Nance-Horan syndrome in females due to a balanced X;1 translocation that disrupts the NHS gene: Familial case report and review of the literature.

The Nance-Horan syndrome is an X-linked disorder characterized by congenital cataract, facial features, microcornea, microphthalmia, and dental anomalies; most of the cases are due to NHS gene mutations on Xp22.13. Heterozygous carrier females generally present less severe features, and up to 30% of the affected males have intellectual disability. We describe two patients, mother and daughter, manifesting Nance-Horan syndrome. The cytogenetic and molecular analyses demonstrated a 46,X,t(X;1)(p22.13;q22) karyotype in each of them. No copy-number genomic imbalances were detected by high-density microarray analysis. The mother had a preferential inactivation of the normal X chromosome; expression analysis did not detect any mRNA isoform of NHS. This is the first report of Nance-Horan syndrome due to a skewed X chromosome inactivation resulting from a balanced translocation t(X;1) that disrupts the NHS gene expression, with important implications for clinical presentation and genetic counseling.

19q13.11 microdeletion concomitant with ins(2;19)(p25.3;q13.1q13.4)dn in a boy: potential role of UBA2 in the associated phenotype.

The 19q13.11 microdeletion syndrome (MIM613026) is a clinically recognisable condition in which a 324-kb minimal overlapping critical region has been recently described. However, genes not included within this region, such as WTIP and UBA2, have been proposed to contribute to the clinical characteristics observed in patients. Using cytogenetic techniques, single nucleotide polymorphism arrays, and the quantitative polymerase chain reaction, we identified a novel case with a 2.49-Mb deletion derived from a de novo chromosomal rearrangement. Based on a review of the literature, we support the notion that UBA2 haploinsufficiency could contribute to the phenotype of this rare genomic disorder. UBA2 belongs to a protein complex with sumoylation activity, and several transcription factors, hormone receptors, and signalling proteins related to brain and sexual development are regulated by this post-translational modification. Additional clinical reports and further research on UBA2 molecular function are warranted.

Trisomy 1q41-qter and monosomy 3p26.3-pter in a family with a translocation (1;3): further delineation of the syndromes.

BACKGROUND: Trisomy 1q and monosomy 3p deriving from a t(1;3) is an infrequent event. The clinical characteristics of trisomy 1q41-qter have been described but there is not a delineation of the syndrome. The 3p25.3-pter monosomy syndrome (MIM 613792) characteristics include low birth weight, microcephaly, psychomotor and growth retardation and abnormal facies. CASE PRESENTATION: A 2 years 8 months Mexican mestizo male patient was evaluated due to a trisomy 1q and monosomy 3p derived from a familial t(1;3)(q41;q26.3). Four female carriers of the balanced translocation and one relative that may have been similarly affected as the proband were identified. The implicated chromosomal regions were defined by microarray analysis, the patient had a trisomy 1q41-qter of 30.3 Mb in extension comprising about 240 protein coding genes and a monosomy 3p26.3-pter of 1.7 Mb including only the genes CNTN6 (MIM 607220) and CHL1 (MIM 607416), which have been implicated in dendrite development. Their contribution to the phenotype, regarding the definition of trisomy 1q41-qter and monosomy 3p26.3-pter syndromes are discussed. CONCLUSION: We propose that a trisomy 1q41-qter syndrome should be considered in particular when the following characteristics are present: postnatal growth delay, macrocephaly, wide fontanelle, triangular facies, frontal bossing, thick eye brows, down slanting palpebral fissures, hypertelorism, flat nasal bridge, hypoplasic nostrils, long filtrum, high palate, microretrognathia, ear abnormalities, neural abnormalities (in particular ventricular dilatation), psychomotor developmental delay and mental retardation. Our patient showed most of these clinical characteristics with exception of macrocephaly, possibly due to a compensatory effect by haploinsufficiency of the two genes lost from 3p. The identification of carriers has important implications for genetic counseling as the risk of a new born with either a der(3) or der(1) resulting from an adjacent-1 segregation is of 25% for each of them, as the products of adjacent-2 or 3:1 segregations are not expected to be viable.

Detection of common chromosomal translocations in small round blue cell pediatric tumors.

BACKGROUND AND AIMS: Recurrent and specific chromosomal translocations have been described in four pediatric sarcomas belonging to the small round blue cell (SRBC) group of tumors. Identification of mRNA chimeras using RT-PCR discriminates among alveolar rhabdomyosarcoma (ARMS), Ewing's sarcoma (ES/pPNET), synovial sarcoma (SS) and desmoplastic small round cell tumor (DSRCT); however, frequencies of these translocations are variable. We present a retrospective study comparing histological examination and occurrence of major chromosomal translocations to validate the diagnosis and to assess the frequency of these molecular markers in a group of 92 small round blue cell (SRBC) tumor samples from Hospital Infantil de Mexico. METHODS: We tested a panel of RT-PCR assays to each RNA tumor sample from formalin-fixed, paraffin-embedded tumors to detect specific mRNA chimeras in 47 ES/pPNET, 19 ARMS, four SS, three DSRCT, and 19 other SRBC tumors. RESULTS: After excluding poor RNA quality samples, we found translocations in 17/31 ES/pPNET (54.8%), 10/19 ARMS (52.6%), 4/4 SS (100%) and 4/4 DSRCT (100%). We found disagreement in only three samples: one ES/pPNET and one embryonal rhabdomyosarcoma harbor a PAX3-FOXO1 translocation (for ARMS), and one neuroepithelioma harboring a EWS-WT1 (for DSRCT). Unsuitable RNA was found in 20/92 samples (21.7%) and was related to necrosis, small amount of tumor tissue, and use of nitric acid in bone biopsies, but was not related to age of the block. CONCLUSIONS: We found a significantly lower occurrence of chromosomal translocations in ES/pPNET compared to reports from other groups. Differences may exist in the frequencies of these molecular markers among different populations.

