Complex chromosome 17p rearrangements associated with low-copy repeats in two patients with congenital anomalies

Recent molecular cytogenetic data have shown that the constitution of complex chromosome rearrangements (CCRs) may be more complicated than previously thought. The complicated nature of these rearrangements challenges the accurate delineation of the chromosomal breakpoints and mechanisms involved. Here, we report a molecular cytogenetic analysis of two patients with congenital anomalies and unbalanced de novo CCRs involving chromosome 17p using high-resolution array-based comparative genomic hybridization (array CGH) and fluorescent in situ hybridization (FISH). In the first patient, a 4-month-old boy with developmental delay, hypotonia, growth retardation, coronal synostosis, mild hypertelorism, and bilateral club feet, we found a duplication of the Charcot-Marie–Tooth disease type 1A and Smith-Magenis syndrome (SMS) chromosome regions, inverted insertion of the Miller-Dieker lissencephaly syndrome region into the SMS region, and two microdeletions including a terminal deletion of 17p. The latter, together with a duplication of 21q22.3-qter detected by array CGH, are likely the unbalanced product of a translocation t(17;21)(p13.3;q22.3). In the second patient, an 8-year-old girl with mental retardation, short stature, microcephaly and mild dysmorphic features, we identified four submicroscopic interspersed 17p duplications. All 17 breakpoints were examined in detail by FISH analysis. We found that four of the breakpoints mapped within known low-copy repeats (LCRs), including LCR17pA, middle SMS-REP/LCR17pB block, and LCR17pC. Our findings suggest that the LCR burden in proximal 17p may have stimulated the formation of these CCRs and, thus, that genome architectural features such as LCRs may have been instrumental in the generation of these CCRs.     

Origin of chromosome rearrangements in two long-lived human keratinocyte lines

Summary We have determined the origin of the extra chromosomal material in the karyotypes of two spontaneously-occurring long-lived human keratinocyte lines, HKC-N2 and HKC-N6. In each case the extra material was derived from the chromosome on which it was located. Possible relationships between the triplication of chromosomal material and the overcoming of cell senescence are discussed.     

Four cases of trisomy 9p syndrome with particular chromosome rearrangements.

The authors present four children, two males and two females, with a 9p duplication, derived from various chromosome rearrangements, diagnosed using clinical, cytogenetic and biochemical evaluations. In particular, GALT dosage allowed them to define with accuracy the different chromosome break-points.     

Primary hypogonadism and 13/15 chromosome translocation in Prader-Labhart-Willi syndrome

A 14-year-old male with Prader-Labhart-Willi syndrome (PLW) had hypogonadism, normal serum gonadotropin levels and 13/15 chromosome translocation. The 24-hour pattern of LH and FSH secretion was normal and comparable to that observed in males at the middle to late stage of puberty. LH rose during sleep and LRH infusion. Basal serum testosterone was low, in the 60-136 ng/dl range, and rose modestly during sleep, LRH and HCG. The 24-hour mean concentrations of androsterone, androsterone sulfate, dehydroepiandrosterone, dehydroepiandrosterone sulfate and prolactin were comparable with normal adolescent males. Biopsy of an undescended testis revealed poor morphology with disorganized spermatogenesis and normal Leydig and Sertoli cells. The 13/15 chromosome aberration was a balanced Robertsonian translocation occurring in his mother and in 5 of 6 siblings, although only the patient had PLW. These data indicate that hypogonadism in PLW is not necessarily hypothalamic-pituitary in origin and that D-chromosome translocations, or deletions per se are not sufficient to explain the etiology of PLW.     

Assessment of X bends in patients with atypical X chromosome phenotypes.

