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.

Parental origin and functional relevance of a de novo UBE3A variant

Sequence analysis of the imprinted UBE3A gene in a 3-year-old girl suspected of having Angelman syndrome had revealed a de novo 3bp in frame deletion predicted to encode a protein lacking the amino acid G538 (based on sequence NM_130838). In order to assess the clinical relevance of this unknown variant, we determined the parental origin and the functional consequences of the deletion. We separated the two chromosomes 15 by microdissection of metaphase spreads and used cytogenetic and molecular markers to demonstrate that the deletion is on the maternal chromosome. For determining the functional consequences of the deletion, we modelled the structure of the deletion mutant based on the wildtype X-ray structure and simulated the molecular dynamics of the wildtype and mutant protein in complex with UcbH7. Our simulations showed that deletion of G538 destroys a network of salt bridges between highly conserved residues in the catalytic cleft of UBE3A. In conclusion, our results strongly suggest that the 3bp deletion is a loss-of-function mutation of the maternal UBE3A allele that has caused Angelman syndrome in our patient. Our study may serve as a paradigm to determine the parental origin of a de novo mutation.

Characterization of 23 small supernumerary marker chromosomes detected at pre-natal diagnosis: The value of fluorescence in situ hybridization

Small supernumerary marker chromosomes (sSMCs) cannot be identified or characterized unambiguously by conventional cytogenetic banding techniques. Until recently, the large variety of marker chromosomes, as well as the limitations in their identification, have presented a diagnostic problem. In order to determine the origin of sSMCs, we used a variety of fluorescence in situ hybridization (FISH) methods, including centromere-specific multicolor FISH, acrocentric specific multicolor FISH, subcentromere-specific multicolor FISH and multicolor FISH with whole chromosome paint probes. Moreover, uniparental disomy testing was in all cases attempted. From a total of 28,000 pre-natal samples from four diagnostic genetics laboratories in Greece, 23 (0.082%) supernumerary marker chromosomes were detected. The mean maternal age was 36.2 years (range 27-43) and the mean gestational age at which amniocentesis was performed was 18.5 weeks (range 16-23). Eighteen markers were de novo and 5 markers were inherited. Molecular cytogenetic methods were applied to determine the chromosomal origin and composition of the sSMC. In total, 17 markers were derived from acrocentric chromosomes (14, 15, 21 and 22) and 6 markers were non-acrocentric, derived from chromosomes 9, 16, 18, 20 and Y. Uniparental disomy was not detected in any of the cases studied. With regard to pregnancy outcome, 13 pregnancies resulted in normal healthy neonates, while 10 pregnancies were terminated due to ultrasound abnormalities. A total of 23 marker chromosomes from 28,000 pre-natal samples (0.082%) were identified. Molecular cytogenetic techniques provided valuable information on the chromosomal origin and composition of all the sSMCs. Especially in cases with normal ultrasound, the FISH results rendered genetic counseling possible in a category of cases previously considered a diagnostic problem. Abnormal outcome was observed in 10 cases (43,5%), 7 of which showed abnormal ultrasound findings. New technologies, such as array-comparative genomic hybridization, should be used in future genotype-phenotype correlation studies, although the high mosaicism rate poses a problem.

Somatic mosaicism in cases with small supernumerary marker chromosomes

Somatic mosaicism is something that is observed in everyday lives of cytogeneticists. Chromosome instability is one of the leading causes of large-scale genome variation analyzable since the correct human chromosome number was established in 1956. Somatic mosaicism is also a well-known fact to be present in cases with small supernumerary marker chromosomes (sSMC), i.e. karyotypes of 47,+mar/46. In this study, the data available in the literature were collected concerning the frequency mosaicism in different subgroups of patients with sSMC. Of 3124 cases with sSMC 1626 (52%) present with somatic mosaicism. Some groups like patients with Emanuel-, cat-eye- or i(18p)- syndrome only tend rarely to develop mosaicism, while in Pallister-Killian syndrome every patient is mosaic. In general, acrocentric and non-acrocentric derived sSMCs are differently susceptible to mosaicism; non-acrocentric derived ones are hereby the less stable ones. Even though, in the overwhelming majority of the cases, somatic mosaicism does not have any detectable clinical effects, there are rare cases with altered clinical outcomes due to mosaicism. This is extremely important for prenatal genetic counseling. Overall, as mosaicism is something to be considered in at least every second sSMC case, array-CGH studies cannot be offered as a screening test to reliably detect this kind of chromosomal aberration, as low level mosaic cases and cryptic mosaics are missed by that.

