Complex genomic alterations and intellectual disability: an interpretative challenge

BACKGROUND

Complex chromosomal rearrangements (CCRs) are structural rearrangements involving more than three chromosomes or having more than two breaks; approximately 70% are not associated with any clinical phenotype. Here, we describe a CCR segregating in a two-generation family.

METHOD

A 4-year-old male was evaluated for developmental delay, mild intellectual disability and epicanthus. Karyotype, fluorescence in situ hybridisation (FISH) analysis and array comparative genomic hybridisation (aCGH) analysis were performed on the patient and of all family members.

RESULT

Array CGH analysis of the proband detected two non-contiguous genomic gains of chromosome 2 at bands q32.3q33.2 and bands q36.1q36.3. Both karyotype and FISH analysis revealed a recombinant chromosome 2 with a direct insertion of regions q32.3q33.2 and q36.1q36.3 into region q12. Both of these regions were also present in their original location. Karyotype and FISH analysis of the father revealed a de novo direct insertion of regions q32.3q33.2 and q36.1q36.3 into region q12. Moreover, a de novo balanced translocation involving the q arm of the same chromosome 2 and the p arm of chromosome 10 was observed in the father of the proband. The single nucleotide polymorphism (SNP) array analysis and haplotype reconstruction confirmed the paternal origin of the duplications. Karyotype, FISH analysis and array CGH analysis of other family members were all normal.

CONCLUSION

This report underlines the importance of using different methods to correctly evaluate the origin and the structure of CCRs in order to provide an appropriate management of the patients and a good estimation of the reproductive risk of the family.

Structural brain anomalies in Cri-du-Chat syndrome: MRI findings in 14 patients and possible genotype-phenotype correlations

INTRODUCTION

Cri-du-Chat Syndrome (CdCS) is a genetic condition due to deletions showing different breakpoints encompassing a critical region on the short arm of chromosome 5, located between p15.2 and p15.3, first defined by Niebuhr in 1978. The classic phenotype includes a characteristic cry, peculiar facies, microcephaly, growth retardation, hypotonia, speech and psychomotor delay and intellectual disability. A wide spectrum of clinical manifestations can be attributed to differences in size and localization of the 5p deletion. Several critical regions related to some of the main features (such as cry, peculiar facies, developmental delay) have been identified. The aim of this study is to further define the genotype-phenotype correlations in CdCS with particular regards to the specific neuroradiological findings.

PATIENTS AND METHODS

Fourteen patients with 5p deletions have been included in the present study. Neuroimaging studies were conducted using brain Magnetic Resonance Imaging (MRI). Genetic testing was performed by means of comparative genomic hybridization (CGH) array at 130 kb resolution.

RESULTS

MRI analyses showed that isolated pontine hypoplasia is the most common finding, followed by vermian hypoplasia, ventricular anomalies, abnormal basal angle, widening of cavum sellae, increased signal of white matter, corpus callosum anomalies, and anomalies of cortical development. Chromosomal microarray analysis identified deletions ranging in size from 11,6 to 33,8 Mb on the short arm of chromosome 5. Then, we took into consideration the overlapping and non-overlapping deleted regions. The goal was to establish a correlation between the deleted segments and the neuroradiological features of our patients.

CONCLUSIONS

Performing MRI on all the patients in our cohort, allowed us to expand the neuroradiological phenotype in CdCS. Moreover, possible critical regions associated to characteristic MRI findings have been identified.

