Deep-intronic variants in CNGB3 cause achromatopsia by pseudoexon activation.

Our comprehensive cohort of 1100 unrelated achromatopsia (ACHM) patients comprises a considerable number of cases (~5%) harboring only a single pathogenic variant in the major ACHM gene CNGB3. We sequenced the entire CNGB3 locus in 33 of these patients to find a second variant which eventually explained the patients' phenotype. Forty-seven intronic CNGB3 variants were identified in 28 subjects after a filtering step based on frequency and the exclusion of variants found in cis with pathogenic alleles. In a second step, in silico prediction tools were used to filter out those variants with little odds of being deleterious. This left three variants that were analyzed using heterologous splicing assays. Variant c.1663-1205G>A, found in 14 subjects, and variant c.1663-2137C>T, found in two subjects, were indeed shown to exert a splicing defect by causing pseudoexon insertion into the transcript. Subsequent screening of further unsolved CNGB3 subjects identified four additional cases harboring the c.1663-1205G>A variant which makes it the eighth most frequent CNGB3 variant in our cohort. Compound heterozygosity could be validated in ten cases. Our study demonstrates that whole gene sequencing can be a powerful approach to identify the second pathogenic allele in patients apparently harboring only one disease-causing variant.

A Female Patient with Xq28 Microduplication Presenting with Myotubular Myopathy, Confirmed with a Custom-Designed X-array.

X-linked myotubular myopathy (XLMTM) is a rare inherited neuromuscular disorder associated with mutations in the MTM1 gene on the Xq28 region. We report a severely affected girl with XLMTM, caused by maternally inherited 661 kb Xq28 microduplication identified by chromosomal microarray analysis and confirmed also on DNA from muscle biopsy with a custom-designed X-chromosome-specific microarray. X-inactivation analysis revealed a skewed inactivation pattern on the proband's muscle biopsy. Muscle biopsy histopathology was indicative of increased variability in fiber diameter, marked and diffuse endomysial proliferation of adipose and connective tissues, as well as predominance of type 1 fibers.

Compound heterozygosity of a paternal submicroscopic deletion and a maternal missense mutation in POR gene: Antley-bixler syndrome phenotype in three sibling fetuses.

BACKGROUND: Antley-Bixler syndrome (ABS) is an exceptionally rare craniosynostosis syndrome that can be accompanied by disordered steroidogenesis, and is mainly caused by mutations in the POR gene, inherited in an autosomal recessive manner. Here we report the prenatal and postmortem findings of three sibling fetuses with ABS as a result of compound heterozygosity of a paternal submicroscopic deletion and a maternal missense mutation in the POR gene. METHODS: Prenatal ultrasound and postmortem examination were performed in three sibling fetuses with termination of pregnancy at 22, 23, and 17 weeks of gestation, respectively. Molecular analysis of fetus 2 and 3 included (a) bidirectional sequencing of exon 8 of the POR gene after amplification of the specific locus by polymerase chain reaction, to detect single nucleotide variants (SNVs) and (b) high resolution comparative genomic hybridization (CGH) positive single nucleotide polymorphism array CGH (aCGH) analysis to detect copy number variants (CNVs), copy neutral areas of loss of heterozygosity and uniparental disomy. RESULTS: The diagnosis of ABS was suggested by the postmortem examination findings. The combination of the POR gene molecular analysis and aCGH revealed a compound heterozygous genotype of a maternal SNV (p.A287P) and a paternal CNV (NC_000007.13:g.(?_75608488)_(75615534_?)del). CONCLUSION: To the best of our knowledge, these sibling fetuses add to the few reported cases of ABS, caused by a combination of a SNV and a CNV in the POR gene. The detailed description of the pathologic and radiographic findings of second trimester fetuses affected with ABS adds novel knowledge concerning the early ABS phenotype, in lack of previous relevant reports. Birth Defects Research (Part A) 106:536-541, 2016. © 2016 Wiley Periodicals, Inc.

Diagnostic exome sequencing to elucidate the genetic basis of likely recessive disorders in consanguineous families.

