Nicolaides-Baraitser syndrome in a patient with hypertrophic cardiomyopathy and SMARCA2 gene deletion.

Nicolaides-Baraitser syndrome is a rare, neuro-developmental disorder caused by heterozygous pathogenic variants in the SMARCA2 gene, involved with chromatin regulation. Cardinal features include intellectual disability, short stature, microcephaly, triangular facies, sparse hair, brachydactyly, prominent interphalangeal joints and seizures. Genetic testing demonstrated a loss within SMARCA2 at 9p24.3 inclusive of basepairs 2094861_2141830 (hg19) in our patient. This case highlights a child with Nicolaides-Baraiter syndrome, a SMARCA2 gene deletion and a novel association of hypertrophic obstructive cardiomyopathy.

Bicoronal and metopic craniosynostosis in association with a de novo unbalanced t(2;7) chromosomal translocation.

We report the case of a developmentally appropriate infant male with a de novo unbalanced chromosome translocation involving bands 2q32.1 and 7p21.3. The child was noted to have metopic and bicoronal craniosynostosis with closely spaced eyes, turricephaly, and flattening of the forehead. © 2016 Wiley Periodicals, Inc.

A case report of primary ciliary dyskinesia, laterality defects and developmental delay caused by the co-existence of a single gene and chromosome disorder.

BACKGROUND: Primary ciliary dyskinesia (PCD) is a rare autosomal recessive disorder characterised by abnormal ciliary motion and impaired mucociliary clearance, leading to recurrent respiratory infections, sinusitis, otitis media and male infertility. Some patients also have laterality defects. We recently reported the identification of three disease-causing PCD genes in the Irish Traveller population; RSPH4A, DYX1C1 and CCNO. We have since assessed an additional Irish Traveller family with a complex phenotype involving PCD who did not have any of the previously identified PCD mutations. CASE PRESENTATION: In this study we report on a family with three children with PCD and various laterality defects. In addition, one child (V:1) has mild-to-moderate developmental delay and one child has speech delay (V:2). Developmental delay is not usually associated with PCD and is likely to be caused by an additional genetic abnormality. Transmission electron microscopy showed variable inner and outer dynein arm defects. Exome sequencing identified a homozygous missense variant in CCDC103 (c.461A > C; p.His154Pro) as the most likely cause of the PCD and laterality defects in this family. However, as mutation in CCDC103 would not account for the developmental delay, array comparative genomic hybridisation was undertaken and identified a maternally inherited gain of ~1.6 Mb (chr17:34,611,352-36,248,918). Gains at this locus are associated with 17q12 duplication syndrome which includes speech and language delay. CONCLUSION: We report on a variable and complex phenotype caused by the co-inheritance of a single gene mutation in CCDC103 and a microduplication at 17q12, both on chromosome 17. The co-existence of a single gene and chromosome disorder is unusual but accounts for the spectrum of clinical features in this family. In addition, our study brings the total number of PCD genes in the Irish Traveller population to four and we suspect additional PCD genes are yet to be identified. Although, on a global scale, PCD is associated with extensive genetic heterogeneity, finding such a high number of causative PCD genes within the relatively small Irish Traveller population was unexpected.

De Novo interstitial deletion 13q33.3q34 in a male patient with double outlet right ventricle, microcephaly, dysmorphic craniofacial findings, and motor and developmental delay.

We describe a 6-year-old male, diagnosed at birth with double outlet right ventricle (DORV), anterior aorta, multiple ventricular septal defects, pulmonary stenosis, microcephaly and mildly dysmorphic craniofacial findings. Chromosomal analysis showed a normal male karyotype but on subsequent array comparative genomic hybridization (array CGH) analysis a de novo 2.5 Mb loss in chromosome 13q at 13q33.3q34, together with an inherited gain at 4p12, were detected. The propositus underwent placement of a Blalock Taussig shunt and subsequently a Glenn and Fontan operation was performed. In this report we propose that COL4A1 and COL4A2 may be candidate genes for congenital heart disease (CHD) in individuals with a deletion in 13q within the 6Mb critical region for cardiac development proposed by Huang et al., [2012].

