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BackgroundKBG syndrome is caused by haploinsufficiency of ANKRD11and is characterised by macrodontia of upper central incisors, distinctive facial features, short stature, skeletal anomalies, developmental delay, brain malformations and seizures. The central nervous system (CNS) and skeletal features remain poorly defined.MethodsCNS and/or skeletal imaging were collected from molecularly confirmed individuals with KBG syndrome through an international network. We evaluated the original imaging and compared our results with data in the literature.ResultsWe identified 53 individuals, 44 with CNS and 40 with skeletal imaging. Common CNS findings included incomplete hippocampal inversion and posterior fossa malformations; these were significantly more common than previously reported (63.4% and 65.9% vs 1.1% and 24.7%, respectively). Additional features included patulous internal auditory canal, never described before in KBG syndrome, and the recurrence of ventriculomegaly, encephalic cysts, empty sella and low-lying conus medullaris. We found no correlation between these structural anomalies and epilepsy or intellectual disability. Prevalent skeletal findings comprised abnormalities of the spine including scoliosis, coccygeal anomalies and cervical ribs. Hand X-rays revealed frequent abnormalities of carpal bone morphology and maturation, including a greater delay in ossification compared with metacarpal/phalanx bones.ConclusionThis cohort enabled us to describe the prevalence of very heterogeneous neuroradiological and skeletal anomalies in KBG syndrome. Knowledge of the spectrum of such anomalies will aid diagnostic accuracy, improve patient care and provide a reference for future research on the effects of ANKRD11variants in skeletal and brain development.

TDP2encodes a 5′-tyrosyl DNA phosphodiesterase required for the efficient repair of double-strand breaks (DSBs) induced by the abortive activity of DNA topoisomerase II (TOP2). To date, only three homozygous variants in TDP2have been reported in six patients from four unrelated pedigrees with spinocerebellar ataxia 23 (SCAR23). By whole-exome sequencing, we identified a novel TDP2splice-site variant (c.636 + 3_636 + 6del) in two Italian siblings (aged 40 and 45) showing progressive ataxia, intellectual disability, speech delay, refractory seizures, and various physical anomalies. The variant caused exon 5 skipping with consequent nonsense-mediated mRNA decay and defective repair of TOP2-induced DSBs, as demonstrated by the functional assays on the patients’ fibroblasts. Our findings further demonstrate the pathogenic role of TDP2biallelic loss-of-function variants in SCAR23 pathogenesis. Considering the age of our patients, the oldest reported to date, and their extensive follow-up, our study delineates in more detail the clinical phenotype related to the loss of TDP2 activity.

Research has been conducted on phylogenic chromosomes XIV and XV. Results suggest that these chromosomes have evolved due to chromosome fission which involved the emergence of new centromeres and the silencing of the ancestral centromere, and that the ancient centromere maps within 15q24-26 hotspot for neocentromere emergence.

Alazami syndrome (MIM#615071) is a rare developmental disorder caused by biallelic variants in the LARP7gene. Hallmark features include short stature, global developmental delay, and distinctive facial features. To date, 23 patients from 11 families have been reported in the literature. Here we describe a 19-year-old man who, in association with the typical features of Alazami syndrome, was diagnosed at the age of 14 years with papillary thyroid carcinoma, harboring the somatic BRAFV600E mutation. Whole exome sequencing revealed two novel LARP7variants in compound heterozygosity, whereas only common variants were detected in genes associated with familial nonmedullary thyroid cancer (MIM#188550). LARP7acts as a tumor suppressor in breast and gastric cancer, and possibly, according to recent studies, in thyroid tumors. Since thyroid cancer is rare among children and adolescents, we hypothesize that the LARP7variants identified in our patient are responsible for both Alazami syndrome and tumor susceptibility. We also provide an overview of the clinical findings in all Alazami syndrome patients reported to date and discuss the possible pathogenetic mechanism that may underlie this condition, including the role of LARP7in tumor susceptibility.

EDITOR--Cryptic telomeric rearrangements are a significant cause of idiopathic mental retardation. Knight et al [1] found 7.4% of these rearrangements in children with moderate to severe mental retardation. Clinical selection [...]

IntroductionPhelan-McDermid syndrome (PMS) is caused by SHANK3haploinsufficiency. Its wide phenotypic variation is attributed partly to the type and size of 22q13 genomic lesion (deletion, unbalanced translocation, ring chromosome), partly to additional undefined factors. We investigated a child with severe global neurodevelopmental delay (NDD) compatible with her distal 22q13 deletion, complicated by bilateral perisylvian polymicrogyria (BPP) and urticarial rashes, unreported in PMS.MethodsFollowing the cytogenetic and array-comparative genomic hybridization (CGH) detection of a r(22) with SHANK3deletion and two upstream duplications, whole-genome sequencing (WGS) in blood and whole-exome sequencing (WES) in blood and saliva were performed to highlight potential chromothripsis/chromoanagenesis events and any possible BPP-associated variants, even in low-level mosaicism.ResultsWGS confirmed the deletion and highlighted inversion and displaced order of eight fragments, three of them duplicated. The microhomology-mediated insertion of partial Alu-elements at one breakpoint junction disrupted the topological associating domain joining NFAM1to the transcriptional coregulator TCF20. WES failed to detect BPP-associated variants.ConclusionsAlthough we were unable to highlight the molecular basis of BPP, our data suggest that SHANK3haploinsufficiency and TCF20misregulation, both associated with intellectual disability, contributed to the patient’s NDD, while NFAM1interruption likely caused her skin rashes, as previously reported. We provide the first example of chromoanasynthesis in a constitutional ring chromosome and reinforce the growing evidence that chromosomal rearrangements may be more complex than estimated by conventional diagnostic approaches and affect the phenotype by global alteration of the topological chromatin organisation rather than simply by deletion or duplication of dosage-sensitive genes.

