Supernumerary ring chromosomes and nuclear blebs in some low-grade malignant soft tissue tumours: atypical lipomatous tumours and dermatofibrosarcoma protuberans

 We investigated the diagnostic significance of supernumerary ring chromosomes in low-grade soft-tissue neoplasms. Chromosome slides were prepared from 123 samples of soft-tissue tumours using the standard trypsin-Giemsa banding technique. Supernumerary ring chromosomes were found in 6 cases of soft tissue tumours: 5 cases of atypical lipomatous tumour (ALT) and 1 case of dermatofibrosarcoma protuberans (DFSP). By chromosome painting with fluorescence in situ hybridization (FISH), the ring chromosome in 1 ALT was painted over its entire length with the chromosome 12 probe. Nuclear blebs and micronuclei, which were observed in each case of ALT, also contained chromosome 12 material; and these structures may represent a topological distribution of ring or giant marker chromosomes in the interphase nuclei. Our findings suggest that supernumerary ring chromosomes are characteristic of some low-grade soft tissue neoplasms including ALT and DFSP. Received: 27 August 1997 / Accepted: 29 December 1997     

Structure and evolution of supernumerary chromosomes in the Pacific giant salamander, Dicamptodon tenebrosus

We examined the genetic make-up and plausible origins of the supernumerary (B) chromosomes of the Pacific giant salamander, Dicamptodon tenebrosus, from the Pacific Northwest of North America. These salamanders have variable numbers of B chromosomes, from 0 to 10 per individual. Salamanders from the most southerly and northerly regions of the species' range have lower average numbers of B chromosomes than salamanders in the middle of the range. To assess how the supernumerary chromosomes originated in D. tenebrosus, B chromosome DNA was isolated by microdissection and amplified by degenerate oligonucleotide-primed PCR. The B chromosome DNA hybridized similarly to genomic DNA from individuals of D. tenebrosus and the related species D. copei and D. ensatus, thus demonstrating that the supernumerary chromosomes were derived from the normal chromosome complement. Unique hybridization bands in both D. copei and D. tenebrosus suggest that the shared sequences have evolved independently. This revised version was published online in July 2006 with corrections to the Cover Date.     

Cytogenetic and molecular analysis of inv dup(15) chromosomes observed in two patients with autistic disorder and mental retardation

A variety of distinct phenotypes has been associated with supernumerary inv dup(15) chromosomes. Although different cytogenetic rearrangements have been associated with distinguishable clinical syndromes, precise genotype-phenotype correlations have not been determined. However, the availability of chromosome 15 DNA markers provides a means to characterize inv dup(15) chromosomes in detail to facilitate the determination of specific genotype-phenotype associations. We describe 2 patients with an autistic disorder, mental retardation, developmental delay, seizures, and supernumerary inv dup(15) chromosomes. Conventional and molecular cytogenetic studies confirmed the chromosomal origin of the supernumerary chromosomes and showed that the duplicated region extended to at least band 15q13. An analysis of chromosome 15 microsatellite CA polymorphisms suggested a maternal origin of the inv dup(15) chromosomes and biparental inheritance of the two intact chromosome 15 homologs. The results of this study add to the existing literature which suggests that the clinical phenotype of patients with a supernumerary inv dup(15) chromosome is determined not only by the extent of the duplicated region, but by the dosage of genes located within band 15q13 and the origin of the normal chromosomes 15. © 1996 Wiley-Liss, Inc.     

Molecular cytogenetic detection of paternal chromosome fragments in allogynogenetic gibel carp, Carassius auratus gibelio Bloch

In gynogenesis, sperm from related species activates egg and embryonic development, but normally does not contribute genetically to the offspring. In gibel carp, Carassius auratus gibelio Bloch, however, gynogenetic offspring often show some phenotypes apparently derived from the heterologous sperm donor. This paternal effect of allogynogenesis is outstanding in an artificial clone F produced by cold treatment of clone E eggs after insemination with blunt-nose black bream (Megaloabrama amblycephala Yin) sperm. Karyotype analysis revealed 5–15 supernumerary microchromosomes in different individuals of clone F in addition to 156 normal chromosomes inherited from the maternal clone E. A painting probe was prepared from the microdissected microchromosomes, and used to investigate the origin of these microchromosomes. Strong positive signals were detected on each microchromosomes of clone F and on 4 pairs of chromosomes in blunt-nose black bream, whereas no signals were detected on the chromosomes of clone E. This result indicates that some paternal chromosome fragments of blunt-nose black bream have been incorporated into the artificial clone F. Therefore, the manipulation of allogynogenesis may provide a unique method to transfer DNA between diverse species for fish breeding. This revised version was published online in July 2006 with corrections to the Cover Date.     

