Sex chromosome markers: characterization using fluorescence in situ hybridization and review of the literature

Prenatal diagnosis of trisomy 21, 18 and 13 by quantitative pyrosequencing of segmental duplications

Chromosomal aberration mostly occurs in chromosomes 21, 18 and 13, with an incidence approximately 1 out of 160 live births in humans, therefore making prenatal diagnosis necessary in clinics. Current methods have drawbacks such as time consuming, high cost, complicated operations and low sensitivity. In this paper, a novel method for rapid and accurate prenatal diagnosis of aneuploidy is proposed based on pyrosequencing, which quantitatively detects the peak height ratio (PHR) of different bases of segmental duplication. A direct polymerase chain reaction (PCR) approach was undertaken, where a small volume of amniotic fluid was used as the starting material without DNA extraction. Single-stranded DNA was prepared from PCR products and subsequently analyzed using pyrosequencing. The PHR between target and reference chromosome of 2.2 for euploid and 3:2 for a trisomy fetus were used as reference. The reference intervals and z scores were calculated for discrimination of aneuploidy. A total of 132 samples were collected, within trisomy 21 (n = 11), trisomy 18 (n = 3), trisomy 13 (n = 2), and unaffected controls (n = 116). A set of six segmental duplications were chosen for analysis. This method had consistent results with karyotyping analysis, a correct diagnosis with 100% sensitivity and 99.9% specificity.

A unique mosaic Turner syndrome patient with androgen receptor gene derived marker chromosome

Patients with Turner syndrome are generally characterized by having short stature with no secondary sexual characteristics. Some abnormalities, such as webbed neck, renal malformations (>50%) and cardiac defects (10%) are less common. The intelligence of these patients is considered normal. Non-mosaic monosomy X is observed in approximately 45% of postnatal patients with Turner syndrome and the rest of the patients have structural abnormalities or mosaicism involving 46,X,i(Xq), 45,X/46,XX, 45,X and other variants. The phenotype of 45,X/46,X,+mar individuals varies by the genetic continent and degree of the mosaicism. The gene content of the marker chromosome is the most important when correlating the phenotype with the genotype. Here we present an 11-year-old female who was referred for evaluation of her short stature and learning disabilities. Conventional cytogenetic investigation showed a mosaic 45,X/46,X,+mar karyotype. Fluorescence in situ hybridization showed that the marker chromosome originated from the X chromosome within the androgen receptor (AR) and X-inactive specific transcript (XIST) genes. Therefore, it is possible that aberrant activation of the marker chromosome, compromising the AR and XIST genes, may modify the Turner syndrome phenotype.

Marker chromosomes

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

Is there a correlation between the proportion of cells with isodicentric Yp at amniocentesis and phenotypic sex?

OBJECTIVES

(1) To present a case with prenatally detected idic Yp. (2) To review literature to assess if there is a correlation between the proportion of amniocytes with idic Yp and phenotypic sex.

METHODS

Seventeen cases were reviewed.

RESULTS

Amniocentesis was done due to positive integrated prenatal screening result. Interphase FISH was normal for chromosomes 13, 18, and 21, but mosaic for cell lines with 1 X and 0 to 2 copies of DYZ3, SRY, or DYZ1(Yq12). Amniocytes had 45,X[28]/46,X,idic(Y)(q11.2)[2].ish idic(Y)(DYZ3 + +, SRY + +). An apparently normal female was born at 37 weeks. The umbilical cord had 45,X[50], but cord blood had 45,X[17]/46,X,idic(Y)[31]/47,X,idic(Y)x2[2]. Review of 17 cases showed that 13 cases with 20 to 100% cells with idic Yp all had a male phenotype. Two cases with 3 and 7% of idic Yp cells had a female phenotype. Two cases with 45,X only at prenatal diagnosis but idic Yp detected postnatally were phenotypic male.