Rare, atypical, and undiagnosed autosomal-recessive disorders frequently occur in the offspring of consanguineous couples. Current routine diagnostic genetic tests fail to establish a diagnosis in many cases. We employed exome sequencing to identify the underlying molecular defects in patients with unresolved but putatively autosomal-recessive disorders in consanguineous families and postulated that the pathogenic variants would reside within homozygous regions. Fifty consanguineous families participated in the study, with a wide spectrum of clinical phenotypes suggestive of autosomal-recessive inheritance, but with no definitive molecular diagnosis. DNA samples from the patient(s), unaffected sibling(s), and the parents were genotyped with a 720K SNP array. Exome sequencing and array CGH (comparative genomic hybridization) were then performed on one affected individual per family. High-confidence pathogenic variants were found in homozygosity in known disease-causing genes in 18 families (36%) (one by array CGH and 17 by exome sequencing), accounting for the clinical phenotype in whole or in part. In the remainder of the families, no causative variant in a known pathogenic gene was identified. Our study shows that exome sequencing, in addition to being a powerful diagnostic tool, promises to rapidly expand our knowledge of rare genetic Mendelian disorders and can be used to establish more detailed causative links between mutant genotypes and clinical phenotypes.

Microduplication 3q13.2q13.31 identified in a male with dysmorphic features and multiple congenital anomalies.

Constitutional microdeletions affecting 3q13.2q13.31 are rare and attempts for genotype-phenotype correlations have only recently been made in a cohort of 28 patients. The major phenotypic features of this rare syndrome are hypotonia, developmental delay, and facial anomalies. In this study, we report on a male infant with a novel reciprocal 3.671 Mb microduplication at the genomic region 3q13.2q13.31 associated with dysmorphic features and multiple congenital anomalies. The current patient was investigated by high-resolution array comparative genomic hybridization (aCGH). This is the first report of a microduplication 3q13.2q13.31 that shares a lot of common clinical features with those carrying the microdeletion. The 3q13.2q13.31 duplicated region in our patient contains nine dosage sensitive genes, amongst them the genes ATG3, CCDC80, KIAA2018, NAA50, ZDHHC23, DRD3, ZBTB20, GAP43, LSAMP. As it is the case for many other well-described reciprocal deletion/duplication syndromes, some have very different clinical features (Williams-Beuren deletion syndrome, WBS/WBS triplication) [Somerville et al. (2005); N Engl J Med 353:1694-1701], while others share similar phenotypic features (22q11.2 microdeletion/microduplication) [Portnoi (2009); Eur J Med Genet 52:88-93]. In conclusion, we describe the main phenotypic features of a possibly novel microduplication 3q13.2q13.31 syndrome. Additionally five of the dosage-sensitive genes and BOC gene are suggested to be responsible for the main phenotypic features. Evaluation of multiple patients with the microduplication is needed for full delineation of this syndrome.

Survivin regulation by HER2 through NF-κB and c-myc in irradiated breast cancer cells.

Radiotherapy is an important treatment modality against cancer resulting in apoptosis and inhibition of cell growth. Survivin is an important cancer biomarker conferring to tumour cells increased survival potential by inhibiting apoptosis. In the present study, we investigated the implication of breast cancer cells features, as hormone receptors and p53 status, in the radio-resistance of breast cancer cells and in the regulation of survivin's expression by nuclear factor (NF)-κB and c-myc. Six breast cancer cell lines Michigan Cancer Foundation (MCF-7), MCF-7/Human Epidermal Growth Factor Receptor (HER)2, M. D. Anderson - Metastatic Breast (MDA-MB-231), SK-BR-3, BT-474 and Human Breast Lactating (HBL-100) were irradiated and cell viability as well as cell cycle distribution were evaluated by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and flow cytometry, respectively. Survivin mRNA and protein levels were evaluated by real time PCR and Western blot analysis. Survivin and HER2 gene knockdown was performed with siRNA technology and investigation of transcription factors binding to survivin and c-myc gene promoters was assessed by chromatin immunoprecipitation. Student's t-test and F-statistics were used for statistical evaluation. Our results demonstrated that only HER2(+) breast cancer cells up-regulated survivin upon irradiation, whereas HER2 knockdown in HER2(+) cells led to survivin's down-regulation. Survivin and especially HER2 knockdown abolished the observed G2/M cell cycle checkpoint and reduced the radio-resistance of HER2 overexpressing breast cancer cells. Additionally, HER2 was found to regulate survivin's expression through NF-κB and c-myc transcription factors. This study revealed the significance of HER2 in the radio-resistance of HER2(+) breast cancer cells through induction of transcription factors NF-κB and c-myc, leading to activation of survivin, a downstream target oncogene preventing apoptosis.

Knowledge and attitudes towards prenatal diagnostic procedures among pregnant women in Greece.