Mosaic inv dup(8p) marker chromosome with stable neocentromere suggests neocentromerization is a post‐zygotic event

Marker chromosomes containing active human neocentromeres have been described in individuals where the chromosomes are non‐mosaic, suggesting that they are mitotically stable, but also in individuals where there is mosaicism, raising the possibility of neocentromere instability. We report two independently ascertained individuals who are mosaic for a supernumerary marker chromosome, shown by reverse chromosome painting to have an 8p origin, resulting in mosaicism for tetrasomy 8p23.1→pter in the patient. The markers have a primary constriction but show no detectable centromeric α‐satellite DNA. The marker in Patient 1 demonstrated no centromere protein CENP‐B binding, but associated with nine different functionally critical centromere proteins. Investigation of peripheral blood lymphocytes from this patient on five separate occasions over a 13‐year period showed 23–46% mosaicism for the marker chromosome with no decrease in incidence. In vitro investigation of primary and secondary sub‐clones of a lymphoblast cell line derived from the patient demonstrated 100% stability of the marker chromosome indicating that neocentromere instability is unlikely to be responsible for the mosaicism in the patient. This and other available data support a general model of neocentromerization as a post‐zygotic event, irrespective of whether the supernumerary chromosome fragment has arisen during meiosis or post‐fertilization at mitosis. © 2001 Wiley‐Liss, Inc.     

De novo supernumerary ring chromosome 7: first report of a non-mosaic patient and review of the literature

The present authors report the case of a 12-year-old-boy with a de novo, non-mosaic supernumerary ring chromosome 7 associated with significant developmental delay and speech difficulty. A review of the literature identified a total of 18 cases with ring chromosomes 7 who can be classified into two groups: (1) patients with a cell line that has 47 chromosomes with a small supernumerary ring chromosome 7 resulting in partial trisomy; and (2) individuals had a cell line with a large ring chromosome replacing one of the normal chromosomes 7 resulting in partial monosomy. A comparison of clinical features in the two groups of patients showed several common features such as growth and mental retardation, and facial dysmorphism, including, ear and eye anomalies. However, patients with partial trisomy have speech difficulty as a distinguishing feature, while patients with partial monosomy have skin lesions as a cardinal feature. All the published cases of ring chromosome 7, irrespective whether they are supernumerary or normal modal number, are mosaics except for one. The present subject is the first case of a de novo, non-mosaic supernumerary ring chromosome 7.     

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.     

Unexpected results in the constitution of small supernumerary marker chromosomes

Traditional approaches for the classification of Small Supernumerary Marker Chromosomes (sSMC), mostly based on FISH techniques, are time-consuming and not always sufficient to fully understand the true complexity of this class of rearrangements. We describe four supernumerary marker chromosomes that, after array-CGH, were interpreted rather differently in respect to the early classification made by conventional cytogenetics and FISH investigations, reporting two types of complex markers which DNA content was overlooked by conventional approaches: 1. the sSMC contains non-contiguous regions of the same chromosome and, 2. the sSMC, initially interpreted as a supernumerary del(15), turns out to be a derivative 15 to which the portion of another chromosome was attached. All are likely derived from partial trisomy rescue events, bringing further demonstration that germline chromosomal imbalances are submitted to intense reshuffling during the embryogenesis, leading to unexpected complexity and changing the present ideas on the composition of supernumerary marker chromosomes.     

The giant B chromosome of the cyprinid fish Alburnus alburnus harbours a retrotransposon-derived repetitive DNA sequence

The cyprinid fish Alburnus alburnus possesses one of the largest supernumerary chromosomes in all vertebrates. In the present study, amplified fragment length polymorphism analyses (AFLP) and fluorescence in-situ hybridization (FISH) were performed in order to characterize these extraordinary chromosomes in detail. Sequence analysis of the B chromosome-specific DNA revealed a strong homology to a Drosophila Gypsy/Ty3 retrotransposon and also to a medaka (Oryzias latipes) one. The sequence is highly abundant on the B chromosome but undetectable in the normal A chromosome complement. It is also absent from the B chromosome of the closely related species, Rutilus rutilus, suggesting a specific spreading of the mobile element during evolution of the giant supernumerary chromosome within A. alburnus. Meitotic chromosomes were in-situ hybridized with the B chromosome-specific probe, documenting that the additional chromosome behaves as an autopaired ring chromosome in diakineses. Our results suggest that the supernumerary chromosome of A. alburnus is not derived from the normal chromosome complement but has evolved independently.     

