A study of ten small supernumerary (marker) chromosomes identified by fluorescence in situ hybridization (FISH)

Small supernumerary marker chromosomes derived from human chromosome 11

Introduction: With only 39 reported cases in the literature, carriers of a small supernumerary marker chromosome (sSMC) derived from chromosome 11 represent an extremely rare cytogenomic condition. Methods: Herein, we present a review of reported sSMC(11), add 18 previously unpublished cases, and closely review eight cases classified as 'centromere-near partial trisomy 11' and a further four suited cases from DECIPHER. Results and discussion: Based on these data, we deduced the borders of the pericentric regions associated with clinical symptoms into a range of 2.63 and 0.96 Mb for chromosome 11 short (p) and long (q) arms, respectively. In addition, the minimal pericentric region of chromosome 11 without triplo-sensitive genes was narrowed to positions 47.68 and 60.52 Mb (GRCh37). Furthermore, there are apparent differences in the presentation of signs and symptoms in carriers of larger sSMCs derived from chromosome 11 when the partial trisomy is derived from different chromosome arms. However, the number of informative sSMC(11) cases remains low, with overlapping presentation between p- and q-arm-imbalances. In addition, uniparental disomy (UPD) of 'normal' chromosome 11 needs to be considered in the evaluation of sSMC(11) carriers, as imprinting may be an influencing factor, although no such cases have been reported. Comprehensively, prenatal sSMC(11) cases remain a diagnostic and prognostic challenge.

Tetrasomy 18p: case report and review of literature

Tetrasomy 18p syndrome (Online Mendelian Inheritance in Man 614290) is a very rare chromosomal disorder that is caused by the presence of isochromosome 18p, which is a supernumerary marker composed of two copies of the p arm of chromosome 18. Most tetrasomy 18p cases are de novo cases; however, familial cases have also been reported. It is characterized mainly by developmental delays, cognitive impairment, hypotonia, typical dysmorphic features, and other anomalies. Herein, we report de novo tetrasomy 18p in a 9-month-old boy with dysmorphic features, microcephaly, growth delay, hypotonia, and cerebellar and renal malformations. We compared our case with previously reported ones in the literature. Clinicians should consider tetrasomy 18p in any individual with dysmorphic features and cardiac, skeletal, and renal abnormalities. To the best of our knowledge, we report for the first time an association of this syndrome with partial agenesis of cerebellar vermis.

Molecular characterization of an analphoid supernumerary marker chromosome derived from 18q22.1➔qter in prenatal diagnosis: a case report

Background

Small supernumerary marker chromosomes (sSMC) occur in 0.072% of unselected cases of prenatal diagnoses, and their molecular cytogenetic characterization is required to establish a reliable karyotype-phenotype correlation. A small group of sSMC are C-band-negative and devoid of alpha-satellite DNA. We report the molecular cytogenetic characterization of a de novo analphoid sSMC derived from 18q22.1→qter in cultured amniocytes.

Results

We identified an analphoid sSMC in cultured amniocytes during a prenatal diagnosis performed because of advanced maternal age. GTG-banding revealed an sSMC in all metaphases. FISH experiments with a probe specific for the chromosome 18 centromere, and C-banding revealed neither alphoid sequences nor C-banding-positive satellite DNA thereby suggesting the presence of a neocentromere. To characterize the marker in greater detail, we carried out additional FISH experiments with a set of appropriate BAC clones. The pattern of the FISH signals indicated a symmetrical organization of the marker, the breakpoint likely representing the centromere of an inverted duplicated chromosome that results in tetrasomy of 18q22.1→qter. The karyotype after molecular cytogenetic investigations was interpreted as follows:

47,XY,+inv dup(18)(qter→q22.1::q22.1→neo→qter)

Conclusion

Our case is the first report, in the prenatal diagnosis setting, of a de novo analphoid marker chromosome originating from the long arm of chromosome 18, and the second report of a neocentromere formation at 18q22.1.

Partial trisomy and tetrasomy of chromosome 21 without Down Syndrome phenotype and short overview of genotype-phenotype correlation. A case report

AIMS

Trisomy of chromosome 21 is associated with Down syndrome (DS) - the commonest genetic cause of mental retardation. We report two unusual cases with partial trisomy of chromosome 21 and tetrasomy of chromosome 21 without DS phenotype. We include a short overview of the genotype-phenotype correlation studies in discussion.

METHODS

Conventional chromosomal analysis, fluorescent in situ hybridisation (FISH), quantitative fluorescent PCR (QFPCR) and Nimblegen targeted chromosome 21 array were used for deciphering the genotypes.