Combined Use of DNA Probes in First-Trimester Prenatal Diagnosis of Hemophilia A

First-trimester prenatal diagnoses of hemophilia A were heretofore obtained by using either intragenic factor VIII markers or linked cxtragcnic polymorphic markers. Postulating that the combined use of all the available intragenic and extragenic markers can render such diagnoses more frequently feasible and more reliable, we carried out ten first-trimester prenatal diagnoses in male fetuses at risk for hemophilia A by DNA analysis of chorionic villus employing in combination the intragenic Bcl I polymorphism and the St 14 (DXS 52) or DX 13 (DXS 15) extragenic probes. A diagnosis of hemophilia was obtained in three fetuses, with a diagnosis of normal fetus obtained in the remaining seven. Seven diagnoses are confirmed by factor VIII assays carried out at the time of abortion, in the mid-Trimester or at birth. A factor VIII probe recognizing Bcl I polymorphism was useful in 4 of 6 diagnoses; St 14, in 5 of 6; and DX 13 in 3 of 5. In two cases, St 14 was the only useful probe for diagnosis. Even though no recombination between extragenic probes and factor VIII gene was detected in this study, when only extragenic markers were informative we advised diagnostic confirmation on fetal plasma obtained by fetoscopy. Hence, first-trimester prenatal diagnosis of hemophilia A is feasible for the great majority of fetuses at risk through combined use of all the available intragenic and extragenic probes, providing key family members are available.

Cryptic deletions are a common finding in "balanced" reciprocal and complex chromosome rearrangements: a study of 59 patients

Using array comparative genome hybridisation (CGH) 41 de novo reciprocal translocations and 18 de novo complex chromosome rearrangements (CCRs) were screened. All cases had been interpreted as "balanced" by conventional cytogenetics. In all, 27 cases of reciprocal translocations were detected in patients with an abnormal phenotype, and after array CGH analysis, 11 were found to be unbalanced. Thus 40% (11 of 27) of patients with a "chromosomal phenotype" and an apparently balanced translocation were in fact unbalanced, and 18% (5 of 27) of the reciprocal translocations were instead complex rearrangements with >3 breakpoints. Fourteen fetuses with de novo, apparently balanced translocations, all but two with normal ultrasound findings, were also analysed and all were found to be normal using array CGH. Thirteen CCRs were detected in patients with abnormal phenotypes, two in women who had experienced repeated spontaneous abortions and three in fetuses. Sixteen patients were found to have unbalanced mutations, with up to 4 deletions. These results suggest that genome-wide array CGH may be advisable in all carriers of "balanced" CCRs. The parental origin of the deletions was investigated in 5 reciprocal translocations and 11 CCRs; all were found to be paternal. Using customized platforms in seven cases of CCRs, the deletion breakpoints were narrowed down to regions of a few hundred base pairs in length. No susceptibility motifs were associated with the imbalances. These results show that the phenotypic abnormalities of apparently balanced de novo CCRs are mainly due to cryptic deletions and that spermatogenesis is more prone to generate multiple chaotic chromosome imbalances and reciprocal translocations than oogenesis.

Otorhinolaringologic manifestation of Smith-Magenis syndrome

Smith-Magenis syndrome (SMS) is a multiple congenital anomaly/mental retardation (MCA/MR) syndrome link to a contiguous-gene deletion syndrome, involving chromosome 1 7p 11.2,whose incidence is estimated to be 1:25,000 livebirth. SMS is characterised by a specific physical, behavioural and developmental pattern. The main clinical features consist of a broad flat midface with brachycefaly, broad nasal bridge, brachydactily, speech delay, hoarse deep voice and peripheral neuropathy. Behavioural abnormalities include hypermotility, self-mutilation and sleep disturbance. This report defines the otorhinolaryngological aspects of a new case of SMS, confirmed by cytogenetic-molecular analysis, in a 9 year old girl affected by chronic otitis media, deafness and sinusitis, who presented with typical clinical signs and symptoms.

Trisomic zygote rescue revealed by DNA polymorphism analysis in confined placental mosaicism

Uniparental disomy can be caused by different genetic mechanisms such as gamete complementation, chromosome duplication in monosomic zygote, or post-zygotic aneuploidy correction. This last mechanism is well documented in human reproduction and is related to placental mosaicism. In the case of a trisomic zygote which has originated by paternal or maternal non-disjunction at the first or second meiotic cell division, mosaicism will result from chromosome loss and restoration of a 'normalized' diploid fetal karyotype. In order to enrich the literature with new observations on this subject, we studied by DNA polymorphism analysis ten cases of confined placental mosaicism (CPM). The finding in placental DNA of three different alleles at polymorphic loci of chromosomes 13, 16, and 20 demonstrated the trisomic status of the zygote in three cases. On the basis of these results, we believe that systematic DNA polymorphism analysis could give useful additional information to improve knowledge on aneuploidy correction in human reproduction.