A supernumerary "G" like chromosome originating from a maternal 13;15 translocation in a nondysmorphic, retarded girl

This paper describes a retarded girl who had a severe seizure disorder and a few minor anomalies, and who was found to have a "G-sized" supernumerary chromosome in all her cells which were examined. Studies of the patient's and her parents' chromosomes by a variety of techniques suggest that the supernumerary chromosome arose following a prezygotic maternal 13;15 translocation.     

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.     

A review of supernumerary and absent limbs and digits of the upper limb

For years people have been enamored by anomalies of the human limbs, particularly supernumerary and absent limbs and digits. Historically, there are a number of examples of such anomalies, including royal families of ancient Chaldea, tribes from Arabia, and examples from across nineteenth century Europe. The development of the upper limbs in a growing embryo is still being elucidated with the recent advent of homeobox genes, but researchers agree that upper limbs develop between stages 12–23 through a complex embryological process. Maternal thalidomide intake during limb development is known to cause limb reduction and subsequent amelia or phocomelia. Additionally, a number of clinical reports have illustrated different limb anomaly cases, with each situation unique in phenotype and developmental abnormality. Supernumerary and absent limbs and digits are not unique to humans, and a number of animal cases have also been reported. This review of the literature illustrates the historical, anatomical, and clinical aspects of supernumerary and absent limbs and digits for the upper limb.     

Comparative Chromosome Banding of Two South-American Species of Rice Rats of the Genus Oligoryzomys (Rodentia, Sigmodontinae)

Comparative analysis of G- and C-banding patterns in two species of pygmy rice rats, namely Oligoryzomys microtis from Peru (Ucayali and Loreto departments) and O. flavescens from Bolivia (Tarija department) established that the diploid number of the former species is 64 (NFa = 66), whereas, in the latter, it varies between 64 and 66 (NFa = 66–68) due to the presence of 0–2 heterochromatic supernumerary or B chromosomes. The G-banding pattern of the euchromatic part of their karyotypes is similar in spite of differences in morphology of the largest and smallest autosomal pairs caused by a centromeric shift and the presence of heterochromatic arms, respectively. In addition, the total quantity of C-heterochromatin is smaller in the karyotype of O. microtis than in that of O. flavescens, resulting in differences in the number and size of chromosome pairs (including sex chromosomes) bearing C-blocks. It follows from present and previous data that these karyotypic features are stable in each of these species and thus may be used as species-specific markers. This revised version was published online in August 2006 with corrections to the Cover Date.     

Identification and characterization of a complex pure mosaic of small supernumerary marker chromosomes involving 11p11.12 → q12.1 and 19p12 → q12 regions in a child featuring multiple congenital anomalies

Unstable, gene‐rich pericentric regions have been associated with various structural aberrations including small supernumerary marker chromosomes (sSMCs). We hereby report on a complex pure mosaic sSMCs derived from chromosomes 11 and 19 in a child featuring multiple congenital anomalies. As indicated by microarray analysis, the sSMCs have involved materials from 11p11.12 → q12.1 and 19p12 → q12 in complex forms (with four cell lines harboring from 1 to 4 sSMCs) in all peripheral blood lymphocytes. The patient featured facial dysmorphism, generalized hypotonia, cryptorchidism, transverse palmar creases, cerebral hemorrhage, atrial septal defect secundum, strabismus, epilepsy, immunodeficiency, and severe cognitive and motor impairment. Literature review indicated this to be a unique sSMCs case simultaneously involving chromosomes 11 and 19, with one sSMC containing materials from the both chromosomes. We propose that the involved chromosomal regions may contain dosage‐sensitive genes which are important for the development, and that the sSMCs derived from multiple origins have formed by a complex mechanism. © 2011 Wiley Periodicals, Inc.     

The evolution of the mammalian Y chromosome

There is a predominant theory for the evolution of the mammalian Y chromosome. This theory hypothesizes that genes for sex determination and male-specific traits, as well as sequences for X-Y meiotic pairing, are conserved on the mammalian Y chromosome across all lineages and that all other Y chromosomal genes or sequences have been or will be lost in each mammalian lineage. There are effects of mouse Y chromosomal genes on behaviors and other traits that are not male specific. Under the predominant theory, these Y chromosomal genes could be the same as the conserved genes for sex determination or malespecific traits, or they could be genes that have been lost from the Y chromosomes of other mammalian lineages and that will eventually be lost from the Y chromosome of the rodent lineage. Recently, the evolution of the primate and rodent Y chromosomes has been studied at the DNA level. These studies are summarized and reviewed in this article. The findings of these studies are not fully consistent with the predominant theory for the evolution of the mammalian Y chromosome. Also, they imply that there are other possibilities for the phylogenetic history of Y chromosomal genes of mice with effects on behavior. These are that Y chromosomal genes with effects on mouse behaviors or other traits could be conserved genes other than those for sex determination or malespecific traits or that they could be novel genes on the Y chromosome of the rodent orMus lineage.     

