Forty four probands with an additional "marker" chromosome

Supernumerary Marker Chromosome Identified in Asian Elephant (Elephas maximus)

We identified a small, supernumerary marker chromosome (sSMC) in two phenotypically normal Asian elephants (Elephas maximus): a female (2n = 57,XX,+mar) and her male offspring (2n = 57,XY,+mar). sSMCs are defined as structurally abnormal chromosomes that cannot be identified by conventional banding analysis since they are usually small and often lack distinct banding patterns. Although current molecular techniques can reveal their origin, the mechanism of their formation is not yet fully understood. We determined the origin of the marker using a suite of conventional and molecular cytogenetic approaches that included (a) G- and C-banding, (b) AgNOR staining, (c) preparation of a DNA clone using laser microdissection of the marker chromosome, (d) FISH with commercially available human painting and telomeric probes, and (e) FISH with centromeric DNA derived from the centromeric regions of a marker-free Asian elephant. Moreover, we present new information on the location and number of NORs in Asian and savanna elephants. We show that the metacentric marker was composed of heterochromatin with NORs at the terminal ends, originating most likely from the heterochromatic region of chromosome 27. In this context, we discuss the possible mechanism of marker formation. We also discuss the similarities between sSMCs and B chromosomes and whether the marker chromosome presented here could evolve into a B chromosome in the future.

Rare partial trisomy and tetrasomy of 15q11-q13 associated with developmental delay and autism spectrum disorder

Background

Small supernumerary marker chromosomes (sSMCs), are additional abnormal chromosomes, which can’t be detected accurately by banding cytogenetic analysis. Abnormal phenotypes were observed in about 30% of SMC carriers. Duplication of chromosome 15 and related disorders, characterized by hypotonia motor delays, autism spectrum disorder (ASD), intellectual disability, and epilepsy including infantile spasms, might be account for 50% of the total sSMCs.

Case presentation

An 11-month-old infant with an sSMC found by banding cytogenetics was referred to our clinic because of developmental retardation and autism spectrum disorder. After several months of rehabilitation treatment, the progress of motor development was obvious, but the consciousness was still far from satisfied. High-resolution karyotype analysis, multiplex ligation-dependent probe amplification and copy number variation sequencing (CNV-Seq) were conducted to confirm the identity of the sSMC. A bisatellited dicentric sSMC was observed clearly in high-resolution karyotype analysis and a 10.16-Mb duplication of 15q11.1q13.2 (3.96 copies) together with a 1.84-Mb duplication of 15q13.2q13.3 (3 copies) was showed by CNV-Seq in the proband. It suggested that the molecular cytogenetic karyotype was 47,XY,+dic(15;15)(q13.2;q13.3). Furthermore, the clinical symptoms of the proband mostly fit 15q duplication related disorders which are characterized by hypotonia motor delays, autism spectrum disorder (ASD), and intellectual disability.

Conclusion

We reported for the first time using CNV-Seq to detect sSMCs and find a partial trisomy and tetrasomy of 15q11-q13 associated with developmental delay and autism spectrum disorder. Our report indicates that CNV-seq is a useful and economical way for diagnosis of dup15q and related disorders.

Genomic characterization of chromosome 8 pericentric trisomy

We present a patient with trisomy 8p11.21q11.21 associated with language, gross motor, fine motor, and cognitive delay. Furthermore, using array-based comparative genomic hybridization, we identify the specific genes duplicated in our patient.

Two cases of recurrent abortion in which isodicentric chromosome 15 was observed in the husbands

We report two cases of women positive for anticardiolipin antibodies who experienced recurrent abortion whose husbands had isodicentric chromosome 15 aberrations who eventually had successful pregnancies. Two women were referred to our hospital due to their medical history of recurrent abortion. Both were diagnosed as being positive for anticardiolipin antibodies and their husbands with isodicentric chromosome 15. After both patients were treated with a Japanese herbal medicine (Sairei-to) and low-dose aspirin for the positive anticardiolipin antibodies, they delivered appropriate-for-date infants at term gestation. Although both husbands were revealed to have isodicentric chromosome 15, and coincidentally both wives were positive for anticardiolipin antibodies, their next pregnancies continued uneventfully as a result of the treatment.

A case of isodicentric chromosome 15 presented with epilepsy and developmental delay

We report a case of isodicentric chromosome 15 (idic(15) chromosome), the presence of which resulted in uncontrolled seizures, including epileptic spasms, tonic seizures, and global developmental delay. A 10-month-old female infant was referred to our pediatric neurology clinic because of uncontrolled seizures and global developmental delay. She had generalized tonic-clonic seizures since 7 months of age. At referral, she could not control her head and presented with generalized hypotonia. Her brain magnetic resonance imaging scans and metabolic evaluation results were normal. Routine karyotyping indicated the presence of a supernumerary marker chromosome of unknown origin (47, XX +mar). An array-comparative genomic hybridization (CGH) analysis revealed amplification from 15q11.1 to 15q13.1. Subsequent fluorescence in situ hybridization analysis confirmed a idic(15) chromosome. Array-CGH analysis has the advantage in determining the unknown origin of a supernumerary marker chromosome, and could be a useful method for the genetic diagnosis of epilepsy syndromes associated with various chromosomal aberrations.

Differences between the pattern of developmental abnormalities in autism associated with duplications 15q11.2-q13 and idiopathic autism

The purposes of this study were to identify differences in patterns of developmental abnormalities between the brains of individuals with autism of unknown etiology and those of individuals with duplications of chromosome 15q11.2-q13 (dup[15]) and autism and to identify alterations that may contribute to seizures and sudden death in the latter. Brains of 9 subjects with dup(15), 10 with idiopathic autism, and 7 controls were examined. In the dup(15) cohort, 7 subjects (78%) had autism, 7 (78%) had seizures, and 6 (67%) had experienced sudden unexplained death. Subjects with dup(15) autism were microcephalic, with mean brain weights 300 g less (1,177 g) than those of subjects with idiopathic autism (1,477 g; p<0.001). Heterotopias in the alveus, CA4, and dentate gyrus and dysplasia in the dentate gyrus were detected in 89% of dup(15) autism cases but in only 10% of idiopathic autism cases (p < 0.001). By contrast, cerebral cortex dysplasia was detected in 50% of subjects with idiopathic autism and in no dup(15) autism cases (p<0.04). The different spectrum and higher prevalence of developmental neuropathologic findings in the dup(15) cohort than in cases with idiopathic autism may contribute to the high risk of early onset of seizures and sudden death.