16q24 deletion involving the ANKRD11 gene, ranging from 137 kb to 2 Mb, have been associated with a microdeletion syndrome characterized by variable cognitive impairment, autism spectrum disorder, facial dysmorphisms with dental anomalies, brain abnormalities essentially affecting the corpus callosum and short stature. On the other hand, patients carrying either deletions encompassing solely ANKRD11 or its loss-of-function variants were reported in association with the KBG syndrome, characterized by a very similar phenotype, including mild-to-moderate intellectual disability, short stature and macrodontia of upper incisors, with inter and intrafamilial variability. To assess whether the haploinsufficiency of ANKRD11-flanking genes, such as ZFPM1, CDH15 and ZNF778, contributed to either the severity of the neurological impairment or was associated with other clinical features, we collected 12 new cases with a 16q24.2q24.3 deletion (de novo in 11 cases), ranging from 343 kb to 2.3 Mb. In 11 of them, the deletion involved the ANKRD11 gene, whereas in 1 case only flanking genes upstream to it were deleted. By comparing the clinical and genetic features of our patients with those previously reported, we show that the severity of the neurological phenotype and the frequency of congenital heart defects characterize the deletions that, besides ANKRD11, contain ZFPM1, CDH15 and ZNF778 as well. Moreover, the presence of thrombocytopenia and astigmatism should be taken into account to distinguish between 16q24 microdeletion syndrome and KBG syndrome. The single patient not deleted for ANKRD11, whose phenotype is characterized by milder psychomotor delay, cardiac congenital malformation, thrombocytopenia and astigmatism, confirms all this data.

Meier-Gorlin syndrome (MGORS) is a rare disorder characterized by primordial dwarfism, microtia, and patellar aplasia/hypoplasia. Recessive mutations in ORC1, ORC4, ORC6, CDT1, CDC6, and CDC45, encoding members of the pre-replication (pre-RC) and pre-initiation (pre-IC) complexes, and heterozygous mutations in GMNN, a regulator of cell-cycle progression and DNA replication, have already been associated with this condition. We performed whole-exome sequencing (WES) in a patient with a clinical diagnosis of MGORS and identified biallelic variants in MCM5. This gene encodes a subunit of the replicative helicase complex, which represents a component of the pre-RC. Both variants, a missense substitution within a conserved domain critical for the helicase activity, and a single base deletion causing a frameshift and a premature stop codon, were predicted to be detrimental for the MCM5 function. Although variants of MCM5 have never been reported in specific human diseases, defect of this gene in zebrafish causes a phenotype of growth restriction overlapping the one associated with orc1 depletion. Complementation experiments in yeast showed that the plasmid carrying the missense variant was unable to rescue the lethal phenotype caused by mcm5 deletion. Moreover cell-cycle progression was delayed in patient’s cells, as already shown for mutations in the ORC1 gene. Altogether our findings support the role of MCM5 as a novel gene involved in MGORS, further emphasizing that this condition is caused by impaired DNA replication.

Chromosome conformation capture methods have identified subchromosomal structures of higher-order chromatin interactions called topologically associated domains (TADs) that are separated from each other by boundary regions. By subdividing the genome into discrete regulatory units, TADs restrict the contacts that enhancers establish with their target genes. However, the mechanisms that underlie partitioning of the genome into TADs remain poorly understood. Here we show by chromosome conformation capture (capture Hi-C and 4C-seq methods) that genomic duplications in patient cells and genetically modified mice can result in the formation of new chromatin domains (neo-TADs) and that this process determines their molecular pathology. Duplications of non-coding DNA within the mouse Sox9 TAD (intra-TAD) that cause female to male sex reversal in humans, showed increased contact of the duplicated regions within the TAD, but no change in the overall TAD structure. In contrast, overlapping duplications that extended over the next boundary into the neighbouring TAD (inter-TAD), resulted in the formation of a new chromatin domain (neo-TAD) that was isolated from the rest of the genome. As a consequence of this insulation, inter-TAD duplications had no phenotypic effect. However, incorporation of the next flanking gene, Kcnj2, in the neo-TAD resulted in ectopic contacts of Kcnj2 with the duplicated part of the Sox9 regulatory region, consecutive misexpression of Kcnj2, and a limb malformation phenotype. Our findings provide evidence that TADs are genomic regulatory units with a high degree of internal stability that can be sculptured by structural genomic variations. This process is important for the interpretation of copy number variations, as these variations are routinely detected in diagnostic tests for genetic disease and cancer. This finding also has relevance in an evolutionary setting because copy-number differences are thought to have a crucial role in the evolution of genome complexity.