OBJECTIVE: To assess knowledge and attitudes towards prenatal diagnostic procedures among pregnant women living in Greece who underwent amniocentesis or chorionic villus sampling in relation to underlying demographic, lifestyle and medical history predictors. METHOD: 354 women, upon receiving the results, were interviewed in person. A structured questionnaire was answered based upon sociodemographic, educational, lifestyle and medical history variables, as well as questions pertaining to the women's knowledge, use and opinion of prenatal tests. Summary statistics and multiple logistic regression analyses were performed. RESULTS: No prior information on prenatal diagnostic procedures was reported in 29% or on prenatal screening tests in 50% of the study subjects. Women with no history of inherited diseases were about threefold more likely to have inadequate knowledge (OR = 2.72, p = 0.01) as were women of non-Greek nationality (OR = 3.27, p = 0.02) as well as those who reported being unaware of the health consequences of smoking during pregnancy (OR = 2.50, p = 0.005). By contrast, women of higher education were over twofold more likely to attain a higher level of knowledge of prenatal diagnostic procedures (OR = 0.51, p = 10(-4)) as were those reported reading the popular press (OR = 0.44, p = 10(-4)). CONCLUSION: In spite of the increased availability of prenatal diagnosis, much more is needed to be done in order to improve the efficiency of prenatal counseling, especially in immigrants and women with a low educational background.

Proliferative and chondrogenic potential of mesenchymal stromal cells from pluripotent and bone marrow cells.

INTRODUCTION: Mesenchymal stromal cells (MSCs) can be derived from a wide range of fetal and adult sources including pluripotent stem cells (PSCs). The properties of PSC-derived MSCs need to be fully characterized, in order to evaluate the feasibility of their use in clinical applications. PSC-MSC proliferation and differentiation potential in comparison with bone marrow (BM)-MSCs is still under investigation. The objective of this study was to determine the proliferative and chondrogenic capabilities of both human induced pluripotent stem cell (hiPSC-) and embryonic stem cell (hESC-) derived MSCs, by comparing them with BM-MSCs. METHODS: MSCs were derived from two hiPSC lines (hiPSC-MSCs), the well characterized Hues9 hESC line (hESC-MSCs) and BM from two healthy donors (BM-MSCs). Proliferation potential was investigated using appropriate culture conditions, with serial passaging, until cells entered into senescence. Differentiation potential to cartilage was examined after in vitro chondrogenic culture conditions. RESULTS: BM-MSCs revealed a fold expansion of 1.18x105 and 2.3x105 while the two hiPSC-MSC lines and hESC-MSC showed 5.88x10¹°, 3.49x108 and 2.88x108, respectively. Under chondrogenic conditions, all MSC lines showed a degree of chondrogenesis. However, when we examined the formed chondrocyte micromasses by histological analysis of the cartilage morphology and immunohistochemistry for the chondrocyte specific markers Sox9 and Collagen II, we observed that PSC-derived MSC lines had formed pink rather than hyaline cartilage, in contrast to BM-MSCs. CONCLUSION: In conclusion, MSCs derived from both hESCs and hiPSCs had superior proliferative capacity compared to BM-MSCs, but they were inefficient in their ability to form hyaline cartilage.

Distal del(4) (q33) syndrome: detailed clinical presentation and molecular description with array-CGH.

The 4q deletion syndrome, comprising all microscopically visible deletions (interstitial and terminal) is a well-recognized distinctive malformation entity, with an estimated incidence of 1:10,000. Here we present the clinical and molecular findings in a 3-year-old male with a de novo distal deletion of 4q33 [46,XY,del(4) (q33)]. Clinical findings of the patient include: hypertelorism, broad nasal bridge, short nose with anteverted nares, long philtrum, thin upper lip, micro-retrognathia, low-set and protruding ears, pre-auricular tag unilaterally, low posterior hairline, clinodactyly of the 5th fingers, tapering fingers, hypospadias, and severe psychomotor retardation. Soon after birth he developed severe hypotonia and feeding difficulties. Echocardiography at 15 months documented aortic supravalvular membrane resulting in mild aortic stenosis and dysplasia of the pulmonary valve. Genome-wide screening using 1 Mb resolution array-CGH and subsequent FISH analyses defined a 18.9-22.9 Mb deletion located at the beginning of 4q33 and extending to the telomere. The description of additional cases with similar distal deletions of 4q33 will allow a more precise prognosis and is therefore of great value for genetic counsellors, while detailed molecular characterization in any well clinically characterized patient is expected to track down individual candidate genes for the specific features of the syndrome.

