Parental origin of apparently balanced de novo complex chromosomal rearrangements investigated by microdissection,whole genome amplification,and microsatellite‐mediated haplotype analysis

Grossmann V, Höckner M, Karmous‐Benailly H, Liang D, Puttinger R, Quadrelli R, Röthlisberger B, Huber A, Wu L, Spreiz A, Fauth C, Erdel M, Zschocke J, Utermann G, Kotzot D. Parental origin of apparently balanced de novo complex chromosomal rearrangements investigated by microdissection, whole genome amplification, and microsatellite‐mediated haplotype analysis. Complex chromosomal rearrangements (CCRs) are rare findings in clinical cytogenetics. As a result of the high risk of unbalanced segregation, familial cases are even rarer and maternal transmission occurs more frequently than paternal transmission. Analogous to Drosophila and mice, as well as to CCRs involving the Y chromosome or a clinically relevant associated deletion, a preferential origin in spermatogenesis has been assumed but not proven directly and systematically thus far. Here, we investigated three healthy adults, one healthy child, and one child with multiple congenital anomalies and various balanced de novo CCRs. The analyses were performed in each case on 10 copies of a derivative chromosome and their normal homologs by glass‐needle microdissection, whole genome amplification (WGA), and microsatellite‐mediated haplotype analysis. With respect to the number of chromosomes involved in each case and in all cases together, the number of chromosomal segments in each case and in all cases together, and the number of breakpoints in each case and in all cases together, the conformity for paternal origin of all derivative chromosomes and maternal origin of their normal homologs makes formation in paternal germline more likely than a postzygotic formation with an accidental uniformity. In conclusion, our results confirm the preferential formation of de novo balanced CCRs in the paternal germline.     

Familial partial trisomy 5p resulting from segregation of an insertional translocation

A case of duplication of segment p13-p15 of the short arm of chromosome 5 as the result of an insertional translocation in a mentally retarded girl with congenital anomalies is reported. Some of the apparently balanced carriers of the inverted insertion showed minor congenital anomalies.     

The complex nature of constitutional de novo apparently balanced translocations in patients presenting with abnormal phenotypes

Objective: To describe the systematic analysis of constitutional de novo apparently balanced translocations in patients presenting with abnormal phenotypes, characterise the structural chromosome rearrangements, map the translocation breakpoints, and report detectable genomic imbalances.

Methods: DNA microarrays were used with a resolution of 1 Mb for the detailed genome-wide analysis of the patients. Array CGH was used to screen for genomic imbalance and array painting to map chromosome breakpoints rapidly. These two methods facilitate rapid analysis of translocation breakpoints and screening for cryptic chromosome imbalance. Breakpoints of rearrangements were further refined (to the level of spanning clones) using fluorescence in situ hybridisation where appropriate.

Results: Unexpected additional complexity or genome imbalance was found in six of 10 patients studied. The patients could be grouped according to the general nature of the karyotype rearrangement as follows: (A) three cases with complex multiple rearrangements including deletions, inversions, and insertions at or near one or both breakpoints; (B) three cases in which, while the translocations appeared to be balanced, microarray analysis identified previously unrecognised imbalance on chromosomes unrelated to the translocation; (C) four cases in which the translocation breakpoints appeared simple and balanced at the resolution used.

Conclusions: This high level of unexpected rearrangement complexity, if generally confirmed in the study of further patients, will have an impact on current diagnostic investigations of this type and provides an argument for the more widespread adoption of microarray analysis or other high resolution genome-wide screens for chromosome imbalance and rearrangement.

     

De novo apparently balanced complex chromosome rearrangement (CCR) involving chromosomes 4, 18, and 21 in a girl with mental retardation: Report and review

We describe a complex and unique, de novo apparently balanced translocation involving chromosomes 4, 18, and 21 with 4 breakpoints, in a patient who was referred for an evaluation of possible fragile-X syndrome. Fluorescence in situ hybridization (FISH) confirmed the complexity of the rearrangement and showed the derivative 21 to be composed of 3 distinct segments derived from chromosomes 21, 18, and 4. The derivative chromosome 18 had undergone a double translocation, the first such event to be described in constitutional complex chromosomal rearrangements (CCRs) involving chromosome 18. A review of these CCRs suggests the existence of a breakpoint “hot spot” on 18q21. Am. J. Med. Genet. 78:44–51, 1998. © 1998 Wiley-Liss, Inc.     