Purpose:Submicroscopic deletions of chromosome band 2p25.3 are associated with intellectual disability and/or central obesity. Although MYT1L is believed to be a critical gene responsible for intellectual disability, so far no unequivocal data have confirmed this hypothesis.Methods:In this study we evaluated a cohort of 22 patients (15 sporadic patients and two families) with a 2p25.3 aberration to further refine the clinical phenotype and to delineate the role of MYT1L in intellectual disability and obesity. In addition, myt1l spatiotemporal expression in zebrafish embryos was analyzed by quantitative polymerase chain reaction and whole-mount in situ hybridization.Results:Complete MYT1L deletion, intragenic deletion, or duplication was observed in all sporadic patients, in addition to two patients with a de novo point mutation in MYT1L. The familial cases comprise a 6-Mb deletion in a father and his three children and a 5' MYT1L overlapping duplication in a father and his two children. Expression analysis in zebrafish embryos shows specific myt1l expression in the developing brain.Conclusion:Our data strongly strengthen the hypothesis that MYT1L is the causal gene for the observed syndromal intellectual disability. Moreover, because 17 patients present with obesity/overweight, haploinsufficiency of MYT1L might predispose to weight problems with childhood onset.Genet Med 17 6, 460–466.

To investigate the molecular defect underlying a large Italian kindred with progressive adult-onset respiratory failure, proximal weakness of the upper limbs, and evidence of lower motor neuron degeneration.

Autosomal dominant dehydrated hereditary stomatocytosis (DHSt) usually presents as a compensated hemolytic anemia with macrocytosis and abnormally shaped red blood cells (RBCs). DHSt is part of a pleiotropic syndrome that may also exhibit pseudohyperkalemia and perinatal edema. We identified PIEZO1as the disease gene for pleiotropic DHSt in a large kindred by exome sequencing analysis within the previously mapped 16q23-q24 interval. In 26 affected individuals among 7 multigenerational DHSt families with the pleiotropic syndrome, 11 heterozygous PIEZO1missense mutations cosegregated with disease. PIEZO1 is expressed in the plasma membranes of RBCs and its messenger RNA, and protein levels increase during in vitro erythroid differentiation of CD34+cells. PIEZO1 is also expressed in liver and bone marrow during human and mouse development. We suggest for the first time a correlation between a PIEZO1mutation and perinatal edema. DHSt patient red cells with the R2456H mutation exhibit increased ion-channel activity. Functional studies of PIEZO1mutant R2488Q expressed in Xenopusoocytes demonstrated changes in ion-channel activity consistent with the altered cation content of DHSt patient red cells. Our findings provide direct evidence that R2456H and R2488Q mutations in PIEZO1alter mechanosensitive channel regulation, leading to increased cation transport in erythroid cells.

Early-onset epileptic encephalopathies (EOEEs) are characterised by epileptic seizures beginning in the first months of life, abnormal background EEG activity, and are associated with severe developmental delay and poor prognosis. Mutations and deletions in the STXBP1gene are associated with Ohtahara syndrome, also known as “early infantile epilepticencephalopathy”. We report an infant affected by EOEE with a 9q34.11 deletion that encompassed the genes STXBP1and SPTAN1. The infant presented with neonatal encephalopathy without epileptic seizures and an EEG pattern varying from highly discontinuous to suppression-burst. This was followed by West syndrome at 2 months with atypical hypsarrhythmia and spasms, easily controlled by therapy. Our findings suggest that molecular analysis of STXBP1should be considered for newborns affected by neonatal encephalopathy associated with a peculiar EEG pattern, even in the absence of neonatal epileptic seizures.

Increased microvessel density contributes to abnormal BM and spleen microenvironment in myelofibrosis (MF). Taking advantage of the JAK2V617F mutation as a marker of malignancy, in the present study, we investigated whether splenic endothelial cells (ECs) obtained from capillaries by laser microdissection or from fresh spleen tissue by cell culture or cell sorting harbored such mutation in patients bearing the mutation in their granulocytes and undergoing splenectomy for therapeutical reasons. To extend the analysis to the ECs of large vessels, endothelial tissue from the splenic vein was also studied. We found JAK2V617F+ ECs in 12 of 18 patients also bearing the mutation in their granulocytes. In 3 patients, the mutation was found in at least 2 different EC samples obtained by laser microdissection, cell culture, or cell sorting. The mutation was detected in the splenic vein ECs of 1 of 6 patients investigated. In conclusion, we provide evidence that some ECs from the spleen and splenic veins of patients with MF bear the JAK2V617F mutation. We suggest that splenic ECs are involved in the process of malignant transformation in MF.