Frequency and Prognostic Impact of ALK Amplifications and Mutations in the European Neuroblastoma Study Group (SIOPEN) High-Risk Neuroblastoma Trial (HR-NBL1).

PURPOSE: In neuroblastoma (NB), the ALK receptor tyrosine kinase can be constitutively activated through activating point mutations or genomic amplification. We studied ALK genetic alterations in high-risk (HR) patients on the HR-NBL1/SIOPEN trial to determine their frequency, correlation with clinical parameters, and prognostic impact. MATERIALS AND METHODS: Diagnostic tumor samples were available from 1,092 HR-NBL1/SIOPEN patients to determine ALK amplification status (n = 330), ALK mutational profile (n = 191), or both (n = 571). RESULTS: Genomic ALK amplification (ALKa) was detected in 4.5% of cases (41 out of 901), all except one with MYCN amplification (MNA). ALKa was associated with a significantly poorer overall survival (OS) (5-year OS: ALKa [n = 41] 28% [95% CI, 15 to 42]; no-ALKa [n = 860] 51% [95% CI, 47 to 54], [P < .001]), particularly in cases with metastatic disease. ALK mutations (ALKm) were detected at a clonal level (> 20% mutated allele fraction) in 10% of cases (76 out of 762) and at a subclonal level (mutated allele fraction 0.1%-20%) in 3.9% of patients (30 out of 762), with a strong correlation between the presence of ALKm and MNA (P < .001). Among 571 cases with known ALKa and ALKm status, a statistically significant difference in OS was observed between cases with ALKa or clonal ALKm versus subclonal ALKm or no ALK alterations (5-year OS: ALKa [n = 19], 26% [95% CI, 10 to 47], clonal ALKm [n = 65] 33% [95% CI, 21 to 44], subclonal ALKm (n = 22) 48% [95% CI, 26 to 67], and no alteration [n = 465], 51% [95% CI, 46 to 55], respectively; P = .001). Importantly, in a multivariate model, involvement of more than one metastatic compartment (hazard ratio [HR], 2.87; P < .001), ALKa (HR, 2.38; P = .004), and clonal ALKm (HR, 1.77; P = .001) were independent predictors of poor outcome. CONCLUSION: Genetic alterations of ALK (clonal mutations and amplifications) in HR-NB are independent predictors of poorer survival. These data provide a rationale for integration of ALK inhibitors in upfront treatment of HR-NB with ALK alterations.

A retrospective study of myeloid leukaemia in children with Down syndrome in Ireland.

BACKGROUND: Acute megakaryoblastic leukaemia (AMKL) is a subtype of myeloid leukaemia and is the most common leukaemia type in children with Down syndrome (DS) under 4 years of age. AMKL is often preceded by a transient neonatal pre-leukaemic syndrome, transient myeloproliferative disorder (TMD). Although TMD often spontaneously resolves, 20-30% of these patients subsequently develop AMKL within the first 4 years of life. AIMS: To perform a retrospective consecutive national audit of all documented cases of childhood TMD and AMKL-DS from 1990 to 2018 at Our Lady's Children's Hospital, Crumlin (OLCHC), Ireland. METHODS: All patients with a diagnosis of AMKL treated consecutively at (OLCHC) between 1990 and 2018 were reviewed. Kaplan-Meier survival curves were constructed. RESULTS: Twenty-seven patients with AMKL-DS were identified. A prior neonatal diagnosis of TMD was described in 10 patients (37%). Nineteen patients (70%) are alive and well, in complete remission, at a median follow-up of 11.4 years. Overall survival (OS) of this cohort has risen from 54% from those treated between the years 1990 and 2004 (n = 13) to 93% for those treated between the years 2005 and 2018 (n = 14). CONCLUSION: High cure rates are observed in AMKL-DS using current polychemotherapy protocols. The finding of a low platelet count at time of diagnosis is in keeping with the knowledge that AMKL-DS is a malignancy of platelet progenitor cells.

