Chromosome 13q neocentromeres: molecular cytogenetic characterization of three additional cases and clinical spectrum

Prenatal identification of an inverted duplicated 13q marker chromosome with a neocentromere

In this case report, we describe a rare prenatal finding of a small marker chromosome. This marker chromosome corresponds to an inverted duplication of the 13q region 13q31.1q34 (or 13q31.1 → qter) with a neocentromere, detected during genetic analysis of a chorionic villus sample in a fetus with multiple congenital anomalies after a normal prenatal screening result by noninvasive prenatal testing.

Case Report: Prenatal Identification of a De Novo Mosaic Neocentric Marker Resulting in 13q31.1→qter Tetrasomy in a Mildly Affected Girl

Partial tetrasomy of distal 13q has a reported association with a variable phenotype including microphthalmia, ear abnormalities, hypotelorism, facial dysmorphisms, urogenital defects, pigmentation and skin defects, and severe learning difficulties. A wide range of mosaicism has been reported, which may, to some extent, account for the variable spectrum of observed phenotypes. We report here a pregnancy conceived using intrauterine insemination in a 32-year-old female with a history of infertility. Non-invasive prenatal screening (NIPS) was performed in the first trimester which reported an increased risk for trisomy 13. Follow-up cytogenetic workup using chorionic villus sampling (CVS) and amniotic fluid samples showed a mosaic karyotype with a small supernumerary marker chromosome (sSMC). Chromosomal microarray analysis (CMA) identified a mosaic 31.34 Mb terminal gain on chr13q31.1q34 showing the likely origin of the sSMC to distal chromosome 13q. Follow-up metaphase FISH testing suggested an inverted duplication rearrangement involving 13q31q34 in the marker chromosome and the presence of a neocentromere. At 21 months of age, the proband has a history of gross motor delay, hypotonia, left microphthalmia, strabismus, congenital anomaly of the right optic nerve, hemangiomas, and a tethered spinal cord. Postnatal chromosome analyses in buccal, peripheral blood, and spinal cord ligament tissues were consistent with the previous amniocentesis and CVS findings, and the degree of mosaicism varied from 25 to 80%. It is often challenging to pinpoint the chromosomal identity of sSMCs using banding cytogenetics. A combination of low-pass genome sequencing of cell-free DNA, chromosomal microarray, and FISH enabled the identification of the precise chromosomal rearrangement in this patient. This study adds to the growing list of clinically identified neocentric marker chromosomes and is the first described instance of partial tetrasomy 13q31q34 identified in a mosaic state prenatally. Since NIPS is now being routinely performed along with invasive testing for advanced maternal age, an increased prenatal detection rate for mosaic sSMCs in otherwise normal pregnancies is expected. Future studies investigating how neocentromeres mediate gene expression changes could help identify potential epigenetic targets as treatment options to rescue or reverse the phenotypes seen in patients with congenital neocentromeres.

Small Supernumerary Ring Chromosome Derived from an Inverted Duplication of 13q11.2q14 in a Fetus with Coarctation of the Aorta

Here, we report a molecular characterization of a small supernumerary marker chromosome (sSMC) derived from the most proximal region of 13q present in a fetus with coarctation of the aorta at ultrasound examination during prenatal diagnosis. Cultured umbilical cord blood cells showed a de novo extra ring-shaped sSMC in 76% of the cells using a standard banding technique. SNP array revealed a tetrasomy of about 28.4 Mb in the long arm of chromosome 13 from band 13q11 to 13q14.11 in the fetus's cells. Metaphase/interphase FISH using specific probes located at 13q11, 13q12.11, and 13q14.11, respectively, demonstrated that the supernumerary ring chromosome was derived from an inverted duplication of the region 13q11q14.11 with a conventional centromere. To the best of our knowledge, this is the first time that an inverted duplication of the most proximal region 13q11q14.11 in a ring chromosome is characterized. The findings we presented here deepen our understanding of the clinical consequences of tetrasomy in this region and may be of help for further studies of critical regions in chromosome 13.

