Swedish survey on extra structurally abnormal chromosomes in 39 105 consecutive prenatal diagnoses: prevalence and characterization by fluorescence in situ hybridization

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.

Cytogenetics in reproductive medicine: the contribution of comparative genomic hybridization (CGH)

Cytogenetic research has had a major impact on the field of reproductive medicine, providing an insight into the frequency of chromosomal abnormalities that occur during gametogenesis, embryonic development and pregnancy. In humans, aneuploidy has been found to be relatively common during fetal life, necessitating prenatal screening of high-risk pregnancies. Aneuploidy rates are higher still during the preimplantation stage of development. An increasing number of IVF laboratories have attempted to improve pregnancy rates by using preimplantation genetic diagnosis (PGD) to ensure that the embryos transferred to the mother are chromosomally normal. This paper reviews some of the techniques that are key to the detection of aneuploidy in reproductive samples including comparative genomic hybridization (CGH). CGH has provided an unparalleled insight into the nature of chromosome imbalance in human embryos and polar bodies. The clinical application of CGH for the purposes of PGD and the future extensions of the methodology, including DNA microarrays, are discussed.

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.

Prenatal diagnosis: molecular genetics and cytogenetics

The technologies developed for the Human Genome Project, the recent surge of available DNA sequences resulting from it and the increasing pace of gene discoveries and characterization have all contributed to new technical platforms that have enhanced the spectrum of disorders that can be diagnosed prenatally. The importance of determining the disease-causing mutation or the informativeness of linked genetic markers before embarking upon a DNA-based prenatal diagnosis is, however, still emphasized. Different fluorescence in situ hybridization (FISH) technologies provide increased resolution for the elucidation of structural chromosome abnormalities that cannot be resolved by more conventional cytogenetic analyses, including microdeletion syndromes, cryptic or subtle duplications and translocations, complex rearrangements involving many chromosomes, and marker chromosomes. Interphase FISH and the quantitative fluorescence polymerase chain reaction are efficient tools for the rapid prenatal diagnosis of selected aneuploidies, the latter being considered to be most cost-effective if analyses are performed on a large scale. There is some debate surrounding whether this approach should be employed as an adjunct to karyotyping or whether it should be used as a stand-alone test in selected groups of women.

Small familial supernumerary ring chromosome 2: FISH characterization and genotype-phenotype correlation

A child and his mother were found to be mosaic for a small supernumerary marker chromosome (SMC) that was identified and characterized by means of fluorescent in situ hybridization. The marker chromosome was derived from the pericentromeric region of chromosome 2; the involvement of proximal 2q was determined by YAC probes. The proband was referred because of psychotic illness and mild mental retardation, whereas his mother presented only minor dysmorphisms. There are only a few published reports concerning SMC(2) or proximal 2q trisomy. We reviewed the previously reported cases in an attempt to establish genotype-phenotype correlations, which are particularly important when SMCs are identified in prenatal diagnosis.

Prenatal diagnosis of a de novo supernumerary marker derived from chromosome 16

Marker chromosomes are supernumerary chromosomes of unknown origin and are seldom found in prenatal diagnosis. Application of fluorescent in situ hybridization (FISH) allows the identification of the chromosomal origin of markers. Estimation of the risk of an abnormal phenotype outcome can be enabled by collecting data on phenotypes associated with markers of the same chromosomal origin. So far only very few cases of prenatal diagnosis of de novo supernumerary markers derived from chromosome 16 have been reported. Here the prenatal diagnosis of a de novo supernumerary marker chromosome 16 is described and the relevant literature discussed.

Relationship between clinical and genetic features in "inverted duplicated chromosome 15" patients

Inverted duplicated chromosome 15 (Inv dup [15]) syndrome is a genetic disorder characterized by psychologic or intellectual language delay; neurologic signs, such as hypotonia, ataxia, and epilepsy; mental retardation ranging from mild to severe; and facial dysmorphisms. All patients present with a psychopathologic impairment that is highly variable in severity but always classifiable as pervasive developmental disorder (PDD). Many genetic mechanisms have been hypothesized to explain the clinical variability. This article describes the neurologic and psychopathologic features of six Inv dup(15) patients, one male and five females, between 8 and 14 years of age, all with a maternal marker chromosome. Four patients were diagnosed with PDD not otherwise specified, whereas two patients received a diagnosis of autism. Epilepsy was present in three patients (two generalized symptomatic and one focal symptomatic), and a correlation between the severity of the disease and its outcome was not always observed. Nevertheless, the influence of gene content of the marker chromosome, particularly the three gamma-aminobutyric acid-A receptor subunit genes, may represent the link between epilepsy, mental retardation, and PDD.

