A novel microdeletion syndrome involving 5q14.3-q15: clinical and molecular cytogenetic characterization of three patients

Molecular karyotyping is being increasingly applied to delineate novel disease causing microaberrations and related syndromes in patients with mental retardation of unknown aetiology. We report on three unrelated patients with overlapping de novo interstitial microdeletions involving 5q14.3-q15. All three patients presented with severe psychomotor retardation, epilepsy or febrile seizures, muscular hypotonia and variable brain and minor anomalies. Molecular karyotyping revealed three overlapping microdeletions measuring 5.7, 3.9 and 3.6 Mb, respectively. The microdeletions were identified using single nucleotide polymorphism (SNP) arrays (Affymetrix 100K and Illumina 550K) and array comparative genomic hybridization (1 Mb Sanger array-CGH). Confirmation and segregation studies were performed using fluorescence in situ hybridization (FISH) and quantitative PCR. All three aberrations were confirmed and proven to have occurred de novo. The boundaries and sizes of the deletions in the three patients were different, but an overlapping region of around 1.6 Mb in 5q14.3 was defined. It included five genes: CETN3, {"type":"entrez-nucleotide","attrs":{"text":"AC093510.2","term_id":"17386257","term_text":"AC093510.2"}}AC093510.2, POLR3G, LYSMD3 and the proximal part of GPR98/MASS1, a known epilepsy gene. Haploinsufficiency of GPR98/MASS1 is probably responsible for the seizure phenotype in our patients. At least one other gene contained in the commonly deleted region, LYSMD3, shows a high level of central nervous expression during embryogenesis and is also, therefore, a good candidate gene for other central nervous system (CNS) symptoms, such as psychomotor retardation, brain anomalies and muscular hypotonia of the 5q14.3 microdeletion syndrome.     

Interstitial del(20)(q11.2q12) - clinical and molecular cytogenetic characterization

A 2-year-old male patient with dysmorphic facial features and multiple congenital anomalies suggestive of a chromosome syndrome is presented. The facial features consisted of a large and high forehead, mild metopic ridging, a small triangular face, depressed nasal bridge, microphthalmia (right more than the left), protruding ears, and mildly prominent anteverted nose with long and smooth philtrum. Cytogenetic analysis showed 46,XY,del(20)(q11.2q12). Parental karyotypes were normal. Molecular characterization of del(20)(q11.2q12) by high-resolution microarray comparative genomic hybridization (arrayCGH) showed an approximately 6.8 Mb deletion. To our knowledge this is the first report of a de novo interstitial del(20)(q11.2q12) characterized by arrayCGH.     

Trisomy 2q35-q37 due to insertion of 2q material into 17q25: clinical, cytogenetic, and molecular cytogenetic characterization

We present a 7-year-old boy with growth retardation, developmental and mental delay, and minor physical abnormalities. The patient had a male karyotype with duplicated material of unknown origin in the long arm of chromosome 17. The origin of the duplicated material was clarified by fluorescence in situ hybridization. Forward chromosome painting showed that the extra material originated from chromosome 2, which was inserted into 17q25. Further characterization of the aberrant chromosome 17 by microdissection and reverse chromosome painting revealed a duplication of bands 2q35 to q37.1. To our knowledge, no other individual with a duplication of this small segment has been described so far. The clinical findings of 13 cases with isolated trisomy 2q are reviewed in relation to the size of the duplicated region. Functional analysis of the duplicated 2q region suggests that critical loci for visceral and central nervous system development in distal trisomy 2q are proximal to 2q33.     

Chromosome 2q37 deletion: clinical and molecular aspects

Terminal deletions of chromosome 2 with breakpoints at or within band 2q37, ranging from visible abnormalities to cryptic, subtelomeric deletions, have been recognized with increasing frequency among children with mild-moderate mental retardation, characteristic facial appearance, and behavioral manifestations which often place them on the autism spectrum. The stereotypic facial characteristics include prominent forehead, thin, highly arched eyebrows, depressed nasal bridge, full cheeks, deficient nasal alae and prominent columella, thin upper lip, and various minor anomalies of the pinnae. Abnormal nipples, including inverted nipples, have been reported in a number of cases. CNS, ocular, cardiac, gastrointestinal, renal, and other GU anomalies have been noted in nearly one-third of patients. Of note, coarctation or hypoplasia of the aorta has been described in several affected children. Wilms tumor, renal dysplasia, and tracheomalacia have been reported only with the most proximal breakpoint at band 2q37.1 while a range of GI anomalies, pyloric stenosis, and diaphragmatic defects have been reported with breakpoints throughout the region. A subset of patients with the most distal deletion present phenotypic features which mimic Albright hereditary osteodystrophy (AHO). In addition to the AHO-like phenotype, later onset findings include seizures and cystic kidneys. Timely diagnosis of this recognizable syndrome provides a basis for genetic counseling, appropriate surveillance, and intervention, and avoids unnecessary and expensive diagnostic testing.     