CD8 locus nuclear dynamics during thymocyte development

Nuclear architecture and chromatin reorganization have recently been shown to orchestrate gene expression and act as key players in developmental pathways. To investigate how regulatory elements in the mouse CD8 gene locus are arranged in space and in relation to each other, three-dimensional fluorescence in situ hybridization and chromosome conformation capture techniques were employed to monitor the repositioning of the locus in relation to its subchromosomal territory and to identify long-range interactions between the different elements during development. Our data demonstrate that CD8 gene expression in murine lymphocytes is accompanied by the relocation of the locus outside its subchromosomal territory. Similar observations in the CD4 locus point to a rather general phenomenon during T cell development. Furthermore, we show that this relocation of the CD8 gene locus is associated with a clustering of regulatory elements forming a tight active chromatin hub in CD8-expressing cells. In contrast, in nonexpressing cells, the gene remains close to the main body of its chromosomal domain and the regulatory elements appear not to interact with each other.

Small supernumerary marker chromosomes 1 with a normal phenotype

Small supernumerary marker chromosomes (sSMCs) are a major problem in prenatal cytogenetic diagnostics. Over two-thirds of cases carrying an sSMC derived from chromosome 1 are associated with clinical abnormalities. We report 3 further cases of such sSMCs that did not show any clinical abnormalities. All 3 sSMCs studied were detected prenatally and characterized comprehensively for their genetic content by molecular cytogenetics using subcentromere-specific multicolor fluorescence in situ hybridization, and for a possibly associated uniparental disomy. After exclusion of additional euchromatin due to the presence of sSMCs and a uniparental disomy, parents opted for continuation of the pregnancies and healthy children were born in all 3 cases. It is important to quickly and clearly characterize prenatal sSMCs. Also, all available sSMC cases need to be collected on a homepage such as the Jena Institute of Human Genetics and Anthropology sSMC homepage (http://www.med.uni-jena.de/fish/sSMC/00START.htm).

Early embryonic chromosome instability results in stable mosaic pattern in human tissues

The discovery of copy number variations (CNV) in the human genome opened new perspectives on the study of the genetic causes of inherited disorders and the aetiology of common diseases. Here, a single-cell-level investigation of CNV in different human tissues led us to uncover the phenomenon of mitotically derived genomic mosaicism, which is stable in different cell types of one individual. The CNV mosaic ratios were different between the 10 individuals studied. However, they were stable in the T lymphocytes, immortalized B lymphoblastoid cells, and skin fibroblasts analyzed in each individual. Because these cell types have a common origin in the connective tissues, we suggest that mitotic changes in CNV regions may happen early during embryonic development and occur only once, after which the stable mosaic ratio is maintained throughout the differentiated tissues. This concept is further supported by a unique study of immortalized B lymphoblastoid cell lines obtained with 20 year difference from two subjects. We provide the first evidence of somatic mosaicism for CNV, with stable variation ratios in different cell types of one individual leading to the hypothesis of early embryonic chromosome instability resulting in stable mosaic pattern in human tissues. This concept has the potential to open new perspectives in personalized genetic diagnostics and can explain genetic phenomena like diminished penetrance in autosomal dominant diseases. We propose that further genomic studies should focus on the single-cell level, to better understand the aetiology of aging and diseases mediated by somatic mutations.

Two siblings with immunodeficiency, facial abnormalities and chromosomal instability without mutation in DNMT3B gene but liability towards malignancy; a new chromatin disorder delineation?

