FISH of supernumerary marker chromosomes (SMCs) identifies six diagnostically relevant intervals on chromosome 22q and a novel type of bisatellited SMC(22)

Supernumerary marker chromosomes (SMCs) are frequently found at pre- and postnatal cytogenetic diagnosis and require identification. A disproportionally large subset of SMCs is derived from the human chromosome 22 and confers tri- or tetrasomy for the cat eye chromosomal region (CECR, the proximal 2 Mb of chromosome 22q) and/or other segments of 22q. Using fluorescence in situ hybridization (FISH) and 15 different DNA probes, we studied nine unrelated patients with an SMC(22) that contained the CECR. Five patients showed the small (type I) cat eye syndrome (CES) chromosome and each one had the larger (type II) CES chromosome, small ring chromosome 22, der(22)t(11;22) extrachromosome, and a novel type of bisatellited SMC(22) with breakpoints outside the low-copy repeats (LCRs22). By size and morphology, the novel bisatellited SMC(22) resembled the typical (types I and II) CES chromosomes, but it might have been associated with the chromosome 22q duplication syndrome, not CES. This SMC included a marker from band 22q12.3 and conferred only one extra copy each of the 22 centromere, CECR, and common 22q11 deletion area. There has been no previous report of a bisatellited SMC(22) predicting the chromosome 22q duplication syndrome. Accounting for the cytogenetic resemblance to CES chromosomes but different makeup and prognosis, we propose naming this an atypical (type III) CES chromosome. In this study, we found six distinct intervals on 22q to be relevant for FISH diagnostics. We propose to characterize SMCs(22) using DNA probes corresponding to these intervals.     

Molecular cytogenetic and clinical studies of 42 patients with marker chromosomes

The molecular cytogenetic characterization and clinical details of 20 patients with marker chromosomes are presented. These 20 patients, together with another 22 patients previously published, represent a cohort in which the chromosomal origin of the marker chromosomes was successfully determined in all but one case. Examination of the pooled data suggests that the satellited markers derived from chromosomes 14, 15 (when metacentric or submetacentric), those whose origin is either 13 or 21, and those small ring autosomal markers derived from both alphoid and satellite II or III pericentric hetero-chromatin of chromosomes 1, 9, 15, and 16 are all associated with a low risk of phenotypic abnormality. The markers identified as i(18p), ring chromosomes derived from various autosomes, and satellited markers derived from chromosome 22 are associated with a high risk of phenotypic abnormality. The phenotype of patients with acrocentric markers derived from chromosome 15 was equivocal, perhaps as a result of imprinting. Additional data are required to confirm these trends. The mild mental retardation and abnormal face of a patient with a small ring chromosome derived from chromosome 4 are described. Identification of patients with small rings originating from particular chromosomes may allow the recognition of new syndromes. © 1992 Wiley-Liss, Inc.     

Molecular cytogenetic and clinical studies of 42 patients with marker chromosomes.

The molecular cytogenetic characterization and clinical details of 20 patients with marker chromosomes are presented. These 20 patients, together with another 22 patients previously published, represent a cohort in which the chromosomal origin of the marker chromosomes was successfully determined in all but one case. Examination of the pooled data suggests that the satellited markers derived from chromosomes 14, 15 (when metacentric or submetacentric), those whose origin is either 13 or 21, and those small ring autosomal markers derived from both alphoid and satellite II or III pericentric heterochromatin of chromosomes 1, 9, 15, and 16 are all associated with a low risk of phenotypic abnormality. The markers identified as i(18p), ring chromosomes derived from various autosomes, and satellited markers derived from chromosome 22 are associated with a high risk of phenotypic abnormality. The phenotype of patients with acrocentric markers derived from chromosome 15 was equivocal, perhaps as a result of imprinting. Additional data are required to confirm these trends. The mild mental retardation and abnormal face of a patient with a small ring chromosome derived from chromosome 4 are described. Identification of patients with small rings originating from particular chromosomes may allow the recognition of new syndromes.     

