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1.  Prenatal diagnosis and molecular cytogenetic analysis of a de novo isodicentric chromosome 18 
Annals of Saudi Medicine  2010;30(6):489-492.
Isodicentric chromosome 18 [idic(18)] is rare structural aberration. We report on a prenatal case described by conventional and molecular cytogenetic analyses. The sonography at 24 weeks of gestation revealed multiple fetal anomalies; radial aplasia and ventricular septal defect were significant features. Routine karyotyping showed a derivative chromosome replacing one normal chromosome 18. The parental karyotypes were normal, indicating that the derivative chromosome was de novo. Array comparative genomic hybridization (array-CGH) revealed 18p11.21→qter duplication and 18p11.21→pter deletion for genomic DNA of the fetus. The breakpoint was located at 18p11.21 (between 12104527 bp and 12145199 bp from the telomere of 18p). Thus, the derivative chromosome was ascertained as idic(18)(qter→p11.21::p11.21→qter). Fluorescent in situ hybridization (FISH) confirmed that the derivative chromosome was idic(18). Our report describes a rare isodicentric chromosome 18 and demonstrates that array-CGH is a useful complementary tool to cytogenetic analysis for reliable identifying derivative chromosome.
doi:10.4103/0256-4947.70578
PMCID: PMC2994170  PMID: 20864786
2.  Homodicentric chromosomes: a distinctive type of dicentric chromosome. 
Journal of Medical Genetics  1981;18(1):54-58.
This report describes two patients with a distinctive type of dicentric autosomal chromosome formed by breakage and union between homologous chromosomes. These stable chromosomes possess two C bands, implying the presence of two centromeric regions. The first child, evaluated for dysmorphic features was shown to have an abnormal chromosome 16, designated as 46, XX, -16, + dic (16) (pter leads to cen leads to q22::p11 leads to qter). The second case is a child with the typical features of trisomy 18 whose karyotype is designated as 46, XX, -18, + dic (18) (qter leads to p11.1 :: p11.3 leads to cen leads to qter). The stability of these chromosomes is presumably in result of centromere suppression and associated premature centromere division of the suppressed centromere. The possible mechanism of formation of these homodicentric chromosomes is presented, and a comparison is made between them and three patients with dicentric X chromosomes.
Images
PMCID: PMC1048659  PMID: 7252999
3.  Trisomy 8 syndrome owing to isodicentric 8p chromosomes: regional assignment of a presumptive gene involved in corpus callosum development. 
Journal of Medical Genetics  1994;31(3):238-241.
Two patients with trisomy 8 syndrome owing to an isodicentric 8p;8p chromosome are described. Case 1 had a 46,XX/46,XX,-8,+idic(8)(p23) karyotype while case 2, a male, had the same abnormal karyotype without evidence of mosaicism. In situ hybridisation, performed in case 1, showed that the isochromosome was asymmetrical. Agenesis of the corpus callosum (ACC), which is a feature of trisomy 8 syndrome, was found in both patients. Although ACC is associated with aneuploidies for different chromosomes, a review of published reports indicates that, when associated with chromosome 8, this defect is the result of duplication of a gene located within 8p21-pter. Molecular analysis in one of our patients led us to exclude the distal 23 Mb of 8p from this ACC region.
Images
PMCID: PMC1049750  PMID: 8014974
4.  Alternate centromere inactivation in a pseudodicentric (15;20)(pter;pter) associated with a progressive neurological disorder. 
Journal of Medical Genetics  1989;26(10):626-630.
A 13 year old male with a severe progressive neurological disorder was found to have a pseudodicentric chromosome resulting from a telomeric fusion 15p;20p. In lymphocytes, the centromeric constriction of the abnormal chromosome was always that of the chromosome 20, while in fibroblasts both centromeres were alternately constricted. Cd staining was positive only at the active centromere, but a weak anticentromere immunofluorescence was present at the inactive one. We suggest that centromere inactivation results from a modified conformation of the functional DNA sequences preventing normal binding to centromere specific proteins. We also postulate that the patient's disorder, reminiscent of a spongy glioneuronal dystrophy as seen in Alper's and Creutzfeldt-Jakob diseases, may be secondary to the presence of the pathogenic isoform of the prion protein encoded by a gene mapped to 20p12----pter.
Images
PMCID: PMC1015713  PMID: 2685311
5.  Neocentric X-chromosome in a girl with Turner-like syndrome 
Background
Neocentromeres are rare human chromosomal aberrations in which a new centromere has formed in a previously non-centromeric location. We report the finding of a structurally abnormal X chromosome with a neocentromere in a 15-year-old girl with clinical features suggestive of Turner syndrome, including short stature and primary amenorrhea.