Cytogenetic characterization of childhood acute lymphoblastic leukemia in Nicaragua.

BACKGROUND: Within the frame of a twinning programme with Nicaragua, The La Mascota project, we evaluated in our study the contribution of cytogenetic characterization of acute lymphoblastic leukemia (ALL) as prognostic factor compared to clinical, morphological, and immunohistochemical parameters. METHODS: All patients with ALL treated at the only cancer pediatric hospital in Nicaragua during 2006 were studied prospectively. Diagnostic immunophenotyping was performed locally and bone marrow or blood samples were sent to the cytogenetic laboratory of Zurich for fluorescence in situ hybridization (FISH) analysis and G-banding. RESULTS: Sixty-six patients with ALL were evaluated. Their mean age at diagnosis was 7.3 years, 31.8% were >or=10 years. Thirty-four patients (51.5%) presented with hyperleucocytosis >or=50 x 10(9)/L, 45 (68.2%) had hepatosplenomegaly. Immunophenotypically 63/66 patients (95%) had a B-precursor, 2 (3%) a T- and 1 (1.5%) a B-mature ALL. FISH analysis demonstrated a TEL/AML1 fusion in 9/66 (14%), BCR/ABL fusion in 1 (1.5%), MLL rearrangement in 2 (3.1%), iAMP21 in 2 (3.1%), MYC rearrangement in 1 (1.5%), and high-hyperdiploidy in 16 (24%). All patients but two with TEL/AML1 fusion and high-hyperdiploidy were clinically and hematologically in the standard risk group whereas those with poor cytogenetic factors had clinical high-risk features and were treated intensively. CONCLUSIONS: Compared to Europe, the ALL population in Nicaragua is older, has a higher proportion of poor prognostic clinical and hematological features and receives more intensive treatment, while patients with TEL/AML1 translocations and high-hyperdiploidy are clinically in the standard risk group. Cytogenetics did not contribute as an additional prognostic factor in this setting.

NRXN1 deletion syndrome; phenotypic and penetrance data from 34 families.

The spectrum of phenotypes associated with heterozygous deletions of neurexin-1 (NRXN1) is diverse and includes: autism spectrum disorder, attention deficit hyperactivity disorder, intellectual disability, seizures, schizophrenia, mood disorders and congenital malformations. Reduced penetrance and variable expressivity of deletions in this gene remain a challenge for genetic counselling. We clinically reviewed 67 NRXN1 deletions from 34 families to document the phenotype and determine odds ratio. Thirty-four probands (5 adults, 29 children (<16 years)) were initially identified from a cohort clinically referred for arrayCGH. A further 33 NRXN1 deletions (16 with established phenotype) from the families were identified following cascade screening. Speech and language delay was a consistent clinical presentation. Pedigree analysis of the inherited group revealed numerous untested relatives with a history of mental health and developmental issues, most notably in the NRXN1ß isoform patients. Our study highlights the complex nature of the NRXN1 phenotype in this population.

Detection of ATM gene deletion/duplication by multiplex ligation-dependant probe amplification in childhood lymphoid malignancies: a report from the Children's Oncology Group.

ATM gene alterations have been described in various lymphoproliferative malignancies suggesting that ATM contributes to lymphomagenesis. Using multiplex ligation-dependant probe amplification (MLPA), we screened 61 childhood lymphoid malignancies for ATM genomic deletion/duplication. Five samples were found to have a complete deletion or duplication. All the three deletions were found in B-precursor ALL (15%), two were submicroscopic, not detected by standard cytogenetic studies. These observations indicate that as in adult ALL, complete ATM submicroscopic deletion is frequent in childhood B-precursor ALL. As previously hypothesized, these results suggest that ATM may act as a tumor suppressor gene in the pathogenesis of childhood B-precursor ALL.