CONCLUSION

(1) We present the first report of prenatally detected idic Yp and Yq12 resulting in an apparently normal female at birth. (2) Finding of > 20% of G-banded amniocytes with idic Yp in the absence of other indicators of foetal structural anomalies seems to correlate with phenotypically normal male in most cases.

Natural history of prenatally diagnosed 46,X,isodicentric Y

OBJECTIVES

The karyotype 46,X,isodicentric Y has rarely been reported in the context of prenatal diagnosis. The literature is replete with descriptions of individuals with 46,X,isodicentric Y/45,X mosaicism, presenting with a spectrum of phenotypes. The postnatal phenotype is believed to depend on the extent of mosaicism in the gonads or other affected tissues. The purpose of this article is to delineate the natural history of this chromosomal abnormality when identified in the context of prenatal diagnosis.

METHODS

We identified a 45,X/46,X,idicY karyotype in the structurally normal male fetus of a woman presenting with an abnormal triple screen. Four other prenatally ascertained cases were found in our files as well as ten in the medical literature.

RESULTS

Of the 15 cases presented here, 11 (73%) were reported as phenotypically normal males, 1 was found to have an epididymal cyst, and 1 had normal male genitalia, but was also found to have a cardiovascular defect. One out of 15 (7%) was found to have female genitalia and was therefore confirmed to have Turner syndrome. In one case, the outcome was not reported.

CONCLUSION

An individual diagnosed prenatally with idic(Y) may in many cases be a normal male, similar to the outcome for prenatally diagnosed 45,X/46,XY.

Small supernumerary marker chromosomes (sSMC) in humans

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

Digoxigenin labelling and laser capture microdissection of male cells

Laser capture microdissection (LMD) is a relatively new technique for the isolation of single cells. The application in forensic investigations has become more and more widespread, especially to select spermatozoa out of mixtures with vaginal cells. In particular in cases with low numbers of sperm it could be profitable to isolate all male cells (e.g. sperm and male epithelial cells) instead of focussing on the sperm only. Therefore, the specific labelling and detection of the male cells in a male/female cell mixture is necessary. In order to label all cells carrying a Y-chromosome we used a digoxigenin labelled chromosome Y hybridisation probe (Q Biogen). The stained cells were isolated with the SL microCut LMD system from Molecular Machines & Industries AG (MMI). At least ten diploid male cells were required to obtain a partial STR profile, with 20 cells, a full profile could be obtained.

Identification of 14 rare marker chromosomes and derivatives by spectral karyotyping in prenatal and postnatal diagnosis

Extra structurally abnormal chromosomes (ESACs) and cryptic rearrangements are often associated with mental retardation and phenotypic abnormalities. In some cases their characterisation, using standard cytogenetic techniques and fluorescence in situ hybridization (FISH), is difficult and time consuming, where a fast and accurate identification is essential, especially when such chromosomal aberrations are found in prenatal diagnosis. A recent molecular technique, spectral karyotyping (SKY), based on the spectral signature of 24 chromosome-specific painting probes labelled with different combinations of five fluorochromes, allows the simultaneous visualisation of all human chromosomes in different colours. We used SKY analysis on 14 cases with rare ESACs or cryptic unbalanced rearrangements found at pre- or postnatal diagnosis. SKY analysis permitted the classification of chromosome rearrangements in all 14 cases analysed in combination with FISH analysis.

Molecular and cytogenetic characterization of extra-structurally abnormal chromosomes (ESACs) found prenatally: outcome and follow-up

A 40-year-old woman underwent amniocentesis at 15.3 weeks of gestation. Chromosome analysis performed using QFQ, DA-DAPI and CBG banding revealed two de novo extra-chromosomal markers (ESACs) in 11 of the 16 colonies analysed. Fluorescence in situ hybridization (FISH) showed that both chromosomes came from the Yq11.22.1 region of the Y chromosome. PCR analysis of genes and STS localized on the Y chromosome excluded the Yp presence specifically of the SRY gene, and most of the euchromatic region of Yq. After extensive genetic counselling and considering both laboratory and second-level ultrasound data, the couple decided to continue the pregnancy. At 37.4 weeks of gestational age, a girl weighing 2750 g was born with an Apgar score of 9/10. A blood sample taken from the umbilical cord showed three cellular lines: mos47,XX, +mar1 ish.der (Y)(wcpY+) [21%]/48,XX, +mar1 ish.der (Y)(wcpY+), +mar2 ish.der (Y)(wcpY+) [41%]/46,XX [38%]. One year after birth, the baby was developing normally and had normal psychomotorial activity.