Delineation of supernumerary marker chromosomes in 38 patients

We present cytogenetic and clinical data on 38 patients with supernumerary marker chromosomes (SMCs). SMCs were characterized using a strategy combining classical banding techniques and molecular cytogenetic studies. Cases were ascertained prenatally, postnatally, and after fetal death. In 26 patients (68%), the SMC originated entirely from acrocentric chromosomes. Among these, most patients carried a der(15). In 11 patients (29%), they were of nonacrocentric origin, including 9 autosomal and 2 gonosomal marker chromosomes. In 1 patient the SMC was of partially acrocentric origin. Patients with small derivatives of chromosome 15 [der(15)] had a normal phenotype. Those with a larger der(15) showed phenotypical abnormalities. Patients with supernumerary marker chromosomes derived from chromosomes 13 or 21, and 14 appeared to have a low risk of abnormalities. Out of this group only 1 patient who carried an additional r(21) had physical anomalies. Patients with an SMC originating from chromosome 22 showed physical abnormalities in 2 out of 6 cases. Supernumerary marker chromosomes identified as i(9p), i(12p), and der(18) were all associated with an abnormal phenotype. Two of the derivatives of chromosome 20 analyzed were correlated with a normal phenotype, while the carrier of the third one showed physical anomalies and motor retardation. Of 2 patients with an extra der(X), 1 was normal and 1 showed an abnormal phenotype. Am. J. Med. Genet. 76:351–358, 1998. © 1998 Wiley-Liss, Inc.     

The identification of small supernumerary marker chromosomes; the experiences of 15,792 fetal karyotyping from Turkey

Small supernumerary marker chromosomes (sSMCs) are often associated with developmental abnormalities and malformations are de novo in approximately 60% of the cases. Fluorescence in situ hybridization (FISH) techniques using various probes provided the possibility to analyze and characterize sSMCs, which is highly important for prenatal diagnosis and genetic counseling. We now present the establishment of a specific strategy to identify the origin and structure of the sSMCs using a combination of conventional banding and classical FISH techniques. Based on this strategy, in a series of 15,792 prenatal karyotypes, 20 cases with sSMCs (prevalence 1.26 per 1000) were diagnosed. Eighteen of these cases were completely analyzed by FISH using commercial probes and Chromoprobe Multiprobe-I System. Out of 20 sSMCs 12 were satellited (10 bisatellited and two monosatellited) (60%) and eight were non-satellited (six ring-like and two isochromosomes) (40%). sSMCs were mostly derived from chromosome 15 (10/20) (50%). Euchromatin material was found in 13 cases by various banding and FISH techniques, while in six of 20 sSMCs there was no evidence of euchromatin material. Parental karyotypes could be evaluated in 15 cases and familial inheritance was found in only three of them (20%). We conclude that the proposed strategy for the identification and characterization of sSMCs is accurate and represents a good alternative to novel FISH techniques for modestly equipped cytogenetic laboratories.     

Characterisation of a satellited non-fluorescent Y chromosome (Y[nfqs]) by FISH.

A fetus was prenatally diagnosed as having a Y(nfqs) chromosome which was inherited from the father. With the QFQ technique, the Yqh was observed to be nonfluorescent and contained cytological satellites which were attached to the terminal long arm. The satellites were positively stained by the Ag-NOR technique suggesting that the NORs were active. A battery of DNA probes was used to characterise the Y(nfqs). Hybridisation experiments using a chromosome 15 specific classical satellite DNA probe (D15Z1) and a Yq telomere DNA probe showed that the additional satellited material on Yq originated from 15p, and that the Yq terminal region had been lost. This is the first reported case in which the origin of cytological satellites on Yq has been determined by FISH, but this does not imply that all satellited Y chromosomes are derived from 15p. However, the clinical significance of this Y(nfqs) chromosome remains obscure.     