RESULTS

Conventional chromosomal analysis revealed one extra copy of derivative chromosome 21 in peripheral blood lymphocytes of the patients. FISH and QF PCR analyses identified duplicated loci (D21Z1, D21S1414, D21S1435) spanning from the centromere to band 21q21. Nimblegen targeted chromosome 21 array specified the range of duplication from the centromere to the band 21q21.3 (19 Mb) in the first case and the range of duplication and triplication resp from centromere to the bands 21q21.3 (15 Mb) and 21q11.2 (4 Mb) resp. in the second case. Additional material was of maternal origin in both cases. The different mechanisms led to the formation of the particular chromosomal imbalances.

CONCLUSION

These findings confirm the conclusion of nonpresence of DS when bands 21q22.2 and 21q22.3 (Down critical region) are not duplicated. The patients had nonspecific phenotypes although some of their features such as "sandal gaps", joint hyperlaxity, hypotonia and brachycephaly are present in patients with DS. Our observation can help to narrow the region responsible for DS and to map the loci accountable for minor features of DS.

Tetrasomy 18p: report of the molecular and clinical findings of 43 individuals

Thus far, the phenotype of tetrasomy 18p has been primarily delineated by published case series and reports. Findings reported in more than 25% of these cases include neonatal feeding problems, growth retardation, microcephaly, strabismus, muscle tone abnormalities, scoliosis/kyphosis, and variants on brain MRI. Developmental delays and cognitive impairment are universally present. The purpose of this study was to more fully describe tetrasomy 18p at both the genotypic and the phenotypic levels. Array CGH was performed on 43 samples from individuals with tetrasomy 18p diagnosed via routine karyotype. The medical records of 42 of these 43 individuals were reviewed. In order to gain additional phenotypic data, 31 individuals with tetrasomy 18p underwent a series of clinical evaluations at the Chromosome 18 Clinical Research Center. Results from the molecular analysis indicated that 42 of 43 samples analyzed had 4 copies of the entire p arm of chromosome 18; one individual was also trisomic for a section of proximal 18q. The results of the medical records review and clinical evaluations expand the phenotypic description of tetrasomy 18p to include neonatal jaundice and respiratory distress; recurrent otitis media; hearing loss; seizures; refractive errors; constipation and gastroesophageal reflux; cryptorchidism; heart defects; and foot anomalies. Additional findings identified in a small number of individuals include hernias, myelomeningocele, kidney defects, short stature, and failure to respond to growth hormone stimulation testing. Additionally, a profile of dysmorphic features is described. Lastly, a series of clinical evaluations to be considered for individuals with tetrasomy 18p is suggested.

Neocentromeres: new insights into centromere structure, disease development, and karyotype evolution

Since the discovery of the first human neocentromere in 1993, these spontaneous, ectopic centromeres have been shown to be an astonishing example of epigenetic change within the genome. Recent research has focused on the role of neocentromeres in evolution and speciation, as well as in disease development and the understanding of the organization and epigenetic maintenance of the centromere. Here, we review recent progress in these areas of research and the significant insights gained.

Characterisation of supernumerary chromosomal markers: a study of 13 cases

Marker chromosomes are defined as 'structurally abnormal chromosomes in which no part can be identified' (ISCN 1995). Supernumerary marker chromosomes (SMC) are 'additional markers' whose origin and composition cannot be determined by conventional cytogenetics. Molecular cytogenetic methods are necessary to identify these additional chromosomal markers. In one third, the SMCs are clinically well-defined in the literature, the remaining two thirds present a major problem for genetic counselling in prenatal diagnosis. At present, different molecular cytogenetic methods are used to determine the origin of SMCs. In this work, we studied 13 SMCs detected by RHG-banding, completed by C-banding and/or NOR-staining. 24-color FISH was used as the primary technique when the chromosomal origin was unknown. Targeted FISH procedures with specific probes (whole chromosome painting, centromeric probe, locus-specific identifier, BAC, etc.) were then performed to confirm and/or specify the chromosomal material present in the SMC. Seven SMCs were found to be associated with phenotypic abnormalities. Five derived from autosomes and two from gonosomes; these are: der(12)t(4;12), dic(15), i(18p), r(19), der(22)t(11;22), r(X), and der(Y). Two markers, r(8) and idic(15), were identified during investigations of infertile couples. Three cases seemed to be phenotypically normal. Four were discovered prenatally: r(2) and r(19) referred for elevated maternal serum markers, der(13/21) referred for advanced maternal age. The fourth SMC, der(14/22), was found during familial investigation following the identification of the same marker in an infertile son. The precise characterisation of the SMCs is of utmost importance for genetic counselling, especially in prenatal diagnosis.