Fluorescence in situ hybridisation analysis and ovarian histology of women with Turner syndrome presenting with Y-chromosomal material: a correlation between oral epithelial cells, lymphocytes and ovarian tissue

The early detection of Y-chromosomal material in women with Turner syndrome (TS) is of great importance due to a relatively high risk of gonadal tumour development. Using fluorescence in situ hybridisation (FISH) analysis, we studied the presence of three different Y-specific sequences (SRY, Ycen and Yq12) in three different tissues (oral epithelial cells, lymphocytes and ovarian tissue) of twelve TS women. We have also described their ovarian histology. Two of the women (17%) had gonadal tumours. In five women where ovarian tissue was available, the presence of Y-chromosomal material in oral epithelial cells and lymphocytes correlated to the presence of Y-chromosomal material in the gonads. We therefore conclude that FISH analysis of oral epithelial cells and/or lymphocytes is a valuable complement to karyotyping for the early detection of Y-chromosomal material in TS women.

Detection of Y-specific sequences in 122 patients with Turner syndrome: nested PCR is not a reliable method

The incidence of Y chromosome sequences in patients with Turner syndrome has been evaluated in several studies, and its frequency varied from 0% to 61%, depending on the molecular methodology used. The aim of our study was to screen for Y chromosome sequences in 122 patients with Turner syndrome without cytogenetic evidence of this chromosome. DNA of 100 normal women was also screened and it was used as a negative control. To identify cryptic Y mosaicism, eight regions of Y chromosome were amplified by PCR. In order to increase the sensitivity of Y sequence detection, a nested PCR of the SRY and TSPY genes was also performed. All patients had several stigmata of Turner syndrome and none of them presented with signs of virilization. The most frequent karyotype was 45,X (54.1%), followed by mosaicism involving structural aberration of the X chromosome. There were 12 patients who carried a marker or ring chromosome. First-round PCR identified Y chromosome sequences in only four patients (3%), and all of them had a chromosome mosaicism with at least one cell lineage with a marker chromosome. After nested PCR, 25% of the patients and 14% of the normal women were positive for the presence of Y sequences. Contamination with extraneous genomic DNA was ruled out by microsatellite studies, but we cannot eliminate the possibility of contamination with PCR products, despite careful handling. We conclude that nested PCR overestimated the frequency of Y sequences in patients with Turner syndrome and should be avoided to prevent false positive results, which lead to unnecessary surgical treatment of these patients.

PCR-PRINS-FISH analysis of structurally abnormal sex chromosomes in eight patients with Turner phenotype

According to cytogenetic analysis, about 50% of Turner individuals are 45,X. The remaining cases have a structurally abnormal X chromosome or are mosaics with a second cell line containing a normal or abnormal sex chromosome. In these mosaics, approximately 20% have a sex marker chromosome whose identity cannot usually be determined by classical cytogenetic methods, requiring the use of molecular techniques. Polymerase chain reaction (PCR), primed in situ labeling (PRINS), and fluorescence in situ hybridization (FISH) analyses were performed in 8 patients with Turner syndrome and 45,X mosaic karyotypes to determine the origin and structure of the marker chromosome in the second cell line. Our data showed that markers were Y-derived in 2 patients and X-derived in the remaining 6 patients. We were also able to determine the breakpoints in the two Y chromosomes. The use of cytogenetic and molecular techniques allowed us to establish unequivocally the origin, X or Y, of the marker chromosomes in the 8 patients with Turner phenotype. This study illustrates the power of resolution and utility of combined cytogenetic and molecular approaches in some clinical cases.