Array comparative genomic hybridization analysis of small supernumerary marker chromosomes in human infertility

Small supernumerary marker chromosomes (sSMC) are structurally abnormal chromosomes that cannot be unambiguously identified by conventional banding cytogenetics. This study describes four patients with sSMC in relation with infertility. Patient 1 had primary infertility. His brother, fertile, carried the same sSMC (patient 2). Patient 3 presented polycystic ovary syndrome and patient 4 primary ovarian insufficiency. Cytogenetic studies, array comparative genomic hybridization (CGH) and sperm analyses were compared with cases previously reported. sSMC corresponded to the 15q11.2 region (patients 1 and 2), the centromeric chromosome 15 region (patient 3) and the 21p11.2 region (patient 4). Array CGH showed 3.6-Mb gain for patients 1 and 2 and 0.266-Mb gain for patient 4. Sperm fluorescent in-situ hybridization analyses found ratios of 0.37 and 0.30 of sperm nuclei with sSMC(15) for patients 1 and 2, respectively (P < 0.001). An increase of sperm nuclei with disomy X, Y and 18 was noted for patient 1 compared with control and patient 2 (P < 0.001). Among the genes mapped in the unbalanced chromosomal regions, POTE B and BAGE are related to the testis and ovary, respectively. The implication of sSMC in infertility could be due to duplication, but also to mechanical effects perturbing meiosis.

Three supernumerary marker chromosomes in a patient with developmental delay, mental retardation, and dysmorphic features

We characterized three supernumerary marker chromosomes (SMCs) simultaneously present in a 2-year- and 10-month-old male patient with mental retardation and dysmorphic features. Peripheral blood chromosome analysis revealed two to three SMCs in 25/26 cells analyzed. The remaining one cell had one SMC. Microarray comparative genomic hybridization (aCGH) showed mosaicism for gains of 5q35.3, 15q11.2q13.3, and 18p11.21q11.1 regions. All three gains contain multiple OMIM genes. FISH studies indicated that one of the SMCs is a dicentric ring 15 with two copies of the 15q11.2q13.3 region including SNRPN/UBE3A and two copies of the 5q35.3 region. One of the der(18)s contains the 18 centromere and 18p11.2 regions, while the other der(18) has a signal for the 18 centromere only. The phenotype of the patient is compared with that of patients with tetrasomy 15q11.2q13.3, trisomy 5q35.3, and trisomy 18p11.2. Our study demonstrates that aCGH and FISH analyses are powerful tools, which complement the conventional cytogenetic analysis for the identification of SMCs.

Characterization of sSMC by FISH and molecular techniques

Small supernumerary marker chromosome (sSMC) is a structurally altered additional chromosome that may not be explicitly clarified by conventional karyotyping alone. About one third of sSMC carriers have abnormal phenotypes and its clinical correlation is difficult, especially in prenatal studies. The present study was aimed at characterizing 19 sSMC identified in 15 patients with dysmorphic features with or without multiple congenital anomalies, conspicuous family history, short stature and/or ambiguous genitalia. All the sSMC were primarily identified by routine cytogenetics studies (performed with banding techniques) from peripheral blood except in one patient, where amniotic fluid was used. All sSMCs were further characterized by array-CGH (using 44 K oligonucleotide probe) and/or fluorescence in situ hybridization (FISH) using multicolor banding (MCB), centromere specific multicolor FISH (cenM-FISH), subcentromere-specific multicolor FISH (subcenM-FISH), micro-dissection and/or reverse FISH. This report demonstrates the worth of advanced molecular (cyto)genetic techniques in characterizing sSMC, their utility in genotype-phenotype correlation and risk of clinical presentation.

A longitudinal follow-up study of autistic symptoms in children and adults with duplications of 15q11-13

We completed a longitudinal follow-up of autistic symptoms in a cohort of children and young adults with duplications of chromosome 15q11-13. In our initial investigation of 29 individuals, tentative conclusions were drawn based on cross-sectional data suggesting that autistic symptoms increased with age, most specifically in the area of social interaction. We were able to re-assess 22 individuals from the original study an average of 7 years later using the same standardized autism screening measure. As predicted, autistic symptoms were found to increase for the younger children in the cohort but remained constant for the older participants. This global change in autistic symptoms among the younger children could not be ascribed to any particular autism subscale and reflects small but cumulatively significant increases across several domains.

Small supernumerary marker chromosome originating from chromosome 10 associated with an apparently normal phenotype

Small supernumerary marker chromosomes (sSMC) originating from chromosome 10 are rare. Only seven cases have been documented, and among those three cases were diagnosed prenatally. We reported on another prenatal diagnosis of a de novo mosaic sSMC in an apparently normal female fetus whose mother had conceived with assisted reproductive technology (ART) procedures. G-banding analysis of amniotic cells was performed. Spectral karyotyping (SKY) and fluorescence in situ hybridization (FISH) studies with chromosome 10-specific alphoid satellite DNA probe were used to identify the chromosome 10 origin of the sSMC. Further FISH study with telomeric sequence probes showed that the sSMC lacked a hybridization signal, suggesting that the marker could be a ring chromosome. FISH studies using BAC clone probes specific for the regions within 10p11.2, 10q11.1, and 10q11.2 showed that the short arm breakpoint was located between 29.8 and 30.7 Mb from the 10p telomere, and that the long arm breakpoint was located less than 43.6 Mb from the 10p telomere. The karyotype of the fetus was 47,XX,+mar. ish der(10)(SKY+ CEP 10+, CTD-2130I7+, RP11-89J23-)/46,XX. Oligonucleotide microarray-based copy number variations (CNV) analysis was also performed and showed a 6.7 Mb duplication from 10p11.2 to 10q11.2 (36.2-42.9 Mb) with Affymetrix SNP-array 6.0 genotype: arr cgh. 10p11.2q11.2(CN_519687 --> CN_541524) X 3. At the 1-year follow-up, the baby did not have any findings of the trisomy 10p syndrome. This observation provided further credence to the concept that additional chromosome material of proximal 10p11.2 may not contribute to the trisomy 10p syndrome phenotype.