Diagnosis of familial Wolf-Hirschhorn syndrome due to a paternal cryptic chromosomal rearrangement by conventional and molecular cytogenetic techniques.

The use of conventional cytogenetic techniques in combination with fluorescent in situ hybridization (FISH) and single-nucleotide polymorphism (SNP) microarrays is necessary for the identification of cryptic rearrangements in the diagnosis of chromosomal syndromes. We report two siblings, a boy of 9 years and 9 months of age and his 7-years- and 5-month-old sister, with the classic Wolf-Hirschhorn syndrome (WHS) phenotype. Using high-resolution GTG- and NOR-banding karyotypes, as well as FISH analysis, we characterized a pure 4p deletion in both sibs and a balanced rearrangement in their father, consisting in an insertion of 4p material within a nucleolar organizing region of chromosome 15. Copy number variant (CNV) analysis using SNP arrays showed that both siblings have a similar size of 4p deletion (~6.5 Mb). Our results strongly support the need for conventional cytogenetic and FISH analysis, as well as high-density microarray mapping for the optimal characterization of the genetic imbalance in patients with WHS; parents must always be studied for recognizing cryptic balanced chromosomal rearrangements for an adequate genetic counseling.

Amplified genes may be overexpressed, unchanged, or downregulated in cervical cancer cell lines.

Several copy number-altered regions (CNAs) have been identified in the genome of cervical cancer, notably, amplifications of 3q and 5p. However, the contribution of copy-number alterations to cervical carcinogenesis is unresolved because genome-wide there exists a lack of correlation between copy-number alterations and gene expression. In this study, we investigated whether CNAs in the cell lines CaLo, CaSki, HeLa, and SiHa were associated with changes in gene expression. On average, 19.2% of the cell-line genomes had CNAs. However, only 2.4% comprised minimal recurrent regions (MRRs) common to all the cell lines. Whereas 3q had limited common gains (13%), 5p was entirely duplicated recurrently. Genome-wide, only 15.6% of genes located in CNAs changed gene expression; in contrast, the rate in MRRs was up to 3 times this. Chr 5p was confirmed entirely amplified by FISH; however, maximum 33.5% of the explored genes in 5p were deregulated. In 3q, this rate was 13.4%. Even in 3q26, which had 5 MRRs and 38.7% recurrently gained SNPs, the rate was only 15.1%. Interestingly, up to 19% of deregulated genes in 5p and 73% in 3q26 were downregulated, suggesting additional factors were involved in gene repression. The deregulated genes in 3q and 5p occurred in clusters, suggesting local chromatin factors may also influence gene expression. In regions amplified discontinuously, downregulated genes increased steadily as the number of amplified SNPs increased (p<0.01, Spearman's correlation). Therefore, partial gene amplification may function in silencing gene expression. Additional genes in 1q, 3q and 5p could be involved in cervical carcinogenesis, specifically in apoptosis. These include PARP1 in 1q, TNFSF10 and ECT2 in 3q and CLPTM1L, AHRR, PDCD6, and DAP in 5p. Overall, gene expression and copy-number profiles reveal factors other than gene dosage, like epigenetic or chromatin domains, may influence gene expression within the entirely amplified genome segments.

Detection of fusion genes in formalin-fixed paraffin-embedded tissue sections of rhabdomyosarcoma by RT-PCR and fluorescence in situ hybridization in Mexican patients.

BACKGROUND AND AIMS: Rhabdomyosarcoma (RMS) is a pediatric tumor whose classification is based on histological criteria according to two main subgroups, embryonal RMS (ERMS) and alveolar RMS (ARMS). The majority but not all ARMS carry the specific PAX3(7)/FKHR translocation. The type of translocation in patients with ARMS defines the prognosis. METHODS: We retrospectively analyzed 30 cases of ARMS in Mexican patients and evaluated the fusion status of the genes using RT-PCR and fluorescence in situ hybridization (FISH) in formalin-fixed paraffin-embedded tissues (FFPET). RESULTS: From 25 samples (83%) with optimal RNA quality, RT-PCR revealed 15 cases (50%) with the t(2;13)/PAX3-FKHR. Only one case (3%) was positive to t(1;13)/PAX7-FKHR and nine cases (30%) were fusion-negative. Correspondingly, using FISH, the t(2;13)/PAX3-FKHR was found positive in 19 cases (63.5%), one case (3%) revealed the t(1;13)/PAX7/FKHR and ten cases (33.5%) were fusion-negative by this method. Five cases were not evaluable by RT-PCR but recovered by FISH. Only four of the total revealed t(2;13); the other was fusion-negative. CONCLUSIONS: FISH technique is more sensitive when FFPET is used to describe the chromosomal translocation of ARMS. These Latino patients showed an association of the t(2;13) in older patients (mean: 9 years) and negative translocation in younger patients (mean: 4 years) (p <0.05). Both t(2;13) and negative-fusion were present in patients with clinical stages III and IV (p <0.05). There was a nonsignificant trend of t(2;13) to lower overall survival than negative-fusion status.