Prenatal diagnosis of a fetus with two balanced de novo chromosome rearrangements

Two apparently balanced chromosome rearrangements were identified in a 17-week fetus by analysis of cultured amniocytes. The fetal karyotype was 46,XX,t(2;16) (q33; q24), inv(7)(p15q11.23). Parental karyotypes were normal, indicating a de novo origin of both chromosome rearrangements in the fetus. The risk of phenotypic abnormality from a de novo reciprocal translocation or inversion has been estimated at approximately 7% [Warburton, 1991]. The risk of abnormality in this fetus was estimated to be a minimum of 14%, based on the additive risk of each rearrangement, equivalent to 3.5% per chromosome breakpoint. The pregnancy was terminated because of the risk of abnormality and the detection of intrauterine growth retardation by ultrasound. In the absence of additional experience, the minimum presumed risk of phenotypic abnormality for de novo, multiple or complex chromosome rearrangements identified prenatally may be estimated as the additive risk of the number of chromosome breakpoints involved. © 1996 Wiley-Liss, Inc.     

A de novo complex chromosomal rearrangement with nine breakpoints characterised by FISH in a boy with mild mental retardation, developmental delay, short stature and microcephaly

A de novo complex chromosome rearrangement (CCR) involving chromosomes 1, 6, 7, 15 and Y was detected in a boy with mental retardation, short stature, and microcephaly. Fluorescence in situ hybridisation (FISH) with whole chromosome painting libraries, band-specific cosmids and telomeric probes was essential for the characterisation of the rearrangement. The CCR was shown to be the result of at least nine chromosomal breaks and involved the alternating insertion of two segments of the short arm of chromosome 1 and two segments of the long arm of chromosome 6 into a novel derived chromosome 7. A non-reciprocal translocation between the distal short arm of the same chromosome 7 and the distal long arm of the Y chromosome was also found, together with a paracentric inversion of the long arm of chromosome 15. The only detectable imbalance was a deletion of the heterochromatic Yq telomeric region. FISH investigations in this case have revealed an additional complexity in this CCR, which has implications for reproductive risk assessment and genetic counselling.     

Balanced into array: genome-wide array analysis in 54 patients with an apparently balanced de novo chromosome rearrangement and a meta-analysis

High-resolution genome-wide array analysis enables detailed screening for cryptic and submicroscopic imbalances of microscopically balanced de novo rearrangements in patients with developmental delay and/or congenital abnormalities. In this report, we added the results of genome-wide array analysis in 54 patients to data on 117 patients from seven other studies. A chromosome imbalance was detected in 37% of all patients with two-breakpoint rearrangements. In 49% of these patients, the imbalances were located in one or both breakpoint regions. Imbalances were more frequently (90%) found in complex rearrangements, with the majority (81%) having deletions in the breakpoint regions. The size of our own cohort enabled us to relate the presence of an imbalance to the clinical features of the patients by using a scoring system, the De Vries criteria, that indicates the complexity of the phenotype. The median De Vries score was significantly higher (P=0.002) in those patients with an imbalance (5, range 1-9) than in patients with a normal array result (3, range 0-7). This study provides accurate percentages of cryptic imbalances that can be detected by genome-wide array analysis in simple and complex de novo microscopically balanced chromosome rearrangements and confirms that these imbalances are more likely to occur in patients with a complex phenotype.     

