Array comparative genomic hybridization in retinoma and retinoblastoma tissues

In retinoblastoma, two RB1 mutations are necessary for tumor development. Recurrent genomic rearrangements may represent subsequent events required for retinoblastoma progression. Array-comparative genomic hybridization was carried out in 18 eye samples, 10 from bilateral and eight from unilateral retinoblastoma patients. Two unilateral cases also showed areas of retinoma. The most frequent imbalance in retinoblastomas was 6p gain (40%), followed by gains at 1q12-q25.3, 2p24.3-p24.2, 9q22.2, and 9q33.1 and losses at 11q24.3, 13q13.2-q22.3, and 16q12.1-q21. Bilateral cases showed a lower number of imbalances than unilateral cases (P = 0.002). Unilateral cases were divided into low-level (≤4) and high-level (÷7) chromosomal instability groups. The first group presented with younger age at diagnosis (mean 511 days) compared with the second group (mean 1606 days). In one retinoma case ophthalmoscopically diagnosed as a benign lesion no rearrangements were detected, whereas the adjacent retinoblastoma displayed seven aberrations. The other retinoma case identified by retrospective histopathological examination shared three rearrangements with the adjacent retinoblastoma. Two other gene-free rearrangements were retinoma specific. One rearrangement, dup5p, was retinoblastoma specific and included the SKP2 gene. Genomic profiling indicated that the first retinoma was a pretumoral lesion, whereas the other represents a subclone of cells bearing 'benign' rearrangements overwhelmed by another subclone presenting aberrations with higher 'oncogenic' potential. In summary, the present study shows that bilateral and unilateral retinoblastoma have different chromosomal instability that correlates with the age of tumor onset in unilateral cases. This is the first report of genomic profiling in retinoma tissue, shedding light on the different nature of lesions named 'retinoma'. (Cancer Sci 2009; 100: 465–471

A comprehensive molecular study on Coffin-Siris and Nicolaides-Baraitser syndromes identifies a broad molecular and clinical spectrum converging on altered chromatin remodeling

Chromatin remodeling complexes are known to modify chemical marks on histones or to induce conformational changes in the chromatin in order to regulate transcription. De novo dominant mutations in different members of the SWI/SNF chromatin remodeling complex have recently been described in individuals with Coffin-Siris (CSS) and Nicolaides-Baraitser (NCBRS) syndromes. Using a combination of whole-exome sequencing, NGS-based sequencing of 23 SWI/SNF complex genes, and molecular karyotyping in 46 previously undescribed individuals with CSS and NCBRS, we identified a de novo 1-bp deletion (c.677delG, p.Gly226Glufs*53) and a de novo missense mutation (c.914G>T, p.Cys305Phe) in PHF6 in two individuals diagnosed with CSS. PHF6 interacts with the nucleosome remodeling and deacetylation (NuRD) complex implicating dysfunction of a second chromatin remodeling complex in the pathogenesis of CSS-like phenotypes. Altogether, we identified mutations in 60% of the studied individuals (28/46), located in the genes ARID1A, ARID1B, SMARCB1, SMARCE1, SMARCA2, and PHF6. We show that mutations in ARID1B are the main cause of CSS, accounting for 76% of identified mutations. ARID1B and SMARCB1 mutations were also found in individuals with the initial diagnosis of NCBRS. These individuals apparently belong to a small subset who display an intermediate CSS/NCBRS phenotype. Our proposed genotype-phenotype correlations are important for molecular screening strategie

Noninvasive Prenatal Diagnosis in a Family at Risk for Fraser Syndrome

NIPT is mainly limited to the screening of aneuploidies. The added value of WES, after an invasive procedure, in malformed fetuses that tested negative by chromosomal microarray, claims for the application of NIPT to the screening of gene sequence variants which are unpredictable with respect to family history and the type of fetal anomalies. Through a screening strategy, WES on cff-DNA can provide clinically relevant information in cases of fetal malformations characterized by high genetic heterogeneity

Noninvasive prenatal diagnosis in a family at risk for Fraser syndrome

NIPT is mainly limited to the screening of aneuploidies. The added value of WES, after an invasive procedure, in malformed fetuses that tested negative by chromosomal microarray, claims for the application of NIPT to the screening of gene sequence variants which are unpredictable with respect to family history and the type of fetal anomalies. Through a screening strategy, WES on cff-DNA can provide clinically relevant information in cases of fetal malformations characterized by high genetic heterogeneity

Next generation sequencing in sporadic retinoblastoma patients reveals somatic mosaicism

In about 50% of sporadic cases of retinoblastoma, no constitutive RB1 mutations are detected by conventional methods. However, recent research suggests that, at least in some of these cases, there is somatic mosaicism with respect to RB1 normal and mutant alleles. The increased availability of next generation sequencing improves our ability to detect the exact percentage of patients with mosaicism. Using this technology, we re-tested a series of 40 patients with sporadic retinoblastoma: 10 of them had been previously classified as constitutional heterozygotes, whereas in 30 no RB1 mutations had been found in lymphocytes. In 3 of these 30 patients, we have now identified low-level mosaic variants, varying in frequency between 8 and 24%. In 7 out of the 10 cases previously classified as heterozygous from testing blood cells, we were able to test additional tissues (ocular tissues, urine and/or oral mucosa): in three of them, next generation sequencing has revealed mosaicism. Present results thus confirm that a significant fraction (6/40; 15%) of sporadic retinoblastoma cases are due to postzygotic events and that deep sequencing is an efficient method to unambiguously distinguish mosaics. Re-testing of retinoblastoma patients through next generation sequencing can thus provide new information that may have important implications with respect to genetic counseling and family care