Small supernumerary marker chromosomes – progress towards a genotype-phenotype correlation

Small supernumerary marker chromosomes (sSMC) are still a major problem in clinical cytogenetics as they are too small to be characterized for their chromosomal origin by traditional banding techniques, but require molecular cytogenetic techniques for their identification. Apart from the correlation of about one third of the sSMC cases with a specific clinical picture, i.e. the i(18p), der(22), i(12p) (Pallister Killian syndrome) and inv dup(22) (cat-eye) syndromes, most of the remaining sSMC have not yet been correlated with clinical syndromes. Recently, we reviewed the available >1600 sSMC cases (Liehr T, sSMC homepage: http://mti-n.mti.uni-jena.de/~huwww/MOL_ZYTO/sSMC.htm). A total of 387 cases (including the 45 new cases reported here) have been molecularly cytogenetically characterized with regard to their chromosomal origin, the presence of euchromatin, heterochromatin and satellite material. Based on analysis of these cases we present the first draft of a basic genotype-phenotype correlation for sSMC for all human chromosomes apart from the chromosomes Y, 10, 11 and 13.

An analphoid marker chromosome inv dup(15)(q26.1qter), detected during prenatal diagnosis and characterized via chromosome microdissection

A small, mosaic, C-band negative marker chromosome was detected in amniocyte cultures during prenatal diagnosis due to advanced maternal age. Following spontaneous premature labor at 29 weeks gestation, a dysmorphic infant was delivered, with flat nasal bridge, short palpebral fissures, micrognathia, high forehead, low-set ears, telecanthus and corneal dystrophy. Additional folds of skin were present behind the neck, and feet, fingers and toes were abnormally long. The child died at age five days, after two days of renal failure. The origin of the marker chromosome was subsequently identified from a cord blood sample, via chromosome microdissection. Through reverse FISH, we found the marker to be an inverted duplication of the region 15q26.1-->qter. FISH with alphoid satellite probe was negative, while whole chromosome 15 paint was positive. Both ends of the marker chromosome were positive for the telomeric TTAGGG probe. These data, plus the G-banding pattern, identified the marker as an analphoid, inverted duplicated chromosome, lacking any conventional centromere. We discuss the etiology and clinical effects of this marker chromosome, comparing it to the few reported cases of "tetrasomy 15q" syndrome. We also discuss the possible mechanisms that are likely responsible for this neocentromere formation.

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.

A series of supernumerary small ring marker autosomes identified by FISH with chromosome probe arrays and literature review excluding chromosome 15

Seven supernumerary small ring marker autosomes were studied. The pantelomere probe (Oncor) in conjunction with scoring for dicentric rings was used to confirm ring morphology. The small rings were identified mainly by FISH with chromosome probe arrays (Cytocell) containing representations from all 24 chromosomes and the rings were derived from chromosomes 7, 8 (three cases), 11, 12, and 14. The effectiveness of the array methodology in identifying markers was tested. Microsatellite DNA data showed biparental disomy (BPD) was present for the rings from chromosomes 7 and 14 thereby excluding UPD, both were de novo but the ring 14 was of paternal origin. The literature on supernumerary small ring autosomes was reviewed excluding chromosome 15. The grade and distribution of mosaicism was invoked as the major determinant of the differences in phenotype and, in addition, variation was attributed to the possibility of different contributions from each chromosome arm. There are 88 published supernumerary small ring cases in total, with phenotypic data attributable to the respective rings in 77 cases and all chromosomes being represented except chromosome 17. Of the prenatally ascertained cases, where there was adequate phenotypic data, 30% had an abnormal phenotype attributable to the ring, and there were 44% familial cases in this group. Of the postnatally ascertained small rings, 75% had an abnormal phenotype attributable to the ring and there were 13% familial cases. This higher abnormality rate is concordant with the considerable ascertainment bias of this latter group and the prenatal data are recommended for genetic counseling. Although data are small there were some differences between the rings derived from different chromosomes. Chromosomes 3 and 8 demonstrate the extremes. Of the supernumerary small r(8) cases reviewed including the three presently described, 8/11 had an abnormal phenotype attributable to the marker but of the small r(3) cases, only 1/6 had an abnormal phenotype. Two of the present r(8) were studied with the GATA4 probe at 8p23.1. The r(8) in case 2 (patient moderately retarded) was comprised mostly of an intact 8p whereas the larger r(8) in case 3 (normal phenotype) was missing 8p23.1 --> pter and had more of 8q contributing to the ring. In other supernumerary rings postnatally ascertained, there is mostly insufficient data but there is an abnormal phenotype in 8/11 cases with multiple small rings, in 5/6 cases with r(20), and in 5/10 with r(1). A novel origin for supernumerary small rings is proposed: that they may originate from incompletely digested superfluous (haploid) pronuclei. The small rings presumptively so formed may occasionally be transfected into the zygote nucleus. The high proportion ( approximately 12.5%) of cases with multiple supernumerary small rings almost always of different centromeric origin is consistent with this concept.