Background

ICF syndrome (standing for Immunodeficiency, Centromere instability and Facial anomalies syndrome) is a very rare autosomal recessive immune disorder caused by mutations of the gene de novo DNA-methyltransferase 3B (DNMT3B). However, in the literature similar clinical cases without such mutations are reported, as well.

Results

We report on a family in which the unrelated spouses had two female siblings sharing similar phenotypic features resembling ICF-syndrome, i.e. congenital abnormalities, immunodeficiency, developmental delay and high level of chromosomal instability, including high frequency of centromeric/pericentromeric rearrangements and breaks, chromosomal fragments despiralization or pulverization. However, mutations in DNMT3B could not be detected.

Conclusion

The discovery of a new so-called 'chromatin disorder' is suggested. Clinical, molecular genetic and cytogenetic characteristics are reported and compared to other 'chromatin disorders'.

New insights into the karyotypic evolution in muroid rodents revealed by multicolor banding applying murine probes

Muroid rodents are composed of a wide range of species characterized by extensive karyotypic evolution. Even if this group includes such important laboratory animal models as domestic mouse (Mus musculus), Norway rat (Rattus norvegicus), Chinese hamster (Cricetulus griseus), and golden hamster (Mesocricetus auratus), comparative cytogenetic studies between rodents are difficult due to the characteristic rapid karyotypic evolution. Molecular cytogenetic methods can help resolve problems of comparing muroid chromosomes. Here, we used cross-species comparative multicolour banding with probes obtained from mouse chromosomes 3, 6, 18, and 19 to study the karyotypes of nine muroid species from the three subfamilies Murinae, Cricetinae, and Arvicolinae. Results from multicolour banding with these murine probes (mcb) allowed us to improve the comparative homology maps between these species and to obtain new insights into their karyotypic evolution. We identified evolutionary conserved chromosomal breakpoints and revealed four previously unrecognized homologous segments, four inversions, and 14 evolutionary new centromeres in the nine muroid species studied. We found Mus apomorphic rearrangements, not seen in other muroids, and defined several subfamily specific chromosome breaks, characteristic for Arvicolinae and Cricetinae. We show that mcb libraries are an effective tool both for the cytogenetic characterisation of important laboratory models such as the rat and hamster as well as elucidating the complex phylogenomics relationships of muroids.

Characterization of double ring chromosome 4 mosaicism associated with bilateral hip dislocation, cortical dysgenesis, and epilepsy

We present the clinical and molecular findings in a Turkish child with a de novo mosaic ring derived from chromosome 4 with multiple cell-lines; the karyotype was 46,XY,r(4)[83]/45,XY, -4[6]/47,XY,r(4),+r(4)[5]/48,XY,r(4),+r(4),+dic r(4)[1]/46,XY[5]. The patient is a 20-month-old male who was the first pregnancy of nonconsanguineous parents. The baby was delivered at term with a birth weight of 1,700 g (<3rd centile) and a length of 46 cm. The baby had feeding difficulties and vomiting problems. He started walking at age 2 years and delayed language was observed. Facial appearance was normal, but the ears were large with abnormal structure. The hands showed bilateral clinodactyly of the 5th fingers. He had mild mental retardation, and epilepsy. Analysis of chromosomes showed 46,XY,r(4)(::p16.3 --> qter::)[67]/46,XY,r(4;4)(::p16.3 --> qter::p16.3 --> qter::)[2]/46,XY[3] by multicolor banding (MCB) technique. Array CGH delineated the size of the terminal deletion as 900 kb in 4p16.3. The Wolf-Hirschhorn critical region was preserved even though our patient had mild mental and motor retardation. While the mosaicism of the ring 4 could affect the phenotype, the deleted 900 kb distal deletion and clinical features of the patient may provide further insight into characteristic phenotype of the 4p- related syndromes.

The case of an infertile male with an uncommon reciprocal X-autosomal translocation: how does this affect male fertility?