Persistence of derivative chromosome 22 after achieving a major molecular response in chronic myeloid leukemia with a cryptic BCR-ABL1 fusion gene

We herein report the findings of a 47-year-old Japanese female with chronic myeloid leukemia (CML) with a cryptic BCR-ABL1 transcript on chromosome 9 and a derivative chromosome 22 unrelated to BCR-ABL1. Although she achieved and continued to demonstrate a major molecular response to imatinib treatment following interferon-alpha, there was persistence of a derivative chromosome 22. A detailed chromosome/molecular studies, including serial karyotyping analysis, finally resulted in the karyotyping at the disease onset to be 47,XX,+del(22)(q11.2), with two genetic evens, namely a cryptic BCR-ABL1 transcript on chromosome 9 and derivative chromosome 22 unrelated to BCR-ABL1. This CML case with these two rare genetic events thus raises diagnostic issues such as the difficulty in making a concise evaluation of the chromosomal/molecular events and an accurate disease prognosis, as well as the difficulty in determining the disease remission status after treatment.

A case of an infertile male with a small supernumerary marker chromosome negative for M-FISH and containing only heterochromatin

AIM

To describe the case of a 32-year-old infertile male with small supernumerary marker chromosome (sSMCs) in 80% of peripheral lymphocytes.

METHODS

G-banding, C-banding, STRP analysis, M-FISH and molecule diagnosis of Y-chromosomal microdeletions were performed to determine the origin of sSMCs.

RESULTS

The karyotype of this patient was established as 47, XY, +mar/46, XY. C-banding showed that the marker chromosome was composed of heterochromatin without visible euchromatic material. No positive result was obtained in STRP, M-FISH and the microdeletion analysis of Y- chromosome.

CONCLUSIONS

The small supernumerary marker chromosome could play a causative role in male infertility although the mechanism remains to be elucidated.

Analphoid supernumerary marker chromosome characterized by aCGH and FISH as inv dup(3)(q25.33qter) de novo in a child with dysmorphic features and streaky pigmentation: case report

BACKGROUND

Small supernumerary marker chromosomes (sSMC) occur in 0.075% of unselected prenatal and in 0.044% of consecutively studied postnatal cases. Individuals with sSMC present with varying phenotype, ranging from normal to extremely mild or severe depending on the chromosomal region involved, the euchromatic content present and degree of mosaicism. Except for chromosomes 15 and 22, the number of reported cases of sSMC is extremely small to provide us with a good genotype-phenotype correlation. Analphoid sSMC are even rarer. To our knowledge only eight cases of analphoid inversion-duplication 3q sSMC are reported so far.

RESULTS

We describe here a one month old female child with several dysmorphic features and with a de novo analphoid supernumerary marker chromosome only in cultured skin fibroblast cells and not in lymphocytes. The marker was characterized as analphoid inversion-duplication 3q25.33-qter by oligo array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH) studies. The final skin fibroblast karyotype was interpreted as 47,XX,+der(3).ish inv dup(3)(qter-q25.33::q25.33-qter)(subtel 3q+,subtel 3q+) de novo.

CONCLUSION

In addition to the eight reported cases of analphoid inversion-duplication 3q supernumerary marker in the literature, this is yet another case of 3q sSMC with a new breakpoint at 3q25.33 and with varying phenotype as described in the case report. Identification of more and more similar cases of analphoid inversion-duplication 3q marker will help in establishing a better genotype-phenotype correlation. The study further demonstrates that aCGH in conjunction with routine cytogenetics and FISH is very useful in precisely identifying and characterizing a marker chromosome, and more importantly help in providing with an accurate genetic diagnosis and better counseling to the family.

Detailed analysis of 15q11-q14 sequence corrects errors and gaps in the public access sequence to fully reveal large segmental duplications at breakpoints for Prader-Willi, Angelman, and inv dup(15) syndromes

BACKGROUND

Chromosome 15 contains many segmental duplications, including some at 15q11-q13 that appear to be responsible for the deletions that cause Prader-Willi and Angelman syndromes and for other genomic disorders. The current version of the human genome sequence is incomplete, with seven gaps in the proximal region of 15q, some of which are flanked by duplicated sequence. We have investigated this region by conducting a detailed examination of the sequenced genomic clones in the public database, focusing on clones from the RP11 library that originates from one individual.

RESULTS

Our analysis has revealed assembly errors, including contig NT_078094 being in the wrong orientation, and has enabled most of the gaps between contigs to be closed. We have constructed a map in which segmental duplications are no longer interrupted by gaps and which together reveals a complex region. There are two pairs of large direct repeats that are located in regions consistent with the two classes of deletions associated with Prader-Willi and Angelman syndromes. There are also large inverted repeats that account for the formation of the observed supernumerary marker chromosomes containing two copies of the proximal end of 15q and associated with autism spectrum disorders when involving duplications of maternal origin (inv dup[15] syndrome).

CONCLUSION

We have produced a segmental map of 15q11-q14 that reveals several large direct and inverted repeats that are incompletely and inaccurately represented on the current human genome sequence. Some of these repeats are clearly responsible for deletions and duplications in known genomic disorders, whereas some may increase susceptibility to other disorders.

Identification of a “cryptic mosaicism” involving at least four different small supernumerary marker chromosomes derived from chromosome 9 in a woman without reproductive success

OBJECTIVE

To characterize the small supernumerary marker chromosomes (sSMCs) present in the female member of an infertile couple who has no further clinical symptoms.

DESIGN

Case report.