Prenatal diagnosis of a small supernumerary, XIST-negative, mosaic ring X chromosome identified by fluorescence in situ hybridization in an abnormal male fetus

Marker or ring X [r(X)] chromosomes of varying size are often found in patients with Turner syndrome. Patients with very small r(X) chromosomes that did not include the X-inactivation locus (XIST) have been described with a more severe phenotype. Small r(X) chromosomes are rare in males and there are only five previous reports of such cases. We report the identification of a small supernumerary X chromosome in an abnormal male fetus. Cytogenetic analysis from chorionic villus sampling was performed because of fetal nuchal translucency thickness and it showed mosaicism 46,XY/47,XY,+r(X)/48,XY,+r(X),+r(X). Fluorescence in situ hybridizations (FISH) showed the marker to be of X-chromosome origin and not to contain the XIST locus. Additional specific probes showed that the r(X) included a euchromatic region in proximal Xq. At 20 weeks gestation, a second ultrasound examination revealed cerebral abnormalities. After genetic counselling, the pregnancy was terminated. The fetus we describe is the first male with a mosaic XIST-negative r(X) chromosome identified at prenatal diagnosis. The phenotype we observed was probably the result of functional disomy of the genes in the r(X) chromosome, secondary to loss of the XIST locus.

Trisomy 17p10-p12 resulting from a supernumerary marker chromosome derived from chromosome 17: molecular analysis and delineation of the phenotype

We report a 5-year-old boy with a small de novo marker chromosome derived from the proximal short arm of chromosome 17. His clinical features include hypotonia, global developmental delay, oval face with large nose and prominent ears, and ligamentous laxity of the fingers. Magnetic resonance imaging of the brain demonstrated mildly delayed myelination. G-band chromosome analysis revealed mosaicism for a small marker chromosome in 85% of the peripheral blood cells analyzed. Fluorescence in situ hybridization and microsatellite polymorphism studies showed that the der(17) was of maternal origin and included genetic material from the 17p10-p12 region, but did not contain the PMP22 gene. One breakpoint mapped within the centromere and the second breakpoint mapped adjacent to the Charcot-Marie-Tooth disease type 1A proximal low-copy repeat (CMT1A-REP). We compare the clinical characteristics of our patient with those previously reported to have a duplication involving the proximal short arm region of chromosome 17 to further delineate the phenotype of trisomy 17pl0-p12.

Tertiary trisomy due to a reciprocal translocation of chromosomes 5 and 21 in a four-generation family

Tertiary trisomy, or double trisomy, is a rare occurrence. We present two individuals with a previously unreported tertiary trisomy for chromosomes 5p and 21q in an eight-generation pedigree. Their phenotypes are compared with other partial trisomies of either 5p or 21q from the literature. The propositus was diagnosed with trisomy 21 at 2 years of age after a karyotype study for short stature and developmental delay. His phenotype was described as atypical for Down syndrome. He presented at 9 years of age because of pervasive behavioral problems and obesity. He was brachycephalic with a flattened nasal bridge, but he lacked other characteristics of trisomy 21. Because of lack of phenotypic evidence of Down syndrome, a repeat karyotype was obtained and showed 47,XY, +der(21)t(5;21)(p15.1; q22.1), incorporating partial trisomies of both chromosomes 5 and 21. Mother had a balanced translocation, 46, XX,t(5;21)(p15.1; q22.1); 8 other relatives were examined. The translocation originated from the maternal great-grandmother, but only the propositus and his mentally retarded aunt had a similar phenotye and the derivative chromosome. Fluorescence in situ hybridization showed absence of band 21q22.2 in the derivative chromosome of the propositus and his aunt, indicating that neither had trisomy for the Down syndrome critical region. These cases represent a unique double partial trisomy of chromosome arms 5p and 21q that occurred because of 3:1 malsegregation of a reciprocal translocation. These cases further demonstrate that phenotypic discordance with cytogenetic results dictate further investigation using advanced cytogenetic hybridization.

Identification of supernumerary marker chromosomes derived from chromosomes 5, 6, 19, and 20 using FISH

A large number of cases with supernumerary marker chromosomes (SMCs) should be compared to achieve a better delineation of karyotype-phenotype correlations. Here we present four phenotypically abnormal patients with autosomal marker chromosomes analysed by fluorescence in situ hybridisation using centromeric, telomeric, and unique sequence probes, as well as forward and reverse painting. We also report the first case, to the best of our knowledge, of an SMC derived from chromosome 5. Furthermore, a marker chromosome 20 in a patient with sex differentiation abnormalities, a double mar(6) in a boy with psychomotor retardation, and the association of r(19) with dup(21q21.2q22.12) are described. Although the mar(6) was very small, the presence of euchromatin was shown, suggesting that the partial trisomy of pericentric region derived sequences is implicated in the aetiology of the abnormal phenotypes.