Hexasomy 13q31.3q34 due to two marker chromosomes with inverted duplication in a fetus with increased nuchal translucency

BACKGROUND

Small supernumerary marker chromosomes are structurally rearranged chromosomes that can be formed from different chromosomal fragments and cannot be identified using chromosomal banding analysis. Their examination has to be complemented by additional analyses like fluorescent in situ hybridization or array comparative genomic hybridization.

METHODS

We report on partial hexasomy of chromosome 13q in a fetus of a pregnant woman referred to genetic counseling because of increased fetal nuchal translucency and increased risk of trisomy 21 and trisomy 18 in first-trimester combined prenatal screening. Using chromosome banding analysis, in situ hybridization and array comparative hybridization we revealed the presence of two marker chromosomes with inverted duplication resulting in hexasomy of a 22.6 Mbp fragment in chromosomal region 13q31.3-13q34 with the lack of chromosome 13 centromere.

RESULTS

The fetus presented dysmorphic facial features, head and body disproportion, wide neck, ambiguous genitalia, incorrect position of the anus, and symmetrical shortening of the long bones were present in our described case. Some of these features were in accordance with other published cases. Other most often described features in tetrasomy were: microphtalmia or other major eye defects, ear abnormalities and deafness, hemangiomata, hypotelorism, severe learning disability and seizures. Despite a low risk of recurrence for small supernumerary marker chromosomes the possibility of germ line mosaicism exists, thus genetic counseling was offered to the examined family.

CONCLUSION

A full characterization of small supernumerary marker chromosomes in fetal karyotype is necessary for pregnancy prognosis and genetic counseling.

Tetrasomy 13q32.2qter due to an apparent inverted duplicated neocentric marker chromosome in an infant with hemangiomas, failure to thrive, laryngomalacia, and tethered cord

BACKGROUND

Approximately 100 small supernumerary marker chromosomes (sSMCs) with a non-α-satellite neocentromere structure have been reported in the literature. Of the few derived from chromosome 13, five have consisted of inverted duplicated segment 13q32qter.

CASE REPORT

We herein describe the sixth case, characterized by genome wide SNP array, conventional cytogenetics and FISH studies. The de novo occurrence of the marker, the poor prognosis and the presence of hemangiomas are consistent with previous cases.

CONCLUSION

We hereby expand the clinical spectrum of this rare cytogenetic disorder and suggest a possible mechanism for the pathogenesis of associated congenital vascular malformations.

Marker chromosomes

Marker chromosomes are a morphologically heterogeneous group of structurally abnormal chromosomes that pose a significant challenge in prenatal diagnosis. Phenotypes associated with marker chromosomes are highly variable and range from normal to severely abnormal. Clinical outcomes are very difficult to predict when marker chromosomes are detected prenatally. In this review, we outline the classification, etiology, cytogenetic characterization, and clinical consequences of marker chromosomes, as well as practical approaches to prenatal diagnosis and genetic counseling.

Origin of a prenatal mosaic supernumerary neocentromeric derivative chromosome 13 determined by QF-PCR

Neocentromeres are mitotically stable human derivative centromeres without alpha-satellite DNA which are able to provide stability to rearranged chromosome fragments that would otherwise be acentric and rapidly lost. A female fetus was found to be mosaic for a supernumerary marker chromosome: 47,XX,+mar[3]/46,XX[36]. The marker was identified by fluorescence in situ hybridization and G-band as an inversion duplication of 13q21→13qter, with a neocentromere present at 13q21, in approximately 9% of colonies examined. Parental blood karyotypes were normal. QF-PCR performed on blood samples from both parents and the second amniotic fluid sample showed evidence of a second maternal allele at markers D13S258 (13q21) and D13S628 (13q31-q32), indicating formation at maternal meiosis I/II. This is the first reported case where the detection and origin of a low-level mosaic prenatal neo(13) were confirmed by QF-PCR.