Several patients with X chromosome structural abnormalities have been more severely affected clinically than expected. Since bends at Xq13-21 have been associated with inactivation, the authors scored bends retrospectively in 62 patients with X chromosome aneuploidy and 21 cases with structural abnormalities of the X chromosome. They found that patients with 2 X inactivation sites where one X was structurally abnormal had significantly fewer cells with X bends than normal 46,XX. In addition, these patients also showed X bends on the normal X more often than would be expected if non-random X inactivation of the abnormal X chromosome was occurring. Five of the 6 patients with a short or long arm deletion or paracentric inversion of Xq were mentally retarded or had other congenital anomalies not usually associated with Turner syndrome. This suggests to them that these clinical findings may be related to interference with X inactivation patterns in cells with a structurally abnormal X chromosome.     

Turner syndrome female with a small ring X chromosome lacking the XIST, an unexpectedly mild phenotype and an atypical association with alopecia universalis

Rearranged X chromosome in Turner syndrome (TS) are generally well tolerated but in cases of ring X chromosomes and of X/autosome translocations the incidence of mental retardation and other congenital abnormalities can be significantly higher. These abnormal phenotypes can be ascribed to failed or partial X inactivation. Here, we report a 10-year-old female who was referred for a cytogenetic analysis because she developed an alopecia universalis. The patient, of normal intelligence, had been found to have traits of TS, especially short stature. A first cytogenetic analysis showed a no mosaic 45,X karyotype. Since, the risk of developing gonadoblastoma in TS patients with mosaicism for a Y derivative chromosome and because association of alopecia universalis and TS is uncommon, fluorescence in situ hybridization (FISH) was performed to search for a second cell population. Our patient was found to have a mosaic 45,X/46,X,+r. FISH analysis using sex chromosome probes permitted us to identify the very small marker as a ring X chromosome, detected in 90% of cells. The ring appeared to be formed almost totally of alphoid sequences with breakpoints in the juxtacentromeric region. The r(X) does not include the XIST locus and may, therefore, not be subject to X-inactivation. Unexpectedly mild phenotype in our patient and its association with alopecia universalis will be discussed.     

Interstitial deletion of chromosome 15: two cases

Summary Two cases of interstitial deletion of chromosome 15 with similar clinical features are presented. In one case, assay of hexosaminidase A enabled us to confirm that the structural gene is located between 15q22 and 15q25 and that it is included in the deletion.     

Molecular analysis of chromosome 9q deletions in two Gorlin syndrome patients.

Gorlin syndrome is an autosomal dominant disorder characterized by multiple basal cell carcinomas, medulloblastomas, ovarian fibromas, and a variety of developmental defects. All affected individuals share certain key features, but there is significant phenotypic variability within and among kindreds with respect to malformations. The gene (NBCCS) maps to chromosome 9q22, and allelic loss at this location is common in tumors from Gorlin syndrome patients. Two recessive cancer-predisposition syndromes, xeroderma pigmentosum group A (XPAC) and Fanconi anemia group C (FACC), map to the NBCCS region; and unusual, dominant mutations in these genes have been proposed as the cause of Gorlin syndrome. This study presents cytogenetic and molecular characterization of germ-line deletions in one patient with a chromosome 9q22 deletion and in a second patient with a deletion of 9q22-q3l. Both have typical features of Gorlin syndrome plus additional findings, including mental retardation, conductive hearing loss, and failure to thrive. That Gorlin syndrome can be caused by null mutations (deletions) rather than by activating mutations has several implications. First, in conjunction with previous analyses of allelic loss in tumors, this study provides evidence that associated neoplasms arise with homozygous inactivation of the gene. In addition, dominant mutations of the XPAC and FACC1 genes can be ruled out as the cause of Gorlin syndrome, since the two patients described have null mutations. Finally, phenotypic features that show variable expression must be influenced by genetic background, epigenetic effects, somatic mutations, or environmental factors, since these two patients with identical alterations (deletions) of the Gorlin syndrome gene have somewhat different manifestations of Gorlin syndrome.     