Phenotypic expression of a spectrum of Neurofibromatosis Type 1 (NF1) mutations identified through NGS and MLPA.

Neurofibromatosis Type 1 (NF1) is caused by mutations of the NF1 gene. The aim of this study was to identify the genetic causes underlying the disease, attempt possible phenotype/genotype correlations and add to the NF1 mutation spectrum. A screening protocol based on genomic DNA was established in 168 patients, encompassing sequencing of all coding exons and adjoining introns using a custom targeted next generation sequencing protocol and subsequent confirmation of findings with Sanger sequencing. MLPA was used to detect deletions/duplications and positive findings were confirmed by RNA analysis. All novel findings were evaluated according to ACMG Standards and guidelines for the interpretation of sequence variants with the aid of in-silico bioinformatic tools and family segregation analysis. A germline variant was identified in 145 patients (86%). In total 49 known and 70 novel variants in coding and non-coding regions were identified. Seven patients carried whole or partial gene deletions. NF1 patients, present with high phenotypic variability even in cases where the same germline disease causing variant has been identified. Our findings will contribute to a better knowledge of the genetic causes and the phenotypic expression related to the disease.

Array-CGH analysis and clinical description of 2q37.3 de novo subtelomeric deletion.

We report on a 13-year-old girl with normal karyotype and a de novo cryptic terminal deletion of chromosome 2q, detected by subtelomeric FISH analysis. Further investigation with array-CGH analysis using the 1Mb resolution Spectral Chip 2600 (Spectral Genomics) confirmed the deletion and also showed a deletion of four additional clones. No other abnormalities were detected by array-CGH. FISH studies using 8 BAC-probes were performed for fine mapping of the deletion and confirmed the array results. FISH analysis showed that the deletion breakpoint lies between clones RP11-84G18 and RP11-83N2 (physical distance between clones 0.36Mb) and extends to the telomere. The size of the deletion was estimated to be about 6.4-6.7Mb. Clinical findings include: developmental delay, severe behavioural disturbances, growth-pubertal retardation, congenital conductive mild hearing loss, growth hormone deficiency, compensate hypothyroidism, dysmorphic facial features, excessive joint hypermobility, brachymetaphalangy, abnormal dermatoglyphics and a history of neonatal laryngomalacia, hypotonia and umbilical hernia. The phenotype of our patient is in keeping with those of the literature, with the exception of cardiovascular, urogenital, neurological anomalies and eczema, which were not observed. The report of the clinical and molecular presentation of similar cases will allow accurate phenotype-genotype correlation and proper genetic counseling of the family.

Genetic polymorphisms in the UGT1A1 gene and breast cancer risk in Greek women.

Uridine diphospho-glucuronosyltransferase 1 (UGT1A1) is involved in estradiol glucuronidation, which may play a central role in the etiology of breast cancer. A common insertion/deletion polymorphism in the TATAA-box of the promoter region of UGT1A1 results in decreased initiation of transcription, and has been associated with breast cancer risk in different ethnic groups. In the present study, the role of the above genetic variation at the UGT1A1 locus in breast cancer susceptibility was investigated in a homogeneous population. Our case-control study included 136 women with breast cancer and 186 healthy female controls of Greek origin. The polymorphism A(TA)nTAA in the promoter region of UGT1A1 gene was studied using the Fragment Analysis Software of an automated DNA sequencer and three genotypes (homozygous 7/7, heterozygous 6/7, and normal homozygous 6/6) were identified. No significant associations were observed between the 7/7 genotype and breast cancer risk, indicating that further studies in Caucasian women are needed to elucidate the role of UGT1A1 polymorphism in breast cancer risk.

Maternal epigenetics and fetal and neonatal growth.