Duplication of the ZIC2 gene is not associated with holoprosencephaly

Cytogenetic testing using genomic microarrays presents a clinical challenge when data regarding the phenotypic consequences of the genomic alteration are not available. We describe a chromosome 13q32.3 duplication discovered by microarray testing in a fetus with a prenatally detected apparently balanced de novo translocation 46,XY,t(2;13)(q37;q32). Microarray analysis on the fetal DNA showed duplications of 384 and 564 kb at the breakpoint regions on chromosomes 2q37.3 and 13q32.3, respectively. There were no disease-associated genes in the duplicated region on chromosome 2q37. The duplicated region on chromosome 13q contains the ZIC2 gene. Haploinsufficiency of ZIC2 is known to cause holoprosencephaly and other brain malformations. Studies in the mouse models have suggested that over expression of ZIC2 may also lead to brain malformations. Fetal MRI of the brain was normal and the family elected to continue the pregnancy. An apparently normal baby was born at term. At 3 months of age a physical exam showed no abnormalities and no developmental delay. This report shows that duplication of ZIC2 is not necessarily associated with brain malformations. We also describe the phenotype from four additional patients with duplications of the region of chromosome 13 containing ZIC2 and three previously described patients with supernumerary marker chromosomes derived from distal chromosome 13. None of the eight patients had holoprosencephaly or brain malformations, indicating that duplication of ZIC2 is not associated with brain anomalies. This information will be useful for counseling in other occurrences of this duplication identified by microarray.

Tetrasomy 13q mosaicism associated with phylloid hypomelanosis and precocious puberty

Various forms of pigmentary dysplasias have been known to be associated with chromosomal mosaicism. One of these disorders, known as phylloid hypomelanosis, has been found to be predominantly associated with abnormalities in chromosome 13. Most of the reported literature involves mosaic trisomy 13 with clinical evidence of abnormal pigmentation in the form of leaf-like or oblong achromic macules following Blaschko's lines. Here, we report on an 8-year-old girl with phylloid hypomelanosis and precocious puberty who was found to have mosaicism for tetrasomy 13q in the form of inverted dup(13)(q21) on her skin fibroblasts as well as peripheral blood karyotype. A higher resolution (244K) chromosomal microarray was done on DNA from skin fibroblasts confirming the breakpoint and gain of distal 13q, which made her tetrasomic for 13q21-qter. This is the first-ever reported association of tetrasomy 13q with phylloid hypomelanosis and precocious puberty. Our report further emphasizes the need to exclude any type of abnormalities of chromosome 13 in patients with phylloid hypopigmentation.

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.

Independent centromere formation in a capricious, gene-free domain of chromosome 13q21 in Old World monkeys and pigs

BACKGROUND

Evolutionary centromere repositioning and human analphoid neocentromeres occurring in clinical cases are, very likely, two stages of the same phenomenon whose properties still remain substantially obscure. Chromosome 13 is the chromosome with the highest number of neocentromeres. We reconstructed the mammalian evolutionary history of this chromosome and characterized two human neocentromeres at 13q21, in search of information that could improve our understanding of the relationship between evolutionarily new centromeres, inactivated centromeres, and clinical neocentromeres.

RESULTS

Chromosome 13 evolution was studied, using FISH experiments, across several diverse superordinal phylogenetic clades spanning >100 million years of evolution. The analysis revealed exceptional conservation among primates (hominoids, Old World monkeys, and New World monkeys), Carnivora (cat), Perissodactyla (horse), and Cetartiodactyla (pig). In contrast, the centromeres in both Old World monkeys and pig have apparently repositioned independently to a central location (13q21). We compared these results to the positions of two human 13q21 neocentromeres using chromatin immunoprecipitation and genomic microarrays.