OBJECTIVE To perform an extensive search for genomic rearrangements by microarray-based comparative genomic hybridization in patients with epilepsy. DESIGN Prospective cohort study. SETTING Epilepsy centers in Italy. PATIENTS Two hundred seventy-nine patients with unexplained epilepsy, 265 individuals with nonsyndromic mental retardation but no epilepsy, and 246 healthy control subjects were screened by microarray-based comparative genomic hybridization. MAIN OUTCOMES MEASURES Identification of copy number variations (CNVs) and gene enrichment. RESULTS Rare CNVs occurred in 26 patients (9.3%) and 16 healthy control subjects (6.5%) (P = .26). The CNVs identified in patients were larger (P = .03) and showed higher gene content (P = .02) than those in control subjects. The CNVs larger than 1 megabase (P = .002) and including more than 10 genes (P = .005) occurred more frequently in patients than in control subjects. Nine patients (34.6%) among those harboring rare CNVs showed rearrangements associated with emerging microdeletion or microduplication syndromes. Mental retardation and neuropsychiatric features were associated with rare CNVs (P = .004), whereas epilepsy type was not. The CNV rate in patients with epilepsy and mental retardation or neuropsychiatric features is not different from that observed in patients with mental retardation only. Moreover, significant enrichment of genes involved in ion transport was observed within CNVs identified in patients with epilepsy. CONCLUSIONS Patients with epilepsy show a significantly increased burden of large, rare, gene-rich CNVs, particularly when associated with mental retardation and neuropsychiatric features. The limited overlap between CNVs observed in the epilepsy group and those observed in the group with mental retardation only as well as the involvement of specific (ion channel) genes indicate a specific association between the identified CNVs and epilepsy. Screening for CNVs should be performed for diagnostic purposes preferentially in patients with epilepsy and mental retardation or neuropsychiatric features.

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and aggressive malignancy derived from precursors of plasmacytoid dendritic cells. We analyzed 21 cases with array-based comparative genomic hybridization (aCGH). Complete or partial chromosomal losses largely outnumbered the gains, with common deleted regions involving 9p21.3 (CDKN2A/CDKN2B), 13q13.1-q14.3 (RB1), 12p13.2-p13.1 (CDKN1B), 13q11-q12 (LATS2), and 7p12.2 (IKZF1) regions. CDKN2A/CDKN2B deletion was confirmed by FISH. This scenario argues for disruption of cell cycle at G1/S transition, representing a genetic landmark of BPDCN, and possibly contributing to its pathogenesis. Statistical analysis of overall survival in our series highlighted an association of poor outcome with biallelic loss of locus 9p21.3. We suggest that, in the absence of reliable parameters for predicting prognosis in BPDCN other than age, tumor stage, and/or clinical presentation, simple methods, such as FISH for CDKN2A/CDKN2B, could help to identify the most aggressive cases.

The aim of this study was to describe in detail the neurological features of nine patients carrying the recently reported microduplication at Xp11.22‐11.23. Clinical and neurological examination, brain magnetic resonance imaging (except for two patients), electroencephalography and a neuropsychological assessment specific for language disturbances were performed in nine patients with microduplication at Xp11.22‐11.23, disclosed by comparative genomic hybridisation array. Six patients were familial cases belonging to three unrelated pedigrees and three were sporadic cases. The patients had the following characteristics: mild dysmorphic facial features (except for two patients), mental retardation with moderate to severe global language deterioration, electroencephalographic epileptiform discharges during wakefulness and especially during sleep or electrical status epilepticus during slow sleep in younger cases, and negative brain magnetic resonance imaging. The main clinical features of this new microduplication syndrome were mild facial dysmorphisms, from increased electroencephalogram abnormalities during sleep to electrical status epilepticus during slow sleep, and mental retardation mainly involving language function in the absence of detectable brain lesions. In the absence of detectable brain lesions, speech delay may be associated with electrical status epilepticus during slow sleep or, alternatively, related to abnormal brain expression of a dosage‐sensitive gene contained within the duplication region.

The molecular characterization of balanced chromosomal rearrangements have always been of advantage in identifying diseasecausing genes. Here, we describe the breakpoint mapping of a de novo balanced translocation t7;12q11.22;q14.2 in a patient presenting with a failure to thrive associated with moderate mental retardation, facial anomalies, and chronic constipation. The localization of the breakpoints and the cooccurrence of Williams–Beuren syndrome and 12q14 microdeletion syndrome phenotypes suggested that the expression of some of the dosagesensitive genes of these two segmental aneuploidies were modified in cells of the proposita. However, we were unable to identify chromosomes 7 andor 12mapping genes that showed disturbed expression in the lymphoblastoids of the proposita. This case showed that positioneffect might operate in some tissues, but not in others. It also illustrates the overlap of phenotypes presented by patients with the recently described 12q14 structural rearrangements. © 2010 WileyLiss, Inc.

Two putative types of circulating endothelial progenitor cells have been recently identified in vitro: (1) endothelial colony-forming cell (ECFC) and (2) colony-forming unit–endothelial cell (CFU-EC). Only the former is now recognized to belong to endothelial lineage. We have used the ECFC and CFU-EC assays to readdress the issue of the clonal relation between endothelial progenitor cells and hematopoietic stem cells in patients with Philadelphia-positive and Philadelphia-negative chronic myeloproliferative disorders. Both ECFCs and CFU-ECs were cultured from peripheral blood mononuclear cells, and either BCR-ABL rearrangement or JAK2-V617F mutation were assessed in both types of endothelial colonies. We found that ECFCs lack the disease-specific markers, which are otherwise present in CFU-ECs, thus reinforcing the concept that the latter belongs to the hematopoietic lineage, and showing that in chronic myeloproliferative disorders the cell that gives rise to circulating ECFC has a distinct origin from the cell of the hematopoietic malignant clone.