Disruption of the ATP8A2 gene in a patient with a t(10;13) de novo balanced translocation and a severe neurological phenotype

Mental retardation is a frequent condition that is clinically and genetically highly heterogeneous. One of the strategies used to identify new causative genes is to take advantage of balanced chromosomal rearrangements in affected patients. We characterized a de novo t(10;13) balanced translocation in a patient with severe mental retardation and major hypotonia. We found that the balanced translocation is molecularly balanced. The translocation breakpoint disrupts the coding sequence of a single gene, called ATP8A2. The ATP8A2 gene is not ubiquitously expressed, but it is highly expressed in the brain. In situ hybridization performed in mouse embryos at different stages of development with the mouse homologue confirms this observation. A total of 38 patients with a similar phenotype were screened for mutations in the ATP8A2 gene but no mutations were found. The balanced translocation identified in this patient disrupts a single candidate gene highly expressed in the brain. Although this chromosomal rearrangement could be the cause of the severe phenotype of the patient, we were not able to identify additional cases. Extensive screening in the mentally retarded population will be needed to determine if ATP8A2 haploinsufficiency or dysfunction causes a neurological phenotype in humans.     

Apparently balanced de novo translocations in patients with abnormal phenotypes: Report of 6 cases

Six patients have been ascertained because of abnormal phenotypes but with apparently balanced de novo translocations. Five of them were mentally retarded with multiple congenital anomalies. The sixth patient had normal mental development but revealed ambiguous genitalia and multiple congenital anomalies. No syndromal diagnosis was possible in any of the six cases. The appearance of apparently balanced reciprocal translocations in association with abnormal phenotype may be coincidental, or the two may be causally related. If the latter is true, the causal relationship may be based upon: I) a submicroscopic chromosomal loss, 2) position effect, or 3) a mutation at the site of the break in one or both translocated chromosomes.     

Low level mosaicism for a balanced 7;14 translocation in the father of an abnormal 7q + child

A child with a 7q + chromosome abnormality had a father with 0.5% mosaicism for a balanced 7;14 translocation. This mosaicism was not found in 100 fibroblasts. This degree of mosaicism is well below the limits usually detected by standard clinical cytogenetic protocols. However, the one abnormal cell cannot be disregarded in this case, since it can serve as an explanation of the child's genotype. This case serves to illustrate the need for detecting subtle degrees of mosaicism for structural anomalies in humans and brings to question the true population frequencies of mosaic balanced translocation carriers.     

Mental retardation in association with a balanced X-autosome translocation and random inactivation of the X chromosomes

A woman whose karyotype shows an apparently balanced reciprocal translocation, 46,X, t(Xq +; 10q —) is described. She is profoundly mentally retarded and shows minor physical abnormalities with normal sexual development. There is a random pattern of late replication of the normal X and the X involved in the translocation, whereas in most balanced X-autosome translocations there is preferential inactivation of the normal X.     

Disruption of EXOC6B in a patient with developmental delay,epilepsy, and a de novo balanced t(2;8) translocation

Most balanced chromosomal aberrations are not associated with a clinical phenotype, however, in some patients they may disrupt gene structure. With the development of various next-generation sequencing techniques, fast and specific analyses of the breakpoint regions of chromosomal rearrangements are possible. Here, we report on a 19-year-old woman with a de novo balanced translocation t(2;8)(p13.2;q22.1) and a severe clinical phenotype including intellectual disability, epilepsy, behavioral features resembling autism, and minor dysmorphic features. By next-generation sequencing, we defined the breakpoints and found disruption of the exocyst complex component 6B (EXOC6B) gene in intron 1 on chromosome 2p13.2 involving two Alu elements with a homology of 81%. No gene was found at the respective breakpoint on chromosome 8. Expression analysis of the EXOC6B in blood lymphocytes and buccal smear revealed reduced expression in the patient in comparison with the control. Our findings in combination with one recently published case and one other patient listed in DECIPHER v5.1 indicate EXOC6B as a gene relevant for intellectual development and electrophysiological stability.     