Two new cases of analphoid marker chromosomes

Supernumerary marker chromosomes (SMCs) without detectable alphoid DNA represent a rare and interesting class of rearranged marker chromosomes. These SMCs are predicted to have a neocentromere and have been referred to as neocentric marker chromosomes (NMCs). We report the molecular cytogenetic characterization of two new cases of neocentromere-containing chromosomes, one on 1q43-44 and one on 15q26. Both cases were examined using fluorescence in situ hybridization (FISH) with various alpha-satellite DNA probes, and no alphoid DNA was detected. In case 1, the NMC originated from the distal long arm of chromosome 1 by chromosomal microdissection and reverse painting. This marker lacked detectable chromosome 1q subtelomeric sequences, and therefore appeared to be a small ring chromosome. After genetic counseling with a high risk for a MCA/MR syndrome (trisomy 1q43 --> q44), the family continued the pregnancy. At age 6 months, the infant demonstrated no congenital or developmental anomalies. This is the first published example of a NMC derived from chromosome 1q. The marker may be one of the smallest, if not the smallest, human NMC reported to date. In case 2, fetal ultrasonography indicated a complex heart defect (abnormal return of lower vena cava, atrial septum malformation) and bilateral hydronephrosis. Molecular cytogenetic analysis showed an inverted duplication of the distal long arm of chromosome 15 (tetrasomy 15q24 --> qter). The pregnancy was terminated. Autopsy demonstrated polycystic left kidney and dysplastic right kidney. Case 2 represents the ninth report of a neocentromere on distal chromosome 15q, suggesting that this region may possibly especially support the formation of neocentromeres.     

Molecular cytogenetic characterization of two small chromosome 8 derived supernumerary mosaic markers

Two small supernumerary mosaic marker chromosomes (SMC) were identified by conventional cytogenetics, one prenatally, the other postnatally. Fluorescence in situ hybridization (FISH) techniques, including 24-color FISH, were applied to identify both SMCs and better characterize their constitution. Patient 1: a 29 year-old man, whose wife had a spontaneous abortion, was found to have a small ring of the pericentromeric region of chromosome 8 (47,XY,+r(8)(p11q11)/46,XY). Patient 2: a 37 year-old woman had amniocentesis. The fetus was found to have a SMC; its presence was confirmed postnatally. Several FISH techniques (24-color, whole chromosome paints, centromeres, telomeres, band 8p22) led to the identification of a small analphoid marker. The marker was an inversion-duplication for part of the short arm of chromosome 8 (47,XY,+inv dup (8)(p23pter)/46,XY). The 24-color FISH allowed us to conclude that both markers originated exclusively from chromosome 8. However, the structure and content of the markers were elucidated using other molecular cytogenetic techniques, showing their complementarity.     

Prenatal identification of de novo marker chromosomes using micro-FISH approach

Chromosome microdissection combined with polymerase chain reaction (PCR) and reverse chromosome painting ('micro-FISH') is a powerful technique for the unequivocal identification of complex or subtle chromosomal aberrations. We have applied this technique to the prenatal diagnosis of three fetuses with de novo marker chromosomes. One small supernumerary satellited marker chromosome was shown to have originated from the fusion of the centromeric heterochromatin of one or both of chromosomes 14 and 22. The second marker was identified as i(9)(p10) while the third marker chromosome was shown to have been derived from the 1p13.1–1q21.3 region. At birth, the clinical outcome correlated well with that expected from the prenatal cytogenetic findings. Our study highlights the importance of the application of 'micro-FISH' to prenatal diagnosis.     

Strategies to identify supernumerary chromosomal markers in constitutional cytogenetics

Supernumerary marker chromosomes (SMCs) are defined as extrastructurally abnormal chromosomes which origin and composition cannot be determined by conventional cytogenetics. SMCs are an heterogeneous group of abnormalities concerning all chromosomes with variable structure and size and are associated with phenotypic heterogeneity. The characterisation of SMCs is of utmost importance for genetic counselling. Different molecular techniques are used to identify chromosomal material present in markers such as 24-colour FISH (MFISH, SKY), centromere specific multicolour FISH (cenMFISH) and derivatives (acroMFISH, subcenMFISH), comparative genomic hybridisation (CGH), arrayCGH, and targeted FISH techniques (banding techniques, whole chromosome painting...). Based on the morphology of SMC with conventional cytogenetic and clinical data, we tried to set up different molecular strategies with all available techniques.     