Two cases with partial trisomy 9p: molecular cytogenetic characterization and clinical follow-up

This paper describes two patients with partial trisomy 9p and partial trisomy 14q due to 3:1 segregation from de novo maternal reciprocal translocations. The breakpoints are different from previously described 9;14 translocations and their 3:1 segregation products. The clinical phenotype of both cases is compatible with the partial trisomy 9p syndrome. We present the follow-up of both patients from birth up to age 7 years. Partial trisomy 9p is a frequently described chromosome abnormality. This does not appear to be related to a breakage sensitive locus on chromosome 9p, since the trisomic fragments of the published cases are heterogeneous. In the two cases described here, GTG-banded karyotyping suggested that the 9p breakpoints were similar; DNA marker analysis, however, showed them to be different. Such DNA studies will be necessary to define the genotype-phenotype relation in partial trisomy 9p syndrome.     

Detailed molecular and clinical characterization of three patients with 21q deletions

Lindstrand A, Malmgren H, Sahlén S, Schoumans J, Nordgren A, Ergander U, Holm E, Anderlid BM,Blennow E. Detailed molecular and clinical characterization of three patients with 21q deletions. We have investigated three patients with 21q deletions, two with developmental delay, dysmorphic features and internal organ malformations, and one with cognitive function within the normal range but with some deficits in gross and fine motor development. All aberrations were characterized by array‐comparative genomic hybridization (array‐CGH). In addition, extensive fluorescence in situ hybridization (FISH) mapping on metaphase chromosomes and mechanically stretched chromosomes was performed on patient 1 who had an extremely complex intrachromosomal rearrangement with 16 breakpoints, four deletions and four duplications. Patients 2 and 3 had interstitial deletions comprising 21q21.1‐21q22.11 and 21q11.2‐21q21.3, respectively. Partial deletions of 21q are rare and these patients display a highly variable phenotype depending on the size and position of the deletion. A review of the literature identified 38 cases with pure 21q deletions. Twenty‐three of these had reliable mapping data. The combined information of present and previous cases suggests that the ITSN1 gene is involved in severe mental retardation in patients with 21q deletion. In addition, a critical region of 0.56 Mb containing four genes, KCNE1, DSCR1, CLIC6 and RUNX1, is associated with severe congenital heart defects, and deletions of the most proximal 15–17 Mb of 21q is associated with mild or no cognitive impairment, but may lead to problems with balance and motor function.     

Pleomorphic liposarcoma: A clinicopathological,immunohistochemical and molecular cytogenetic study of 32 additional cases

The purpose of this study is to report the author's experience with 32 cases of pleomorphic liposarcoma to further broaden the clinicopathological spectrum. The tumours occurred equally in males and females with ages ranging from 11 to 83 years (median, 56 years). Tumour site included the extremities (17 cases), abdomen/retroperitoneum (4 cases), internal organs (5 cases), thoracic cavity/mediastinum (2 cases), orbit, neck, groin and scrotum (1 case each). The diagnostic pleomorphic lipoblasts were identified in 31 primary tumours and one recurrent tumor but varied widely in proportion between cases or different areas of the same tumor. Four tumors contained sheets or focal aggregates of lipoblasts with epithelioid morphology. The nonlipogenic component in 26 cases had an appearance of undifferentiated pleomorphic sarcoma, whereas in six cases it was consistent with intermediate to high grade myxofibrosarcoma. The pleormorphic and epithelioid lipoblasts displayed variable expression of S100 protein. There was no signal of amplified MDM2 gene in 10 cases tested by fluorescence in situ hybridization. This study further illustrates that pleomorphic liposarcoma is a distinctive entity with no relationship to either well differentiated liposarcoma or dedifferentiated liposarcoma. Albeit very rare, pleomorphic liposarcoma can occur in teenaged patients and internal organs.     