CONCLUSION

We show that a gene-desert region at 13q21 of approximately 3.9 Mb in size possesses an inherent potential to form evolutionarily new centromeres over, at least, approximately 95 million years of mammalian evolution. The striking absence of genes may represent an important property, making the region tolerant to the extensive pericentromeric reshuffling during subsequent evolution. Comparison of the pericentromeric organization of chromosome 13 in four Old World monkey species revealed many differences in sequence organization. The region contains clusters of duplicons showing peculiar features.

Molecular cytogenetic identification and characterization of a de novo supernumerary neocentromeric derivative chromosome 13

We report a young girl with microphthalmia, conductive deafness, aortic isthmus stenosis, laryngomalacia, and laryngeal stenosis carrying a de novo supernumerary neocentromeric derivative chromosome 13. For the precise identification and characterization of the eu- and heterochromatic content of the marker chromosome, straightforward molecular cytogenetic analyses were performed, such as chromosome microdissection, FISH with different probes (e.g. wcp, alphoid centromeric probes, BAC), centromere-specific multicolor FISH (cenM-FISH), and multicolor banding (MCB). The analyses demonstrated that the marker consisted of an inverted duplication (partial tetrasomy) of the distal portion of chromosome 13 that was separated from the endogenous chromosome 13 centromere. Using an all-centromere probe and multicolor cenM-FISH, no alpha-satellite DNA hybridization signal was detectable on any portion of the derivative chromosome. The presence of a functional and active neocentromere on the derivative chromosome 13 was confirmed by positive immunofluorescence signals with CENP-C antibodies. BAC-FISH confirmed the cytogenetic localization of the neocentromere in band 13q31.3. Thus the patient had a mosaic conventional karyotype mos 47,XX,+inv dup(13)(qter-->q21.3::q21.3-->q31.3-->neo-->q31.3-->qter)[6]/46,XX [49].

Mosaic monosomy of a neocentric ring chromosome maps brachyphalangy and growth hormone deficiency to 13q31.1-13q32.3

We describe a boy with moderate intellectual disability associated with distinctive hand malformations (hypoplastic and angel-shaped middle phalanges) and partial growth hormone (GH) deficiency associated with mosaic deletion of 13q31.1-13q32.3. The deleted segment was mapped to a 20-Mb region bounded by BACs RP11-1143C2 and RP11-139C1, narrowing the previously described locus for hand malformations at this region and suggesting that a locus for GH deficiency is also present at this location. The deleted segment contains at least three candidate genes, glypican-5, FARP1 and SOX21, that may be contributing to the phenotype in this boy. In a significant proportion (approximately 50%) of cells, the deleted region is present as a supernumerary ring chromosome stabilized by the formation of a neocentromere at 13q31-q32, within a region with a known propensity for neocentromere formation. The ring chromosome appears to be prone to low-level misdivision and loss in vitro which, in vivo, must be countered by selection for the balanced karyotype because the level of mosaicism has remained stable over 13 years.

Small supernumerary marker chromosomes (sSMC) in humans

Small supernumerary marker chromosomes (sSMC), defined as additional centric chromosome fragments too small to be identified or characterized unambiguously by banding cytogenetics alone, are present in 0.043% of newborn children. Several attempts have been made to correlate certain sSMC with a specific clinical picture, resulting in the description of several syndromes such as the i(18p)-, der(22)-, i(12p)- (Pallister Killian syndrome) and inv dup(22)- (cat-eye) syndromes. However, most of the remaining sSMC including minute-, ring-, inverted-duplication- as well as complex-rearranged chromosomes, have not yet been correlated with clinical syndromes, mostly due to problems in their comprehensive characterization. Here we present an overview of sSMC, including the first attempt to address problems of nomenclature and their modes of formation, problems connected with mosaicism plus familial occurrence. The review also discusses the frequency of sSMC in prenatal, postnatal, and clinical cases, their chromosomal origin and their association with uniparental disomy. A short review of the up-to-date approaches available for sSMC characterization is included. Clinically relevant correlations concerning the presence of a specific sSMC and its phenotypic consequences should become available soon.