Turner综合征患儿标记染色体的来源研究

目的 了解Turner综合征患儿标记染色体的来源，以指导遗传咨询及治疗。方法 在染色体核型分析的基础上，对32例Turner综合征患者进行回顾性分析。对3例含有标记染色体的患儿进一步用荧光原位杂交技术研究标记染色体的来源。结果 3例含有标记染色体的Turner综合征患儿中，确定1例患儿的标记染色体来源于Y染色体，含有性别决定基因；1例来源于X染色体；另外1例未能确定其来源，该标记染色体可能来源于性染色体的其他片段或其他端着丝粒染色体。结论 Turner综合征患者的标记染色体大多来源于性染色体（X染色体、Y染色体），也可能来源于其他端着丝粒染色体。有必要同时应用X染色体和Y染色体特异性探针对Turner综合征患者进行标记染色体的荧光原位杂交分析，以明确标记染色体的来源。     

Involvement of chromosomes 17 and 22 in dermatofibrosarcoma protuberans

Literature on the cytogenetics of dermatofibrosarcoma protuberans (DFSP) is limited; only I0 cases with chromosome aberrations have been reported. They are karyotypically characterized by the presence of supernumerary ring(s), either as the sole cytogenetic abnormality or together with a few additional structural or numerical changes. We report the cytogenetic and fluorescence in situ hybridization (FISH) analysis of three new DFSP, one primary and two recurrent tumors. In two cases we found a supernumerary ring as the sole change, whereas the third had two copies of a marker chromosome and monosomy of chromosome 22. Sequences of chromosomes I7 and 22 were identified by FISH in the supernumerary rings and in the markers. The fluorescence pattern suggested that additional sequences were present in the two rings, but showed that the marker chromosomes were entirely painted by chromosome 17 and 22 probes. The findings indicate that juxtaposition and/or amplification of chromosome 17 and 22 sequences could be crucial in the pathogenesis of DFSP. © 1995 Wiley-Liss, Inc.     

Pallister-Killian syndrome: tetrasomy of 12pter-->12p11.22 in a boy with an analphoid, inverted duplicated marker chromosome

Supernumerary marker chromosomes (SMCs) without detectable alphoid DNA are predicted to have a neocentromere and have been referred to as mitotically stable neocentromere marker chromosomes (NMCs). Here we report the molecular cytogenetic characterization of a new case of Pallister-Killian syndrome (PKS) in a boy with an analphoid, inverted duplicated NMC derived from 12pter-->12p11.22 in his fibroblasts by using high-resolution comparative genetic hybridization (HR-CGH), multiplex fluorescent in situ hybridization (FISH) and bacterial artificial chromosome (BAC)-FISH mapping analyses with various alpha-satellite DNA probes, subtelomere probes and BAC-DNA probes. Precise identification of SMCs and NMCs is of essential importance in genetic counseling. HR-CGH is a more informative and often a faster way of precisely identifying the origin of SMCs. This case is the third report of PKS with an NMC containing an inverted duplication of partial 12p with available clinical data. These observations may help to determine the critical region for PKS and the mechanisms leading to the origin of the NMC derived from 12pter-->12p11.22 - a region that appears to be susceptible to the formation of neocentromeres. The use of subtelomeric probe PCP12p in buccal cells appears superior to the use of the centromere probe D12Z3 for the diagnosis of the PKS.     

Marker chromosomes: cytogenetic characterization and implications for prenatal diagnosis

Satellited marker chromosomes were identified in four individuals from unrelated families; one was first encountered in cultured amniotic fluid cells obtained for prenatal diagnostic studies. We present cytogenetic characterization of these marker chromosomes and clinical findings in the individuals carrying them. Identification of a marker chromosome in amniotic fluid cell cultures presents problems in genetic counseling, as it is often difficult to determine the clinical significance of such a finding. Chromosome-banding techniques now allow the precise identification of satellited marker chromosomes originating from chromosome 15. Presence of a supernumerary bisatellited der(15) marker chromosome containing the proximal long arm of 15 has been associated with mental and developmental retardation. Application of chromosome-banding techniques was useful in characterization of the marker chromosomes and providing prenatal genetic counseling.     