Interstitial duplications of chromosome region 15q11q13: Clinical and molecular characterization

Duplications of chromosome region 15q11q13 often occur as a supernumerary chromosome 15. Less frequently they occur as interstitial duplications [dup(15)]. We describe the clinical and molecular characteristics of three patients with de novo dup(15). The patients, two males and one female (ages 3–21 years), had nonspecific findings that included autistic behavior, hypotonia, and variable degrees of mental retardation. The extent, orientation, and parental origin of the duplications were assessed by fluorescent in situ hybridization, microsatellite analyses, and methylation status at D15S63. Two patients had large direct duplications of 15q11q13 [dir dup(15)(q11q13)] that extended through the entire Angelman syndrome/Prader-Willi syndrome (AS/PWS) chromosomal region. Their proximal and distal breaks, at D15S541 or D15S9 and between D15S12 and D15S24, respectively, were comparable to those found in the common AS/PWS deletions. This suggests that duplications and deletions may be the reciprocal product of an unequal recombination event. These two duplications were maternally derived, but the origin of the chromatids involved in the unequal crossing over in meiosis differs. In one patient, the duplication originated from two different maternal chromosomes, while in the other patient it arose from the same maternal chromosome. The third patient had a much smaller duplication that involved only D15S11 and parental origin could not be determined. There was no obvious correlation between phenotype and extent of the duplication in these patients. Am. J. Med. Genet. 79:82–89, 1998. © 1998 Wiley-Liss, Inc.     

Chromosome 6q deletions: a report of two additional cases and a review of the literature

Here we report on two additional cases of distal 6q deletions with one case showing a terminal deletion of chromosome 6 (46,XY, del(6)(pter----q26:)) and one case showing an interstitial deletion of chromosome 6 (46,XY, del(6)(pter----q23::q25----qter)). The association of retinal abnormalities in 6q deletions is supported, and the additional manifestations of skin hyperextensibility, sacral abnormality, and imperforate anus are described.     

Distal 3p deletion syndrome: detailed molecular cytogenetic and clinical characterization of three small distal deletions and review

The distal 3p deletion syndrome is characterized by developmental delay, low birth weight and growth retardation, micro- and brachycephaly, ptosis, long philtrum, micrognathia, and low set ears. We have used FISH and BACs in order to map three 3p deletions in detail at the molecular level. The deletions were 10.2-11 Mb in size and encompassed 47-51 known genes, including the VHL gene. One of the deletions was interstitial, with an intact 3p telomere. In nine previously published patients with 3p deletions, the size of the deletion was estimated using molecular or molecular cytogenetic techniques. The genotype, including genes of interest, and the phenotype of these cases are compared and discussed. The localization of the proximal breakpoint in one of our patients suggests that the previously identified critical region for heart defects may be narrowed down, now containing three candidate genes. We can also conclude that deletion of the gene ATP2B2 alone is not enough to cause hearing impairment, which is frequently found in patients with 3p deletion. This is the third reported case with an interstitial deletion of distal 3p.     

Genomic microarray analysis reveals distinct locations for the CENP-A binding domains in three human chromosome 13q32 neocentromeres

Human neocentromeres are fully functional centromeres that provide mitotic stability to rearranged chromosomes that have separated from endogenous centromeres. A disproportionate number of neocentromeres has been observed in certain regions such as chromosome 3q (n=6), 15q (n=9) and 13q32 (n=7), suggesting that these regions contain DNA sequences with a high propensity for neocentromere formation. Therefore, we have addressed the role of primary DNA sequence in neocentromere formation by asking whether multiple independent neocentromeres that were cytologically localized to chromosome 13q32 are in fact localized to the same underlying genomic DNA. Analysis of four independent 13q32 neocentromeres using simultaneous FISH with ordered YAC probes and immunofluorescence with antibodies to CENP-C have localized three neocentromeres to a distal approximately 7 Mb domain in chromosome 13q32, and one to an overlapping proximal domain of approximately 7 Mb. DNA was obtained from three of these neocentromeres by CENP-A chromatin immunoprecipitation (ChIP) and used to screen ordered BACs using both a slot-blotted BAC pool approach and a genomic microarray that contiguously spans 13q31.3-13q33.1. The CENP-A binding domains from each of these neocentromeres was identified to distinct genomic locations of approximately 130, 215 and 275 kb within an approximately 6.5 Mb region. Thus, the lack of coincidence of these neocentromeres to the same underlying DNA sequence refutes the idea of a DNA sequence based neocentromere 'hotspot' in 13q32 and further supports the sequence-independent epigenetic formation of human neocentromeres. The screening of genomic microarrays with ChIP DNA provides a powerful method to identify mammalian DNA sequences associated with particular functional chromatin states.     

Chromosome rearrangements at 12q13 in two cases of chondrosarcomas.

We analyzed the karyotypes of two moderately differentiated (grade 2) chondrosarcomas. Case 1 had a reciprocal translocation between chromosomes 6 and 12, t(6;12)(q25;q13) in most of the cells analyzed, as well as trisomies of chromosomes 7, 8, 11, 17, 19, and 21 and tetrasomy of chromosome 19. A reciprocal translocation involving chromosomes 12 and 19, t(12;19)(q13;q13), was noted as a highly clonal abnormality in the other case. Some cells had t(12;19) as the sole chromosome abnormality. Thus, chromosome rearrangements involving the long arm of chromosome 12 at the same region (q13) were commonly identified in the two tumors. These findings suggest that the rearrangements at 12q13 are nonrandom acquired changes that characterize a subgroup of chondrosarcomas.     