Result
G-banded chromosome analysis revealed a mosaic female karyotype involving two abnormal cell lines. One cell line (84% of analyzed metaphases) had a structurally abnormal X chromosome (duplication of the long arm and deletion of the short arm) and a normal X chromosome. The other cell line (16% of cells) exhibited monosomy X. C-banding studies were negative for the abnormal X chromosome. FISH analysis revealed lack of hybridization of the abnormal X chromosome with both the X centromere-specific probe and the “all human centromeres” probe, a pattern consistent with lack of the X chromosome endogenous centromere. A FISH study using an XIST gene probe revealed the presence of two XIST genes, one on each long arm of the iso(Xq), required for inactivation of the abnormal X chromosome. R-banding also demonstrated inactivation of the abnormal X chromosome. An assay for centromeric protein C (CENP-C) was positive on both the normal and the abnormal X chromosomes. The position of CENP-C in the abnormal X chromosome defined a neocentromere, which explains its mitotic stability. The karyotype is thus designated as 46,X,neo(X)(qter- > q12::q12- > q21.2- > neo- > q21.2- > qter)[42]/45,X[8], which is consistent with stigmata of Turner syndrome. The mother of this patient has a normal karyotype; however, the father was not available for study.
Conclusion
To our knowledge, this is the first case of mosaic Turner syndrome involving an analphoid iso(Xq) chromosome with a proven neocentromere among 90 previously described cases with a proven neocentromere.
doi:10.1186/1755-8166-5-29
PMCID: PMC3477003  PMID: 22682421
Neocentromere; Turner Syndrome; X-inactivation; Mosaicism
6.  Large inverted repeats within Xp11.2 are present at the breakpoints of isodicentric X chromosomes in Turner syndrome 
Human Molecular Genetics  2010;19(17):3383-3393.
Turner syndrome (TS) results from whole or partial monosomy X and is mediated by haploinsufficiency of genes that normally escape X-inactivation. Although a 45,X karyotype is observed in half of all TS cases, the most frequent variant TS karyotype includes the isodicentric X chromosome alone [46,X,idic(X)(p11)] or as a mosaic [46,X,idic(X)(p11)/45,X]. Given the mechanism of idic(X)(p11) rearrangement is poorly understood and breakpoint sequence information is unknown, this study sought to investigate the molecular mechanism of idic(X)(p11) formation by determining their precise breakpoint intervals. Karyotype analysis and fluorescence in situ hybridization mapping of eight idic(X)(p11) cell lines and three unbalanced Xp11.2 translocation lines identified the majority of breakpoints within a 5 Mb region, from ∼53 to 58 Mb, in Xp11.1–p11.22, clustering into four regions. To further refine the breakpoints, a high-resolution oligonucleotide microarray (average of ∼350 bp) was designed and array-based comparative genomic hybridization (aCGH) was performed on all 11 idic(X)(p11) and Xp11.2 translocation lines. aCGH analyses identified all breakpoint regions, including an idic(X)(p11) line with two potential breakpoints, one breakpoint shared between two idic(X)(p11) lines and two Xp translocations that shared breakpoints with idic(X)(p11) lines. Four of the breakpoint regions included large inverted repeats composed of repetitive gene clusters and segmental duplications, which corresponded to regions of copy-number variation. These data indicate that the rearrangement sites on Xp11.2 that lead to isodicentric chromosome formation and translocations are probably not random and suggest that the complex repetitive architecture of this region predisposes it to rearrangements, some of which are recurrent.
doi:10.1093/hmg/ddq250
PMCID: PMC2916707  PMID: 20570968
7.  The inv dup (15) or idic (15) syndrome (Tetrasomy 15q) 
The inv dup(15) or idic(15) syndrome displays distinctive clinical findings represented by early central hypotonia, developmental delay and intellectual disability, epilepsy, and autistic behaviour. Incidence at birth is estimated at 1 in 30,000 with a sex ratio of almost 1:1. Developmental delay and intellectual disability affect all individuals with inv dup(15) and are usually moderate to profound. Expressive language is absent or very poor and often echolalic. Comprehension is very limited and contextual. Intention to communicate is absent or very limited. The distinct behavioral disorder shown by children and adolescents has been widely described as autistic or autistic-like. Epilepsy with a wide variety of seizure types can occur in these individuals, with onset between 6 months and 9 years. Various EEG abnormalities have been described. Muscle hypotonia is observed in almost all individuals, associated, in most of them, with joint hyperextensibility and drooling. Facial dysmorphic features are absent or subtle, and major malformations are rare. Feeding difficulties are reported in the newborn period.