SETTING(S)

Faculty of medicine and institute of human genetics and anthropology.

PATIENT(S)

A young, healthy, nonconsanguineous couple asked for genetic evaluation for infertility.

INTERVENTION(S)

Intracytoplasmic sperm injection, conventional and molecular cytogenetic analyses.

MAIN OUTCOME MEASURE(S)

We characterized the sSMCs present in a woman, who was a member of an infertile couple, by molecular cytogenetic techniques.

RESULT(S)

The G-banding technique showed that a marker chromosome was present in some of the examined cells describing the 47,XX,+mar[30]/46,XX[70] karyotype. Subsequently, using new fluorescence in situ hybridization (FISH) techniques, four distinguishable sSMCs (cryptic mosaicism), all derived from chromosome 9, were observed, including minute and ring chromosomes. This heterogeneity was impossible to detect by the conventional G-banding technique or conventional FISH technique that were used before the new FISH techniques (subcentromere-specific multicolor-FISH [subcenM-FISH]) and specific probe for the 9q12 band. In each metaphase with sSMCs, only one or two markers were observed. On the basis of the FISH analyses, the patient's karyotype was defined as 47,XX,+min(9)(:p12-->q12:)/47,XX,+min(9)(:p12-->q12::q12-->p12:)/47,XX,+r(9)(::p12-->q12::)/47,XX,+r(9)(::p12-->q12::p12-->q12::)x2/46,XX.

CONCLUSION(S)

The presence of sSMCs derived from chromosome 9 could influence the couple's infertility. The new subcenM-FISH techniques are very useful in the characterization of cryptic mosaicisms of marker chromosomes. Additionally, the hypothesis that the 9p12 chromosomal band is an euchromatic variant region without any phenotypic impact other than possible infertility is supported by this case study since the woman shows a normal phenotype.

Molecular cytogenetic characterization of eight small supernumerary marker chromosomes originating from chromosomes 2, 4, 8,18, and 21 in three patients

Small supernumerary marker chromosomes (sSMCs) are a morphologically heterogeneous group of additional structurally abnormal chromosomes that cannot be identified unambiguously by conventional banding techniques alone. Molecular cytogenetic methods enable detailed characterization of sSMCs; however, in many cases interpretation of their clinical significance is problematic. The aim of our study was to characterize precisely sSMCs identified in three patients with dysmorphic features, psychomotor retardation and multiple congenital anomalies. We also attempted to correlate the patients' genotypes with phenotypes by inclusion of data from the literature. The sSMCs were initially detected by G-banding analysis in peripheral blood lymphocytes in these patients and were subsequently characterized using multicolor fluorescence in situ hybridization (M-FISH), (sub)centromere-specific multicolor FISH (cenM-FISH, subcenM-FISH), and multicolor banding (MCB) techniques. Additionally, the sSMCs in two patients were also studied by hybridization to whole-genome bacterial artificial chromosome (BAC) arrays (array-CGH) to map the breakpoints on a single BAC clone level. In all three patients, the chromosome origin, structure, and euchromatin content of the sSMCs were determined. In patient RS, only a neocentric r(2)(q35q36) was identified. It is a second neocentric sSMC(2) in the literature and the first marker chromosome derived from the terminal part of 2q. In the other two patients, two sSMCs were found, as M-FISH detected additional sSMCs that could not be characterized in G-banding analysis. In patient MK, each of four cell lines contained der(4)(:p11.1-->q12:) accompanied by a sSMC(18): r(18)(:p11.2-->q11.1::p11.2-->q11.1:), inv dup(18)(:p11.1-->q11.1::q11.1-->p11.1:), or der(18) (:p11.2-->q11.1::q11.1-->p11.1:). In patient NP, with clinical features of trisomy 8p, three sSMCs were characterized: r(8)(:p12-->q11.1::q11.1-->p21:) der(8) (:p11.22-->q11.1::q11.1-->p21::p21-->p11.22:) and der(21)(:p11.1-->q21.3:). The BAC array results confirmed the molecular cytogenetic results and refined the breakpoints to the single BAC clone resolution. However, the complex mosaic structure of the marker chromosomes derived from chromosomes 8 and 18 could only be identified by molecular cytogenetic methods. This study confirms the usefulness of multicolor FISH combined with whole-genome arrays for comprehensive analyses of marker chromosomes.

A new heritable fragile site at 15q13 in a three-generation family

Here, we describe a family ascertained through recurrent spontaneous abortions in which a new heritable fragile site located at 15q13 is segregating. The fragile site was present in nine members of a three-generation family and expressed spontaneously in a high proportion of the metaphases varying from 88 to 95% under standard culture conditions in all the carriers. This didn't change under folate deficiency.

Trisomy of 19.4 Mb region of chromosome 22 and subtelomeric 17p identified in a male without clinical affectation

Supernumerary marker chromosomes (SMCs) have a reported frequency in the prenatal and newborn population ranging from 0.04% to 0.08% and about 37% of diagnosed SMCs are associated with an abnormal phenotype. Around 7.5% of them are derived from chromosome 22. SMCs(22) that result in tri- or tetrasomy of band 22q11.2 are associated with Cat-eye syndrome (CES), a syndrome of variable penetrance and affectation. CES-like phenotype has been also related to 22q11.2 interstitial duplications and der(22) syndrome. The 22q11.2 region, also involved in the velocardiofacial microdeletional syndrome, presents high susceptibility to chromosomal rearrangements due to the presence of low-copy repeats sequences (LCR22). Another region in the genome rich in LCR is 17p and five recurrent disorders have been mapped on the region 17p11-p13. Some chromosomal imbalances affecting the 17p13.3 subtelomeric region have been reported, related to cryptic unbalanced translocations and associated, in most cases, to mental retardation and dysmorphic features. We report on a healthy male carrier of a SMC that was identified as a +der(22)t(17;22)(p13.3;q11.2) consequence of an abnormal 3:1 segregation of the paternal t(17;22) and we have determined the approximate size of the trisomic regions, comparing the obtained results with other reported imbalances involving 22q11.2 and 17pter.

