truncation (MCTT) syndrome or CEBALID (Craniofacial defects, dysmorphic Ears, Brain Abnormalities, Language delay, and Intellectual Disability) and suggested to be caused by dominantly acting truncated protein MN1 instead of haploinsufficiency. As a proto-oncogene, MN1 is also involved in familial meningioma. In this study, we present a novel case of MCTT syndrome in a female patient presenting with craniofacial anomalies and rhombencephalosynapsis, harboring a de novo pathogenic variant in the MN1 gene: c.3686_3698del, p.(Met1229Argfs*87).

Noninvasive fetal sex determination in maternal plasma: a prospective feasibility study.

PURPOSE: To prospectively validate a protocol for noninvasive fetal sex determination in maternal plasma and demonstrate its applicability to clinical practice. METHODS: Peripheral blood from 404 pregnant women undergoing prenatal invasive testing was collected from 6 to 23 weeks of gestation. Real-time PCR was performed for the SRY gene and multicopy DYS14 marker sequence located within the TSPY gene by the TaqMan minor groove binder probe assay as a first-line test. Owing to a false-positive result, amplification of repetitive motifs of the DAZ gene region was also tested as a second-line test performed in the last 232 patients enrolled in our series. A diagnostic algorithm was designed using a combination of these three markers. Fetal gender determined by noninvasive prenatal diagnosis (NIPD) was compared with that diagnosed by quantitative fluorescent PCR after invasive testing or ultrasound. RESULTS: A single false-positive result was obtained in the first 172 pregnancies. Reporting criteria were modified in the subsequent 232 pregnancies, giving an overall sensitivity and specificity of 100% (95% CI 99.8-100%) and 99.5% (95% CI 98.1-100%), respectively. Pregnancy outcome was obtained in all cases, including 221 male-bearing and 183 female-bearing pregnancies. CONCLUSION: NIPD for fetal sex determination in maternal plasma is highly accurate and clinically applicable if robust reporting criteria are applied.

Fragile X Syndrome Caused by Maternal Somatic Mosaicism of FMR1 Gene: Case Report and Literature Review.

Fragile X syndrome (FXS) is caused by an abnormal expansion of the number of trinucleotide CGG repeats located in the 5' UTR in the first exon of the FMR1 gene. Size and methylation mosaicisms are commonly observed in FXS patients. Both types of mosaicisms might be associated with less severe phenotypes depending on the number of cells expressing FMRP. Although this dynamic mutation is the main underlying cause of FXS, other mechanisms, including point mutations or deletions, can lead to FXS. Several reports have demonstrated that de novo deletions including the entire or a portion of the FMR1 gene end up with the absence of FMRP and, thus, can lead to the typical clinical features of FXS. However, very little is known about the clinical manifestations associated with FMR1 gene deletions in mosaicism. Here, we report an FXS case caused by an entire hemizygous deletion of the FMR1 gene caused by maternal mosaicism. This manuscript reports this case and a literature review of the clinical manifestations presented by carriers of FMR1 gene deletions in mosaicism.

Hereditary cerebral small vessel disease: Assessment of a HTRA1 variant using protein stability predictors and 3D modelling.

Cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy (CARASIL) is an autosomal recessive vascular disorder caused by biallellic variants in HTRA1. Recently, it has been reported that several heterozygous mutations in HTRA1 are responsible for a milder late-onset cerebral small vessel disease (CSVD) with an autosomal dominant pattern of inheritance. The majority of them are missense that affects the Htr1A protease activity due to a dominant-negative effect caused by defective trimerization or monomer activation. The molecular mechanism related to the structural destabilization of the protein supports the practical utility of integrating computational stability predictors to prioritize candidate variants in this gene. In this work, we report a family with several members diagnosed with subcortical ischemic events and progressive cognitive impairment caused by the novel c.820C > G, p.(Arg274Gly) heterozygous variant in HTRA1 segregating in an autosomal dominant manner and propose its molecular mechanism by a three-dimensional model of the protein's structure.