Molecular cytogenetics

In the past decade, clinical cytogenetics has undergone remarkable advancement as molecular biology techniques have been applied to conventional chromosome analysis. The limitations of conventional banding analysis in the accurate diagnosis and interpretation of certain chromosome abnormalities have largely been overcome by these new technologies, which include fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH), and multicolor FISH (M-FISH, SKY, and Rx-FISH). Clinical applications include diagnosis of microdeletion and microduplication syndromes, detection of subtelomeric rearrangements in idiopathic mental retardation, identification of marker and derivative chromosomes, prenatal diagnosis of trisomy syndromes, and gene rearrangements and gene amplification in tumors. Molecular cytogenetic methods have expanded the possibilities for precise genetic diagnoses, which are extremely important for clinical management of patients and appropriate counseling of their families.

A non-sex chromosome marker in a patient with an atypical Ullrich-Turner phenotype and mosaicism of 46,X,mar/46,XX

The absence of a sex chromosome in conjunction with the presence of a marker chromosome generally implicates a sex chromosome origin for such marker chromosomes. These types of findings are frequently associated with Ullrich-Turner syndrome. We report a patient that presented with an atypical Ullrich-Turner phenotype and a cytogenetic mosaicism of 46,X,mar/46,XX. The marker chromosome was derived from chromosome 20, not from the X or Y chromosome. The patient's clinical features are described and discussed relative to the cytogenetic findings. This case further demonstrates the necessity of marker chromosome identification for accurate phenotype-karyotype correlation.

AZFc deletion detected in a newborn with prenatally diagnosed Yq deletion

A case of prenatally diagnosed Yq deletion is described. Fluorescence in situ hybridisation (FISH) was used to identify the abnormal chromosome and to exclude mosaicism. Based on the cytogenetic result and the ultrasound investigation the pregnancy was continued. A newborn with normal male genitalia was delivered. Microdeletion analysis of the Yq showed the absence of the AZFc region. This type of deletion has been described as being associated with azoospermia or oligozoospermia with a progressive decrease of sperm number over time. Long-term andrological follow-up of the newborn will be necessary with eventual cryoconservation of sperm at early adulthood. The present report proposes that AZF analysis combined with FISH has an important role in accurate genetic counselling in sex chromosome anomalies.

Molecular mechanisms for constitutional chromosomal rearrangements in humans

Cytogenetic imbalance in the newborn is a frequent cause of mental retardation and birth defects. Although aneuploidy accounts for the majority of imbalance, structural aberrations contribute to a significant fraction of recognized chromosomal anomalies. This review describes the major classes of constitutional, structural cytogenetic abnormalities and recent studies that explore the molecular mechanisms that bring about their de novo occurrence. Genomic features flanking the sites of recombination may result in susceptibility to chromosomal rearrangement. One such substrate for recombination is low-copy region-specific repeats. The identification of genome architectural features conferring susceptibility to rearrangements has been accomplished using methods that enable investigation of regions of the genome that are too small to be visualized by traditional cytogenetics and too large to be resolved by conventional gel electrophoresis. These investigations resulted in the identification of previously unrecognized structural cytogenetic anomalies, which are associated with genetic syndromes and allowed for the molecular basis of some chromosomal rearrangements to be delineated.

Application of multicolor fluorescent in situ hybridization for enhanced characterization of chromosomal abnormalities in congenital disorders

OBJECTIVE

To determine the efficacy of multicolor fluorescent in situ hybridization (M-FISH), which paints each chromosome in a unique color, for identification of congenital derivative and marker chromosomes. MATERIAL, METHODS AND CASES: Commercially available M-FISH probes were used to label each chromosome in a specific fluorescent color. Six representative cases involving derivative chromosomes, markers, and subtle anomalies were analyzed by M-FISH.

