Complex chromosome re-arrangement 45,X,t(Y;9) in a girl with sex reversal and mental retardation

A rare familial rearrangement of chromosomes 9 and 15 associated with intellectual disability: a clinical and molecular study

Background

There are many reports on rearrangements occurring separately in the regions of chromosomes 9p and 15q affected in the case under study. 15q duplication syndrome is caused by the presence of at least one extra maternally derived copy of the Prader–Willi/Angelman critical region. Trisomy 9p is the fourth most frequent chromosome anomaly with a clinically recognizable syndrome often accompanied by intellectual disability. Here we report a new case of a patient with maternally derived unique complex sSMC resulting in partial trisomy of both chromosomes 9 and 15 associated with intellectual disability.

Case presentation

We characterise a supernumerary derivative chromosome 15: 47,XY,+der(15)t(9;15)(p21.2;q13.2), likely resulting from 3:1 malsegregation during maternal gametogenesis. Chromosomal analysis showed that a phenotypically normal mother is a carrier of balanced translocation t(9;15)(p21.1;q13.2). Her 7-year-old son showed signs of intellectual disability and a number of physical abnormalities including bilateral cryptorchidism and congenital megaureter. The child’s magnetic resonance imaging showed changes in brain volume and in structural and functional connectivity revealing phenotypic changes caused by the presence of the extra chromosome material, whereas the mother’s brain MRI was normal. Sequence analyses of the microdissected der(15) chromosome detected two breakpoint regions: HSA9:25,928,021-26,157,441 (9p21.2 band) and HSA15:30,552,104-30,765,905 (15q13.2 band). The breakpoint region on chromosome HSA9 is poor in genetic features with several areas of high homology with the breakpoint region on chromosome 15. The breakpoint region on HSA15 is located in the area of a large segmental duplication.

Conclusions

We discuss the case of these phenotypic and brain MRI features in light of reported signatures for 9p partial trisomy and 15 duplication syndromes and analyze how the genomic characteristics of the found breakpoint regions have contributed to the origin of the derivative chromosome. We recommend MRI for all patients with a developmental delay, especially in cases with identified rearrangements, to accumulate more information on brain phenotypes related to chromosomal syndromes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13039-021-00565-y.

EARLY-ONSET GONADOBLASTOMA IN A 13-MONTH-OLD INFANT WITH 46,XY COMPLETE GONADAL DYSGENESIS IDENTIFIED WITH PRENATAL TESTING: A CASE OF CHROMOSOME 9p DELETION

Objective

Individuals with 46,XY complete gonadal dysgenesis (CGD) are at high risk of developing gonadal neoplasms. Chromosome 9p monosomy with deletion of the DMRT1 gene, a key transcription factor in testicular development, is one of the known causes of 46,XY CGD. Noninvasive prenatal testing (NIPT) is being increasingly used, and can identify disorders of sexual development (DSDs).

Methods

We report the case of a 46,XY infant with phenotypically female external genitalia, müllerian structures including uterus and fallopian tubes, and bilateral streak gonads who was found to have unilateral gonadoblastoma at 13 months. 46,XY DSD was suggested prenatally when discordance between NIPT and fetal ultrasound was noted.

Results

Genetic investigation revealed a deletion of 12.5 million base pairs at chromosome 9p24.3, which includes the doublesex and MAB-3-related transcription factor-1 (DMRT1) gene.

Conclusion

Current guidelines recommend gonadectomy at the time of diagnosis in cases of 46,XY CGD, and our patient had gonadoblastoma at 13 months. 46,XY DSD, including rare disorders such as CGD, will be increasingly identified before birth with more widespread use of NIPT, raising the question about the appropriate timing of gonadectomy in prenatal diagnoses. Our case supports the current recommendation to perform gonadectomy as early as possible after diagnosis.

Unbalanced Y;7 Translocation between Two Low-Similarity Sequences Leading to SRY-Positive 45,X Testicular Disorders of Sex Development

Unbalanced translocations of Y-chromosomal fragments harboring the sex-determining region Y gene (SRY) to the X chromosome or an autosome result in 46,XX and 45,X testicular disorders of sex development (DSD), respectively. Of these, Y;autosome translocation is an extremely rare condition. Here, we identified a 20-year-old man with a 45,X,t(Y;7)(q11.21;q35) karyotype, who exhibited unilateral cryptorchidism, small testis, intellectual disability, and various congenital anomalies. The fusion junction of the translocation was blunt, and the breakpoint-flanking regions shared only 50% similarity. These results indicate that Y;autosome translocations can occur between 2 low-similarity sequences, probably via nonhomologous end joining. Furthermore, translocations of a Ypterq11.21 fragment to 7q35 likely result in normal or only mildly impaired male-type sexual development, along with various clinical features of 7q deletion syndrome, although their effects on adult testicular function remain to be studied.