Prenatal identification of a marker chromosome 16 by chromosome microdissection and reverse FISH

Prenatal cytogenetic analysis of cultured amniocytes was performed after an increased foetal nuchal translucency thickness was detected by ultrasound in week 17 of a pregnancy. Analysis of GTG-banded chromosomes showed a small marker chromosome in six of the 12 colonies analysed. The supernumerary abnormal chromosome appeared to be positive with DA/DAPI staining and C-banding. The parents' karyotypes were normal. Using microFISH and FISH with band-specific probes, we found the marker appeared to be derived from chromosome region (16)(p13.1-->q12.2). Accurate identification of the marker chromosome was important for prenatal counselling: the marker chromosome contained euchromatic sequences, the foetus was carrying mosaic trisomy 16, and based on the literature the prognosis for the foetus was unfavourable and the pregnancy was terminated.

Identification, characterization and clinical implications of two markers detected at prenatal diagnosis

OBJECTIVES

Marker chromosomes are relatively rare in the general population as its identification at prenatal diagnosis. In this article, we identified and characterized two de novo supernumerary marker chromosomes in a mosaic form at prenatal diagnosis.

METHODS

The two cases presented were detected during prenatal diagnosis at 17 and 15 weeks of gestation. The analyses were performed due to the advanced maternal age. In both cases, parent's karyotypes were normal. The identification of the marker chromosomes was possible by FISH techniques.

RESULTS

One marker chromosome was derived from chromosome 5 and the other from chromosome 6. Both children are well at the moment.

CONCLUSION

The two cases described in the present paper, join to the ones already described in the literature. However these results are the first ones without any phenotypical anomalies, at least until the present. Every new characterization of marker chromosomes at prenatal diagnosis should be reported for determining a genotype-phenotype correlation, and thus be used for genetic counselling and risk evaluation.

Three new cases with a supernumerary ring chromosome 1

We report on three cases with a cytogenetically identical ring chromosome containing euchromatin from the long arm of chromosome 1 (r[1][::p11.1-->q21.1::]). Two cases were newborn males (Cases 1 and 2) and the third one was prenatally identified as female (Case 3). Mosaicism was present in all three cases in different degrees, i.e. 48%, 25% and 14% of the cells, respectively. Clinical signs and symptoms vary between the three cases. The results of our three cases are compared with those from the literature.

Characterization of six marker chromosomes by comparative genomic hybridization

We applied comparative genomic hybridization (CGH) in six patients with de novo prenatal or postnatal extra marker chromosomes (MC). In four cases, MCs were mosaic and in one of them, the MC was detected in less than 50% of the cells. In three cases, CGH identified the origin of the extra MCs. In the other three, two prenatal cases and one child with an abnormal phenotype, CGH showed normal profiles. Among these cases, a normal profile and entirely C-band positive was identified suggesting that MC did not contain euchromatin. Genetic imbalances detected by CGH were as follow: a gain of 8p10-p12 in a boy with facial dysmorphism, hyperactivity and speech delay, a gain of 8q10-q12 in a healthy man with a history of spontaneous abortions, and a gain of 15q11-q13 in a girl with speech delay, and motor skill and object manipulation difficulties. Clinical data of these patients were compared with those reported in the literature. We conclude that CGH is a very useful and powerful tool for characterizing prenatal or postnatal MCs, even when the mosaicism is present and the MCs are present in less than 50% of the cells.

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

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

Supernumerary marker chromosomes in man: parental origin, mosaicism and maternal age revisited

The details of all cytogenetic abnormalities diagnosed in the Wessex Regional Genetics Laboratory (WRGL) since 1967 to the present day have been recorded in the Salisbury Treasury of Interesting Chromosomes (STOIC). From this resource, we identified 137 patients with constitutional autosomal supernumerary marker chromosomes (SMC) ascertained in four principal groups: (i) 37% with abnormal phenotypes; (ii) 7% couples with reproductive difficulties; (iii) 47% antenatal diagnoses and (iv) 9% miscellaneous. Overall, 81 (59%) SMCs were mosaics and 56 (41%) nonmosaics. Of the 109 cases with known parental origins, 70% were de novo, 19% maternally and 11% paternally inherited. The chromosomal origins of 112/137 (82%) of the SMCs have been determined by fluorescence in situ hybridization (FISH). In all, 36/112 (32%) were derived from nonacrocentric autosomes, and 76/112 (68%) from the acrocentric autosomes 13/21, 14, 15 and 22. Of these acrocentric SMCs, 39 (51%) were derived from chromosome 15, so that SMC(15) constituted 39/112 (35%) of all SMCs with known chromosomal origins. The frequencies with which mosaicism was observed varied considerably according to the chromosomal origin of the SMCs and accounted for 8/39 (20%) SMC(15), 13/37 (35%) SMCs from other acrocentrics and 25/36 (69%) of nonacrocentric SMCs. The data were analysed for parental age effects, and only de novo SMC(15)s were found to be associated with a significantly increased maternal age.

First small supernumerary ring chromosome carrying 10q euchromatin in a patient with mild phenotype characterized by molecular cytogenetic techniques and review of the literature

We report the identification and characterization of the first supernumerary ring chromosome 10 containing a considerable proportion of 10q euchromatin by microdissection and reverse painting in a female patient presenting with short stature. Fluorescence in situ hybridization studies showed that the marker chromosome originates from chromosome 10 and includes the euchromatic bands p11.2 and q11.2. The supernumerary marker chromosome 10 was found in 14% of the peripheral blood lymphocytes analyzed. This constitutional mosaic could be confirmed in oral mucosa cells as a second cell system (16%) by interphase FISH using an alphoid centromeric probe for chromosome 10. Parental karyotypes were normal, uniparental disomy for the normal chromosomes 10 could be excluded by microsatellite analysis. The karyotype of the patient detected in peripheral blood cells can be described as mos 47,XX,+mar.rev ish r(10)(p11.2q11.2)(wcp10+,cep10+)/46,XX.