Chromosome region 15q11q13, known for its instability, is highly susceptible to clinically relevant genomic rearrangements, such as supernumerary marker chromosomes formed by the inverted duplication of proximal chromosome 15. Inv dup(15) results in tetrasomy 15p and partial tetrasomy 15q. The large rearrangements, containing the Prader-Willi/Angelman syndrome critical region (PWS/ASCR), are responsible for the inv dup(15) or idic(15) syndrome. Diagnosis is achieved by standard cytogenetics and FISH analysis, using probes both from proximal chromosome 15 and from the PWS/ASCR. Microsatellite analysis on parental DNA or methylation analysis on the proband DNA, are also needed to detect the parent-of-origin of the inv dup(15) chromosome. Array CGH has been shown to provide a powerful approach for identifying and detecting the extent of the duplication. The possible occurrence of double supernumerary isodicentric chromosomes derived from chromosome 15, resulting in partial hexasomy of the maternally inherited PWS/ASCR, should be considered in the differential diagnosis. Large idic(15) are nearly always sporadic. Antenatal diagnosis is possible. Management of inv dup(15) includes a comprehensive neurophysiologic and developmental evaluation. Survival is not significantly reduced.
The inv dup(15) or idic(15) syndrome can also be termed "tetrasomy 15q". About 160 patients have been reported in the medical literature [1-5].
doi:10.1186/1750-1172-3-30
PMCID: PMC2613132  PMID: 19019226
8.  Early recurrence in standard-risk medulloblastoma patients with the common idic(17)(p11.2) rearrangement 
Neuro-Oncology  2012;14(7):831-840.
Medulloblastoma is diagnosed histologically; treatment depends on staging and age of onset. Whereas clinical factors identify a standard- and a high-risk population, these findings cannot differentiate which standard-risk patients will relapse and die. Outcome is thought to be influenced by tumor subtype and molecular alterations. Poor prognosis has been associated with isochromosome (i)17q in some but not all studies. In most instances, molecular investigations document that i17q is not a true isochromosome but rather an isodicentric chromosome, idic(17)(p11.2), with rearrangement breakpoints mapping within the REPA/REPB region on 17p11.2. This study explores the clinical utility of testing for idic(17)(p11.2) rearrangements using an assay based on fluorescent in situ hybridization (FISH). This test was applied to 58 consecutive standard- and high-risk medulloblastomas with a 5-year minimum of clinical follow-up. The presence of i17q (ie, including cases not involving the common breakpoint), idic(17)(p11.2), and histologic subtype was correlated with clinical outcome. Overall survival (OS) and disease-free survival (DFS) were consistent with literature reports. Fourteen patients (25%) had i17q, with 10 (18%) involving the common isodicentric rearrangement. The presence of i17q was associated with a poor prognosis. OS and DFS were poor in all cases with anaplasia (4), unresectable disease (7), and metastases at presentation (10); however, patients with standard-risk tumors fared better. Of these 44 cases, tumors with idic(17)(p11.2) were associated with significantly worse patient outcomes and shorter mean DFS. FISH detection of idic(17)(p11.2) may be useful for risk stratification in standard-risk patients. The presence of this abnormal chromosome is associated with early recurrence of medulloblastoma.
doi:10.1093/neuonc/nos086
PMCID: PMC3379796  PMID: 22573308
FISH; idic(17)(p11.2); i17q; medulloblastoma; pediatric oncology
9.  Paradoxical worsening of seizure activity with pregabalin in an adult with isodicentric 15 (IDIC-15) syndrome involving duplications of the GABRB3, GABRA5 and GABRG3 genes 
BMC Neurology  2013;13:43.
Background
Isodicentric 15 syndrome (IDIC-15) is due to partial duplications of chromosome 15 that may includes the q11–13 region that includes genes encoding the α5 (GABRA5) and β3 - γ3 (GABRB3) receptor subunits. The disease causes intellectual and physical developmental delay, seizures, intellectual disability and behavioral disorders that may be related to abnormal GABA receptor function and morphology. Seizures are often severe and may be refractory to treatment. There are however no specific guidelines for the treatment of the seizures and it is unknown whether drugs that affect the GABAergic system have a different effect in IDIC-15 seizures.
Case presentation
We report the case of an adult individual with IDIC-15 whose complex-partial seizures worsened dramatically after the introduction of pregabalin, with increased seizure frequency, frequent generalization, and appearance of new seizure pattern. Her cognitive function and verbal skills also worsened during treatment with pregabalin. Her seizures and cognitive skills quickly improved after pregabalin was discontinued and treatment with lacosamide started.
Discussion
As her genetic testing confirmed that her region of duplication included GABA receptor encoding genes, it is plausible that the worsening of seizures were due to induction of an abnormal GABAergic response to pregabalin.
Conclusion
As her genetic testing confirmed that her region of duplication included GABA receptor encoding genes, it is plausible that the worsening of seizures were due to induction of an abnormal GABAergic response to pregabalin.This case may help define proper therapeutic strategies for the treatment of IDIC-15 associated seizures.
doi:10.1186/1471-2377-13-43
PMCID: PMC3660219  PMID: 23663378
IDIC-15; GABA receptors; Pregabalin; Seizures; Lacosamide
10.  Structural aberration of the X chromosome in a patient with gonadal dysgenesis: an approach to karyotype-phenotype correlation. 
Journal of Medical Genetics  1981;18(3):228-231.