Segregation of a supernumerary del(15) marker chromosome in sperm

Supernumerary marker chromosomes (SMC) can be associated with both normal and abnormal phenotypes. In addition, SMC are found at higher frequency in males with infertility. We identified a SMC, characterized as a del(15)(q11.2) chromosome, in a phenotypically normal male. Using fluorescence in situ hybridization (FISH), we examined the segregation of the del(15) chromosome in sperm from this patient. Only 6.23% of sperm nuclei showed disomy using a chromosome 15 alpha-satellite FISH probe, instead of the expected 50%. In addition, FISH analysis showed no increase for non-disjunction of chromosome 18, excluding an interchromosomal effect for this chromosome. The significant decrease in sperm bearing the del(15) may be due to tissue-specific mosaicism or a result of some form of selection against the del(15) during spermatogenesis. This finding provides a basis for the observation that SMC(15) are less likely to be inherited from a paternal carrier.

Rapid identification of a small dicentric supernumerary marker derived from chromosome 16 with a modified FISH technique on amniotic fluid

Small supernumerary marker chromosomes are seldom found in prenatal diagnosis and the majority of them are difficult to identify. The only possibility to give a more precise prognosis is by establishing its origin. FISH is the best technique to identify the chromosomal origin, but in the majority of cases large amounts of chromosomal material are needed and this is time consuming. We have used a modification of the FISH technique that allows the hybridization of several probes on one slide. Using this method, we have identified the first de novo mosaic dicentric supernumerary marker derived from chromosome 16 (smaller than chromosome 21) in amniotic fluid. The gestation and the follow-up of the baby were normal.

A brief history of human autosomes

Comparative gene mapping and chromosome painting permit the tentative reconstruction of ancestral karyotypes. The modern human karyotype is proposed to differ from that of the most recent common ancestor of catarrhine primates by two major rearrangements. The first was the fission of an ancestral chromosome to produce the homologues of human chromosomes 14 and 15. This fission occurred before the divergence of gibbons from humans and other apes. The second was the fusion of two ancestral chromosomes to form human chromosome 2. This fusion occurred after the divergence of humans and chimpanzees. Moving further back in time, homologues of human chromosomes 3 and 21 were formed by the fission of an ancestral linkage group that combined loci of both human chromosomes, whereas homologues of human chromosomes 12 and 22 were formed by a reciprocal translocation between two ancestral chromosomes. Both events occurred at some time after our most recent common ancestor with lemurs. Less direct evidence suggests that the short and long arms of human chromosomes 8, 16 and 19 were unlinked in this ancestor. Finally, the most recent common ancestor of primates and artiodactyls is proposed to have possessed a chromosome that combined loci from human chromosomes 4 and 8p, a chromosome that combined loci from human chromosomes 16q and 19q, and a chromosome that combined loci from human chromosomes 2p and 20.

Frequencies of chromosomal abnormalities at amniocentesis: over 20 years of cytogenetic analyses in one laboratory

Prenatal diagnosis of chromosomal disorders has been performed for more than 20 years, mainly for advanced maternal age. Chromosomal abnormality rates derived from second trimester amniocentesis have mainly come from a collection of small-scale studies from North America and Western Europe. Accurate risk estimates for chromosomal abnormalities are important tools for the physician or obstetrician who would need to make referrals to a prenatal genetic center. This paper presents amniocentesis rates of clinically significant cytogenetic abnormalities for various indications, including advanced maternal age, previous chromosomal abnormality, parental structural rearrangement and a family history of aneuploidy as defined in the text. These data come from a Canadian prenatal diagnosis laboratory with more than 20 years experience in second trimester cytogenetic analysis. They show that the overall frequency of chromosomal abnormalities for advanced maternal age (> or = 35 years) is 1.79%. In this group, 21% of all abnormalities are structural rearrangements (including markers) and less than half of all abnormalities are trisomy 21. The advanced maternal age specific risk of aneuploidies at second trimester is 1.24%. Recurrence risk for aneuploidy after a previous one is 1.29%. However, it is much higher (4.84%) for women of > or = 35 years. When a parent's brother, sister, nephew or niece is affected, the risk of occurrence of aneuploidies (0.24%) is not elevated. When there is a balanced translocation in one of the parents, the overall risk is 10.2% for unbalanced translocations and 37.3% for balanced translocations.