Mosaic trisomy (8)(p22 --> pter) in a fetus caused by a supernumerary marker chromosome without alphoid sequences

OBJECTIVE

Our objective was to characterise a marker chromosome in cultured amniocytes of a fetus with a mos 47,XX,+mar[3]/46,XX[14] karyotype.

METHODS

The indication for prenatal cytogenetic analysis of cultured amniocytes was advanced maternal age. Classic banding techniques (GTG- and C-banding) were performed. Microdissection combined with reverse painting was used to disclose the exact origin of the marker; the result was confirmed by chromosome painting and FISH with band-specific probes.

RESULTS

Analysis of GTG-banded chromosomes showed a small marker chromosome in 3 of the 17 colonies analysed. Subsequently, C-banding showed no alphoid sequences, suggesting the presence of a neocentromere. The parent's karyotypes were normal. After normal ultrasound findings, the parents decided to continue the pregnancy. Chromosome analysis in peripheral blood after birth demonstrated that the marker chromosome was present in 50% of the lymphocytes. Using microFISH, the marker was further characterised and appeared to be derived from chromosome region (8)(p22 --> pter).

CONCLUSION

Accurate identification of the marker chromosome was very important for prenatal counselling. Combining the results of GTG- and C-banding analysis with the results of the (micro)FISH, we concluded that the patient's karyotype is: mos 47,XX,+mar.rev ish der(8)(p22 --> pter)[50]/46,XX[50].

Prenatal diagnosis of minute supernumerary marker chromosomes

The identification of supernumerary marker chromosomes (SMC) at prenatal diagnosis is problematic, particularly for the prediction of phenotype. The assessment of phenotypic risk is based on the size, morphology and origin of the SMC. Fluorescence in situ hybridization (FISH) characterization and family studies are also employed to aid in determining the significance of a prenatally ascertained SMC. Generally, SMC containing euchromatin are more likely to be associated with abnormal phenotypes and SMC without euchromatin are more likely to result in normal phenotypes. The smallest of SMC, minute SMC (minSMC) appear as dot-like or centric fragments and are particularly difficult to identify and characterize. Previous empirical observations suggested that the risk of phenotypic abnormality in prenatally ascertained minSMC was < or = 5%. We identified minSMC in chorionic villus samples (CVS) or amniocytes from 11 unrelated pregnancies. The chromosomal origin of each minSMC was identified by sequential FISH analysis with chromosome-specific centromere probes. Further FISH analysis with whole chromosome paint probes was undertaken to assess each minSMC for the presence or absence of euchromatin, since the presence of euchromatin may be associated with a higher risk of abnormality. Two minSMC were shown to have euchromatin. The first, a minSMC(12) was found in CVS but not confirmed in amniocytes, indicating confined placental mosaicism. The second, a minSMC derived from chromosome 19, was associated with ultrasound abnormalities. Apart from a case with mild speech delay, the remaining minSMC cases without detectable euchromatin had a normal outcome at birth and/or on longer term follow-up. Additional FISH analyses with a telomeric repeat probe showed no signal on any of the minSMC tested, suggesting that they were ring chromosomes in structure. These data further support the concept that minSMC containing euchromatin are more likely to be associated with an abnormal phenotype, although as more data are collected, this may vary by chromosome of origin. The absence of detectable euchromatin, while not guaranteeing a normal result, is most likely to have a normal outcome. The present report and previous studies do not yet allow any significant adjustment of the empirical < or = 5% risk estimate for minSMC identified at prenatal diagnosis. However, reporting of additional cases with characterization of the minSMC and particularly with long-term follow-up will, in time, allow for more accurate risk estimates and provide prognostic information.

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

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

Clinical findings and cytogenetic analysis of small supernumerary ring chromosomes 7: report of two new cases

Two new patients, mosaic for a small supernumerary ring chromosome 7 are described. There are only seven published reported concerning supernumerary ring chromosome 7 and we reviewed the previously reported cases in an attempt to establish genotype-phenotype correlations, which are particularly important for genetic counselling and clinical genetics. Our first case was a 20 months old girl who was referred for a mild motor developmental delay, an asymmetric facial appearance, a plagiocephaly and a short nose with anteverted nostrils. Our second case was a 9 years old boy who was referred for a IQ at the lower end of the normal range (? 80), obesity, hyperactivity and some dysmorphic features including hypertelorism and down slanting palpebral fissures. In both cases, chromosome analysis after G and R banding and FISH showed a small ring chromosome 7 in respectively 76% and 50% of consecutively scored metaphases. Both ring chromosomes were labelled by FISH using the Williams Syndrome locus probe (Elastin Gene D7S486). Comparison between these two cases and previously published cases allowed to delineate frequent clinical findings. A mild mental retardation was found in the majority of patients. which is an important data for genetic counselling.

Chromosome aberrations in a schizophrenia population

Cytogenetic abnormalities with schizophrenia may provide a valuable clue to the identification of target loci and successful search for major genes. We have performed chromosomal examinations by using the GTG banding technique on 134 schizophrenics. In 43 patients (32%), random numerical and structural aberrations were detected. Structural aberrations predominated and usually consisted of deletions and inversion of various chromosomes. Numerical changes were present in one or two cells in 14 cases including trizomy 21, marker and acentric chromosomes, and 47,XXY. The seven cases with pericentric inversion and enlargement of the heterochromatin region of chromosome 9 (inv(9); 9qh+) were observed in the study. The incidence (5.2%) of inv(9) and 9qh+ in our schizophrenic patients were found higher than the general population, suggesting that a susceptibility locus for schizophrenia may be located at pericentromeric region of chromosome 9. Our study have detected 1q21, 7q23, inv(9), 9qh+, 11q23, 21q22, 22q11-13 and Xp11-q13 suggested that these chromosomal lesions are prevalent in schizophrenics. The reason for this might be that these anomalies increase risk for schizophrenia in a relatively nonspecific way, such as contributing to disruption of normal embryogenesis of the nervous system.