Pathological and sub-pathological changes in European rabbit bones: Two reference cases to be applied to the analysis of archaeological assemblages.

OBJECTIVE: To provide prevalence data for future comparative analysis of the health status of rabbits (Oryctolagus cuniculus) accumulated in the archaeological record. MATERIALS: Two contrasting assemblages were analysed for pathological and sub-pathological changes: 1) an assemblage of domestic modern rabbit bones; and 2) a non-anthropogenic accumulation of archaeological rabbit remains. METHODS: The lesions observed macroscopically, under magnification, and radiographically in both assemblages are quantified and described. RESULTS: In the first assemblage, pathological and sub-pathological changes mostly affected the lower limb bones and primarily took two forms: diaphyseal periosteal proliferation and hypervascularised distal physes. Differential diagnosis of the periosteal proliferation suggests that pododermatitis is the most probable cause. In the second assemblage fractures were the most common lesions, but isolated examples of hypervascularised physes, periosteal proliferation, and musculo-skeletal stress markers were also identified. The pathological changes recorded is typical of a naturally-accumulated population of wild rabbits. CONCLUSIONS: The prevalence of pathological and sub-pathological skeletal changes in the rabbits, and thus their health status, are closely related to living conditions. This study demonstrates the value of systematically recording pathologies in rabbit bones. SIGNIFICANCE: We contribute new data to help understand rabbit interactions with humans in the past and also the environment they inhabited. LIMITATIONS: Working with modern samples frequently means only incomplete skeletons are available for study. In these cases lesion prevalence always needs to be interpreted with caution. SUGGESTIONS FOR FURTHER RESEARCH: Paleopathological studies of rabbit remains are remarkable for their absence. Further exhaustive research in this area is advised.

Investigating Neolithic caprine husbandry in the Central Pyrenees: Insights from a multi-proxy study at Els Trocs cave (Bisaurri, Spain).

Sheep remains constitute the main archaeozoological evidence for the presence of Early Neolithic human groups in the highlands of the Southern Pyrenees but understanding the role of herding activities in the Neolithisation process of this mountain ecosystem calls for the analysis of large and well-dated faunal assemblages. Cova de Els Trocs (Bisaurri, Huesca, Spain), a cave located at 1564 m a.s.l on the southern slopes of the Central Pyrenees, is an excellent case study since it was seasonally occupied throughout the Neolithic (ca. 5312-2913 cal. BC) and more than 4000 caprine remains were recovered inside. The multi-proxy analytical approach here presented has allowed us to offer new data elaborating on vertical mobility practices and herd management dynamics as has not been attempted up until now within Neolithic high-mountain sites in the Iberian Peninsula. For the first time, δ18O and δ13C stable isotope analyses offer direct evidence on both the regular practice of altitudinal movements of sheep flocks and the extended breeding season of sheep. Autumn births are recorded from the second half of the fifth millennium cal. BC onwards. Age-at-death distributions illustrate the progressive decline in caprine perinatal mortality together with the rising survival rate of individuals older than six months of age and the larger frequency of adults. This trend alongside the 'off-season' lambing signal at the implementation of husbandry techniques over time, probably aiming to increase the size of the flocks and their productivity. Palaeoparasitological analyses of sediment samples document also the growing reliance on herding activities of the human groups visiting the Els Trocs cave throughout the Neolithic sequence. In sum, our work provides substantial arguments to conclude that the advanced herding management skills of the Early Neolithic communities arriving in Iberia facilitated the anthropisation process of the subalpine areas of the Central Pyrenees.

Towards a Change in the Diagnostic Algorithm of Autism Spectrum Disorders: Evidence Supporting Whole Exome Sequencing as a First-Tier Test.