An 18-year-old female with some stigmata of pure dysgenesis had a chromosome constitution of 46,X,dir dup(X) (pter leads to q27: :q21 leads to qter). The abnormal chromosome was always late replicating. The clinical and cytogenetic picture is compared with that of patients with X;X translocation and some problems of karyotype-phenotype correlation are discussed.
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PMCID: PMC1048711  PMID: 7241547
11.  DDX11L: a novel transcript family emerging from human subtelomeric regions 
BMC Genomics  2009;10:250.
Background
The subtelomeric regions of human chromosomes exhibit an extraordinary plasticity. To date, due to the high GC content and to the presence of telomeric repeats, the subtelomeric sequences are underrepresented in the genomic libraries and consequently their sequences are incomplete in the finished human genome sequence, and still much remains to be learned about subtelomere organization, evolution and function. Indeed, only in recent years, several studies have disclosed, within human subtelomeres, novel gene family members.
Results
During a project aimed to analyze genes located in the telomeric region of the long arm of the human X chromosome, we have identified a novel transcript family, DDX11L, members of which map to 1pter, 2q13/14.1, 2qter, 3qter, 6pter, 9pter/9qter, 11pter, 12pter, 15qter, 16pter, 17pter, 19pter, 20pter/20qter, Xpter/Xqter and Yqter. Furthermore, we partially sequenced the underrepresented subtelomeres of human chromosomes showing a common evolutionary origin.
Conclusion
Our data indicate that an ancestral gene, originated as a rearranged portion of the primate DDX11 gene, and propagated along many subtelomeric locations, is emerging within subtelomeres of human chromosomes, defining a novel gene family. These findings support the possibility that the high plasticity of these regions, sites of DNA exchange among different chromosomes, could trigger the emergence of new genes.
doi:10.1186/1471-2164-10-250
PMCID: PMC2705379  PMID: 19476624
12.  Cytogenetic and clinical characteristics of a case involving complete duplication of Xpter-->Xq13. 
Journal of Medical Genetics  1996;33(3):237-239.
True isochromosomes for Xp probably do not exist in a liveborn. We describe a rare case of complete Xp duplication and retention of the inactivation centre at Xq13. Cytogenetically, it is described as a nonmosaic 46,X,psu idic(X)(q13). Complete duplication of Xpter-->Xq13 was confirmed by banded analysis and FISH probes for X centromere, Xp21, XIST locus, and whole chromosome paints for X and Y. The abnormal X was always late replicating. Clinically, the patient was short statured, had primary amenorrhoea, and incomplete development of secondary sexual characteristics, but otherwise was phenotypically normal. There are no non-mosaic reported cases with complete duplication of i(Xp) confirmed by FISH or molecular techniques. Those cases with partial duplication of Xp and presence of the inactivation centre share the traits of amenorrhoea and poor secondary sexual development. To develop a clinical profile of duplication of Xp (in presence of Xq13) there is a need to study more cases.
Images
PMCID: PMC1051876  PMID: 8728700
13.  Copy number alterations in small intestinal neuroendocrine tumors determined by array comparative genomic hybridization 
BMC Cancer  2013;13:505.
Background
Small intestinal neuroendocrine tumors (SI-NETs) are typically slow-growing tumors that have metastasized already at the time of diagnosis. The purpose of the present study was to further refine and define regions of recurrent copy number (CN) alterations (CNA) in SI-NETs.
Methods
Genome-wide CNAs was determined by applying array CGH (a-CGH) on SI-NETs including 18 primary tumors and 12 metastases. Quantitative PCR analysis (qPCR) was used to confirm CNAs detected by a-CGH as well as to detect CNAs in an extended panel of SI-NETs. Unsupervised hierarchical clustering was used to detect tumor groups with similar patterns of chromosomal alterations based on recurrent regions of CN loss or gain. The log rank test was used to calculate overall survival. Mann–Whitney U test or Fisher’s exact test were used to evaluate associations between tumor groups and recurrent CNAs or clinical parameters.
Results
The most frequent abnormality was loss of chromosome 18 observed in 70% of the cases. CN losses were also frequently found of chromosomes 11 (23%), 16 (20%), and 9 (20%), with regions of recurrent CN loss identified in 11q23.1-qter, 16q12.2-qter, 9pter-p13.2 and 9p13.1-11.2. Gains were most frequently detected in chromosomes 14 (43%), 20 (37%), 4 (27%), and 5 (23%) with recurrent regions of CN gain located to 14q11.2, 14q32.2-32.31, 20pter-p11.21, 20q11.1-11.21, 20q12-qter, 4 and 5. qPCR analysis confirmed most CNAs detected by a-CGH as well as revealed CNAs in an extended panel of SI-NETs. Unsupervised hierarchical clustering of recurrent regions of CNAs revealed two separate tumor groups and 5 chromosomal clusters. Loss of chromosomes 18, 16 and 11 and again of chromosome 20 were found in both tumor groups. Tumor group II was enriched for alterations in chromosome cluster-d, including gain of chromosomes 4, 5, 7, 14 and gain of 20 in chromosome cluster-b. Gain in 20pter-p11.21 was associated with short survival. Statistically significant differences were observed between primary tumors and metastases for loss of 16q and gain of 7.