Increasing complexity of the karyotype in 50 human gliomas. Progressive evolution and de novo occurrence of cytogenetic alterations

We studied the karyotypes of eight differentiated gliomas, 19 anaplastic gliomas, and 23 glioblastomas (GBM). Normal stemlines were present in 70% of the differentiated and anaplastic gliomas; abnormalities were mostly characterized by loss of sex chromosomes. In GBM, on the contrary, only 13% of the stemlines were normal and three groups, 45,XO, near-diploid, and near tetraploid, could be identified. The most frequent alterations among GBM were: total or partial loss of chromosome 10 in nine cases, structural abnormalities of chromosome 9 in seven cases, and loss of the Y chromosome in stemline clones of seven cases. Less frequent abnormalities included chromosomes 7, 1, 3, and 19. Our data support the cytogenetic model of gliomas as multi-stage tumors. GBM, in particular, can originate from the evolution of astrocytomas but can also develop de novo. In both cases loss of genetic material on chromosome 10 seems to play a crucial role.

Prenatal confirmation of trisomy 12 mosaicism by fetal skin biopsy

Trisomy 12 mosaicism diagnosed at 16 weeks' amniocentesis in a 42-year-old woman was not confirmed at 18 weeks' gestational age in amniotic fluid or fetal blood. Fetal skin biopsy performed at the same time did, however, allow the detection of trisomy 12 in 1 of 14 fibroblasts analysed. Fetal skin biopsy can be included within the diagnostic procedures to be performed when a level III mosaicism is found in the amniotic fluid.

Multiple clonal chromosome abnormalities in Peyronie's disease

Numerical and structural chromosome aberrations were found in cell plaque metaphases from 9 of 14 patients with Peyronie's disease. In two cases there was evidence of clonal evolution for some of the chromosomal aberrations observed. The Y chromosome was the most frequently involved in numerical changes. Four of 9 cases with abnormal karyotype showed more than one abnormal, cytogenetically unrelated clone. Our findings suggest the possibility of a multiclonal origin for this benign tumor, and confirm the presence of chromosome instability in this cell growth disorder.

Genetic amniocentesis: 505 cases performed before the sixteenth week of gestation

Between May 1987 and November 1988, 505 early amniocentesis within the 15th week of gestation were performed at the First Department of Obstetrics and Gynaecology, 'L. Mangiagalli' of the University of Milan and at the Department of Obstetrics and Gynaecology of 'Gaslini' hospital in Genoa. A total number of ten abnormal fetal karyotypes were diagnosed. In addition, one case of pseudomosaicism (not confirmed on fetal blood) and one case of osteogenesis imperfecta type II (observed at ultrasound examination) were also detected. Eleven pregnancies were therefore terminated because of an abnormal fetus. Out of 494 pregnancies (excluding terminated pregnancies) there were 16 fetal losses within the 28th week; ten of these occurred in the 2 weeks following the procedure. There were 475 live-births, of which 447 were term deliveries and the other 28 deliveries occurred before the 37th week of gestation.

Seven cases of trisomy 3 mosaicism in chorionic villi

This paper describes seven cases of confined chorionic mosaicism with trisomy 3. The chromosomally abnormal cell line in chorionic villi was revealed in three cases at diagnostic CVS and in four cases at the evacuation of the uterine cavity after a missed abortion had been diagnosed by ultrasound. In two of these cases, the abortion occurred after apparently normal development of the fetus during the second trimester of pregnancy. An evaluation of the effect of confined chorionic mosaicism with trisomy 3 on the viability of the conceptus has been attempted.