Clonal structural chromosomal rearrangements in lymphocytes of four patients with Werner's syndrome

Multiple numerical and structural chromosome abnormalities were found in cultured lymphocytes of four patients with Werner's syndrome. The proportion of metaphases with structural and/or numerical aberrations varied from 30 to 44% and several of them were clonal. These results confirm definitively that Werner's syndrome is a chromosome rearrangement syndrome and that these non-constitutional chromosome changes are not exclusive of cultured fibroblasts but present also in lymphocytes.     

Persistence of chromosome rearrangements in peripheral lymphocytes from patients treated with melphalan for ovarian carcinoma

Summary Chromosome aberrations were studied in peripheral lymphocytes from 50 patients treated with melphalan against ovarian carcinoma. The chromosome analyses were carried out 4–132 months (mean 57 months) after the end of melphalan therapy. Most of the patients were studied several times during four years. The mean frequency of cells with chromosome and chromatid aberrations was 5.4% in the patients and 2.3% in an untreated control group. The highest aberration frequency (average 18%) was found in a patient who later developed gastric carcinoma. The dominating types of berrations in the patients were chromosome exchanges occurring as single marker chromosomes or as multiple chromosome rearrangements. These types of aberrations were found in only 0.3% of the control cells as compared to 3.8% of the patient cells. Patients with a high total dose of melphalan (above 420 mg) and a long duration of the therapy (average 22.5 months) had a higher frequency of cells with aberrations (6.3%) than patients with a lower total dose (below 420 mg) and a shorter therapy (12 months) (4.2%). No additive effect of radiation therapy was observed on the aberration frequency.This work was supported by grants from the Swedish Cancer Society (1179), and the Swedish Medical Research Council (3681)     

Molecular analysis of the sex-determining region from the Y chromosome in two patients with Frasier syndrome.

In the Frasier syndrome there is an association between XY gonadal dysgenesis and chronic renal failure. Owing to an observed sex reversal, the Y chromosomes of two girls with this syndrome have been analyzed. Using molecular-biology techniques, no major alterations of the known sex-determining area of the Y chromosome were found. Furthermore, the sequence did not reveal impairment of the recently described testis-determining factor SRY. These data suggest that in the Frasier syndrome, XY sex reversal and renal failure could be the result of either faulty gene(s) located downstream in the sex differentiation pathway during embryogenesis, or impaired SRY regulation. Preliminary results on the Wilms' tumor suppressor gene WT1, a candidate for acting downstream to SRY, are also provided.     

Unstable chromosome rearrangements associated with male recombination in Drosophila melanogaster

The male recombination second chromosome 23.5 MRF isolated from the same Greek natural population with the second chromosome 31.1 MRF induced high frequencies of chromosome rearrangements, including specific deletions and duplications. A number of the duplications recovered were found to be highly unstable. The duplicated chromosome segments of the unstable duplications had been either completely or partially lost. The loss occurred most probably by excision of the corresponding segments and not by unequal crossing-over involving sister chromatids. As regards the unstable deletions, they became either shorter or longer or they showed complete restoration. Hypotheses explaining the high frequencies of the unstable chromosome mutations detected are discussed.     

No evidence for a paternal interchromosomal effect from analysis of the origin of nondisjunction in Down syndrome patients with concomitant familial chromosome rearrangements.

The parental origin of the extra chromosome 21 was determined with DNA polymorphisms in seven families in whom the proband and one of the parents carried an additional chromosome rearrangement (balanced translocation or pericentric inversion) not involving chromosome 21. The balanced rearrangement was inherited from the mother in two families and from the father in five families, whereas the additional chromosome 21 was derived from the mother in all seven families. These findings are not in agreement with the hypothesis of a paternal interchromosomal effect. The latter would imply that a balanced rearrangement in the father would favor nondisjunction during meiosis in the germ cells.     