Association Array comparative genomic hybridization in retinoma and retinoblastoma tissues

In retinoblastoma, two RB1 mutations are necessary for tumor development. Recurrent genomic rearrangements may represent subsequent events required for retinoblastoma progression. Array-comparative genomic hybridization was carried out in 18 eye samples, 10 from bilateral and eight from unilateral retinoblastoma patients. Two unilateral cases also showed areas of retinoma. The most frequent imbalance in retinoblastomas was 6p gain (40%), followed by gains at 1q12-q25.3, 2p24.3-p24.2, 9q22.2, and 9q33.1 and losses at 11q24.3, 13q13.2-q22.3, and 16q12.1-q21. Bilateral cases showed a lower number of imbalances than unilateral cases (P = 0.002). Unilateral cases were divided into low-level (£4) and high-level (³7) chromosomal instability groups. The first group presented with younger age at diagnosis (mean 511 days) compared with the second group (mean 1606 days). In one retinoma case ophthalmoscopically diagnosed as a benign lesion no rearrangements were detected, whereas the adjacent retinoblastoma displayed seven aberrations. The other retinoma case identified by retrospective histopathological examination shared three rearrangements with the adjacent retinoblastoma. Two other gene-free rearrangements were retinoma specific. One rearrangement, dup5p, was retinoblastoma specific and included the SKP2 gene. Genomic profiling indicated that the first retinoma was a pretumoral lesion, whereas the other represents a subclone of cells bearing 'benign' rearrangements overwhelmed by another subclone presenting aberrations with higher 'oncogenic' potential. In summary, the present study shows that bilateral and unilateral retinoblastoma have different chromosomal instability that correlates with the age of tumor onset in unilateral cases. This is the first report of genomic profiling in retinoma tissue, shedding light on the different nature of lesions named 'retinoma'. (Cancer Sci 2009; 100: 465-471) R etinoblastoma (RB, OMIM#180200) is the most common primary intraocular malignancy in children, initiated by the inactivation of both alleles of the RB1 tumor-suppressor gene. (4,5) Unlike RB, which is typically opaque white, RN appears as a translucent gray retinal mass, frequently associated with calcification and retinal pigment epithelial hyperplasia. Recently, it has been demonstrated that the two mutational events inactivating the RB1 gene are already present in RN. (4) Using quantitative polymerase chain reaction (PCR) and fluorescence in situ hybridization on specific candidate genes, it has also been shown that RN display low-level copy number changes involving higher levels of amplification in adjacent RB. (4) At some point this instability can lead to further genomic rearrangements (M3-Mn) that result in tumor progression. (9) These data strongly suggest that these changes may represent M3-Mn events driving tumor progression in RB. In this scenario, RN represents a very interesting tissue to study the timing of genomic instability in RB development. However, molecular studies in this lesion are limited by sample availability as patients with only RN are not treated, and the coexistence of RN and RB in enucleated eyes is not frequently observed. Here, we used a high-resolution array-CGH technique to analyze genomic rearrangements in 18 RB eye samples, 10 from bilateral and eight from unilateral patients. In two unilateral cases, we also investigated genomic imbalances in two areas of RN adjacent to RB. (5) In one case (#16), clinically diagnosed RN was observed to progress to RB, whereas in the other case (#15) RN was identified by retrospective histopathological examination. Materials and Methods Tissue sample collection. We collected 18 formalin-fixed paraffinembedded eye samples from enucleated RB patients archived in the Department of Human Pathology and Oncology of the University of Siena. After surgery, enucleated eyes were immersion-fixed in buffered formalin for 48 h. After fixation, sampling, paraffin embedding, and cutting were carried out according to the usual pathological methods. The group of samples included 10 bilateral cases (one familial and nine sporadic) and eight sporadic unilateral cases. For each patient we have the corresponding DNA sampl

Coffin-Siris and Nicolaides-Baraitser syndromes are a common well recognizable cause of intellectual disability

Nicolaides-Baraitser and Coffin-Siris syndromes are emerging conditions with overlapping clinical features including intellectual disability and typical somatic characteristics, especially sparse hair, low frontal hairline, large mouth with thick and everted lips, and hands and feet anomalies. Since 2012, mutations in genes encoding six proteins of the BAF complex were identified in both conditions.publisher: Elsevier articletitle: Coffin–Siris and Nicolaides–Baraitser syndromes are a common well recognizable cause of intellectual disability journaltitle: Brain and Development articlelink: http://dx.doi.org/10.1016/j.braindev.2014.08.009 content_type: article copyright: Copyright © 2014 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.status: publishe