Autism spectrum disorder (ASD) is a prevalent and extremely heterogeneous neurodevelopmental disorder (NDD) with a strong genetic component. In recent years, the clinical relevance of de novo mutations to the aetiology of ASD has been demonstrated. Current guidelines recommend chromosomal microarray (CMA) and a FMR1 testing as first-tier tests, but there is increasing evidence that support the use of NGS for the diagnosis of NDDs. Specifically in ASD, it has not been extensively evaluated and, thus, we performed and compared the clinical utility of CMA, FMR1 testing, and/or whole exome sequencing (WES) in a cohort of 343 ASD patients. We achieved a global diagnostic rate of 12.8% (44/343), the majority of them being characterised by WES (33/44; 75%) compared to CMA (9/44; 20.4%) or FMR1 testing (2/44; 4.5%). Taking into account the age at which genetic testing was carried out, we identified a causal genetic alteration in 22.5% (37/164) of patients over 5 years old, but only in 3.9% (7/179) of patients under this age. Our data evidence the higher diagnostic power of WES compared to CMA in the study of ASD and support the implementation of WES as a first-tier test for the genetic diagnosis of this disorder, when there is no suspicion of fragile X syndrome.

Genetic turnovers and northern survival during the last glacial maximum in European brown bears.

The current phylogeographic pattern of European brown bears (Ursus arctos) has commonly been explained by postglacial recolonization out of geographically distinct refugia in southern Europe, a pattern well in accordance with the expansion/contraction model. Studies of ancient DNA from brown bear remains have questioned this pattern, but have failed to explain the glacial distribution of mitochondrial brown bear clades and their subsequent expansion across the European continent. We here present 136 new mitochondrial sequences generated from 346 remains from Europe, ranging in age between the Late Pleistocene and historical times. The genetic data show a high Late Pleistocene diversity across the continent and challenge the strict confinement of bears to traditional southern refugia during the last glacial maximum (LGM). The mitochondrial data further suggest a genetic turnover just before this time, as well as a steep demographic decline starting in the mid-Holocene. Levels of stable nitrogen isotopes from the remains confirm a previously proposed shift toward increasing herbivory around the LGM in Europe. Overall, these results suggest that in addition to climate, anthropogenic impact and inter-specific competition may have had more important effects on the brown bear's ecology, demography, and genetic structure than previously thought.

Noninvasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield.

OBJECTIVE: The aim of this study was to determine if the use of different mappers for NIPT may vary the results considerably. METHODS: Peripheral blood was collected from 217 pregnant women, 58 pathological (34 pregnancies with trisomy 21, 18 with trisomy 18, and 6 with trisomy 13) and 159 euploid. MPS was performed following a manufacturer's modified protocol of semiconductor sequencing. Obtained reads were mapped with two different software programs: TMAP and HPG-Aligner, comparing the results. RESULTS: Using TMAP, 57 pathological samples were correctly detected (sensitivity 98.28%, specificity 93.08%): 33 samples as trisomy 21 (sensitivity 97.06%, specificity 99.45%), 16 as trisomy 18 (sensibility 88.89%, specificity 93.97%), and 6 as trisomy 13 (sensibility 100%, specificity 100%). 11 false positives, 1 false negative, and 2 samples incorrectly identified were obtained. Using HPG-Aligner, all the 58 pathological samples were correctly identified (sensibility 100%, specificity 96.86%): 34 as trisomy 21 (sensibility 100%, specificity 98.91%), 18 as trisomy 18 (sensibility 100%, specificity 98.99%), and 6 as trisomy 13 (sensibility 100%, specificity 99.53%). 5 false positives were obtained. CONCLUSION: Different mappers use slightly different algorithms, so the use of one mapper or another with the same batch file can provide different results.

[Phenotypic variability of the 1q21.1 microdeletion syndrome in members of the same family: relevance of detection of neuropsychiatric disorders for diagnosis of genetic syndromes]. / Variabilidad del fenotipo del sindrome de microdelecion 1q21.1 dentro de una misma familia: importancia de la deteccion de trastornos neuropsiquiatricos para el diagnostico de sindromes geneticos.