MLPA vs multiprobe FISH: comparison of two methods for the screening of subtelomeric rearrangements in 50 patients with idiopathic mental retardation

Subtelomeric rearrangements not visible by conventional cytogenetic analysis have been reported to occur in approximately 5% of patients with unexplained mental retardation (MR). As the prevalence of MR is high, many patients need to be screened for these chromosomal abnormalities routinely. Multiplex ligation-dependent probe amplification (MLPA) is a new technique for measuring sequence dosage, allowing large number of samples to be processed simultaneously and thus significantly reducing laboratory work. We have assessed its performance for the detection of subtelomeric rearrangements by comparing the results with those of our previous multiprobe fluorescence in situ hybridization (FISH) assay. We have tested 50 patients with idiopathic MR, dysmorphic features, congenital malformations, and/or familial history of MR. Our results show a high degree of concordance between the two techniques for the 50 samples tested. On the basis of these results, we conclude that MLPA is a rapid, accurate, reliable, and cost-effective alternative to FISH for the screening of subtelomeric rearrangements in patients with idiopathic MR.     

Smith-Lemli-Opitz syndrome in a female with a de novo,balanced translocation involving 7q32: Probable Disruption of an SLOS gene

A 3-month-old infant girl had manifestations of the Smith-Lemli-Opitz syndrome (SLOS) including typical positional anomalies of the limbs, apparent Hirschsprung disease, cataracts, ptosis, anteverted nares, cleft of the posterior palate, small tongue, broad maxillary alveolar ridges, and abnormally low serum cholesterol levels. Chromosomal analysis showed a de novo balanced translocation interpreted as 46,XX,t(7;20)(q32.1;q13.2). We hypothesize that the translocation breakpoint in this case interrupts one SLOS allele and that the other allele at the same locus has a more subtle mutation that was inherited from the other parent. This case, as well as cytogenetic observations in other SLOS cases, suggests that SLOS could be due to autosomal recessive mutation at a gene in 7q32. © 1994 Wiley-Liss, Inc.     

Cytogenetic findings in 200 children with mental retardation and multiple congenital anomalies of unknown cause

We report a cytogenetic study of 200 children with mental retardation and three or more major or minor congenital anomalies. In all cases, the chromosomes were studied with conventional staining methods (nonbanding) and with at least one of the following techniques: Q, G, or R banding. In a few patients, C banding and in vitro differentiation with BUDR and acridine orange (R banding) were also used. In patients with structural abnormality, parental chromosomes were studied using the same techniques. A chromosome abnormality was found in 42 patients (21%). Of these, 16 (8%) had complete or mosaic aneuploidies (11 autosomal and 5 gonosomal); and 26 (13%) had structural defects. In 21 of the latter the structural abnormality occurred as a de novo rearrangement, and in 5 the defect was inherited from a parent carrier of a balanced rearrangement. The contribution of chromosome aberrations to the cause of (idiopathic) MCA/MR syndromes is discussed.     

Emerging patterns of cryptic chromosomal imbalance in patients with idiopathic mental retardation and multiple congenital anomalies: a new series of 140 patients and review of published reports

Background

Chromosomal abnormalities are a major cause of mental retardation and multiple congenital anomalies (MCA/MR). Screening for these chromosomal imbalances has mainly been done by standard karyotyping. Previous array CGH studies on selected patients with chromosomal phenotypes and normal karyotypes suggested an incidence of 10–15% of previously unnoticed de novo chromosomal imbalances.

Objective

To report array CGH screening of a series of 140 patients (the largest published so far) with idiopathic MCA/MR but normal karyotype.

Results

Submicroscopic chromosomal imbalances were detected in 28 of the 140 patients (20%) and included 18 deletions, seven duplications, and three unbalanced translocations. Seventeen of 24 imbalances were confirmed de novo and 19 were assumed to be causal. Excluding subtelomeric imbalances, our study identified 11 clinically relevant interstitial submicroscopic imbalances (8%). Taking this and previously reported studies into consideration, array CGH screening with a resolution of at least 1 Mb has been undertaken on 432 patients with MCA/MR. Most imbalances are non‐recurrent and spread across the genome. In at least 8.8% of these patients (38 of 432) de novo intrachromosomal alterations have been identified.

Conclusions

Array CGH should be considered an essential aspect of the genetic analysis of patients with MCA/MR. In addition, in the present study three patients were mosaic for a structural chromosome rearrangement. One of these patients had monosomy 7 in as few as 8% of the cells, showing that array CGH allows detection of low grade mosaicisims.