SKY reveals a high frequency of unbalanced translocations involving chromosome 6 in t(12;21)-positive acute lymphoblastic leukemia.

The G-band cryptic t(12;21)(p13;q22) is the most common chromosomal rearrangement in childhood acute lymphoblastic leukemia (ALL). To investigate the nature of additional chromosomal events in this group of patients spectral karyotyping (SKY) following G-banding analysis was performed in 14 cases. From these cases six showed structural aberrations of chromosome 6, including both simple deletions and unbalanced translocations, and involved both q (n=4) and p (n=3) arms. The results show that rearrangements of 6p are also non-random events t(12;21)-positive ALL. This study illustrates the value of a combined SKY and G-banding approach in identifying novel karyotypic events in childhood ALL.

Karyotypic characterization of infant embryonal rhabdomyosarcoma.

Despite embryonal rhabdomyosarcoma (eRMS) representing the most frequent form of RMS, the karyotypic characterization of this tumor subtype is still incomplete. We report the karyotypic analysis of two new cases of infant-onset eRMS. Both cases had a hyperdiploid karyotype, including gain of chromosomes 2 and 8. Only one of the cases showed a structural aberration, an unbalanced rearrangement involving 4p. These cases, together with a review of the literature, suggest that a karyotypic subgroup exists in infant eRMS that is defined by hyperdiploidy (<53 chromosomes) and includes gain of chromosomes 2, 8, 11, and 17, with few or no structural aberrations. Hence, this report illustrates that distinct karyotypic subgroups may be found in eRMS, which ultimately may be shown to have prognostic relevance.

SKY analysis of childhood neural tumors and cell lines demonstrates a susceptibility of aberrant chromosomes to further rearrangements.

Malignant solid tumors are commonly characterized by a large number of complex structural and numerical chromosomal alterations, which often reflect the level of genomic instability and can be associated with disease progression. The aim of this study was to evaluate whether chromosomes that harbor primary aberrations have a higher susceptibility to accumulate further alterations. We used spectral karyotyping (SKY), to compare the individual chromosomal instability of two chromosome types: chromosomes that have a primary aberration and chromosomes without an aberration, in 13 primary childhood neural tumors and seven cell lines. We found that chromosomes that contain a primary aberration are significantly (p-value<0.001) more likely to gain further structural rearrangements or to undergo numerical changes (22.6%, 36 of 159 chromosomes) than chromosomes with no initial aberration (4.9%, 54 of 1099 chromosomes). These results are highly suggestive that aberrant chromosomes in solid tumors have a higher susceptibility to accumulate further rearrangements than "normal" chromosomes.

Array comparative genomic hybridization reveals unbalanced gain of the MYCN region in Wilms tumors.

Wilms tumor (WT) is one of the most common solid tumors in childhood. It is characterized by a nonrandom pattern of chromosomal aberrations whose clinical significance is still uncertain. To gain further insight into different genetic events and their corresponding biological role, conventional cytogenetics and array comparative genomic hybridization (array CGH) were performed on 13 tumor samples. In two of these, array CGH revealed, together with other aberrations, a low-level amplification and an unbalanced gain in the region of chromosome bands 2p23 approximately p24 that encompass the MYCN gene. Both events were confirmed with a MYCN-specific fluorescence in situ hybridization probe, which showed a signal pattern consistent with a small homogenous staining region in one case. In addition, mRNA expression levels for MYCN were determined by quantitative reverse-transcriptase polymerase chain reaction and revealed that gain of chromosomal material was reflected in enhanced levels of MYCN mRNA in both tumors, whereby also additional tumors showed increased MYCN expression. Therefore, our findings suggest that WT is an additional childhood tumor where MYCN gain might play an important role in tumor development.

Early Bilateral Gonadoblastoma in a Young Child with Mosaicism for Turner Syndrome and Trisomy 18 with Y Chromosome.