INTRODUCTION: 1q21.1 microdeletion syndrome is a caused by a recurrent deletion of the 1q21.1 copy-number variant, which spans 800 kb and includes at least seven genes. It is associated with a variable phenotype. Neuropsychiatric abnormalities have been previously described in many of the previously reported cases, but its true prevalence is unknown. AIM: To illustrate the phenotypic variability in 1q21.1 microdeletion syndrome. CASE REPORTS: Four individuals of the same kindred harboring a 1.74-Mb deletion within 1q21.1 are included. In our patients a heterogeneous phenotype is recognized. Neuropsychiatric disorders or more specifically impulse control disorders were common to all the four cases that we present. CONCLUSIONS: 1q21.1 microdeletion syndrome is phenotypically heterogeneous even among members of the same family. Behavioral or neuropsychiatric abnormalities are frequent. Paucisymptomatic forms with individuals presenting exclusively psychiatric disorders have been identified.

TITLE: Variabilidad del fenotipo del sindrome de microdelecion 1q21.1 dentro de una misma familia: importancia de la deteccion de trastornos neuropsiquiatricos para el diagnostico de sindromes geneticos.Introduccion. El sindrome de microdelecion 1q21.1 esta causado por una delecion recurrente de aproximadamente 800 kb que incluye al menos siete genes y se asocia a un fenotipo variable. Esta variacion en el numero de copias patogenica puede aparecer de novo o ser heredada de uno de los progenitores. La presencia de trastornos psiquiatricos se ha descrito en muchos de los casos publicados, pero se desconoce su prevalencia exacta. Objetivo. Exponer la variabilidad fenotipica de los individuos que presentan una microdelecion 1q21.1. Casos clinicos. Se incluyen cuatro individuos portadores de una delecion de 1,74 Mb en 1q21.1, todos miembros de la misma familia. El estudio genetico del caso indice se llevo a cabo mediante array de hibridacion genomica comparada, y el del resto de familiares mediante hibridacion in situ fluorescente, con una sonda especifica para la region delecionada. Los individuos presentan un fenotipo heterogeneo, y es comun a todos ellos la presencia de alteraciones psiquiatricas o del comportamiento, con un claro predominio de la presencia de trastornos relacionados con las dificultades para el control de impulsos en sus diferentes subtipos. Conclusiones. El sindrome de microdelecion 1q21.1 es fenotipicamente heterogeneo, incluso entre los miembros de una misma familia. Destaca la presencia de alteraciones psiquiatricas o del comportamiento como rasgo comun en todos los pacientes que presentamos. Existen formas paucisintomaticas en las que el individuo portador de la delecion presenta exclusivamente alteraciones psiquiatricas.

Encefalopatía epiléptica del lactante: lo prioritario es un buen estudio genético / Infantile epileptic encephalopathy: a good genetic study should be a priority

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Chromosomal anomalies in patients with short stature.

BACKGROUND: The incidence of chromosomal anomalies in patients with short stature (SS) was studied in order to determine the value of routine karyotyping in this population. METHODS: This study was a retrospective evaluation of 972 patients (719 females and 253 males) with SS. Chromosomal analysis was performed on cultured peripheral lymphocytes. RESULTS: The incidence of chromosome aberrations in males was 2.77% (7/253) and in females 9.8% (71/719). Several groups were made according to clinical features and familial antecedents of SS. We observed different incidence rates of chromosomal anomalies among groups of patients, mainly in females. The incidence in the group without familial antecedents was 18.89%, however, in females with familial antecedents it was 4.45%. In females with isolated SS we detected karyotype anomalies in the 3.98%, while in patients with phenotypic features, amenorrhoea and SS the incidence was 77.78%. In females the most frequent anomaly was Turner syndrome, present in 55 patients (77.46%). CONCLUSION: Karyotype analysis is recommended for all girls with unexplained SS and associated abnormalities. In females with isolated SS a cost-benefit analysis must be done in each case.