Ring chromosome 8 syndrome: further characterization

We describe two de novo cases of extra r(8) confirmed by fluorescent in situ hybridization (FISH). Based on these two and eight additional cases of extra r(8) confirmed by FISH, the phenotype is better documented. One of our patients had minor facial anomalies, near-normal growth, and neurological development. She had a ring in each cell analyzed. The second had minor craniofacial anomalies and growth and mental retardation. He had a small or double-sized ring in each cell. The phenotype of these 10 cases ranges from almost normal in an adult with 10% mosaicism to variable degrees of minor anomalies, growth retardation, and mental retardation overlapping the mosaic +8 syndrome.

Neocentromere at 13q32 in one of two stable markers derived from a 13q21 break

A 10-month-old girl with psychomotor retardation, microcephaly, bilateral microphthalmia, and postaxial polydactyly of the feet was karyotyped using banding techniques and (single or dual color) fluorescent in situ hybridization (FISH) with four probes: D13Z1/D21Z1, pancentromeric, pantelomeric, and a mix of 13q subtelomeric and 13/21 alphoid repeats. She was found to have a 47-chromosome karyotype in which a normal 13 was replaced by two stable markers derived from a breakpoint at 13q21.1, namely a del(13)(q21.1) and an isofragment(13) (qter-->q21.1::q21.1-->qter). The latter had a single C-negative but Cd-positive primary constriction at 13q32 which, however, was not obvious in about 12% of the cells. FISH studies showed that the small 13q- had the 13-centromere and a 13q telomere (as shown for a specific 13q subtelomeric signal) onto the broken end whereas the isofragment lacked alphoid signals but had 13q subtelomeric sequences on both ends. Parental karyotypes were normal. The patient's rearrangement represents the eighth chromosome-13-derived marker with a nonalphoid neocentromere located at 13q. All in all, such neocentromeres have been described in 29 markers derived from chromosomes 2, 3, 8-11, 13-15, 20, and Y, and plausibly result from the epigenetic activation of a latent centromere, which may even be a telomere with neocentric activity. The 13q telomere found in the del(13q) was probably captured from the homologous chromosome.

Multiplex-FISH for pre- and postnatal diagnostic applications

For >3 decades, Giemsa banding of metaphase chromosomes has been the standard karyotypic analysis for pre- and postnatal diagnostic applications. However, marker chromosomes or structural abnormalities are often encountered that cannot be deciphered by G-banding alone. Here we describe the use of multiplex-FISH (M-FISH), which allows the visualization of the 22 human autosomes and the 2 sex chromosomes, in 24 different colors. By M-FISH, the euchromatin in marker chromosomes could be readily identified. In cases of structural abnormalities, M-FISH identified translocations and insertions or demonstrated that the rearranged chromosome did not contain DNA material from another chromosome. In these cases, deleted or duplicated regions were discerned either by chromosome-specific multicolor bar codes or by comparative genomic hybridization. In addition, M-FISH was able to identify cryptic abnormalities in patients with a normal G-karyotype. In summary, M-FISH is a reliable tool for diagnostic applications, and results can be obtained in </=24 h. When M-FISH is combined with G-banding analysis, maximum cytogenetic information is provided.

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.

Molecular cytogenetic evidence for a common breakpoint in the largest inverted duplications of chromosome 15

Chromosomes from 20 patients were used to delineate the breakpoints of inverted duplications of chromosome 15 (inv dup[15]) that include the Prader-Willi syndrome/Angelman syndrome (PWS/AS) chromosomal region (15q11-q13). YAC and cosmid clones from 15q11-q14 were used for FISH analysis, to detect the presence or absence of material on each inv dup(15). We describe two types of inv dup(15): those that break between D15S12 and D15S24, near the distal boundary of the PWS/AS chromosomal region, and those that share a breakpoint immediately proximal to D15S1010. Among the latter group, no breakpoint heterogeneity could be detected with the available probes, and one YAC (810f11) showed a reduced signal on each inv dup(15), compared with that on normal chromosomes 15. The lack of breakpoint heterogeneity may be the result of a U-type exchange involving particular sequences on either homologous chromosomes or sister chromatids. Parent-of-origin studies revealed that, in all the cases analyzed, the inv dup(15) was maternal in origin.

FISH and molecular study of autosomal supernumerary marker chromosomes excluding those derived from chromosomes 15 and 22: I. Results of 26 new cases

The chromosomal origins and in some cases the molecular composition of 26 autosomal supernumerary marker chromosomes (SMC) were identified using combined fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR) techniques. Fifteen were de novo, 4 maternally and 2 paternally transmitted and in 5 cases the parental origin is not known. Eleven cases were non-mosaic and fifteen cases had SMC cell lines ranging from 8-87%. Ten cases were ascertained prenatally, nine postnatally with abnormal phenotypes, three with poor reproductive histories and four co-incidentally. Five SMC were small rings from chromosomes 3, 6 (2 cases), 20 and 21; 8 were bisatellited from chromosomes 13/21 (4 cases), 14 (3 cases) and 14/22 (1 case). The remaining 13 appeared to be minutes comprising centromeric material only from chromosomes 1, 4, 12, 13/21 (2 cases), 14 (3 cases), 16 (2 cases), 19; 5/19, and a centric fusion involving 13 or 21 and 14. Euchromatin was detected in 9 out of 18 SMC tested with paints and/or PCR, and abnormal phenotypes were most commonly observed in patients with small ring shaped SMCs containing euchromatic sequences. Uniparental paternal isodisomy (UPD) for chromosome 6 was detected in one patient but was the only example of UPD for the normal homologues in association with an autosomal SMC in an overall total of 30 cases examined.