Clinical applications of comparative genomic hybridization

PURPOSE

Comparative genomic hybridization (CGH) is a powerful DNA-based cytogenetic technique that allows the entire genome to be scanned for chromosomal imbalances without requiring the sample material to be mitotically active. During the past 2 years we received many requests from various medical centers around the country to use CGH to resolve the identity of aberrant chromosomal material.

METHODS

We report the use of CGH for the evaluation of 12 clinical postnatal cases in which traditional cytogenetic analysis yielded ambiguous results. This series consisted of five marker chromosomes, five unbalanced translocations, and two intrachromosomal duplications.

RESULTS

Identification and characterization of the additional unknown chromosomal material was achieved with use of CGH. All CGH findings were validated by traditional fluorescence in situ hybridization and other specialized staining techniques. CONCLUSLONS: These results demonstrate the effective use of CGH as a focused, single-step method for the identification of chromosomal material of unknown origin.

Prenatal diagnosis of mosaicism for tetrasomy 18p: cytogenetic, fish and morphological findings

A case of mosaicism for tetrasomy 18p detected prenatally is reported. We believe this is the second case where fetal anomalies were found at autopsy.

Delineation of supernumerary marker chromosomes in 38 patients

We present cytogenetic and clinical data on 38 patients with supernumerary marker chromosomes (SMCs). SMCs were characterized using a strategy combining classical banding techniques and molecular cytogenetic studies. Cases were ascertained prenatally, postnatally, and after fetal death. In 26 patients (68%), the SMC originated entirely from acrocentric chromosomes. Among these, most patients carried a der(15). In 11 patients (29%), they were of nonacrocentric origin, including 9 autosomal and 2 gonosomal marker chromosomes. In 1 patient the SMC was of partially acrocentric origin. Patients with small derivatives of chromosome 15 [der(15)] had a normal phenotype. Those with a larger der(15) showed phenotypical abnormalities. Patients with supernumerary marker chromosomes derived from chromosomes 13 or 21, and 14 appeared to have a low risk of abnormalities. Out of this group only 1 patient who carried an additional r(21) had physical anomalies. Patients with an SMC originating from chromosome 22 showed physical abnormalities in 2 out of 6 cases. Supernumerary marker chromosomes identified as i(9p), i(12p), and der(18) were all associated with an abnormal phenotype. Two of the derivatives of chromosome 20 analyzed were correlated with a normal phenotype, while the carrier of the third one showed physical anomalies and motor retardation. Of 2 patients with an extra der(X), 1 was normal and 1 showed an abnormal phenotype.

FISH and molecular study of autosomal supernumerary marker chromosomes excluding those derived from chromosomes 15 and 22: I. Results of 26 new cases

The chromosomal origins and in some cases the molecular composition of 26 autosomal supernumerary marker chromosomes (SMC) were identified using combined fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR) techniques. Fifteen were de novo, 4 maternally and 2 paternally transmitted and in 5 cases the parental origin is not known. Eleven cases were non-mosaic and fifteen cases had SMC cell lines ranging from 8-87%. Ten cases were ascertained prenatally, nine postnatally with abnormal phenotypes, three with poor reproductive histories and four co-incidentally. Five SMC were small rings from chromosomes 3, 6 (2 cases), 20 and 21; 8 were bisatellited from chromosomes 13/21 (4 cases), 14 (3 cases) and 14/22 (1 case). The remaining 13 appeared to be minutes comprising centromeric material only from chromosomes 1, 4, 12, 13/21 (2 cases), 14 (3 cases), 16 (2 cases), 19; 5/19, and a centric fusion involving 13 or 21 and 14. Euchromatin was detected in 9 out of 18 SMC tested with paints and/or PCR, and abnormal phenotypes were most commonly observed in patients with small ring shaped SMCs containing euchromatic sequences. Uniparental paternal isodisomy (UPD) for chromosome 6 was detected in one patient but was the only example of UPD for the normal homologues in association with an autosomal SMC in an overall total of 30 cases examined.