A rare unbalanced Y:autosome translocation in a Turner syndrome patient

BACKGROUND

Y:autosome translocations are reported to be associated with male infertility and azoospermia. Female cases with Y:autosome translocation are extremely rare.

CASE PRESENTATION

We report a unique case of a rare unbalanced translocation t(Y;13) in a 12-year-old girl with Turner syndrome. Combined cytogenetic testing helped to demonstrate the detail of rare chromosomal structural rearrangement in this patient.

CONCLUSIONS

The presented case showed femaleness phenotype and failure of masculinization with presence of Y chromosome and the SRY gene. She was treated with growth hormone (GH) therapy after confirming the presence of only female internal gonad with laparoscopy.

Unbalanced translocation involving partial trisomy 9p and partial monosomy yq with neurodevelopmental delays

We present a 4-year-old Honduran boy with mild neurodevelopmental delays, growth delays, dysmorphic features, and small genitalia. Chromosome analysis initially revealed a single X chromosome and a marker chromosome derived from the short arm of chromosome 9 which was consistent with Turner syndrome as only 1 sex chromosome could be identified. However, on further analysis, he was found to have an unbalanced translocation involving the short arm of chromosome 9 and the long arm of the Y chromosome. The translocation resulted in partial trisomy 9p and partial monosomy Yq. The patient's clinical features are felt to be the result of partial trisomy 9p. In addition, partial monosomy Yq is associated with male infertility. Testing of the patient's parents was normal, indicating this was a de novo translocation. Additional evaluations of this child and his parents allowed an accurate assessment of his diagnosis, long-term prognosis, and chance of recurrence.

Another rare case of a child with de novo terminal 9p deletion and co-existing interstitial 9p duplication: clinical findings and molecular cytogenetic study by array-CGH

Trisomy 9p is the fourth most common chromosome abnormality found in liveborns. We report on a rare case of partial trisomy 9p complicated by partial monosomy 9p. Clinical manifestation included craniofacial abnormalities typical for trisomy 9p syndrome, developmental delay, mental retardation and brain anomaly in the form of Dandy-Walker malformation. The cytogenetic abnormality was investigated with FISH and array-CGH to characterize the breakpoints of the complex rearrangement. The patient's karyotype was 46,XX,der(9)del(9)(p24)dup(9)(p21p24)dn.arr 9p24.3p24.2 (1-2,414,485)×1,9p24.2p21.3(2,414,485-24,101,280)×3. The cytogenetic rearrangement led to a 2.4-Mb deletion of 9p24.2pter and a 21.6-Mb duplication of 9p24.2p21.3. The clinical and cytogenetic findings in our and other similar patients are compared.

A new multicolor fluorescence in situ hybridization probe set directed against human heterochromatin: HCM-FISH

A new multicolor fluorescence in situ hybridization (mFISH) probe set is presented, and its possible applications are highlighted in 25 clinical cases. The so-called heterochromatin-M-FISH (HCM-FISH) probe set enables a one-step characterization of the large heterochromatic regions within the human genome. HCM-FISH closes a gap in the now available mFISH probe sets, as those do not normally cover the acrocentric short arms; the large pericentric regions of chromosomes 1, 9, and 16; as well as the band Yq12. Still, these regions can be involved in different kinds of chromosomal rearrangements such as translocations, insertions, inversions, amplifications, and marker chromosome formations. Here, examples are given for all these kinds of chromosomal aberrations, detected as constitutional rearrangements in clinical cases. Application perspectives of the probe set in tumors as well as in evolutionary cytogenetic studies are given.