Molecular and fluorescence in situ hybridization characterization of the breakpoints in 46 large supernumerary marker 15 chromosomes reveals an unexpected level of complexity

Supernumerary marker chromosomes (SMCs) of chromosome 15, designated "SMC(15)s," are the most common SMC in humans, accounting for as much as 60% of all those observed. We report the characterization of 46 large SMC(15)s, using both fluorescence in situ hybridization and polymerase chain reaction analysis within and distal to the Prader-Willi/Angelman syndrome critical region (PWACR). Our aim was to establish detailed information on origin, content, and breakpoints, to address the formation of SMC(15)s, and to facilitate genotype-phenotype correlations. For all patients in whom we were able to establish the parental origin, the SMC(15)s were maternally derived. Two patients were observed who had familial SMC(15)s, both inherited from the mother; however, in all remaining patients for whom parental samples were available, the SMC(15)s were shown to have arisen de novo. With one exception, all the SMC(15)s were shown to include the entire PWACR. Detailed investigations of the distal breakpoints categorized the SMC(15)s into two groups. Group A, representing approximately two-thirds of the SMC(15)s, had a breakpoint beyond the standard distal PWS/AS deletion breakpoint BP3, at a position close to the microsatellite marker D15S1010 and the bacterial artificial chromosome 10I10. The group B SMC(15)s were shorter, with more variable breakpoints located around BP3. The majority of the SMC(15)s were shown to have asymmetrical breakpoints, with the two inverted arms of the SMC being unequal in length. Our study revealed an unexpected level of complexity and heterogeneity among SMC(15)s that is not seen in other chromosome 15 rearrangements, such as deletions and duplications. This suggests that multiple mechanisms are involved in the formation of large SMC(15)s.

Partial hexasomy of chromosome 15

Marker chromosomes originating from chromosome 15, often referred to as inv dup(15), is the most common marker chromosome found in humans. The large marker 15 that contains the Prader-Willi syndrome (PWS)/Angelman syndrome (AS) chromosome region is usually associated with an abnormal phenotype of moderate to severe mental retardation, seizures, poor motor coordination, behavioral problems, and mild dysmorphic features. We report here an infant boy with two copies of the large inv dup(15). A 10-day-old infant was found to have infantile spasms, microcephaly, hypotonia, and lethargy. Lymphocyte chromosome analysis revealed a 48,XY, +2mar karyotype. Fluorescence in situ hybridization with probes rRNA, D15Z4, D15S11, and GABRB3 demonstrated that both markers were chromosome 15 in origin and contained the Prader-Willi/Angelman syndrome chromosome region. Therefore, this patient is hexasomic for the PWS/AS region. The phenotype of this patient does not appear to be significantly more severe than patients with one copy of the large inv dup(15) at birth, however, follow-up evaluation of the patient at 21 months of age shows that this patient has frequent and severe seizure activity, severe bilateral hearing loss, and cortical blindness.

Characterization of a supernumerary ring chromosome 1 mosaicism in two cell systems by molecular cytogenetic techniques and review of the literature

We report on a 4-year-old boy with developmental delay and microcephaly with an additional small marker chromosome derived from chromosome 1 and detected in 14% of T-lymphocytes by conventional cytogenetics and in 9% of buccal smear cells by interphase FISH. Using molecular cytogenetic techniques, the marker chromosome was characterized as an extra ring chromosome consisting of euchromatic material from the proximal short arm of chromosome 1. We compare the cytogenetic data and the phenotype of our patient to those previously described cases with marker chromosome 1 mosaicism. We conclude that in addition to the straightforward molecular cytogenetic characterization of the euchromatic content of the ring chromosome, the investigation of a second cell system gives additional information about the tissue specific distribution of the supernumerary marker chromosome (SMC) and provides more reliable data for further karyotype/phenotype correlations and the prediction of the phenotypic outcome in prenatal cases.

SKY assessment of two karyotypes with 0-6 supernumerary marker/ring chromosomes and review of previously reported cases with two or more markers

A 7-month-old boy with developmental delay and congenital abnormalities and a 58-year-old man with mental retardation, impaired speech, and dysmorphic features were referred for cytogenetic studies. The peripheral blood chromosome studies of Patient 1 had a de novo mosaic karyotype with 2-6 supernumerary marker chromosomes. Patient 2 had a mosaic karyotype with 1-5 supernumerary marker chromosomes and normal cells. All markers appeared to have a centromere by C-banding and also by fluorescence in situ hybridization (FISH) using all centromere probe for Patient 1. The majority of the markers appeared like rings. Except for one marker in Patient 1 and 2-3 markers in Patient 2 with discernible >5 Mb euchromatin, the rest of the markers were minute and some appeared to have barely discernible euchromatin in C-banding or FISH. Spectral karyotyping (SKY) was attempted to determine the origin of the marker chromosomes. Because some markers had barely any euchromatin, their classification was not clear cut and they were identified as derived from more than one chromosome. The SKY classification of the markers in Patient 1 was 1, 3, 5, 7, 11, 15, and 22 and in Patient 2 was 1, 5, 6, or 7. Patient 2 was lost to further follow-up studies. To confirm the recurring SKY classifications in Patient 1, centromere probes for chromosomes 1, 3, 5, 7, 11, 15, and 22 were used. The markers were negative for 1, 3, and 11 but positive for 7, 15, and 22 and probably 5. Since 5 centromere probe cross hybridizes with 1 and 19, the weak signal on the marker/s in successive hybridization did not give a definitive answer. Also, the 5 paint probe was not conclusive because of the minute size of the marker. In some metaphases, two markers were derived from 5 or 22. For clinical considerations, the marker derived from 7, although variable in size, appeared to consistently have euchromatin, followed by 15, while 22 and 5 markers were mostly centromeric heterochromatin. The elastin gene probe that maps to 7q11.23, SNRPN gene that maps to 15q11.2, and TUPLE gene that maps to 22q11.2 did not give a signal on the markers. As expected for a majority of ring chromosomes, the pan telomere probe did not hybridize to any of the markers. This highly unusual karyotype was confirmed in the buccal epithelium using a mix of centromere 7 and 15 probes and the combination 14/22 probe. The ratio of additional FISH signals in the buccal mucosal cells was comparable to the ratios observed in the peripheral blood. In this study, we have attempted to consolidate the data on >/=2 marker cases to understand the analysis constraints, the range of clinical abnormalities, and the mechanisms involved. The literature was surveyed for multiple markers cases. A majority of the reported cases had two markers, either derived from the same chromosome or from two different chromosomes or two cell lines with different markers derived from the same chromosome. Cases with three or more markers were rare. The nature and extent of euchromatin content of the multiple markers appears to determine the phenotype. Frequently, multiple marker cases had small to minute markers. The clinical presentation varied from mild to severe. While two bisatellited markers may be associated with infertility, the phenotype in other cases ranged from borderline intelligence and mild dysmorphism to developmental delay, mental retardation, and congenital abnormalities.