Conclusion
Our results revealed recurrent CNAs in several candidate regions with a potential role in SI-NET development. Distinct genetic alterations and pathways are involved in tumorigenesis of SI-NETs.
doi:10.1186/1471-2407-13-505
PMCID: PMC3819709  PMID: 24165089
Small intestine; Neuroendocrine tumor; Carcinoid; Array CGH; Chromosome 18
14.  Multiple copies of BCR-ABL fusion gene on two isodicentric Philadelphia chromosomes in an imatinib mesylate-resistant chronic myeloid leukemia patient 
Oncology Letters  2013;5(5):1579-1582.
The so-called Philadelphia (Ph) chromosome is present in more than 90% of chronic myeloid leukemia (CML) cases. Amplification or duplication of the BCR-ABL gene has been found to be one of the key factors leading to drug resistance to imatinib mesylate (IM). In the present study, we identified the presence of isodicentric Ph chromosomes [idic(Ph)] in an IM-resistant patient. Fluorescence in situ hybridization (FISH) analysis on metaphase chromosomes confirmed the heterogeneity and amplification of the fused BCR-ABL gene. FISH analysis superimposed on G-banding confirmed the presence of idic(Ph) chromosomes. Reverse transcription-polymerase chain reaction (RT-PCR) products revealed the presence of the BCR-ABL fusion transcript b3a2. The idic(Ph) chromosomes in CML were shown to be fused at the satellite regions of the short arms. The patient did not respond to IM chemotherapy and did not achieve remission. In this study, the impact of the idic(Ph) chromosomes on genomic instability, heterogeneity and amplification of the BCR-ABL gene in IM-resistant patients is discussed.
doi:10.3892/ol.2013.1225
PMCID: PMC3678658  PMID: 23761821
chronic myeloid leukemia; isodicentric Philadelphia chromosomes; fluorescence in situ hybridization; imatinib mesylate
15.  Trisomy 1q41-qter and monosomy 3p26.3-pter in a family with a translocation (1;3): further delineation of the syndromes 
BMC Medical Genomics  2014;7:55.
Background
Trisomy 1q and monosomy 3p deriving from a t(1;3) is an infrequent event. The clinical characteristics of trisomy 1q41-qter have been described but there is not a delineation of the syndrome. The 3p25.3-pter monosomy syndrome (MIM 613792) characteristics include low birth weight, microcephaly, psychomotor and growth retardation and abnormal facies.
Case presentation
A 2 years 8 months Mexican mestizo male patient was evaluated due to a trisomy 1q and monosomy 3p derived from a familial t(1;3)(q41;q26.3). Four female carriers of the balanced translocation and one relative that may have been similarly affected as the proband were identified. The implicated chromosomal regions were defined by microarray analysis, the patient had a trisomy 1q41-qter of 30.3 Mb in extension comprising about 240 protein coding genes and a monosomy 3p26.3-pter of 1.7 Mb including only the genes CNTN6 (MIM 607220) and CHL1 (MIM 607416), which have been implicated in dendrite development. Their contribution to the phenotype, regarding the definition of trisomy 1q41-qter and monosomy 3p26.3-pter syndromes are discussed.
Conclusion
We propose that a trisomy 1q41-qter syndrome should be considered in particular when the following characteristics are present: postnatal growth delay, macrocephaly, wide fontanelle, triangular facies, frontal bossing, thick eye brows, down slanting palpebral fissures, hypertelorism, flat nasal bridge, hypoplasic nostrils, long filtrum, high palate, microretrognathia, ear abnormalities, neural abnormalities (in particular ventricular dilatation), psychomotor developmental delay and mental retardation. Our patient showed most of these clinical characteristics with exception of macrocephaly, possibly due to a compensatory effect by haploinsufficiency of the two genes lost from 3p. The identification of carriers has important implications for genetic counseling as the risk of a new born with either a der(3) or der(1) resulting from an adjacent-1 segregation is of 25% for each of them, as the products of adjacent-2 or 3:1 segregations are not expected to be viable.
doi:10.1186/1755-8794-7-55
PMCID: PMC4170088  PMID: 25223409
Chromosomal rearrangement; Trisomy 1q41-qter; Monosomy 3p26.3-pter; Balanced translocation
16.  Dicentric X isochromosomes in man. 
Journal of Medical Genetics  1976;13(6):496-500.