Molecular genetic analysis of partial 9p trisomy in two Chinese families with mental retardation and facial anomaly

Mental retardation is defined by significant limitations in intellectual function and adaptive behavior that occur before 18 years of age. Many chromosomal diseases come with mental retardation. We reported two Chinese families with partial trisomy 9p and other chromosome partial monosomy, clinical features of mental retardation and mild facial and pinkie anomalies. In the family 1, we showed that the proband carried a trisomy 9p21.3→pter and monosomy 21q22.3→qter by using fluorescence in situ hybridization analysis. Molecular genetic analysis defined the precise breakpoint on chromosome 9p between markers D9S1846 and D9S171, an interval of about 2.9 Mb on 9p21.3, and the breakpoint on chromosome 21q between markers D21S1897 and D21S1446, a region of about 1.5 Mb on 21q22.3. In the family 2, a patient with trisomy 9p21.3→pter and monosomy 5p15.33→pter, and a de novo maternal balanced translocation between chromosomes 5 and 9 was identified in his mother. Cytogenetic and molecular genetic analysis defined the precise breakpoints on chromosome 9p21.3 and chromosome 5p15.33. Further clinical investigation found that any individual had no refractoriness eczema disease except the proband in this family. These results further implicate that trisomy 9p is associated with mental retardation, and that there may be key gene duplication on chromosome 9p21.3→9pter responsible for mental retardation and mild facial anomaly. This result has been applied successfully in prenatal diagnosis of the second family.

Array-CGH study of partial trisomy 9p without mental retardation

Partial trisomy 9p is one of the most common detected autosomal structural anomalies, so the phenotype-genotype correlation of this rearrangement has been well described. Despite variation in size of the 9p duplications, trisomy 9p syndrome is characterized by typical dysmorphic features and a variable but constant psychomotor and mental retardation. Previously reported phenotype genotype correlation studies proposed that the critical region for phenotype is located in 9p22. We report here on a new patient with partial trisomy 9p13.3→9pter in an 8-year-old boy with typical trisomy 9p dysmorphic features but a normal mental development. Cytogenetics investigations showed that our patient karyotype was 47,XY,+ der(22)t(9;22)(p13.q11) inherited by a 3:1 disjunction of a maternal reciprocal translocation t(9;22)(p13.q11). FISH and array CGH analysis were used to better characterize duplicated chromosomal regions and showed a large duplication of chromosome 9p13.3→9pter associated to microduplication in 22q11.1. The size of the duplications in chromosomes 9p and 22q were estimated about 33.9 and 2.67 Mb, respectively. The comparison between this case and those reported in the literature allows us to support that all syndromes show variability and that not all partial trisomies 9p are associated with intellectual disability.

[Chromosome 9P deletion: Gonadal dysgenesis associated with mental retardation and hypoplasia of the corpus callosum: A contiguous gene syndrome?]

BACKGROUND

Many genes are involved in testicular differentiation. The alterations of these genes are responsible for sexual differentiation disorders with 46 XY karyotype.

CASE

We report the case of a newborn who had an interscrotal hypospadias, palpable gonads and hypoplastic penis. Karyotype 46 XY. Abdominal ultrasound revealed testes and absence of Müllerian remnants. There was a good response to the short gonadotrophin test. At one year he had signs of psychomotor retardation and hypotonia. The magnetic resonance revealed frontal-temporal atrophy and a decrease in the corpus callosum. Testicular biopsy was compatible with gonadal dysgenesis. A preoperative cystography showed a vaginal remnant. Due to the presence of a sexual differentiation disorder, psychomotor retardation and facial dysmorphism, we requested a high-resolution karyotype: deletion 46, XY, del (9p) (p23-pter). Ish tel (9p-).

DISCUSSION

Many genes are involved in testicular differentiation, some of which also affect the development of other tissues. In the short arm of chromosome 9, two genes, DMRT1 and DMRT2, are involved in sexual differentiation. Their alterations have also been described as causing mental retardation. In the evaluation of 46,XY disorders of sex differentiation, the accompanying signs are very important for guiding the genetic study.

Trisomy 9p and Prader-Willi syndromes in an infant resulting from a de-novo unbalanced t(9;15) translocation

Trisomy 9p is a well-described dysmorphic syndrome. The physical features include hypertelorism, down-slanting palpebral fissures, deep-set eyes, down-turned corners of the mouth, and mild skeletal anomalies including hypoplastic terminal phalanges. We report an infant born with some of the typical features of trisomy 9p syndrome, as well as additional features that include extreme joint hyperlaxity with subluxation of the knees and elbows, arachnodactyly, and total anomalous pulmonary venous return. The karyotype revealed an unbalanced chromosome complement. Specifically, a derivative chromosome from a de-novo unbalanced translocation of chromosomes 9 and 15 resulted in partial trisomy of 9pter to 9q13 and deletion of the long arm of chromosome 15 proximal to band q13. Fluorescence in-situ hybridization studies and methylation analysis by Southern blotting revealed deletion of the SNRPN locus on the paternally derived chromosome 15, consistent with Prader-Willi syndrome. This infant represents the first reported case of trisomy 9p syndrome with total anomalous pulmonary venous return and hypoplasia of the amygdala and hippocampus, with the additional finding of Prader-Willi syndrome resulting from a derivative chromosome arising from an unbalanced de-novo t(9;15) translocation.