We report on the case of a 17‐year‐old boy with clinical features compatible with Lowry–Wood syndrome: microcephaly, short stature, multiple epiphyseal dysplasia, tapetoretinal degeneration, and mental retardation. Bilateral restricted elbow extension, knock knees and hip dislocation were also present. Radiographs showed evidence of radial dislocation due to the absence of the radial heads, lateral dislocation of both patellae, multiple epiphyseal dysplasia that was more severe at the proximal femoral epiphyses, and dislocation of both hips with severe hip dysplasia. The patient developed a behavioral disorder at age 15. Conventional karyotyping was normal (46,XY). Molecular karyotyping, performed through array‐based competitive genomic hybridization, showed copy number variants that were probably benign. We suggest that multiple joint dislocations, including the patellae, may be a sign of Lowry–Wood syndrome. © 2009 Wiley‐Liss, Inc.

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We identified a duplication of 22q13.1q13.2 in a 10yearold girl and demonstrated that this duplication was the recombinant product of a maternal intrachromosomal insertion. Phenotypic characteristics included prominent forehead, small lowset ears, hypertelorism, epicanthal folds, small palpebral fissures, short philtrum, and syndactyly. MRI of the brain revealed high signal abnormalities in the periventricular white matter, a hypoplastic corpus callosum, underrotated hippocampus on the left and atrophic hippocampus on the right. Since age 5, the childs behavior has shown cyclic maniacal episodes with severely disorganized mood and behavior. Psychiatric and cognitive assessment led to a diagnosis of bipolar disorder not otherwise specified, manic episodes, attention deficit hyperactivity disorder and moderate mental retardation. ArrayCGH revealed an interstitial duplication of 6.9 Mb at chromosome 22q: dup22q13.1q13.2. FISH using BAC clones confirmed the arrayCGH results and demonstrated that the duplication was inverted. Gbanding analysis in the propositas mother revealed a banding pattern suggestive of an intrachromosomal insertion, as demonstrated by dualcolor FISH with BACs that were duplicated in the proposita and multicolorbanding MCB based on microdissection derived regionspecific libraries for chromosome 22. Our findings suggest that in both seemingly de novo deletions and duplications, the parent transmitting the imbalance should be investigated for possible balanced rearrangements. This report reinforces previous evidence that chromosome imbalances, and thus gene dosage effects, may be at the basis of some psychiatric disorders. Stringent correlations between submicroscopic imbalances, specific behavioral phenotypes and brain imaging will possibly help in dissecting complex behavioral traits. © 2008 WileyLiss, Inc.

Chromosomal abnormalities may cause autism by disrupting a gene or by providing a permissive genetic environment for mutations elsewhere in the genome to become expressed as autism. We report here on a patient with an apparently balanced de novo translocation of chromosomes 1q and 5q. He presented with minor dysmorphic features and renal malformations, mental retardation, and autism. Further characterization of the chromosomal rearrangement by FISH revealed a deletion in chromosome 1 from q23.3 to q24.2 corresponding to a region of rising interest in the research of autism susceptibility genes. The array‐CGH technique gave better resolution of the breakpoints and the size of the deletion was calculated to be 4.97 Mb. © 2007 Wiley‐Liss, Inc.

Approximately 40 patients with terminal duplication of the distal short arm of chromosome 7 have been reported, the smallest being dup(7)(p21). We report here on a patient with a smaller duplication, dup(7)(p22.1), detected on G‐banding and characterized by array‐CGH. We establish phenotype–karyotype correlations with the reported patients with other 7p duplications. © 2006 Wiley‐Liss, Inc.

Cytogenetic analysis of a young woman with gonadal dysgenesis and bilateral gonadoblastoma shared a male karyotype with a rearranged Y chromosome, interpreted as a pericentric inversion. The breakpoints, defined by fluorescent in situ hybridization (FISH), were located on the very distal short arm on band Yp11.31 and in the middle of the Yq12 long arm heterochromatic region. FISH analysis documented that the short arm breakpoint was 93 Kb distal to SRY and disrupted the CD99 gene, which was transposed to the distal portion of Yq12. The proposita's phenotype was similar to that of XY individuals with gonadal dysgenesis but without signs of Ullrich—Turner syndrome. There were no mutations in the SRY gene. Cytogenetic analysis in the proposita's father showed mosaicism of a normal Y chromosome and several different rearrangements, such as deletion of a heterochromatin portion at band Yq12.2, a fragile site at the same band, structural rearrangements between the Y‐chromosome and other autosomes, Y‐chromosome aneuploidies, and “Premature Centromere Division” (PCD) anomaly. The proposita's inverted Y chromosome appears to have originated from paternal Y chromosome instability. The patient's female phenotype could be due to SRY CpG methylation‐mediated positional effects (PEV). © 2005 Wiley‐Liss, Inc.