Forty-two supernumerary marker chromosomes (SMCs) in 43,273 prenatal samples: chromosomal distribution, clinical findings, and UPD studies

Fluorescence in situ hybridization (FISH) analyses were performed on supernumerary marker chromosomes (SMCs) detected in 43,273 prenatal diagnoses over a period of 11 years, 1993-2003. A total of 42 pregnancies with SMC were identified, indicating a prevalence of one in 1032. A total of 15 SMCs were endowed with detectable euchromatin (prevalence, 1/2884), including six SMCs containing the cat eye critical region (CECR) on chromosome 22q11.21 (1/7212). De novo SMCs were found in 29 pregnancies (1/1492), including 14 euchromatic SMCs (48.2%). Follow-up studies were available for 24 cases. Nine pregnancies (37.5%) were terminated; two children (8.3%) were born with Pallister-Killian syndrome and cat eye syndrome (CES), respectively; 13 children (54.1%) showed apparently normal development. Familial SMCs were identified in 13 pregnancies (1/3328) from 11 unrelated women. They were all acrocentric. In all, 10 were heterochromatic and one was an extra der(22)t(11;22) chromosome. A total of 12 cases were available for follow-up. One pregnancy was terminated due to anhydramnios, spina bifida, and cystic-dysplastic kidneys; one child suffered from a der(22) syndrome; 10 children (83.3%) appeared unaffected. Studies for uniparental disomy were performed on seven pregnancies and revealed a case of maternal heterodisomy for chromosome 22. So far this is the largest FISH study of prenatally ascertained SMCs and the first study with detailed data on the prevalence. Findings illustrate the spectrum and clinical outcomes of prenatally diagnosed SMCs, and indicate a higher frequency of SMCs than generally assumed.     

Chromosomal aberrations in neuroblastoma cell lines identified by cross species color banding and chromosome painting

We have studied cytogenetic rearrangements in karyotypes of five neuroblastoma cell lines [SK-N-AS, SK-N-SH, SH-SY5Y, SK-N-MC, SMS-KCNR] by G-banding, cross species color banding (RxFISH), and fluorescence in situ hybridization (FISH) with chromosome painting probes. Each neuroblastoma cell line had unique modal karyotypic characteristics and showed a variable number of numerical and structural clonal cytogenetic aberrations. The number of rearranged chromosomes in SK-N-AS, SK-N-SH, SH-SY5Y, SK-N-MC, and SMS-KCNR was 11, 3, 7, 14 (tetraploid, 20-21), and 6, respectively. The origins of abnormal chromosomes were effectively analyzed by RxFISH and FISH with multiple chromosome painting probes. The chromosomal origin of the homogeneously staining region in SH-SY5Y was identified as coamplification of chromosome bands 2p13 and 2p24 by chromosome microdissection and FISH. The non-random rearrangements of chromosomes were determined on 1p34 approximately p36, 6q16 approximately q21, 8q24, 9q34, 11q13 approximately q23, 16q23 approximately q24, 17q21, and 22q31. These results may provide useful information for further molecular characterization of neuroblastoma.     

Molecular cytogenetic analysis of the monoblastic cell line U937. karyotype clarification by G-banding,whole chromosome painting,microdissection and reverse painting,and comparative genomic hybridization

Previous reports on the analysis of the human monoblastic cell line U937 had described several sublines containing unidentified rearrangements and marker chromosomes. In order to determine the true nature of the rearrangements, conventional banding analysis was carried out with various combinations of molecular cytogenetic techniques: comparative genomic hybridization, fluorescence in situ hybridization (FISH) with whole chromosome painting probes, and microdissection and reverse painting FISH. The origins of the marker chromosomes were identified and the composite karyotype is described.     