Detection of trisomy 12 and centromeric alterations in CLL by interphase- and metaphase-FISH

We have studied trisomy 12 in chronic lymphocytic leukemia (CLL) by fluorescence in situ hybridization (FISH) with an alpha-satellite centromeric probe for chromosome 12 on both dividing and non-dividing cells. Trisomy for chromosome 12 was demonstrated in four of these patients (15.3%) using FISH on interphase cells. The percentage of trisomic cells ranged from 10% to 65% of nuclei. The hybridization signals in the trisomic and disomic nuclei were of a broadly similar size and nature. Interestingly, three of the remaining CLL patients, who exhibited disomy for chromosome 12, showed a marked difference in size of the hybridization signals in interphase nuclei. This was also demonstrated in metaphase spreads. In addition, metaphase FISH studies revealed a supernumerary marker chromosome in three out of 26 patients with CLL.

Centromere DNA dynamics: latent centromeres and neocentromere formation

Images

Mosaicism for a small supernumerary ring X chromosome in a dysmorphic, growth-retarded male: mos47,XXY/48,XXY, +r(X)

Supernumerary ring X [r(X)] chromosomes are often found in patients with Turner syndrome. The phenotypic effects of the r(X) chromosome are variable, and largely depend on the presence or absence of the X inactivation (XIST) locus. Ring(X) chromosomes in males are rare and have been previously reported in only four cases, with 47,XY, + r(X) or mos47,XY, +r(X)/46,XY karyotypes. These patients all had developmental delay and dysmorphic features. We describe a 2.5-year-old male patient with facial dysmorphia, growth retardation, microcephaly, global developmental delay, and microphallus. Cytogenetic analysis from peripheral blood lymphocytes and fibroblasts identified mosaicism for two cell lines: mos48,XXY, + r(?X)/47,XXY. Fluorescence in situ hybridization (FISH) with an X chromosome paint showed the ring chromosome to be X chromosome derived. This is the first case of an r(X) chromosome described in a 47,XXY patient. FISH analysis of the r(X) chromosome with an XIST probe showed that the XIST locus was absent. Functional disomy of genes in the r(X) chromosome most likely accounts for the abnormal phenotype in the proband.

A molecular and FISH approach to determining karyotype and phenotype correlations in six patients with supernumerary marker(22) chromosomes

In a cytogenetic, molecular, and clinical study of patients with autosomal supernumerary marker chromosomes (SMC), 6 out of 72 (8.3%) were shown by fluorescence in situ hybridisation (FISH) to be derived from chromosome 22. PCR microsatellite analysis and FISH using primers and cosmids from proximal 22q showed 3 of the 6 to contain euchromatin. The first, a de novo nonmosaic bisatellited, dicentric SMC, was acsertained in a patient with cat eye syndrome and Duane anomaly. Microsatellite analysis showed the SMC was maternal in origin with euchromatin extending to D22S427, i.e., proximal to the DiGeorge syndrome critical region (DGSCR). The second, a nonmosaic bisatellited, dicentric marker, was found in a child with severe hypotonia and developmental delay and had been inherited from the patient's phenotypically normal father. FISH showed the SMC to contain euchromatin extending into the DGSCR. The third, a de novo SMC, was ascertained antenatally and was shown to contain 22q euchromatin extending distal to the DGSCR. The 19-week terminated fetus was phenotypically normal at autopsy. Two of the three SMC(22)s not containing detectable proximal 22q euchromatin were ascertained coincidentally in phenotypically normal individuals, whereas the third, the only mosaic with a minority euploid cell line, was found in a patient with mild developmental delay. These results suggest that SMC(22)s devoid of proximal 22q euchromatin are not associated with adverse phenotypic effects whereas SMC(22)s containing euchromatin may be found in individuals with phenotypes ranging from cat eye syndrome to normal.