A molecular and FISH approach to determining karyotype and phenotype correlations in six patients with supernumerary marker(22) chromosomes

In a cytogenetic, molecular, and clinical study of patients with autosomal supernumerary marker chromosomes (SMC), 6 out of 72 (8.3%) were shown by fluorescence in situ hybridisation (FISH) to be derived from chromosome 22. PCR microsatellite analysis and FISH using primers and cosmids from proximal 22q showed 3 of the 6 to contain euchromatin. The first, a de novo nonmosaic bisatellited, dicentric SMC, was acsertained in a patient with cat eye syndrome and Duane anomaly. Microsatellite analysis showed the SMC was maternal in origin with euchromatin extending to D22S427, i.e., proximal to the DiGeorge syndrome critical region (DGSCR). The second, a nonmosaic bisatellited, dicentric marker, was found in a child with severe hypotonia and developmental delay and had been inherited from the patient's phenotypically normal father. FISH showed the SMC to contain euchromatin extending into the DGSCR. The third, a de novo SMC, was ascertained antenatally and was shown to contain 22q euchromatin extending distal to the DGSCR. The 19-week terminated fetus was phenotypically normal at autopsy. Two of the three SMC(22)s not containing detectable proximal 22q euchromatin were ascertained coincidentally in phenotypically normal individuals, whereas the third, the only mosaic with a minority euploid cell line, was found in a patient with mild developmental delay. These results suggest that SMC(22)s devoid of proximal 22q euchromatin are not associated with adverse phenotypic effects whereas SMC(22)s containing euchromatin may be found in individuals with phenotypes ranging from cat eye syndrome to normal.

FISH characterization of small supernumerary marker chromosomes in two Prader-Willi patients

A small supernumerary chromosome was observed in two Prader-Willi syndrome (PWS) patients. The clinical diagnosis of PWS was confirmed by the ascertainment of the deletion of region 15q11-13 in one case and uniparental disomy (UPD) of the same region in the other. The markers were negative for dystamycinA/DAPI banding, did not contain NOR-positive satellites, and had an appearance consistent with a very small ring chromosome. Fluorescent in situ hybridization (FISH) analysis with the "all human centromere" probe indicated the presence of centromeric sequences in both markers. Chromosomal in situ suppression hybridization with chromosome specific libraries demonstrated that the small markers in the deleted and UPD patient originated from chromosome 15 and X, respectively. To the best of our knowledge these are the only PWS patients reported with a supernumerary marker chromosome other than inv dup(15) characterized by FISH.

Small extra ring chromosome derived from chromosome 10p: clinical report and characterisation by FISH

We present a case with a small extra ring chromosome which was found in 66% of lymphocytes on routine cytogenetic examination. FISH analyses, using centromere specific and single copy probes, showed that the extra ring chromosome was derived from the most proximal part of 10p, close to the centromere. The patient has a unilateral cleft lip and palate, mild dysmorphic features, and mild mental retardation. Only a limited number of extra ring chromosomes have been characterised so far. To our knowledge, this is the first reported patient with an extra ring chromosome derived from chromosome 10p.

Incidence and significance of chromosome mosaicism involving an autosomal structural abnormality diagnosed prenatally through amniocentesis: a collaborative study

Among 179,663 prenatal diagnosis cases collected from ten institutions and two publications, 555 (0.3 per cent) were diagnosed as having chromosome mosaicism. Of these, 57 (10.3 per cent) were mosaic for an autosomal structural abnormality, 28 (5 per cent) for a sex chromosome structural abnormality, and 85 (15.3 per cent) were mosaic for a marker chromosome. Ninety-five cases of prenatally diagnosed mosaicism with a structural abnormality in an autosome and a normal cell line, and with a known phenotypic outcome, were collected for karyotype-phenotype correlations through our collaboration (40 cases), a prior survey (26 cases), and published reports (29 cases). They included 13 balanced reciprocal translocations, one unbalanced reciprocal translocation, four balanced Robertsonian translocations, four unbalanced Robertsonian translocations, four inversions, 17 deletions, three ring chromosomes, 19 i(20q), seven +i(12p), six other isochromosomes, and 17 partial trisomies resulting from a duplication or other rearrangement. All cases mosaic for a balanced structural rearrangement resulted in a normal phenotype. All cases of 46/46,i(20q) resulted in normal liveborns. Five of seven cases with 46/47,+i(12p) had an abnormal phenotype compatible with Killian-Pallister syndrome. The overall risk for an abnormal outcome for a mosaic case with an unbalanced structural abnormality, excluding 46/46,i(20q) and 46/47,+i(12p), is 40.4 per cent. In the same category, the study also suggested a correlation between the percentage of abnormal cells and an abnormal phenotype. For mosaicism involving a terminal deletion, the possibility of a familial fragile site should be considered.