Chromosomal dynamics of human neocentromere formation

Neocentromeres are rare human chromosomal aberrations where a new centromere has formed in a previously non-centromeric location. The emergence of new centromeres on a chromosome that already contains an endogenous centromere would be a highly deleterious event which would lead to dicentricity and mitotic instability. Nonetheless, neocentromere formation appears to provide a mechanism for the acquisition of a new centromere. Neocentromeres are most often observed on chromosomal arm fragments that have separated from an endogenous centromere, and therefore actually lead to mitotic stability of what would have been an acentric fragment. Neocentromeres have recently also been observed on apparently unrearranged chromosomes where the endogenous centromere has been inactivated. Furthermore, the process of centromere repositioning during primate chromosomal evolution may depend on the acquisition and subsequent fixation of neocentromeres. This remarkable plasticity in the position of centromeres has important implications for human cytogenetics and chromosome evolution, and provides an opportunity to further our understanding of the process of centromere formation and structure.

A new neocentromere locus on chromosome 13 resulting in mosaic tetrasomy for distal 13q and an asymmetric phenotype

An 8-year-old girl was referred to the Genetics Centre with mild developmental delay, mild dysmorphic features, and a head circumference on the 98th centile. She was noted to have large irregular ear lobes, torticollis, and mild hemihypertrophy. Karyotype analysis of cultured peripheral lymphocytes and skin fibroblasts revealed the presence of a symmetrical supernumerary marker chromosome in 13% of cells from both tissue types. Further analysis showed that this marker chromosome originated from the distal region of chromosome 13 and contained no centromeric alpha-satellite DNA. The marker chromosome was not found in blood from the parents. This case represents a novel symmetrical structure with a previously unreported neocentromere locus, leading to an unusual phenotype. Similar cases of individuals with a chromosome 13 with a neocentromere have been reported. They are reviewed and compared with the current case. The importance of scanning metaphases for abnormalities in individuals presenting with asymmetry is emphasized.

Human supernumeraries: are they B chromosomes?

In humans, the presence of supernumerary chromosomes is an unusual phenomenon, which is often associated with developmental abnormalities and malformations. In contrast to most animal and plant species, the extensive knowledge of the human genome and the ample set of molecular and cytogenetic tools available have permitted to ascertain not only that most human supernumerary chromosomes (HSCs) derive from the A chromosome set, but also the specific A chromosome from which most of them arose. These extra chromosomes are classified into six types on the basis of morphology and size. There are both heterochromatic and euchromatic HSCs, the latter being more detrimental. Most are mitotically stable, except some producing individual mosaicism. No information is available on the HSC transmission rate since extensive familial studies are not usually performed generally because of death of the relatives or lack of cooperation. The main B chromosome property failing in HSCs seems to be their population spread as polymorphisms, since most HSCs seem to correspond to extra A chromosomes or centric fragments spontaneously arisen in the analysed individual or one of his/her parents. However, we cannot rule out at this moment, that more intensive studies on population distribution and frequency of those HSCs most closely resembling B chromosomes (i.e. those heterochromatic and thus less detrimental) would reveal possible HSCs polymorphisms. Although HSCs cannot be considered B chromosomes, some of them might be a source for future B chromosomes. The best candidates would be heterochromatic HSCs, which might manage to drive in either sex. To ascertain this possibility, research on inheritance and population studies would be very helpful in combination with the powerful cytogenetic and molecular tools available for our species.