Four cases of Turner's syndrome are presented in which an apparent X isochromosome i(Xq) has been found to possess two regions of centromeric heterochromatin. It is suggested that these chromosomes were isodicentric structures capable of functioning as monocentric elements as a result of the inactivation of one centromere. The prevalence of mosaicism is believed to be a consequence of the dicentric nature of these chromosomes, and it is considered possible that a high proportion of X isochromosmes are structurally dicentric. Banding patterns showed that the exchange site involved in the formation of the dicentric chromosome was different in at least three of the cases.
Images
PMCID: PMC1013476  PMID: 1018308
17.  Severe phenotype resulting from an active ring X chromosome in a female with a complex karyotype: characterisation and replication study. 
Journal of Medical Genetics  1998;35(11):932-938.
We report on the characterisation of a complex chromosome rearrangement, 46,X,del(Xq)/47,X,del(Xq),+r(X), in a female newborn with multiple malformations. Cytogenetic and molecular methods showed that the del(Xq) contains the XIST locus and is non-randomly inactivated in all metaphases. The tiny r(X) chromosome gave a positive FISH signal with UBE1, ZXDA, and MSN cosmid probes, but not with a XIST cosmid probe. Moreover, it has an active status, as shown by a very short (three hour) terminal BrdU pulse followed by fluorescent anti-BrdU antibody staining. The normal X is of paternal origin and both rearranged chromosomes originate from the same maternal chromosome. We suggest that both abnormal chromosomes result from the three point breakage of a maternal isodicentric idic(X)(q21.1). Finally, the phenotype of our patient is compared to other published cases and, despite the absence of any 45,X clone, it appears very similar to those with a 45,X/46,X,r(X) karyotype where the tiny r(X) is active.
Images
PMCID: PMC1051487  PMID: 9832041
18.  Multiple forms of atypical rearrangements generating supernumerary derivative chromosome 15 
BMC Genetics  2008;9:2.
Background
Maternally-derived duplications that include the imprinted region on the proximal long arm of chromosome 15 underlie a complex neurobehavioral disorder characterized by cognitive impairment, seizures and a substantial risk for autism spectrum disorders[1]. The duplications most often take the form of a supernumerary pseudodicentric derivative chromosome 15 [der(15)] that has been called inverted duplication 15 or isodicentric 15 [idic(15)], although interstitial rearrangements also occur. Similar to the deletions found in most cases of Angelman and Prader Willi syndrome, the duplications appear to be mediated by unequal homologous recombination involving low copy repeats (LCR) that are found clustered in the region. Five recurrent breakpoints have been described in most cases of segmental aneuploidy of chromosome 15q11-q13 and previous studies have shown that most idic(15) chromosomes arise through BP3:BP3 or BP4:BP5 recombination events.
Results
Here we describe four duplication chromosomes that show evidence of atypical recombination events that involve regions outside the common breakpoints. Additionally, in one patient with a mosaic complex der(15), we examined homologous pairing of chromosome 15q11-q13 alleles by FISH in a region of frontal cortex, which identified mosaicism in this tissue and also demonstrated pairing of the signals from the der(15) and the normal homologues.
Conclusion
Involvement of atypical BP in the generation of idic(15) chromosomes can lead to considerable structural heterogeneity.
doi:10.1186/1471-2156-9-2
PMCID: PMC2249594  PMID: 18177502
19.  Balanced reciprocal whole arm translocation t(3;9): analysis by fluorescence in situ hybridisation. 
Journal of Medical Genetics  1994;31(1):74-75.
A patient with Turner phenotype was found to carry two de novo chromosome aberrations: a 45,X line and a whole arm reciprocal translocation t(3;9). Fluorescence in situ hybridisation on metaphase cells using alpha satellite DNA for chromosome 3 and beta satellite and 'classical' satellite DNA for chromosome 9 showed that the centromeric region of chromosome 3 was retained in the 3q9q translocation derivative, as was the secondary constriction heterochromatin of chromosome 9. No signals were observed in the 3p9p derivative with the three probes. This suggests that the breakpoints were on 3p11 and 9q11. The karyotype was 45,X,t(3;9)(3qter-->3p11::9q11-->9qter; 9qter-->9q11::3p11-->3pter).
Images
PMCID: PMC1049606  PMID: 8151645
20.  Clinically abnormal case with paternally derived partial trisomy 8p23.3 to 8p12 including maternal isodisomy of 8p23.3: a case report 
Background
Because of low copy repeats (LCRs) and common inversion polymorphisms, the human chromosome 8p is prone to a number of recurrent rearrangements. Each of these rearrangements is associated with several phenotypic features. We report on a patient with various clinical malformations and developmental delay in connection with an inverted duplication event, involving chromosome 8p.
Methods
Chromosome analysis, multicolor banding analysis (MCB), extensive fluorescence in situ hybridization (FISH) analysis and microsatellite analysis were performed.
Results
The karyotype was characterized in detail by multicolor banding (MCB), subtelomeric and centromere-near probes as 46,XY,dup(8)(pter->p23.3::p12->p23.3::p23.3->qter). Additionally, microsatellite analysis revealed the paternal origin of the duplication and gave hints for a mitotic recombination involving about 6 MB in 8p23.3.