Infertility is defined as the inability to conceive after one year of regular unprotected intercourse. Constitutional numerical and/or structural chromosomal aberrations like sex-chromosome aberrations are one of the possible factors involved in fertility problems. Reciprocal translocations between an X-chromosome and an autosome are rarely seen in men. Male carriers of an X-autosome translocation are invariably sterile, regardless of the position of the breakpoint in the X-chromosome. Breakpoints in autosomal chromosomes could also be involved in male infertility. In this paper, we describe a 31-year-old male with azoospermia. GTG banding with high resolution multicolor-banding (MCB) techniques revealed a karyotype 46,Y,t(X;1)(p22.3;q25), and we discuss how the breakpoint of this translocation could affect male infertility. As a conclusion, cytogenetic evaluation of infertile subjects with azoospermia should be considered in the first place before in vitro fertilisation procedures are planned.

Partial deletion of the long arm of chromosome 13 (q32q33.2) associated with mental retardation, choanal atresia and fish mouth

13q deletion syndrome is characterized by mental and motor retardation, craniofacial dysmorphic facial appearance and various congenital malformations. In this article, we present a new case with 13q deletion syndrome phenotypically characterized by fish mouth, choanal atresia and severe mental and motor retardation. In order to determine the certain localization of deleted region high resolution multicolor-banding technique was performed and the karyotype determined as 46,XX,del(13)(q32q33.2). To come in future to a genotype-phenotype correlation, it is very important to delineate the deleted region in such cases in detail by cytogenetic/ molecular cytogenetic methods.

First case of a neocentromere formation in an otherwise normal chromosome 7

According to cytogenetic and molecular cytogenetic characterization, an otherwise not-altered chromosome 7 formed a neocentromere in band 7q32.1 in a clinically normal female. The alpha satellite sequence D7Z1 remained in its place but was not used for formation of the primary chromosomal incision. Similar observations of centromere repositioning have been made for chromosomes 3 (2x), 4, 8 and Y (2x). Even though data is available for some neocentromeres whose positions are correlated with evolutionary new centromeres for 7q32.1, no correlation could be found for an ancestral inactivated centromere in any of the presently living primates. Overall, we report a new case of centromere repositioning at a position not known to harbor an ancestral inactivated centromere.

A small supernumerary marker chromosome present in a Turner syndrome patient not derived from X- or Y-chromosome: a case report

Background

Small supernumerary marker chromosomes (sSMC) can be present in numerically abnormal karyotypes like in a 'Turner-syndrome karyotype' mos 45,X/46,X,+mar.

Results

Here we report the first case of an sSMC found in Turner syndrome karyotypes (sSMC^T) derived from chromosome 14 in a Turner syndrome patient. According to cytogenetic and molecular cytogenetic characterization the karyotype was 46,X,+del(14)(q11.1). The present case is the third Turner syndrome case with an sSMC^T not derived from the X- or the Y-chromosome.

Conclusion

More comprehensive characterization of such sSMC^T might identify them to be more frequent than only ~0.6% in Turner syndrome cases according to available data.

High-throughput sequencing of microdissected chromosomal regions

The linkage of disease gene mapping with DNA sequencing is an essential strategy for defining the genetic basis of a disease. New massively parallel sequencing procedures will greatly facilitate this process, although enrichment for the target region before sequencing remains necessary. For this step, various DNA capture approaches have been described that rely on sequence-defined probe sets. To avoid making assumptions on the sequences present in the targeted region, we accessed specific cytogenetic regions in preparation for next-generation sequencing. We directly microdissected the target region in metaphase chromosomes, amplified it by degenerate oligonucleotide-primed PCR, and obtained sufficient material of high quality for high-throughput sequencing. Sequence reads could be obtained from as few as six chromosomal fragments. The power of cytogenetic enrichment followed by next-generation sequencing is that it does not depend on earlier knowledge of sequences in the region being studied. Accordingly, this method is uniquely suited for situations in which the sequence of a reference region of the genome is not available, including population-specific or tumor rearrangements, as well as previously unsequenced genomic regions such as centromeres.