Characterization of a de novo unbalanced Y;autosome translocation in a 45,X mentally retarded male and literature review

OBJECTIVE

To describe the molecular and cytogenetic characterization of a de novo unbalanced Y;autosome translocation in a 45,X mentally retarded male.

DESIGN

Descriptive case study and literature review.

SETTING

Tertiary medical center.

PATIENT(S)

A 17-year-old 45,X mentally retarded male with no stigmata of Turner syndrome.

INTERVENTION(S)

Molecular and cytogenetic investigations, physical examination, and hormonal assays.

MAIN OUTCOME MEASURE(S)

Cytogenetic analysis, fluorescence in situ hybridization (FISH), array comparative genomic hybridization (CGH), and polymorphic DNA marker analysis.

RESULT(S)

The FISH showed a Y/18p translocation. Array CGH revealed a loss of distal chromosome 18p material and a loss of part of Yq material corresponding to deletions of chromosomal segments of 18pter-->18p11.2 and Yq11.221-->Yqter. Polymorphic DNA markers analysis showed that the X chromosome was of maternal origin and the deletion of 18p was of paternal origin.

CONCLUSION(S)

This study confirms the usefulness of array CGH in the detection of subtle chromosomal rearrangements resulting in an unbalanced Y;autosome translocation.

A 9p13-->p24 duplication coupled with a whole 22q translocation onto 9p24

We report on a 3-year-old girl with a typical 9p trisomy syndrome, whose 45-chromosome karyotype includes a 9p+. As assessed by G, C and Ag-NOR bands, the rearranged chromosome resulted from a 9p13-->p24 direct duplication coupled with a translocation of the whole 22q onto 9pter, had heterochromatin at the junction site, lacked both nucleolar organizing regions (NORs) and centromere dots at the unconstricted fusion point, and was present in all metaphases scored. FISH results: a 9p subtelomere probe gave a diminished signal on the 9p+ precisely at the duplication junction 9p24::9p13, but no labeling was observed at the 9;22 translocation site; a pancentromeric alphoid probe labeled all centromeres, and gave a distinct signal at the 9pter;22cen junction. Hence, her karyotype was 45,XX,rea(9;22)(9qter-->9p24::9p13-->9p24::22p10-->22qter).ish rea(9;22) (9psubtel+dim,pancen+). Parental chromosomes were normal. The distinctiveness of the present centromere-telomere fusion rests on the coupling of an intrachromosomal distal duplication with a whole-arm translocation including alphoid DNA onto the duplicated segment. The centromeric inertia of the residual alphoid DNA in the present case compares with the variable functional status of the chromosome 22 centromere in true heterodicentrics involving such a chromosome.

Ovotestes and XY sex reversal in a female with an interstitial9q33.3-q34.1 deletion encompassingNR5A1 andLMX1B causing features of genitopatellar syndrome

We describe our findings in a 46,XY female with a clinical features of Genitopatellar syndrome (GPS) and confirmed hermaphroditism with ovotestes, and five additional patients with GPS. GPS is a genetic disorder characterized by renal and genital anomalies, joint dislocation, aplastic or hypoplastic and often displaced patellae, minor facial anomalies, and mental retardation. The genital anomalies clearly distinguish GPS from nail-patella syndrome (NPS) that has similar features, but additionally shows hypoplastic finger- and toenails as found in the 46,XY female. In our patients no mutation was found in the coding regions of WNT4, WNT7A, TBX4, and LMX1B. Fluorescent in situ hybridization (FISH) and array-based comparative genome hybridization (aCGH) analysis showed a 3 Mb deletion of LMX1B, NR6A1, and NR5A1 (SF1) in the 46,XY female. This is the first report of a microdeletion causing haploinsuffiency of LMX1B and NR5A1. The deletion of LMX1B is responsible for the knee anomalies and the deletion of NR5A1 likely causes the sex reversal. Cytogenetic analysis of the five additional patients with diagnosed GPS failed to identify a similar microdeletion, or inversion of a potentially regulatory element between the two genes. This suggests that the locus 9q33-9q34 can be excluded for GPS and that the presented case is unique in its combination of GPS and NPS features caused by a microdeletion associated with loss of function of LMX1B and NR5A1.