Association of transgene integration sites with chromosome rearrangements in hexaploid oat

Transgene loci in 16 transgenic oat (Avena sativa L.) lines produced by microprojectile bombardment were characterized using phenotypic and genotypic segregation, Southern blot analysis, and fluorescence in situ hybridization (FISH). Twenty-five transgene loci were detected; 8 lines exhibited single transgene loci and 8 lines had 2 or 3 loci. Double FISH of the transgene and oat C- and A/D-genome-specific dispersed and clustered repeats showed no preferences in the distribution of transgene loci among the highly heterochromatic C genome and the A/D genomes of hexaploid oat, nor among chromosomes within the genomes. Transgene integration sites were detected at different locations along individual chromosomes, although the majority of transformants had transgenes integrated into subtelomeric and telomeric regions. Transgene integration sites exhibited different levels of structural complexity, ranging from simple integration structures of two apparently contiguous transgene copies to tightly linked clusters of multiple copies of transgenes interspersed with oat DNA. The size of the genomic interspersions observed in these transgene clusters was estimated from FISH results on prometaphase chromosomes to be megabases long, indicating that some transgene loci were significantly larger than previously determined by Southern blot analysis. Overall, 6 of the 25 transgene loci were associated with rearranged chromosomes. These results suggest that particle bombardment-mediated transgene integration may result from and cause chromosomal breakage and rearrangements. Received: 29 July 1999 / Accepted: 9 November 1999     

Preferential paternal origin of microdeletions caused by prezygotic chromosome or chromatid rearrangements in Sotos syndrome

Sotos syndrome (SoS) is characterized by pre- and postnatal overgrowth with advanced bone age; a dysmorphic face with macrocephaly and pointed chin; large hands and feet; mental retardation; and possible susceptibility to tumors. It has been shown that the major cause of SoS is haploinsufficiency of the NSD1 gene at 5q35, because the majority of patients had either a common microdeletion including NSD1 or a truncated type of point mutation in NSD1. In the present study, we traced the parental origin of the microdeletions in 26 patients with SoS by the use of 16 microsatellite markers at or flanking the commonly deleted region. Deletions in 18 of the 20 informative cases occurred in the paternally derived chromosome 5, whereas those in the maternally derived chromosome were found in only two cases. Haplotyping analysis of the marker loci revealed that the paternal deletion in five of seven informative cases and the maternal deletion in one case arose through an intrachromosomal rearrangement, and two other cases of the paternal deletion involved an interchromosomal event, suggesting that the common microdeletion observed in SoS did not occur through a uniform mechanism but preferentially arose prezygotically.     

New chromosome 11p15 epigenotypes identified in male monozygotic twins with Beckwith-Wiedemann syndrome

Beckwith-Wiedemann syndrome (BWS) is an overgrowth syndrome demonstrating heterogeneous molecular alterations of two imprinted domains on chromosome 11p15. The most common molecular alterations include loss of methylation at the proximal imprinting center, IC2, paternal uniparental disomy (UPD) of chromosome 11p15 and hypermethylation at the distal imprinting center, IC1. An increased incidence of female monozygotic twins discordant for BWS has been reported. The molecular basis for eleven such female twin pairs has been demonstrated to be a loss of methylation at IC2, whereas only one male monozygotic twin pair has been reported with this molecular defect. We report here two new pairs of male monozygotic twins. One pair is discordant for BWS; the affected twin exhibits paternal UPD for chromosome 11p15 whereas the unaffected twin does not. The second male twin pair is concordant for BWS and both twins of the pair demonstrate hypermethylation at IC1. Thus, this report expands the known molecular etiologies for BWS twins. Interestingly, these findings demonstrate a new epigenotype-phenotype correlation in BWS twins. That is, while female monozygotic twins with BWS are likely to show loss of imprinting at IC2, male monozygotic twins with BWS reflect the molecular heterogeneity seen in BWS singletons. These data underscore the need for molecular testing in BWS twins, especially in view of the known differences among 11p15 epigenotypes with respect to tumor risk.