The microphthalmia with linear skin defects (MLS) syndrome (MIM 309801) is a severe and rare developmental disorder, which is inherited as an X‐linked dominant trait with male lethality. In the vast majority of patients, this syndrome is associated with terminal deletion of the Xp22.3 region. Thirty‐five cases have been described to date in the literature since the first description of the syndrome in the early 1990s. We now report on the clinical, cytogenetic, and molecular characterization of 11 patients, 7 of whom have not been described previously. Seven of these patients have chromosomal abnormalities of the short arm of the X‐chromosome, which were characterized and defined by fluorescence in situ hybridization (FISH) analysis. Intriguingly, one of the patients displays an interstitial Xp22.3 deletion, which to the best of our knowledge is the first reported for this condition. Finally we report on the identification and molecular characterization of four cases with clinical features of MLS but apparently normal karyotypes, verified by FISH analysis using genomic clones spanning the MLS minimal critical region, and with genome‐wide analysis using a 1 Mb resolution BAC microarray. These patients made it possible to undertake mutation screening of candidate genes and may prove critical for the identification of the gene responsible for this challenging and intriguing genetic disease. © 2005 Wiley‐Liss, Inc.

We report on a 5p− azoospermic male not showing the clinical features diagnostic for the cri‐du‐chat syndrome but for a breathy, raspy voice. The 5p deletion breakpoint, determined by fluorescent in situ hybridization (FISH) analysis with BAC clones, maps 8.5 Mb far from the short arm telomere in 5p15.31. Genotype/phenotype correlations in this subject, including his neuropsychological assessment, led us to define that the gene for the cat‐like cry and one gene responsible for mild mental retardation with speech delay map both in the distal 8.5 Mb of chromosome 5 short arm. © 2005 Wiley‐Liss, Inc.

We report a four generations family with multiple exostoses segregating with a reciprocal translocation t(8;19)(q24.11;q13.13) in 8 members of three generations. FISH investigations detected a breakage of the dosage-sensitive EXT1 gene. Although three members of the family died perinatally from unknown causes and one carrier had four spontaneous abortions, the translocation was discovered only when the cytogenetic analysis was requested in an affected male because of oligozoospermia. In fact, it is well known that infertile males may be carriers of reciprocal or Robertsonian translocations with a higher frequency than the general population. This family stresses the importance of requesting the cytogenetic analysis in all cases in which a dominant disease segregates with repeated miscarriages and/or newborn deaths of unknown cause. © 2003 Wiley-Liss, Inc.

We report on the multistep progression to the correct genetic diagnosis in an apparently new syndrome of mental retardation and multiple congenital anomalies, including hypogenitalism and polymicrogyria. We had previously reported it as an X-linked condition affecting four members (three males and one female) of a family [Zollino et al., 1992: Am J Med Genet 43:452–457]. Two of the four patients, both males, presented with a brain abnormality that was initially described as pachygyria, while the remaining two (one male and one female) did not. Our present study includes a clinical follow-up on the patients, neuroradiological reexamination of one patient, X linkage studies and X inactivation analyses, and finally molecular cytogenetics, which allowed us to establish definitely the genetic causes of the condition. After the detection of a subtle t(1;12)(q44;p13.3) balanced translocation in healthy carriers, two unbalanced segregation products were observed in different patients, resulting in 1q44qter monosomy and 12p13.3pter trisomy in patients with polymicrogyria and severe psychomotor delay, 12p13.3pter monosomy and 1q44qter trisomy in the other two patients without polymicrogyria, with less severe mental retardation and less distinctive physical anomalies. Thus, this condition is no longer to be considered X-linked, but the result of cryptic autosomal imbalance. Furthermore, this study identified an approximately 14 Mb interval in 1q44qter pathogenetically related to polymicrogyria. © 2003 Wiley-Liss, Inc.

We studied the case of a girl with a partial 9p duplication, dup(9)(p22.1 → p13.1). Molecular cytogenetics studies defined the chromosome 9 rearrangement as a direct duplication of 20 Mb from D9S1213 to D9S52. Microsatellite analysis demonstrated the presence of a double dosage of the paternal alleles and demonstrated that the duplication occurred between sister chromatids. The patient's phenotype was almost normal, with a few minor anomalies (dolichocephaly, crowded teeth, high arched palate) and normal IQ. The breakpoint's location in this patient and previously reported cases suggest that the critical region for the 9p duplication syndrome lies within a 6-Mb portion of chromosome 9p22 between markers D9S267 and D9S1213. © 2002 Wiley-Liss, Inc.

Male to female sex reversal has been described in patients with deletions of chromosome 9p, and a region critical for sex reversal has been localized to p24.3, at the tip of the chromosome (TD9). It was proposed that the sex reversal may arise by haploinsufficiency for a gene localized to the minimum deletion. The 9p24.3 genes DMRT1and DMRT2are the favorite TD9candidates to date, in virtue of their sequence similarity to doublesexand mab-3,sexual regulators in Drosophilaand Caenorhabditis elegans,respectively. The hypothesis of sex reversal by combined haploinsufficiency for the two genes was put forward to explain the lack of mutations in either gene in XY sex-reversed females. Here we describe a XY sex-reversed patient carrying a novel 9p deletion that extends over less than 700 kb of genomic DNA. This region defines the smallest interval for sex reversal found to date. DMRT1and DMRT2map outside this region. Our data do not support the hypothesis of combined haploinsufficiency for DMRT1and DMRT2.Nevertheless, DMRT1localizes very close to the deletion breakpoint and has a pattern of expression compatible with a role in sex determination. It therefore remains a candidate gene for 9p sex reversal.