Conclusion
A comprehensive analysis of the derivative chromosome 8 suggested a previously unreported mechanism of formation, which included an early mitotic aberration leading to maternal isodisomy, followed by an inverted duplication of the 8p12p23.3 region.
doi:10.1186/1755-8166-2-14
PMCID: PMC2715415  PMID: 19566937
21.  Association of cytogenetic abnormalities in a neuroblastoma and fragile sites expression. 
British Journal of Cancer  1988;58(3):287-291.
A 15 month old boy with a stage IV right suprarenal gland neuroblastoma showed a number of raised biochemical parameters, whilst catecholamines and skeletal survey were normal. Treatment with peptichemio failed to give a clinical response. Histological evidence of neuroblastoma infiltration in the bone marrow aspirate was absent. Immunofluorescence on sedimented cells was negative using antibody UJ223.8, PI153/3 and H11; only UJ308 and to a lesser extent UJ13A gave positive results. After 21 days, however, the same cells in culture showed highly differentiated dendritic processes. Thirty-seven percent metaphases from bone marrow aspirate showed the following karyotype 45XY, del (1) (p32), and two markers. Mar1 = der (2) t (2; 2) (2qter----2q14::2p24----2qter). Mar2 = der (15) t (15; 2) (15qter----15p11::2p11----2pter). Treatment with methotrexate reduced the aberrant mitoses rate to 2%. N-myc in situ hybridisation showed significant signal on both markers confirming the cytogenetic interpretation. Peripheral blood lymphocytes at 72 h showed a higher level of breaks per cell than control. After treatment with aphidicolin (APC) or methotrexate (MTX) for the last 24 h, to induce fragile sites, the incidence of breaks per cells was increased. Moreover 11.4% of APC-induced breaks were in 1p31-32 (mean of normal controls = 2.3%). The mother presented an increased sensitivity to the inducibility of fragile sites, while the father's lymphocytes showed values within the control range. The genetic changes produced by the abnormalities on chromosomes 1 and 2 might be related to tumour progression. Furthermore this is the first description of correlation between a high frequency of fragile site 1p31-32 induced by APC in the patient's lymphocytes and deletion of 1p32 in tumour cells. The interpretation of these findings and of other similar correlations needs further study.
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PMCID: PMC2246604  PMID: 3179179
22.  Role of ATRX in chromatin structure and function: implications for chromosome instability and human disease 
Reproduction (Cambridge, England)  2011;142(2):221-234.
Functional differentiation of chromatin structure is essential for the control of gene expression, nuclear architecture, and chromosome stability. Compelling evidence indicates that alterations in chromatin remodeling proteins play an important role in the pathogenesis of human disease. Among these, α-thalassemia mental retardation X-linked protein (ATRX) has recently emerged as a critical factor involved in heterochromatin formation at mammalian centromeres and telomeres as well as facultative heterochromatin on the murine inactive X chromosome. Mutations in human ATRX result in an X-linked neurodevelopmental condition with various degrees of gonadal dysgenesis (ATRX syndrome). Patients with ATRX syndrome may exhibit skewed X chromosome inactivation (XCI) patterns, and ATRX-deficient mice exhibit abnormal imprinted XCI in the trophoblast cell line. Non-random or skewed XCI can potentially affect both the onset and severity of X-linked disease. Notably, failure to establish epigenetic modifications associated with the inactive X chromosome (Xi) results in several conditions that exhibit genomic and chromosome instability such as fragile X syndrome as well as cancer development. Insight into the molecular mechanisms of ATRX function and its interacting partners in different tissues will no doubt contribute to our understanding of the pathogenesis of ATRX syndrome as well as the epigenetic origins of aneuploidy. In turn, this knowledge will be essential for the identification of novel drug targets and diagnostic tools for cancer progression as well as the therapeutic management of global epigenetic changes commonly associated with malignant neoplastic transformation.
doi:10.1530/REP-10-0380
PMCID: PMC3253860  PMID: 21653732
23.  Screening for subtelomeric rearrangements in 210 patients with unexplained mental retardation using multiplex ligation dependent probe amplification (MLPA) 
Journal of Medical Genetics  2004;41(12):892-899.
Background: Subtelomeric rearrangements contribute to idiopathic mental retardation and human malformations, sometimes as distinct mental retardation syndromes. However, for most subtelomeric defects a characteristic clinical phenotype remains to be elucidated.
Objective: To screen for submicroscopic subtelomeric aberrations using multiplex ligation dependent probe amplification (MLPA).
Methods: 210 individuals with unexplained mental retardation were studied. A new set of subtelomeric probes, the SALSA P036 human telomere test kit, was used.