Characterization of an analphoid, neocentromere-positive inv dup 8p marker chromosome using multiplex whole chromosome and sub-telomere FISH analyses

A 30-year-old male patient with mild mental retardation was found to have a small supernumerary marker chromosome (SMC) in 90% of his peripheral blood cells and in 100% of his fibroblast cells. Multiplex whole chromosome and sub-telomere FISH analyses were used to determine that this SMC is an inverted duplicated distal chromosome 8p fragment. Although it was negative for alpha-DNA sequences, this marker had a functional kinetochore (neocentromere) demonstrated by a positive signal with a CENP-C antibody. Apparently intact 8p telomeres at the marker's ends were demonstrated by using a telomere repeat FISH probe. The patient's phenotypically normal mother on G-banding analysis had a small marker chromosome in 8% of her peripheral blood cells in two cultures of the first specimen studied. The marker was not seen in any subsequent maternal peripheral blood or fibroblast specimens. Although it was impossible to further characterize the maternal SMC, it was suggested that the mother had the same marker as the one seen in the proband. Inverted duplicated chromosomal fragments are the most frequent type of analphoid markers. Stable inverted duplicated 8p marker chromosomes were previously reported in three other patients. They all apparently occurred de novo and were found to be positive for kinetochore-associated proteins. Evidence for the possible inheritance of an inverted-duplicated, analphoid SMC was not shown to-date. This study also demonstrates a practical, straightforward approach for analphoid marker characterization in clinical laboratory settings, using whole chromosome multiplex and subtelomere-specific FISH analyses. FISH probes for all sub-telomere chromosomal regions are commercially available and the large majority of analphoid marker chromosomes involve telomere regions.

Prenatal diagnosis of a karyotypically normal pregnancy in a mother with a supernumerary neocentric 13q21 -->13q22 chromosome and balancing reciprocal deletion

An adult female patient with a history of miscarriages was found to be carrying a stable supernumerary chromosome. The patient also carried a reciprocal paracentric deletion in chromosome 13q21/22. Microdissection and reverse fluorescence in situ hybridization FISH revealed that this supernumerary chromosome was derived from region 13q21 --> 13q22. The presence of a neocentromere on this supernumerary chromosome was confirmed by the absence of detectable alpha satellite DNA using FISH and the presence of centromere proteins CENP-C and CENP-A using immunofluorescence. The absence of telomere sequences suggests that the marker is a ring chromosome (r(13)). FISH using ordered BACs from the chromosome region 13q21 --> 13q31 permitted the precise positioning of the r(13) chromosome and the corresponding deletion to chromosome bands 13q21.32 --> 13q22.2. BAC 280J7 from within the r(13) was used as a FISH probe for the prenatal analysis of amniocytes at 16 weeks of gestation, which revealed a normal karyotype for the fetus. This r(13) chromosome represents the first description of chromosome 13 of the rarer class of neocentric chromosomes that are derived from interstitial deletions. It represents the first example of prenatal diagnosis in a phenotypically normal female that was ascertained to carry a neocentric marker. The presence of such a neocentric marker/deletion karyotype in a parent presents unique possible karyotypic outcomes for conceptions and unusual challenges for genetic counseling.

Neocentromeres: role in human disease, evolution, and centromere study

The centromere is essential for the proper segregation and inheritance of genetic information. Neocentromeres are ectopic centromeres that originate occasionally from noncentromeric regions of chromosomes. Despite the complete absence of normal centromeric alpha-satellite DNA, human neocentromeres are able to form a primary constriction and assemble a functional kinetochore. Since the discovery and characterization of the first case of a human neocentromere in our laboratory a decade ago, 60 examples of constitutional human neocentromeres distributed widely across the genome have been described. Typically, these are located on marker chromosomes that have been detected in children with developmental delay or congenital abnormalities. Neocentromeres have also been detected in at least two types of human cancer and have been experimentally induced in Drosophila. Current evidence from human and fly studies indicates that neocentromere activity is acquired epigenetically rather than by any alteration to the DNA sequence. Since human neocentromere formation is generally detrimental to the individual, its biological value must lie beyond the individual level, such as in karyotype evolution and speciation.