Handling small supernumerary marker chromosomes in prenatal diagnostics

Small supernumerary marker chromosomes (sSMCs) are structurally abnormal chromosomes that cannot be thoroughly characterized by conventional banding cytogenetics and are equal in size or smaller than chromosome 20. They are present in 0.075% of prenatal cases and, overall, approximately 3 million people worldwide are carriers of a sSMC. In prenatal cases with ultrasound abnormalities, sSMCs are found in up to approximately 0.2% of the cases. First described in 1961, it is now known that sSMCs have no phenotypic effects in approximately 70% of de novo cases. Nonetheless, in at least 30-50% of prenatally detected sSMC cases, the pregnancy is terminated; that is, for a certain percentage of potentially healthy children with a sSMC, an abortion is induced. This situation can only be improved by providing increased amounts of and more reliable information on sSMCs. This article provides an overview on current state-of-the-art technologies and how sSMC analysis can be optimized in prenatal diagnostics.

Molecular cytogenetic characterisation of a mosaic add(12)(p13.3) with an inv dup(3)(q26.31 --> qter) detected in an autistic boy

BACKGROUND

Inverted duplications (inv dup) of a terminal chromosome region are a particular subset of rearrangements that often results in partial tetrasomy or partial trisomy when accompanied by a deleted chromosome. Associated mosaicism could be the consequence of a post-zygotic event or could result from the correction of a trisomic conception. Tetrasomies of distal segments of the chromosome 3q are rare genetic events and their phenotypic manifestations are diverse. To our knowledge, there are only 12 cases reported with partial 3q tetrasomy. Generally, individuals with this genomic imbalance present mild to severe developmental delay, facial dysmorphisms and skin pigmentary disorders.

RESULTS

We present the results of the molecular cytogenetic characterization of an unbalanced mosaic karyotype consisting of mos 46,XY,add(12)(p13.3) [56]/46,XY [44] in a previously described 11 years old autistic boy, re-evaluated at adult age. The employment of fluorescence in situ hybridization (FISH) and multicolor banding (MCB) techniques identified the extra material on 12p to be derived from chromosome 3, defining the additional material on 12p as an inv dup(3)(qter --> q26.3::q26.3 --> qter). Subsequently, array-based comparative genomic hybridization (aCGH) confirmed the breakpoint at 3q26.31, defining the extra material with a length of 24.92 Mb to be between 174.37 and 199.29 Mb.

CONCLUSION

This is the thirteenth reported case of inversion-duplication 3q, being the first one described as an inv dup translocated onto a non-homologous chromosome. The mosaic terminal inv dup(3q) observed could be the result of two proposed alternative mechanisms. The most striking feature of this case is the autistic behavior of the proband, a characteristic not shared by any other patient with tetrasomy for 3q26.31 --> 3qter. The present work further illustrates the advantages of the use of an integrative cytogenetic strategy, composed both by conventional and molecular techniques, on providing powerful information for an accurate diagnosis. This report also highlights a chromosome region potentially involved in autistic disorders.

Diagnostic applications of fluorescence in situ hybridization

BACKGROUND

Fluorescence in situ hybridization (FISH) assays are indispensable in diagnostics and research. Routine application of this so-called molecular cytogenetic technique on human chromosomes started in 1986. Since then, a huge variety of different approaches for chromosomal differentiation based on FISH has been described. It was established to characterize marker chromosomes identified in conventional banding analysis as well as cryptic rearrangements not resolved by standard cytogenetics.

OBJECTIVE/METHOD

Even though molecular cytogenetics, like banding cytogenetics for almost 40 years, is often called dead now, it offers unique possibilities of single cell analysis. Thus, a review is presented here on the available diagnostic-relevant FISH methods and probe sets applied in routine pre- and postnatal clinical as well as tumor cytogenetics.

CONCLUSION

Molecular cytogenetics is a fast, straightforward and reliable tool that is indispensable in cytogenetic diagnostics. It is and will continue to be of high clinical impact in diagnostics, especially in the overwhelming majority of routine cytogenetic laboratories that cannot afford and do not need high-throughput chip-based platforms for their daily work.