Mosaic Turner syndrome (TSM) commonly occurs in the form of 45,X/46,XX and 45,X/46,X,i(X)(q10). Mosaicism for a Y chromosome, 45,X/46,XY, has been well documented and is associated with increased risk of gonadoblastoma (GB). To date, there are only six reported cases of TSM with a trisomy 18 karyotype, and only two of these were phenotypically female with 45,X/47,XY,+18 karyotype. We present the case of a phenotypically female infant born with dysmorphic features. G-banded karyotype and interphase FISH of blood showed 45,X in 95% and 47,XY,+18 (trisomy 18) in 5% of cells analysed. However, interphase FISH of buccal cells showed only the presence of the 45,X cell line. Due to the presence of Y chromosome material, elective gonadectomy was performed at 13 months of age. There were bilateral streak ovaries with early evidence of GB bilaterally, a rudimentary uterus and bilateral fallopian tubes with unilateral ectopic adrenal tissue identified histologically. Interphase FISH of the gonadal tissue was similar to the blood findings with 45,X in 86% of cells and 47,XY,+18 in 14% of cells analysed. This case highlights a rare karyotype of TSM and trisomy 18 in the same patient and is the first reporting the associated finding of bilateral GB.

ATM promoter analysis in childhood lymphoid malignancies: a brief communication.

ATM promoter hypermethylation has been recently reported in adult carcinomas, but no information is available concerning the methylation status of ATM gene promoter in childhood B-precursor acute lymphoblastic leukaemia (ALL). Furthermore, involvement of somatic ATM promoter mutations in cancer is not known. We report a complete ATM gene promoter analysis in 74 childhood lymphoid malignancies.

Cytogenetics of pineoblastoma: four new cases and a literature review.

Pineoblastoma represents a class of primitive neuroectodermal tumors (PNET) with poorly differentiated neuroepithelial cells that are histologically indistinguishable from medulloblastomas. It is a rare tumor, typically arising in childhood, and to date only a few cytogenetic cases have been published. We report four new cases in which conventional cytogenetics demonstrated the presence of an abnormal clone. The tumors showed a variety of ploidy levels, from hypodiploid to hypertetraploid. Both structural and numerical aberrations were frequent, and in three out of the four cases a large degree of cell-to-cell variation was observed. The most frequently involved chromosome in structural rearrangements was chromosome 1, observed in three of the four cases. The short arm was involved in two of the three cases; in the third case, the anomaly was in the long arm. Two cases showed unbalanced gain of chromosome 17q, one of them showing i(17)(q10). Together, the four cases illustrate the complex karyotypic nature of this tumor type and represent a step toward determining whether a nonrandom cytogenetic picture exists and how this may be related to other associated tumor types.

ATM alterations in childhood non-Hodgkin lymphoma.

ATM gene alterations and impaired ATM protein expression have been described in various adult lymphoproliferative malignancies, suggesting that ATM contributes to lymphomagenesis. The present study investigated the prevalence of ATM gene and ATM protein expression alterations in sporadic childhood non-Hodgkin lymphoma (NHL). Twenty-seven cases of NHL were screened for ATM mutations by denaturing high-performance liquid chromatography (DHPLC). Direct and indirect criteria, including in silico tools, were used to classify the gene alterations. The methylation status of the ATM promoter CpG island was determined in 25 samples; ATM protein expression was assessed by Western blot in 9 lymphomas. ATM alterations were detected in 12 NHLs (44%). Ten different heterozygous base substitutions were identified in 10 NHLs (37%). Five samples (19%) were found to harbor a gene alteration considered to be a mutation or a rare variant potentially pathogenic. In one case, an ATM mutation was found in the germline. Four NHLs (44%) showed reduced or absent ATM protein expression. Except for one sample, no definite genetic or epigenetic alteration was identified to account for impaired ATM protein expression. These observations document a high prevalence of ATM gene and protein expression alterations, suggesting that ATM is involved in childhood NHL.