Results: A subtelomeric aberration was identified in 14 patients (6.7%) (10 deletions and four duplications). Five deletions were de novo; four were inherited from phenotypically normal parents, suggesting that these were polymorphisms. For one deletion, DNA samples of the parents were not available. Two de novo submicroscopic duplications were detected (dup 5qter, dup 12pter), while the other duplications (dup 18qter and dup 22qter) were inherited from phenotypically similarly affected parents. All clinically relevant aberrations (de novo or inherited from similarly affected parents) occurred in patients with a clinical score of ⩾3 using an established checklist for subtelomeric rearrangements. Testing of patients with a clinical score of ⩾3 increased the diagnostic yield twofold to 12.4%. Abnormalities with clinical relevance occurred in 6.3%, 5.1%, and 1.7% of mildly, moderately, and severely retarded patients, respectively, indicating that testing for subtelomeric aberrations among mildly retarded individuals is necessary.
Conclusions: The value of MLPA is confirmed. Subtelomeric screening can be offered to all mentally retarded patients, although clinical preselection increases the percentage of chromosomal aberrations detected. Duplications may be a more common cause of mental retardation than has been appreciated.
doi:10.1136/jmg.2004.023671
PMCID: PMC1735655  PMID: 15591274
24.  A long non-coding RNA is required for targeting centromeric protein A to the human centromere 
eLife  2014;3:e03254.
The centromere is a specialized chromatin region marked by the histone H3 variant CENP-A. Although active centromeric transcription has been documented for over a decade, the role of centromeric transcription or transcripts has been elusive. Here, we report that centromeric α-satellite transcription is dependent on RNA Polymerase II and occurs at late mitosis into early G1, concurrent with the timing of new CENP-A assembly. Inhibition of RNA Polymerase II-dependent transcription abrogates the recruitment of CENP-A and its chaperone HJURP to native human centromeres. Biochemical characterization of CENP-A associated RNAs reveals a 1.3 kb molecule that originates from centromeres, which physically interacts with the soluble pre-assembly HJURP/CENP-A complex in vivo, and whose down-regulation leads to the loss of CENP-A and HJURP at centromeres. This study describes a novel function for human centromeric long non-coding RNAs in the recruitment of HJURP and CENP-A, implicating RNA-based chaperone targeting in histone variant assembly.
DOI: http://dx.doi.org/10.7554/eLife.03254.001
eLife digest
Before a cell divides, it copies its chromosomes. Initially, the two copies of each chromosome remain linked via their centromeres. These regions also serve as the attachment sites for the proteins that pull these two copies apart, and eventually segregate the chromosomes equally between the two newly formed cells.
Chromosome segregation is the main function of centromeres; and in most organisms, the DNA in these regions is highly repetitive and is not thought to encode any proteins. However, it has been observed that cells need enzymes called RNA polymerases—which transcribe stretches of DNA into RNA molecules—to be able to separate the copies of their chromosomes correctly. This suggests that RNAs transcribed from centromeres might be required for cell division, but the identity and function of these RNAs remained elusive.
Quénet and Dalal have now discovered that an RNA polymerase localizes to the DNA in human centromeres and produces RNA molecules during the early stages of the cell cycle. Two proteins—one called CENP-A and another that functions as its chaperone—that normally bind to the centromere and determine its structure were found less often in this region of the chromosome if the activity of the RNA polymerase was inhibited. Quénet and Dalal identified a specific RNA molecule that is transcribed from the centromeric DNA, which directly binds to the CENP-A protein and its chaperone before CENP-A is assembled onto the centromeric DNA. Reducing the levels of this RNA within the cells made them unable to separate their chromosomes correctly during cell divisions. Quénet and Dalal also demonstrated that this centromeric RNA is needed to specifically target both the CENP-A protein, via its chaperone, to the centromere.
The findings of Quénet and Dalal demonstrate that RNAs produced from a specific part of the chromosome can help target DNA-binding proteins back to that region's DNA sequence. Following on from this work, the next challenge will be to determine if other RNA molecules are used for the same purpose in humans and other species.
DOI: http://dx.doi.org/10.7554/eLife.03254.002
doi:10.7554/eLife.03254
PMCID: PMC4145801  PMID: 25117489
histone variants; chromatin; centromeres; CENP-A; epigenetics; lncRNA; human
25.  A duplication/deficient X chromosome in a girl with mental retardation and dysmorphic features. 
Journal of Medical Genetics  1988;25(4):264-267.
A structurally abnormal X chromosome was found in a nine year old girl with mild mental retardation and dysmorphic features. Subsequent clinical examination at 18 years of age showed tall stature and gonadal dysgenesis. Re-examination of her karyotype using a variety of banding techniques on prometaphase chromosomes allowed the identification of the abnormal chromosome as a duplication/deficient X chromosome, 46,Xder X(pter----q28::p11.2----pter). The clinical features are discussed in terms of karyotype/phenotype correlation.
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PMCID: PMC1015512  PMID: 3367354

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