The application of comparative genomic hybridization as an additional tool in the chromosome analysis of acute myeloid leukemia and myelodysplastic syndromes

In acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) there are frequently complex karyotypes with multiple structurally altered chromosomes, many of which are marker chromosomes of unknown origin. The aim of this study was to apply comparative genomic hybridization (CGH) to cases of AML or MDS in transformation submitted for routine cytogenetic analysis to investigate whether this approach would yield any further information and, if possible, to predict which cases would benefit from CGH analysis. Nineteen cases with AML or MDS in transformation were analyzed. CGH revealed nine cases with gains or losses of chromosomal material. In six of these cases the chromosomal location of this material was not apparent from cytogenetic analysis especially when multiple markers were present. By using fluorescence in situ hybridization (FISH) with specific libraries for the chromosome regions that showed discordance between CGH and conventional cytogenetics, we were able to identify the chromosome location of material within the karyotype. In this group of six patients, four cases of an unbalanced translocation involving regions of chromosomes 5 and 17 were characterized. Three of these cases had additional abnormalities, including two cases with regions of amplification in which oncogenes are located (MYC, MLL) and one case with a dic(7;21)(p10;p10). In all six cases it was possible to characterize complex chromosomal aberrations such as derivative chromosomes, marker chromosomes, and ring chromosomes. This study demonstrates that CGH can detect true gain and loss of critical chromosome regions more accurately than conventional karyotyping in cases with very complex karyotypes, and can thus prove useful in predicting prognosis and pinpointing areas of the genome that require further study. Also, CGH can be a useful technique to identify the origin of marker chromosomes, and it can assist in choice of probes for confirmatory FISH, when there is no clue provided from the analysis of G-banded chromosomes.     

Characterization of an analphoid supernumerary marker chromosome derived from 15q25-->qter using high-resolution CGH and multiplex FISH analyses

Supernumerary marker chromosomes (SMCs) without detectable alphoid DNA are predicted to have a neocentromere and have been referred to as mitotically stable neocentromere marker chromosomes (NMCs). We report the molecular cytogenetic characterization of a new case with analphoid NMC derived from 15q25-->qter using high-resolution comparative genomic hybridization (HR-CGH) and multiplex fluorescence in situ hybridization analyses with various alpha-satellite DNA probes, all-human-centromere probe (AHC), whole chromosome painting probes, and a subtelomere probe. The propositus is a dysmorphic infant who, at age 3 months, showed accelerated growth, partial deafness, and a phenotype similar to that of the eight previously reported cases of distal 15q tetrasomy. Chromosome studies showed that he had a de novo extra SMC in 80% of cells examined. HR-CGH revealed rev ish enh(15)(q25qter). Molecular cytogenetic analysis and molecular DNA polymorphism study demonstrated that this extra SMC is an NMC containing an inverted duplication of the distal long arm of chromosome 15 (tetrasomy 15q25-->qter) which originated paternally, i.e. ish der(15)(qte-->q25::q25[neocen]-->qter)(AHC-, CEP15-, WCP15+, PCP15q++). This case further elucidates the phenotype related to tetrasomy of this specific chromosome segment and represents a new report of a neocentromere on distal chromosome 15q suggesting that this region appears to be susceptible to the formation of neocentromeres.     

FISH approach to determine cat eye syndrome chromosome breakpoints of a patient with cat eye syndrome type II

We report a 19-year-old man with craniofacial dysmorphic features, anorectal malformations, eye colobomas, orthopaedic anomalies, and mild neurodevelopmental delay. Cat eye syndrome (CES) was suspected, and confirmed by cytogenetic analysis which showed the presence of a supernumerary bisatellited chromosome, identified by fluorescence in situ hybridization (FISH) as invdup(22). The marker was further analyzed with six BAC clones located at the 22q11.1 and 22q11.2 regions; this analysis allowed correct assignment at low copy repeat 4 on chromosome 22 (LCR22-4) of the two breakpoints, confirming the presence of a CES chromosome type II. The patient's phenotype is considered in the light of the cytogenetic, and FISH investigations results and other patients reported in literature. Molecular definition of the breakpoints at the LCR22-4 copy confirms the role of different chromosome 22-specific LCRs in CES chromosomes generation, as well as in other chromosome 22 germ line rearrangements. Our report confirms that, unlike other conditions, i.e. the invdup(15) bisatellited dicentric marker, the CES phenotype does not appear to correlate with the size of the marker chromosome. Additional cases are necessary to be able to draw more specific genotype-phenotype correlations and to determine the outcome of patients with CES, especially when this rare condition is diagnosed in prenatal age.