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The human X chromosome is known to contain several disease genes yet to be cloned. In the course of a project aimed at the construction of a transcription map of the Xp22 region, we fully characterized a novel cDNA,Cxorf5(HGMW-approved symbol, alias71-7A), previously mapped to this region but for which no sequence information was available. We isolated and sequenced the full-length transcript, which encodes a predicted protein of unknown function containing a large number of coiled-coil domains, typically present in a variety of different molecules, from fibrous proteins to transcription factors. We showed that theCxorf5cDNA is ubiquitously expressed, undergoesalternative splicing, and escapes X inactivation. Furthermore, we precisely mapped two additionalCxorf5-related loci on the Y chromosome and on chromosome 5. By virtue of its mapping assignment to the Xp22 region,Cxorf5represents a candidate gene for at least four human diseases, namely spondyloepiphiseal dysplasia late, oral-facial-digital syndrome type 1, craniofrontonasal syndrome, and a nonsyndromic sensorineural deafness.

By screening an expressed sequence tag database, we identified a novel human gene, SLC7A4, encoding a solute carrier family 7 [cationic amino acid (CAA) CAT-4 transporter, y+system] member 4. The SLC7A4 cDNA is 2325 nt long and includes 78, 1911, and 336 nt in the 5′ noncoding, coding, and 3′-noncoding regions, respectively. SLC7A4 displays high homology with SLC7A1 and SLC7A2, two previously known CAA transporters. By chromosomalin situhybridization and YAC identification, SLC7A4 was mapped to 22q11.2, the commonly deleted region of the velocardiofacial syndrome (VCFS, Shprintzen syndrome). In a patient affected by VCFS, deletion of SLC7A4 was demonstrated by chromosomal FISH. By Northern analysis, an abundant transcript was detected in brain, testis, and placenta. Microinjection of SLC7A4 mRNA intoXenopus laevisoocytes demonstrates a significant stimulation of CAA transport.

The case of a 4-month-old male with a de novo partial trisomy for chromosome 14 involving the p13?q24 portion is reported. He presented with growth and psychomotor retardation, peculiar facies due to nose-mouth anomalies, monolateral microphtalmia, high arched palate, and anomalies of hands and feet. These symptoms are found also in the other 8 cases of partial trisomy 14 reported in the literature. This confirms a characteristic chromosomal syndrome although the breaking points on the extra chromosome 14 are not the same in the 9 cases. The clinical picture of our case calls for careful investigations of the chronology of bone age and of the immunologic situation in further cases of total and partial trisomy 14.

Ten patients with inverted duplication of 8p (inv dup 8p) were studied with cytogenetic, biochemical and molecular techniques. The duplication for the region 8p12-p22 was always associated with a deletion of the locus D8S7 (mapped in 8p23.1) as demonstrated with the probe pSW50 by both in situ hybridization and Southern blot. Restriction fragment length polymorphisms detected by probes pSW50 (1 case) and by pG2LPL35 (locus LPL) (two cases) were informative as to a maternal origin of the anomaly. The activity of glutathione reductase, whose gene maps in the duplicated region at 8p21.1, was increased in all patients. The recognizable phenotype of inv dup 8p includes neonatal hypotonia, prominent forehead, large mouth with everted lower lip, abnormally shaped large ears, brain malformations and severe mental retardation. Our findings indicate that the chromosome rearrangement is homogeneous at least for the presence of the deletion and support the hypothesis of a common mechanism of origin.

In situ hybridization of a telomeric (TTA-GGG)n sequence to metaphases from three cases of ring chromosome, involving respectively chromosomes 4, 16, and 20, showed the presence of the cognate sequences in all three rings. To investigate whether these ring chromosomes originated by telomere-telomere fusion, we determined, by in situ hybridization, whether telomere-associated sequences and/or specific distal sequences were still present in the ring chromosomes. The finding that these sequences were preserved in all the ring chromosomes strongly indicates that they originated by telomere-telomere fusion. All three subjects carrying the ring chromosomes are affected by the so-called ring syndrome, with failure to thrive, minor dysmorphic signs and no major anomalies. The r(4) patient has the ring in mosaic form with a normal cell line and has normal intelligence. The r(16) and the r(20) patients have moderate mental retardation and suffer from seizures. We conclude that the ring syndrome, even in its more severe manifestation, is caused by ring chromosome instability.

Stable dicentric chromosomes behave as monocentrics because one of the centromeres is inactive. The cause of centromere inactivation is unknown; changes in centromere chromatin conformation and loss of centromeric DNA elements have been proposed as possible mechanisms. We studied the phenomenon of inactivation in two Y centromeres, having as a control genetically identical active Y centromeres. The two cases have the following karyotypes: 45,X/46,X,i(Y)(q12) and 46,XY/ 47,XY,+t(X;Y)(p22.3;p11.3). The analysis of the behaviour of the active and inactive Y chromosome centromeres after Da-Dapi staining, CREST immunofluorescence, and in situ hybridization with centromeric probes leads us to conclude that, in the case of the isochromosome, a true deletion of centromeric chromatin is responsible for its stability, whereas in the second case, stability of the dicentric (X;Y) is the result of centromere chromatin modification.