Rapid identification of multiple supernumerary ring chromosomes with a new FISH technique

Multiple supernumerary ring chromosomes are a rare cytogenetic finding which is poorly understood. With the introduction of FISH techniques, their chromosomal origin can now be defined clearly. The techniques described previously are complicated and time consuming. We report a new rapid technique which has been used to investigate two new cases. Multiple probes were hybridised to a single slide by means of marking the underside with a diamond pen to form a grid of squares, pipetting fixed cell suspension into the centre of each square, forming a rubber solution grid on the denatured, dehydrated slide following the lines on the underside, adding a mixture of probes into each square, and sealing the slide with a silicone rubber rim and a covering slide. The type of probe and the size, dimensions, and number of squares in the grid can be tailored to individual cases. The two new cases examined here are mosaic for three (case 1) and four (case 2) supernumerary ring chromosomes derived from different chromosomes. Normal cell lines were also present. The karyotypes were established as 47,XY,+r(4)/47,XY,+r(17)/.../48,XY,+r(17),+r(20)/ 49,XY,+r(4),+r(17),+r(20)/46,XY for case 1 and 47,XX,+r(4)/47,XX,+r(8)/47,XX,+r (10)/48,XX,+r(X),+r(4)/... /49,XX,+r(X),+r (8),+r(10)/46,XX for case 2. Our findings suggest that the ring chromosomes were formed during meiosis, perhaps involving complex rearrangements, resulting in a germ cell containing all markers, with subsequent loss of markers during cell division. Our second case also shows that the outcome is not invariably mental or physical handicap.

dup(10q) lacking alpha-satellite DNA in bone marrow cells of a patient with acute myeloid leukemia

A marker chromosome was identified in leukemic cells on an AML patient. The G-banding pattern resembled on i(10q), but its centromeric position was not clear; in some cells it had a telocentric shape, in others a metacentric or acentric shape. The origin of the marker chromosome was confirmed by FISH, using chromosome-10-specific painting. To determine the centromeric position, C-banding and alpha-satellite probes were applied in FISH, and none of them gave a positive signal. Despite the absence of the centromeric alpha-satellite sequences and the constricted feature of the centromere, the essential centromeric activity was retained in this chromosome, namely, the separation of sister chromatids in anaphase.

Mosaic tetrasomy 15q25-->qter in a newborn infant with multiple anomalies

We describe a premature boy with metopic craniosynostosis, facial anomalies, atrial-septal defect, hydronephrosis and flexion contractures of lower limbs, and mosaic tetrasomy 15q25-->qter. The extra chromosome material was present in the form of an acentric marker. A number of clinical manifestations observed in this child were also found in 3 previously reported patients who were trisomic for the same part of chromosome 15 and in 2 patients who were tetrasomic for a larger segment of 15q.

Characterization by fluorescence and electron microscopy in situ hybridization of a double Y isochromosome

A patient with mixed gonadal dysgenesis and Y isochromosomes i(Y) is described. Lymphocyte cultures from peripheral blood contained a high proportion of 45,X cells and several other cell lines with two different marker chromosomes (mars). These markers had either a monocentric (mar1) or a dicentric appearance (mar2). Following high-resolution GTG, RBG, QFQ, and CBG bandings, five cell lines were identified; 45,X/46,X,+mar1/46,X,+mar2/47,X,+mar1x2/47,X,+mar2x 2. The percentages were 66/6/26/1/1%, respectively. Chromosome banding analyses were insufficient for characterization of the markers. In situ hybridization of specific probes for the Y centromere and its short arm showed, both in fluorescence and electron microscopy (EM), two different Y rearrangements. Mar1 is an isochromosome for the short arm i(Yp) and mar2 is a dicentric which was shown by EM to be a double isochromosome Yp, inv dup i(Yp). The breakpoint producing mar1 is within the centromere and the one producing mar2 is within one of the short arms of the Y isochromosome. The findings of different cell populations in peripheral blood lymphocytes indicate the postzygotic instability of this i(Yp).

Deletion or triplication of the alpha 3 (VI) collagen gene in three patients with 2q37 chromosome aberrations and symptoms of collagen-related disorders

Two new cases of del(2)(q37.1) and one case of partial trp(2)(q37) are studied by FISH with cosmid probes from the COL6A3 and PAX3 genes mapped in 2q37.3 and 2q36, respectively. While the PAX3 gene dosage appeared unaffected, the COL6A3 gene was found to be deleted and triplicated, respectively. This finding could explain features of connective tissue disorders such as joint laxity and hypotonia or joint stiffness and epiphyseal dysplasia, particularly documented by congenital dislocation of the radial head. Karyotype-phenotype correlations with reference to published cases are discussed.

Marker chromosome identification by micro-FISH

Micro-FISH was used to elucidate the chromosomal origin of marker chromosomes in three patients. Ten copies of marker chromosomes were collected with microneedles from GTG banded metaphases, transferred to a collecting drop and amplified by means of DOP-PCR. The PCR products were labeled with biotin-14-dATP and used as FISH probes for hybridization to normal metaphase chromosomes and to metaphase chromosomes of the patients (reverse painting). With the generation of chromosome region-specific painting probes by PCR amplification of microdissected DNA and subsequent FISH it was possible to identify the marker chromosomes in all patients. One marker appeared to be derived from the centromere region of the X-chromosome and the proximal third of the long arm, one from the centromere region of chromosome 17 and one marker chromosome was identified as an isochromosome 18p.