Inactive ribosomal cistrons are spread throughout the B chromosomes of Rattus rattus (Rodentia, Muridae). Implications for their origin and evolution

In-situ hybridization with a rDNA probe has demonstrated the presence of non-transcribed ribosomal genes in the B chromosomes of the black rat Rattus rattus. To test whether methylation of ribosomal DNA present in the B chromosomes could account for their inactivation, we performed in-situ digestions and Southern analyses of DNA digested with the isoschizomers MspI and HpaII. Our results suggest that the accessory chromosomes of this species have originated from one of the smaller NOR-carrying chromosome pairs. In the course of evolution, repetitive sequences invaded this supernumerary element and its ribosomal DNA content was dispersed throughout the chromosome and inactivated by heterochromatinization and methylation. This revised version was published online in July 2006 with corrections to the Cover Date.     

Characterization of a supernumerary small marker X chromosome in two females with similar phenotypes

We describe two female patients mosaic for a cell line with an extra marker X chromosome in addition to a normal 46,XX cell line. To our knowledge, these cases are the first reports of females who had a cell line with a supernumerary marker X chromosome in addition to a normal cell line. They also had strikingly similar manifestations, including small hands and feet, minor facial anomalies, obesity, and mental retardation. The DNA content of the mar(X) chromosomes was investigated by fluorescent in situ hybridization using pericentromeric probes. The XIST gene, which is necessary for initiation of X-inactivation, was deleted from both marker chromosomes, suggesting that these chromosomes were not subject to inactivation. The short arm breakpoints of the mar(X)s were between the DNA markers DXS423E on Xp11.21 and UBE1 on Xp11.23. In Patient 1, mar(X) contained the androgen receptor gene and the DNA marker DXS1, both mapping to Xq11.2, whereas in Patient 2 the chromosome breakpoint was proximal to these markers. We suggest that the similar phenotypes of these patients may be due to the overexpression of genes in the common pericentromeric region of the X chromosome. Am. J. Med. Genet. 76:45–50, 1998. © 1998 Wiley-Liss, Inc.     

Applications of comparative genomic hybridisation in constitutional chromosome studies

G band cytogenetic analysis often leads to the discovery of unbalanced karyotypes that require further characterisation by molecular cytogenetic studies. In particular, G band analysis usually does not show the chromosomal origin of small marker chromosomes or of a small amount of extra material detected on otherwise normal chromosomes. Comparative genomic hybridisation (CGH) is one of several molecular approaches that can be applied to ascertain the origin of extra chromosomal material. CGH is also capable of detecting loss of material and thus is also applicable to confirming or further characterising subtle deletions. We have used comparative genomic hybridisation to analyse 19 constitutional chromosome abnormalities detected by G band analysis, including seven deletions, five supernumerary marker chromosomes, two interstitial duplications, and five chromosomes presenting with abnormal terminal banding patterns. CGH was successful in elucidating the origin of extra chromosomal material in 10 out of 11 non-mosaic cases, and permitted further characterisation of all of the deletions that could be detected by GTG banding. CGH appears to be a useful adjunct tool for either confirming deletions or defining their breakpoints and for determining the origin of extra chromosomal material, even in cases where abnormalities are judged to be subtle. We discuss internal quality control measures, such as the mismatching of test and reference DNA in order to assess the quality of the competitive hybridisation effect on the X chromosome.     

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 de novo supernumerary genomic discontinuous ring chromosome 21 in a child with mild intellectual disability

Small supernumerary marker chromosomes (sSMCs) are structurally abnormal extra chromosomes that cannot be unambiguously identified or characterized by conventional banding techniques alone, and they are generally equal in size or smaller than chromosome 20 of the same metaphase spread. Small supernumerary ring chromosomes (sSRCs), a smaller class of marker chromosomes, comprise about 10% of the cases. For various reasons these marker chromosomes have been the most difficult to characterize; although specific syndromes have not yet been defined, 60% of cases are associated with an abnormal phenotype. The chromosomal material involved, the degree and tissutal distribution of mosaicism, and the possible presence of uniparental disomy, are the important factors determining whether or not the ring chromosome will give rise to symptoms. Using conventional and molecular cytogenetics approaches we identified a de novo chromosome 21 sSRC in a child with speech delay and mild intellectual disability. By using aCGH analysis and SNP arrays, we report the presence of two discontinuous regions of chromosome 21 and the paternal origin of the sSRC. A thorough neuropsychiatric evaluation is also provided. Only few other cases of complex discontinuous ring chromosomes have been described in detail.