A complex balanced three-break-point rearrangement between chromosome 2 and chromosome 7 and a balanced reciprocal translocation between chromosome 5 and chromosome 20, were found associated in a girl and in her mother and grandmother. All three of them have microcephaly, low stature, peculiar asymmetric facies and slight mental retardation. We postulate that one (or more) of the five chromosome break-points disrupted one (or more) gene, leading to the expression of the syndrome and to its segregation with the chromosome rearrangement in three generation. Our finding confirms the efficiency of balanced translocations for gene mapping, althought it has led only to the exclusion mapping of all chromosomes except 2, 5, 7 and 20.

Aicardi's syndrome, which is characterized by agenesis of the corpus callosum, specific chorioretinal abnormalities, and defects of vertebrae and ribs, is considered a probable X-linked dominant trait with male lethality. All features of this syndrome were seen in a girl with a de novo balanced X/3 translocation (46,X,t(X;3)(p22;q12)). It is hypothesized that the clinical picture is the consequence of chromosome breakage within the Aicardi locus. Then, unusual X-inactivation patterns in blood and fibroblasts of this patient can be explained by somatic selection against cells with the Aicardi phenotype.

H-Y antigen was examined in six patients exhibiting the characteristic features of Turner syndrome. Five of the patients were of the karyotype 45,X, and one was a mosaic 45,X/46,Xi(Xq). H-Y antigen was detected in all of them, however, compared to male controls, their antigen titer was reduced. Within the intermediate range between female and male controls, considerable interindividual variation was detected among the patients which could be due at least in part to biological variation. The findings permit the inference that the H-Y structural gene is not Y-linked, and support the assumptions of an X-linked gene escaping inactivation and of it controlling the expression of the H-Y structural gene. It is probable that the structural gene itself is autosomal. The results also suggest that male gonadal differentiation is dependent on a threshold level of H-Y antigen concentration.

Eight patients are reported with a de nov extra inverted duplicated chromosome 15. The abnormal chromosome was considered to be the same in all cases, but its precise delineation remained uncertain and was defined as either 15qter?15q12::15q12?15pter or 15pter?15q11::15q13?15pter. Analysis with various techniques of the satellite regions of the bisatellited chromosomes demonstrated maternal derivation in six and paternal derivation in one of the seven families. A nonsister chromatid exchange between the two homologous chromosomes 15 is considered a likely origin of the inv dup(15) in the cases with maternal derivation; in the only case of paternal derivation, however, the abnormal chromosome originated from one single chromosome 15. The clinical findings confirm that patients with inv dup(15) have mental and developmental retardation and are frequently affected by seizures, while severe physical malformations are absent.

Summary Eleven patients with the so-called Cat Eye syndrome are reported including a more detailed description of the original cases reported by Schnid and Fraccaro. All cases had, in addition to a normal karyotype, a small extra G-like chromosome which appeared to be an isochromosome for the juxtacentromeric region (pter→q11) of an acrocentric chromosome. None were mosaics. Clinical findings and further cytogenetic studies in a few cases suggest that these markers probably derive from a No. 22 chromosome.

Two 46,XX sibs, one of female, one of male gender, and both with ambiguous external genitalia and ovotestis, were H-Y positive. The mother was H-Y negative. It is assumed that the underlying mutation was transmitted by the father, resulting in an autosomal dominant mode of inheritance. The common origin and the nature of the mutation leading to XX sex reversal are discussed.

Prominent intensely fluorescent satellites on one chromosome 22 seem to have been transferred, during gametogenesis of a male carrier of a balanced 10/22 translocation, from the normal 22 to the translocated 22 in his daughter and son, both carriers of the translocation. Prenatal diagnosis was performed in the carrier daughter and in the chromosomally normal female foetus the satellites have jumped back to one normal chromosome 22. The phenomenon is probably due to exchanges between the short arms of chromosome 22 at meiotic pairing in the father and in his daughter. These observations give a warning for caution in the use of marker variants for paternity tests and prenatal diagnosis.

A deletion of the Y chromosome at the distal portion of band q11 was found in 6 men with normal male habitus but with azoospermia. Five of them were found during a survey of 1170 subfertile males while the sixth was karyotyped because of slight bone abnormalities. These findings, together with a review of the literature, suggest that on the distal portion of the nonfluorescent segment of the long arm of the Y, factors are located controlling spermatogenesis.

The human TRIP-1 (transforming growth factor-β (TGBβ)-receptor interacting protein-1) cDNA encodes a protein able to associate specifically with the type II TGFβ receptor. It is phosphorylated on serine and threonine by this receptor kinase which makes it a strong candidate as part of the TGFβ signal transduction pathway. We have isolated the genomic sequence of TRIP-1 and found that the complete coding region is organised into 11 exons ranging from 39 to 397 bp and spanning approximately 9 kb of genomic DNA. The 5′ flanking region lacks a TATA box but is GC-rich, suggesting that it is a constitutively expressed gene which is in agreement with its wide pattern of expression. Fluorescence in situ hybridisation mapped the TRIP-1 gene to chromosome 1p34.1 whereas a pseudogene is located on chromosome 7q32.