10p11.2 to 10q11.2 is a yet unreported region leading to unbalanced chromosomal abnormalities without phenotypic consequences

Directly transmitted unbalanced chromosomal abnormalities (UBCA) or euchromatic variants (EV) were recently reported for >50 euchromatic regions of almost all human autosomes. UBCA and EV are comprised of a few megabases of DNA, and carriers are in many cases clinically healthy. Here we report on partial trisomies of chromosome 10 within the pericentromeric region which were detected by standard G banding. Those were referred for further delineation of the size of these duplicated regions for molecular cytogenetics and/or array-CGH. Partial trisomies of chromosome 10 in the pericentromeric region were identified prenatally in seven cases. A maximum of three copies of the region from 10p12.1 to 10q11.22 was observed in all cases without apparent clinical abnormalities. The imbalances were either caused by a direct duplication in one familial case or by de novo small supernumerary marker chromosomes (sSMC). Thus, we report a yet unrecognized chromosomal region subject to UBCA detected in seven unrelated cases. To the best of our knowledge, this is the first report of a UBCA in the pericentromeric region of chromosome 10 that is not correlated with any clinical consequences.

The hierarchically organized splitting of chromosomal bands for all human chromosomes

BACKGROUND

Chromosome banding is widely used in cytogenetics. However, the biological nature of hierarchically organized splitting of chromosomal bands of human chromosomes is an enigma and has not been, as yet, studied.

RESULTS

Here we present for the first time the hierarchically organized splitting of chromosomal bands in their sub-bands for all human chromosomes. To do this, array-proved multicolor banding (aMCB) probe-sets for all human chromosomes were applied to normal metaphase spreads of three different G-band levels. We confirmed for all chromosomes to be a general principle that only Giemsa-dark bands split into dark and light sub-bands, as we demonstrated previously by chromosome stretching. Thus, the biological band splitting is in > 50% of the sub-bands different than implemented by the ISCN nomenclature suggesting also a splitting of G-light bands. Locus-specific probes exemplary confirmed the results of MCB.

CONCLUSION

Overall, the present study enables a better understanding of chromosome architecture. The observed difference of biological and ISCN band-splitting may be an explanation why mapping data from human genome project do not always fit the cytogenetic mapping.

Characterization of a prenatally assessed de novo supernumerary minute ring chromosome 20 in a phenotypically normal male

Background

The heterogeneous group of small supernumerary marker chromosomes (sSMCs) presents serious counseling problems, especially if they are present de novo and diagnosed prenatally. The incidence has been estimated at 1 in 1000 prenatal samples. We present a case of mosaic sSMC diagnosed prenatally after amniocentesis. The sSMC was characterized by various molecular cytogenetic techniques and determined to be a r(20) chromosome. After genetic counseling, the parents decided to continue the pregnancy, and a boy with minor phenotypic variants was born after 39 weeks of pregnancy. The case is compared with four other cases of prenatally detected r(20) mosaicism.

Results

Here we describe a 3 months old male child with normal pre- and postnatal development and with a de novo ring supernumerary marker chromosome in amniocytes cultures. Using new fluorescence in situ hybridization (FISH) techniques, three distinguishable sSMCs (cryptic mosaicism), all derived from chromosome 20, were observed, including ring and minute chromosomes. This heterogeneity was impossible to detect by the conventional G-banding technique or conventional FISH technique that were used before the application of new FISH techniques (subcentromere-specific multicolor-FISH [subcenM-FISH]) and a probe, specific for the 20p12.2 band. The sSMC present in 25% of the cells was present as r(20)(::p12.2~12.3->q11.1::)[5]/r(20;20)(::p12.1->q11.1::q11.1 >p12.1::)[2]/min(20;20)(:p12.1->q11.1::q11.1->p12.1:)[1]. The final karyotype was 47,XY,+r(20)[25%]/46,XY[75%].

Conclusion

We emphasize the importance of application of molecular cytogenetics in a prenatally diagnostic laboratory and description of more cases to enable a better genetic counseling and risk evaluation.