A novel mechanism for the origin of supernumerary marker chromosomes

A ring chromosome 3 and a 47th chromosome formed by the portions of 3p and 3q distal to the r(3) breakpoints were found in a girl with mental retardation and minor facial anomalies. The supernumerary chromosome 3, rea(3), had a primary constriction inside its 3p portion (3p23) and was consistently stable both in lymphocytes and fibroblasts. In situ hybridization with alphoid probes revealed that the r(3) maintained its wild-type-centromere, whereas the rea(3) showed no alphoid-related signals. This case and a similar one recently reported demonstrate that acentric fragments can acquire a new centromere and become stable, and that supernumerary marker chromosomes can also originate by the junction of the acentric portions distal to the centric region forming a ring. The possibility of such a chromosome segregating will depend on its ability to (re)activate a new centromere.

Complete and precise characterization of marker chromosomes by application of microdissection in prenatal diagnosis

A straightforward and extremely efficient reverse chromosome painting technique is described which allows the rapid and unequivocal identification of any cytogenetically unclassifiable chromosome rearrangement. This procedure is used to determine the origin of unknown marker chromosomes found at prenatal diagnosis. After microdissection of the marker chromosome and amplification of the dissected fragment by a degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), fluorescence in situ hybridization (FISH) to aberrant and normal metaphase chromosomes with the marker-derived probe pool is performed. With this strategy, marker chromosomes present in amniotic fluid samples were successfully identified in three cases. The origin of the supernumerary markers was ascertained as deriving from 3p(p12-cen), 18p(pter-cen) and 9p(p12-cen), respectively. Since a specific FISH signal on chromosomes can be obtained within 2 working days using a probe generated without any pretreatment from one chromosomal fragment only and without additional image processing devices, this technique is considered to be highly suitable for routine application in pre- and postnatal cytogenetic analysis.

Identification of a supernumerary marker derived from chromosome 17 using FISH

We report on a 15-year-old girl with mental retardation, obesity, short stature and minor anomalies. She had 47 chromosomes with a minute extra ring which was identified by FISH to be derived from chromosome 17.

Supernumerary chromosome marker (1) in a developmentally delayed child

A 15-month-old boy with mild developmental delay and several minor anomalies was found to be mosaic 46,XY/47,XY ,+mar(1). The marker r(1) was a small de novo ring identified by FISH with a painting type DNA probe.

A 10-year survey, 1980-1990, of prenatally diagnosed small supernumerary marker chromosomes, identified by FISH analysis. Outcome and follow-up of 14 cases diagnosed in a series of 12,699 prenatal samples

A cytogenetic survey and follow-up studies were made of 14 cases with supernumerary marker chromosomes, identified among 12,699 prenatal samples, investigated at our institution over a 10-year period from 1980 to 1990. FISH (fluorescence in situ hybridization) techniques were employed to identify the chromosomal origin of the marker chromosomes. Five cases were familial, all derived from acrocentric chromosomes, and all without apparent phenotypic effects in the children. Nine cases represented de novo aberrations. In two cases (one with a marker from chromosome 14 or 22, the other with a ring-like marker derived from chromosome 17), the pregnancies continued and apparently normal babies were delivered at term, but the child with a marker derived from chromosome 17 showed slight psychomotor retardation at 2 years of age. All other pregnancies with de novo markers were terminated. In three cases, significant abnormalities were found at autopsy. One of these had an isochromosome 12p and the phenotype was consistent with Pallister-Killian syndrome. In conclusion, marker chromosome identification, as well as clinical follow-up, is essential for the purpose of improving genetic counselling.

A small supernumerary marker chromosome X identified by in situ hybridization

Cytogenetic analysis of a girl with moderate mental retardation and dysmorphic features revealed a 46,XX/47,XX,+mar karyotype. Fluorescence in situ hybridization using chromosome specific alpha satellite probes showed that the supernumerary marker originated from the X chromosome. To our knowledge, this is the first reported case of a female patient mosaic for a supernumerary small marker chromosome derived from X, and hence mosaic for trisomy of the pericentric region of the X chromosome.

Marker chromosome 21 identified by microdissection and FISH

A child without Down syndrome but with developmental delay, short stature, and autistic behavior was found to be mosaic 46,XX/47,XX,+mar(21) de novo. The marker was a small ring or dot-like chromosome. Microdissection of the marker was performed. The dissected fragments were biotinylated with sequence-independent PCR as a probe pool for fluorescence in situ hybridization (FISH). FISH results suggested an acrocentric origin of the marker. Subsequent FISH with alpha-satellite DNA probes for acrocentric chromosomes, and chromosome-specific 21 and 22 painting probes confirmed its origin from chromosome 21.