Variabilidad del fenotipo del síndrome de microdeleción 1q21.1 dentro de una misma familia: importancia de la detección de trastornos neuropsiquiátricos para el diagnóstico de síndromes genéticos / Phenotypic variability of the 1q21.1 microdeletion syndrome in members of the same family: relevance of detection of neuropsychiatric disorders for diagnosis of genetic syndromes

Introducción. El síndrome de microdeleción 1q21.1 está causado por una deleción recurrente de aproximadamente 800 kb que incluye al menos siete genes y se asocia a un fenotipo variable. Esta variación en el número de copias patogénica puede aparecer de novo o ser heredada de uno de los progenitores. La presencia de trastornos psiquiátricos se ha descrito en muchos de los casos publicados, pero se desconoce su prevalencia exacta. Objetivo. Exponer la variabilidad fenotípica de los individuos que presentan una microdeleción 1q21.1. Casos clínicos. Se incluyen cuatro individuos portadores de una deleción de 1,74 Mb en 1q21.1, todos miembros de la misma familia. El estudio genético del caso índice se llevó a cabo mediante array de hibridación genómica comparada, y el del resto de familiares mediante hibridación in situ fluorescente, con una sonda específica para la región delecionada. Los individuos presentan un fenotipo heterogéneo, y es común a todos ellos la presencia de alteraciones psiquiátricas o del comportamiento, con un claro predominio de la presencia de trastornos relacionados con las dificultades para el control de impulsos en sus diferentes subtipos. Conclusiones. El síndrome de microdeleción 1q21.1 es fenotípicamente heterogéneo, incluso entre los miembros de una misma familia. Destaca la presencia de alteraciones psiquiátricas o del comportamiento como rasgo común en todos los pacientes que presentamos. Existen formas paucisintomáticas en las que el individuo portador de la deleción presenta exclusivamente alteraciones psiquiátricas (AU)

Introduction. 1q21.1 microdeletion syndrome is a caused by a recurrent deletion of the 1q21.1 copy-number variant, which spans 800 kb and includes at least seven genes. It is associated with a variable phenotype. Neuropsychiatric abnormalities have been previously described in many of the previously reported cases, but its true prevalence is unknown. Aim. To illustrate the phenotypic variability in 1q21.1 microdeletion syndrome. Case reports. Four individuals of the same kindred harboring a 1.74-Mb deletion within 1q21.1 are included. In our patients a heterogeneous phenotype is recognized. Neuropsychiatric disorders or more specifically impulse control disorders were common to all the four cases that we present. Conclusions. 1q21.1 microdeletion syndrome is phenotypically heterogeneous even among members of the same family. Behavioral or neuropsychiatric abnormalities are frequent. Paucisymptomatic forms with individuals presenting exclusively psychiatric disorders have been identified (AU)

Chromosomal anomalies in cryptorchidism and hypospadias.

PURPOSE: We studied the incidence of chromosomal anomalies in patients with cryptorchidism and hypospadias to determine the value of routine karyotyping in this population. MATERIALS AND METHODS: Blood samples from 984 patients with cryptorchidism and/or hypospadias were studied for chromosome analysis. RESULTS: Chromosomal anomalies were detected in 27 of the 916 patients (2.94%) with cryptorchidism and in 7 of the 100 (7%) with hypospadias. There were chromosomal aberrations in 13 of the 706 patients (1.84%) with isolated cryptorchidism (no additional congenital abnormalities) and in 14 of the 210 (6.67%) with cryptorchidism with associated anomalies. We identified normal karyotypes in 26 patients with isolated hypospadias, although 7 of the 74 (9.46%) with hypospadias and additional abnormalities had chromosomal aberrations. CONCLUSIONS: It is important to perform karyotyping in these patients, mainly when they show associated abnormalities other than cryptorchidism or hypospadias. However, cost-benefit analysis must be done in each case.