De novo 13q partial duplication identified by cytogenetic, biochemical and molecular approaches

A 3.5-month-old female infant manifesting dysmorphic facies, developmental delay and failure to thrive was referred for cytogenetic evaluation. Peripheral lymphocytes revealed three chromosomally distinct cell lines: 46,XX/46,XX,10p+/47,XX,10p+,+mar. Dermal fibroblasts revealed only the 46,XX,10p+cell line. High resolution G-, R-, and Q-banding suggested that the extra chromosomal material (10p+) represented a duplication of the segment 13q14----13qter. Parental karyotypes were normal. As absolute identification of de novo chromosomal abnormalities, based solely on cytogenetic studies, is sometimes difficult, both biochemical and molecular approaches were undertaken to elucidate this abnormality in more detail. Dosage effects were examined using esterase D (localized to 13q14.1) and the DNA probes p1E8 and p9A7 (localized to 13q22 and 13q31/32, respectively). These studies suggested the presence of only 2 copies of esterase D, but 3 copies of both DNA probes, allowing identification of the breakpoint at 13q14.2.     

15q13q14 deletions: phenotypic characterization and molecular delineation by comparative genomic hybridization

We report on a detailed phenotypic characterization of two patients with novel de novo deletions involving 15q13q14, a chromosomal region immediately distal to the Prader-Willi/Angelman syndrome critical interval. Both cases were detected by the clinical array-based comparative genomic hybridization (array-CGH) and were precisely delineated through the high-density Agilent 244 K oligonucleotide array. The comparison of our patients with previously reported deletion cases involving the 15q13q14 region demonstrated a recurrent pattern of developmental anomalies including mild dysmorphic features, cleft palate/bifid uvula, congenital heart defects (PFO or ASD), developmental delay, and learning disabilities. The potential role of the genes within the deleted region in the pathogenesis of these various phenotypic abnormalities is discussed.     

Chromosome 11q13 and atopic asthma

Asthma is a complex syndrome in which bronchial inflammation and smooth muscle hyperactivity lead to labile airflow obstruction. The commonest form of asthma is that due to atopy, which is an immune disorder where production of IgE to inhaled antigens leads to bronchial mucosal inflammation. The ultimate origins of asthma are interactive environmental and genetic factors. The genetics is acknowledged to be heterogeneous, and one chromosomal region of interest and controversy has been 11q13. To clarify the nature of the chromosome 11q13 effect in atopy and asthma, we conducted a genetic association study in subjects with marked atopic asthma and matched controls, which incorporated the study of 13 genetic variants over a distance of 10-12 cM and which took account of detailed immune and clinical phenotyping. Association with high IgE levels was limited to the interval flanked by D11S1335 and CD20 in a 0.8-Mb interval and was greatest for variants of Fc epsilonRIbeta and HTm4; these variants also associated with asthma (recurrent wheeze with labile airflow obstruction and need for regular inhaler treatment). At the more telomeric marker, D11S480, variants associated with asthma, but not with high IgE levels. The data might support the possibility of multiple loci relevant to atopic asthma on chromosome 11q13.     

Partial trisomy 12q: clinical and cytogenetic observations

High resolution chromosome banding showed a male infant with profound mental retardation, hypertonia and multiple congenital anomalies to have the karyotype 46,XY,-der (2),t(2;12)(q37.3;q24.13)pat. Most of the clinical findings were compatible with those of the previously described cases with partial trisomy 12q. Some of the clinical features seem to disappear with increasing age.     

Scapuloiliac dysostosis (Kosenow syndrome, pelvis-shoulder dysplasia) spectrum: three additional cases

We report on 3 patients (2 sibs and an unrelated adult woman) with scapuloiliac dysostosis (Kosenow syndrome, Pelvis-Shoulder Dysplasia) each of whom has additional abnormalities not previously reported in the literature. The clinical spectrum of this entity is discussed along with possible inheritance patterns.     

Ring Y chromosome: cytogenetic and molecular characterization

A female patient with Turner syndrome and the karyotype mos45,X/46,X,r(Y)/46,XY is described. Physical mapping of the ring chromosome by Y-specific single-copy and moderately repeated DNA sequences as molecular probes showed that, in addition to the heterochromatic part of Yq, a considerable portion of the Yp has also been lost in the course of the rearrangement. Thus, molecular findings provide independent support that this structurally abnormal sex chromosome is a ring Y and agree with the generally accepted model of ring formation requiring breaks in both chromosome arms. Clinical consequences of Y chromosome mosaicism in patients with Turner syndrome are discussed.