Prenatal diagnosis of occipital encephalocele, mega-cisterna magna, mesomelic shortening, and clubfeet associated with pure tetrasomy 20p

We present the first case of a fetus with pure tetrasomy 20p proven by cord-blood sampling at 24 weeks of gestation. This case was diagnosed in utero with multiple congenital anomalies including occipital encephalocele, mega-cisterna magna, mesomelic shortening, and clubfeet. An analysis of GTG-banded chromosomes of 20 metaphase cells was performed. Female karyotype [47,XX, +i(20)(p10)] was revealed in all cells. Pure tetrasomy 20p was confirmed using fluorescent in situ hybridization (FISH) with a telomere probe for chromosome 20p in all seven metaphase cells. The pregnancy was terminated because of associated multiple anomalies and severe oligohydramnios. The postmortem examination confirmed the prenatal diagnosis.

Double supernumerary isodicentric chromosomes derived from 15 resulting in partial hexasomy

We report two unrelated patients each with two supernumerary marker chromosomes (SMCs) derived from chromosome 15, and thus resulting in partial hexasomy. Hexasomy in the one case (family 1) was diagnosed at prenatal diagnosis and did not include the Prader-Willi/Angelman critical region (PWACR). The double SMCs were also found in the mother, the pregnancy continued to term, and an apparently phenotypically normal child was born. This represents the first report of transmission of double SMCs from mother to child. In the second case (family 2), the hexasomy did include the PWACR and was de novo in origin. This patient manifested severe psychomotor retardation, clefting of the soft palate, hypotonia, seizure-like episodes, and other phenotypic features. The aberrant phenotype is attributable to the hexasomy for the PWACR gene loci. The normal homologs of chromosome 15 proved to be biparental in origin while the two SMCs appeared maternal.

Tetrasomy 15q25.3 --> qter resulting from an analphoid supernumerary marker chromosome in a patient with multiple anomalies and bilateral Wilms tumors

We describe a girl who had been followed since birth for apparent Shprintzen-Goldberg syndrome (SGS), with macrosomia, long fingers and toes, and craniosynostosis, and presented at 4 years of age with bilateral Wilms tumors (also called nephroblastoma). Cytogenetic analysis of her peripheral blood revealed a de novo supernumerary marker chromosome. This stable marker chromosome is present in 19 of 20 lymphocytes analyzed, as well as in all 40 tumor cells (20 from each tumor) studied. Classical and molecular cytogenetic studies indicate that the marker is derived from an inverted duplication of chromosome 15q25.3 --> qter and contains a neocentromere. The presence of this marker chromosome in our patient results in tetrasomy 15q25.3 --> qter. The relationship between her genotype and phenotype are discussed in light of genes, including IGF1R and FES, mapped to the aneusomic segment.

Supernumerary marker chromosomes derived from chromosome 15: analysis of 32 new cases

Small supernumerary marker chromosomes (SMC) are a heterogeneous group of chromosomes with an estimated frequency of approximately 0.14-0.72 per 1000 newborns and higher frequencies in particular populations such as the mentally retarded or infertile males. With a frequency of about 50%, derivatives of chromosome 15 represent the most common SMC. Here we present the results of a detailed analysis of 32 SMC(15) carriers who were ascertained in pre- or post-natal routine cytogenetic diagnostics. SMC(15) with euchromatic content led to mental and psychomotor retardation. In contrast, SMC(15) without euchromatin were found to have no influence on the carrier's phenotype but were detected with a high incidence among infertile males. The majority of SMC(15) are pseudodicentric homologous rearrangements. Based on our investigations a further characterization of der(15) was possible.

Unique case of mosaicism involving two morphologically similar marker chromosomes of different centric origin in a patient with developmental delay

A five-year-old Caucasian male presented with developmental delay, minor dysmorphic features, and hyperactivity. Cytogenetic analysis showed the presence of a marker chromosome in the majority of cells analyzed. Fluorescence in situ hybridization (FISH) analyses using several alpha satellite probes, including D13Z1/D21Z1, did not reveal any signal on the marker chromosome. Subsequent multicolor FISH (M-FISH) indicated the marker to be derived from chromosome 13, and FISH with a chromosome 13 paint confirmed this finding. The absence of D13Z1/D21Z1 signal on the marker suggested that it was analphoid in nature. Comparative genomic hybridization (CGH) was utilized to further characterize the region of chromosome 13 from which the marker originated, and unexpectedly revealed a gain of chromosomal material at both the centromeric regions of chromosomes 3 and 13. In view of the CGH results, extensive FISH studies with D3Z1 and D13Z1/D21Z1 were performed and revealed the presence of four cell lines comprising one normal cell line (50.5%), a cell line with a chromosome 3 derived marker (19%), a cell line containing a marker derived from chromosome 13 (20%), and a cell line with both markers (10.5%). As the two markers appeared morphologically similar by GTG banding, all 47,XY metaphases in the initial analysis were thought to comprise only a single marker. This is the first report, to our knowledge, of the presence of a chromosome 3 and a chromosome 13 marker in mosaic condition in a congenital disorder. In light of our experience, we urge caution in interpreting karyotypes with marker chromosomes. Our case illustrates the limitations of fluorescent DNA probes and sampling errors.