PURPOSE OF REVIEW: The article provides an update on new insights of factors altering inherited maternal epigenome that ultimately affect fetal and neonatal growth. RECENT FINDINGS: A number of new publications have identified mechanisms through which maternal nutrition, environmental exposures such as stress and toxic substances altering expression of imprinted genes during pregnancy can influence fetal and neonatal phenotype and susceptibility to disease development later in life. The possible causes of metabolic syndrome by in-utero epigenetic alterations of genes involved in energy metabolism (PPARγ and PPARα), microRNAs, arginine methyltransferases, lysine demethylases, and histone deacetylaces have been elucidated. Moreover associations between methylation of key genes (NRC31, HSD11ß1/2, GFI1) involved in the hypothalamic-pituitary-adrenal axis have been identified. Alcohol exposure during pregnancy was found to alter methylation patterns of several imprinted genes (H19, SLC22A18, SLC6A3, DRD4). Finally alterations in vulnerable epigenetic marks of imprinted genes such as H19/IGF2, during early stages of embryonic development result in intrauterine growth restriction. SUMMARY: All these investigations continue to provide new insights for improved clinical management of in-utero development.

Short stature and dysmorphology associated with defects in the SHOX gene.

Since its discovery in 1997, knowledge about the SHOX gene ( Short stature HOmeoboX-containing gene) has rapidly advanced. Although originally described as causing idiopathic short stature, SHOX mutations are also responsible for growth retardation in Léri-Weill dyschondrosteosis, Langer mesomelic dysplasia and Turner syndrome. Furthermore, SHOX has a broad functional scope and leads to a variety of different morphological-skeletal stigmata associated with these syndromes. This article reviews clinical and molecular data associated SHOX gene defects. Functional ongoing studies are expected to improve our understanding of the SHOX gene as comprising part of a genetic process responsible for normal growth and bone development.

Genomic screening of ABCA4 and array CGH analysis underline the genetic variability of Greek patients with inherited retinal diseases.

BACKGROUND: Retinal dystrophies are a clinically and genetically heterogeneous group of disorders which affect more than two million people worldwide. The present study focused on the role of the ABCA4 gene in the pathogenesis of hereditary retinal dystrophies (autosomal recessive Stargardt disease, autosomal recessive cone-rod dystrophy, and autosomal recessive retinitis pigmentosa) in patients of Greek origin. MATERIALS AND METHODS: Our cohort included 26 unrelated patients and their first degree healthy relatives. The ABCA4 mutation screening involved Sanger sequencing of all exons and flanking regions. Evaluation of novel variants included sequencing of control samples, family segregation analysis and characterization by in silico prediction tools. Twenty five patients were also screened for copy number variations by array-comparative genomic hybridization. RESULTS: Excluding known disease-causing mutations and polymorphisms, two novel variants were identified in coding and non-coding regions of ABCA4. Array-CGH analysis revealed two partial deletions of USH2A and MYO3A in two patients with nonsyndromic autosomal recessive retinitis pigmentosa. CONCLUSIONS: The ABCA4 mutation spectrum in Greek patients differs from other populations. Bioinformatic tools, segregation analysis along with clinical data from the patients seemed to be crucial for the evaluation of genetic variants and particularly for the discrimination between causative and non-causative variants.

An interstitial deletion at 8q23.1-q24.12 associated with Langer-Giedion syndrome/ Trichorhinophalangeal syndrome (TRPS) type II and Cornelia de Lange syndrome 4.

BACKGROUND: There are three distinct subtypes of Trichorhinophalangeal syndrome (TRPS); TRPS type I, TRPS type II and TRPS type III. Features common to all three subtypes include sparse, slowly growing scalp hair, laterally sparse eyebrows, a bulbous tip of the nose (pear-shaped), and protruding ears. Langer-Giedion syndrome (LGS) or TRPS type II is a contiguous gene syndrome on 8q24.1, involving loss of functional copies of the TRPS1 and EXT1 genes. We report a male patient that was referred to the Department of Medical Genetics due to hypotonia and dysmorphic facial features. RESULTS: Cytogenetic and array- Comparative Genomic Hybridization (aCGH) analysis revealed that the patient was a carrier of an interstitial deletion at 8q23.1-q24.12 of 12,5 Mb. Parental karyotype indicated that the father carried an apparently balanced insertion: 46, ΧΥ, der(10)ins(10;8)(q22;q23q24). CONCLUSIONS: This is the first report of an apparently balanced insertion including chromosomes 8 and 10 contributing to the etiology of LGS/ TRPS type II. Τimely diagnosis of parental balanced chromosomal rearrangements can reduce the risk of subsequent miscarriages as well as abnormal offspring.

Erratum to: An interstitial deletion at 8q23.1-q24.12 associated with Langer-Giedion syndrome/ Trichorhinophalangeal syndrome (TRPS) type II and Cornelia de Lange syndrome 4.

[This corrects the article DOI: 10.1186/s13039-015-0169-9.].