RESULTS

Three familial, rather subtle derivative chromosomes were identified by M-FISH with relative ease. A small ring that was unidentifiable by banded-chromosome analysis was identified by M-FISH. A case of a subtle telomeric anomaly could not be resolved without the use of telomeric-specific probes. The M-FISH results were confirmed by individual chromosome-specific painting probes.

CONCLUSION

M-FISH was helpful for identifying a wide range of congenital chromosomal anomalies. However, for subtle chromosomal abnormalities, use of locus-specific probes may be necessary.

Advances in laboratory evaluation of Turner syndrome and its variants: beyond cytogenetics studies

Turner syndrome is a clinically defined phenotype that is characterized by partial or complete X chromosome monosomy. A host of cytogenetic aberrations and mosaicism have been associated with this syndrome. Some individuals, Turner syndrome variants, have cytogenetic findings consistent with Turner syndrome, but exhibit atypical clinical phenotypes. Recently, several molecular tests have been presented to allow for the refined clinical study of Turner syndrome and its variants.

Identification of Y chromatin directly in gonadal tissue by fluorescence in situ hybridization (FISH): significance for Ullrich-Turner syndrome screening in the cytogenetics laboratory

The presence of Y chromatin in individuals with Ullrich-Turner syndrome (UTS) confers a risk for gonadoblastoma. In mosaic cases, little is known about Y chromatin distribution in gonads. Fluorescence in situ hybridization (FISH) is a direct approach to assess the extent of Y chromatin mosaicism in gonads. Gonadal tissue from four patients with mosaic karyotypes were analyzed by routine cytogenetics and FISH with X and Y centromere probes. Y chromatin was present in gonads in varying percentages in these patients. The distribution of Y chromatin in gonads of UTS individuals did not completely correlate with that found in blood lymphocytes. The finding of Y chromatin in the blood samples from these patients prompted the development of a screening strategy in our cytogenetics laboratory to detect low-level Y chromatin mosaicism in patients with UTS.

Utility of multicolor fluorescent in situ hybridization in clinical cytogenetics

PURPOSE

Multicolor FISH (M-FISH) was introduced in 1996 to scan all 24 chromosomes in different fluorescent colors by use of a specific filter set and computer software. However, the clinical utility of M-FISH has been limited because of the lack of commercial availability of reagents and hardware. We have evaluated M-FISH for identification of markers, derivative chromosomes, and complex karyotypes.

METHODS

We present our findings based on a representative sample of one normal and six abnormal cases from a variety of tissue types. The results of M-FISH were confirmed by other well-established FISH probes.

RESULTS

M-FISH analyses were successful in all six cases. The derivative chromosomes, ring, and a complex karyotype were resolved.

CONCLUSIONS

We find M-FISH to be an invaluable tool for a high degree of accuracy and efficiency for chromosome identification. The limitations similar to spectral karyotyping system (SKY) include the inability to detect intrachromosomal anomalies, abnormalities involving the p-arms of acrocentrics and areas rich in highly repetitive DNA. In addition, there are some concerns of misinterpretation due to overlap of fluorophore combinations of different chromosomes, especially for subtle insertional translocations.

Karyotype-phenotype correlation in females with X chromosome abnormalities

In mammals, females have a pair of X chromosomes, whereas males have one X chromosome and one Y chromosome, which is much smaller and contains fewer genes than a X chromosome. One of the pair of X chromosomes is inactivated in females. The inactivated X chromosome is late-replicating, heterochromatic, and genetically unexpressed. An X inactivation center (XIC) located at a proximal region on Xq is thought to control inactivation of an X chromosome. There has been increasing scientific interest in the relationship between chromosomal and clinical findings in different chromosomal aberrations, whether affecting the sex chromosomes or the autosomes. The genetic and molecular implications of the karyotype/phenotype controversy have recently been considered with the aim of better understanding the interplay of specific genes carried on different chromosomes in organ development and differentiation. Karyotype/phenotype correlation showed the gradation of severity of clinical phenotype to be related to the number of X chromosomes.