The yolk sac in early pregnancy failure

An attempt was made to visualize the yolk sac in 845 patients scheduled for chorionic villi sampling. The distribution of yolk sac diameters and the interpolating growth curve up to 11 weeks of development were analyzed in 239 pregnant women who were delivered of normal infants. The highest visualizing rate of the yolk sac in normal pregnancies was 97 at 7 weeks of gestation. A total of 130 miscarriages occurred before chorionic villi sampling. In these cases, the diameter of the yolk sac versus crown-rump length tended to be larger than found in normal pregnancies. The visualizing rate of the yolk sac in miscarriages after the embryo had been formed was significantly higher in those women who demonstrated fetal heart activity (82.1%) than in those who did not (54.5%). On the other hand, the yolk sac was observed in 44% of miscarriages without a visible embryo. These findings suggest different types of missed abortion. An abnormal karyotype was observed in 23 of 29 chromosomal analyses performed on aborted specimens. An abnormal karyotype was observed in all eight cases with only a yolk sac-like structure within the gestational sac.

Combined use of DNA probes in first-trimester prenatal diagnosis of hemophilia A

First-trimester prenatal diagnoses of hemophilia A were heretofore obtained by using either intragenic factor VIII markers or linked extragenic polymorphic markers. Postulating that the combined use of all the available intragenic and extragenic markers can render such diagnoses more frequently feasible and more reliable, we carried out ten first-trimester prenatal diagnoses in male fetuses at risk for hemophilia A by DNA analysis of chorionic villus employing in combination the intragenic Bcl I polymorphism and the St 14 (DXS 52) or DX 13 (DXS 15) extragenic probes. A diagnosis of hemophilia was obtained in three fetuses, with a diagnosis of normal fetus obtained in the remaining seven. Seven diagnoses are confirmed by factor VIII assays carried out at the time of abortion, in the mid-trimester or at birth. A factor VIII probe recognizing Bcl I polymorphism was useful in 4 of 6 diagnoses; St 14, in 5 of 6; and DX 13 in 3 of 5. In two cases, St 14 was the only useful probe for diagnosis. Even though no recombination between extragenic probes and factor VIII gene was detected in this study, when only extragenic markers were informative we advised diagnostic confirmation on fetal plasma obtained by fetoscopy. Hence, first-trimester prenatal diagnosis of hemophilia A is feasible for the great majority of fetuses at risk through combined use of all the available intragenic and extragenic probes, providing key family members are available.

Prevalence and distribution of chromosome abnormalities in a sample of first trimester internal abortions

Cytogenetic analysis was performed directly on villus material from 202 samples obtained at the evacuation of the uterine cavity in cases of retained abortion in the first trimester, identified as such by ultrasound examination. A precise delineation of the karyotype was obtained in 94% of the cases, while the efficiency of karyotype analysis in samples of spontaneous abortion was not higher than 50%. An abnormal chromosome constitution was found in 145 fetuses (76.7%) of which 117, including mosaics, were aneuploid (70%), 16 polyploid (8.5%) and 12 had structural abnormalities (6.3%). The relative proportion of chromosome abnormalities in this material is higher than that found in spontaneous abortion for trisomies and double trisomies, but lower for 45,X and polyploidy. The method was found to be efficient in obtaining fetal karyotypes also in those cases in which the villous material was scarce (1 mg), and thus it seems appropriate for routine cytogenetic studies in the first trimester abortions.

First trimester fetal karyotyping: one thousand diagnoses

Cytogenetic investigations for diagnostic purposes were performed on 1000 first trimester samples of chorionic villi (CVS) in two laboratories using similar techniques. Fetal karyotyping was the primary indication for CVS in 912 and maternal age was the major indication in 758 of them. The risk category "previous child/fetus with chromosome abnormality" included 74 diagnoses, while the category "chromosome abnormality in one of the parents" included 38 diagnoses. Sex determination was the primary indication for CVS in 53 pregnancies. The overall incidence of chromosomal abnormalities was 70, of which 47 were balanced and 23 unbalanced. The results are detailed for each of the risk categories and the incidence of abnormal karyotypes is given for each year of maternal age. In the maternal age of 35-37 years the incidence of unbalanced karyotypes was 2.9% and in the years 38 onwards it was 6.6%. The incidence of unbalanced karyotypes was about 4% when the sampling was made in the weeks 9 to 12 but six abnormal karyotypes were found among 39 CVS performed at the eight week of gestation. The 11 trisomies of the type not found at birth were clustered between the 8th and the 10th week of pregnancy. The technical problems encountered in this experience and the preliminary estimates of fetal loss are discussed.