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• 22 of 146 patients (15 %) with epilepsy showed relevant copy number variants (CNVs). • "Epilepsy and global developmental delay/intellectual disability " group showed the highest prevalence of clinically relevant CNVs. • Chromosomes 1, 2, 16, and X showed higher CNVs incidence. • aCGH is a suitable first-line genetic test for the epilepsy-plus subgroup. • This study highlights the significance of aCGH in unraveling the genetic basis of epilepsy and have implications for precision medicine. Epilepsy, a neurological disorder characterized by recurring unprovoked seizures due to excessive neuronal excitability, is primarily attributed to genetic factors, accounting for an estimated 70 % of cases. Array-comparative genomic hybridization (aCGH) is a crucial genetic test for detecting copy number variants (CNVs) associated with epilepsy. This study aimed to analyze a cohort of epilepsy patients with CNVs detected through aCGH to enhance our understanding of the genetic underpinnings of epilepsy. A retrospective cross-sectional study was conducted using the aCGH database from the Genetics Department of the Faculty of Medicine of the University of Porto, encompassing 146 patients diagnosed with epilepsy, epileptic encephalopathy, or seizures. Clinical data were collected, and aCGH was performed following established guidelines. CNVs were classified based on ACMG standards, and patients were categorized into four groups according to their clinical phenotype. Among the 146 included patients, 94 (64 %) had at least one CNV, with 22 (15.1 %) classified as pathogenic or likely pathogenic. Chromosomes 1, 2, 16, and X were frequently implicated, with Xp22.33 being the most reported region (8 CNVs). The phenotype "Epilepsy and global developmental delay/intellectual disability" showed the highest prevalence of clinically relevant CNVs. Various CNVs were identified across different groups, suggesting potential roles in epilepsy. This study highlights the significance of aCGH in unraveling the genetic basis of epilepsy and tailoring treatment strategies. It contributes valuable insights to the expanding knowledge in the field, emphasizing the need for research to elucidate the diverse genetic causes of epilepsy. [ABSTRACT FROM AUTHOR]

Introduction: Gestational (GC) (derived from the placenta) and non-gestational (NGC) choriocarcinomas are trophoblastic diseases originated from abnormal proliferation of trophoblastic cells. These rare tumors share similar morphology and pathological features and differ on chemotherapy response, genetic origin and prognosis. In this study, the genomic profile of choriocarcinomas was performed according to their origin (GC or NGC) aiming to better understand these poorly characterized diseases.Methods: Thirteen patients were included in this study; 10 presented previous history of hydatidiform mole and six developed metastasis. Twelve polymorphic microsatellite markers (D15S659, APOC2, D5S816, BAT25, D3S1614, D3S1311, D1S1656, APC-D5S346, D3S1601, D18S70, D8S1110 and D11S1999) were investigated to distinguish GC from NGC. All choriocarcinomas were evaluated by copy number alterations using array CGH.Results: Eight cases were classified as GC and five as NGC. Although potentially polymorphic, NGC exhibited significant gain of 21p11. Rare copy number alterations (CNA) were detected as a frequent event in GC including gains of 1p36.33-p36.32 (3 cases), 17q25.3 (4 cases), and losses of 9q33.1 (5 cases), 17q21.3 (3 cases) and 18q22.1 (4 cases) (varying from 724 to 3,053 Kb).Discussion: Two tumor suppressor genes are candidates to be involved in GC: TRIM32 (9q33.1) and CDH19 (18q22.1). Gains of CBX2, CBX4 and CBX8 were frequently found in high risk prognostic score in GC. The in silico functional interaction analysis revealed the involvement of PTEN and PI3K-Akt signaling pathways. These data pointed out significant genomic alterations in GC, opening new avenues to better characterize the pathobiology of this disease. [ABSTRACT FROM AUTHOR]

The past few years have seen extraordinary advances in prenatal genetic practice led by 2 major technological advances; next-generation sequencing of cell-free DNA in the maternal plasma to noninvasively identify fetal chromosome abnormalities, and microarray analysis of chorionic villus sampling and amniotic fluid samples, resulting in increased cytogenetic resolution. Noninvasive prenatal screening of cell-free DNA has demonstrated sensitivity and specificity for trisomy 21 superior to all previous screening approaches with slightly lower performance for other common aneuploidies. These tests have rapidly captured an increasing market share, with substantial reductions in the number of chorionic villus sampling and amniocentesis performed suggesting that physicians and patients regard such screening approaches as an equivalent replacement for diagnostic testing. Simultaneously, many clinical programs have noted significant decreases in patient counseling. In 2012 the Eunice Kennedy Shriver National Institute of Child Health and Human Development funded a blinded comparison of karyotype with the emerging technology of array comparative genomic hybridization showing that in patients with a normal karyotype, 2.5% had a clinically relevant microdeletion or duplication identified. In pregnancies with an ultrasound-detected structural anomaly, 6% had an incremental finding, and of those with a normal scan, 1.6% had a copy number variant. For patients of any age with a normal ultrasound and karyotype, the chance of a pathogenic copy number variant is greater than 1%, similar to the age-related risk of aneuploidy in the fetus of a 38 year old. This risk is 4-fold higher than the risk of trisomy 21 in a woman younger than 30 years and 5- to 10-fold higher than the present accepted risk of a diagnostic procedure. Based on this, we contend that every patient, regardless of her age, be educated about these risks and offered the opportunity to have a diagnostic procedure with array comparative genomic hybridization performed. [ABSTRACT FROM AUTHOR]

Background: Extranodal natural killer–/T-cell lymphoma, nasal type (ENKTCL-NT) is a highly aggressive lymphoma and prognosis is usually poor. The genetic background of primary cutaneous cases is poorly understood. Objective: We sought to evaluate the clinicopathologic features of cutaneous ENKTCL-NT, and the prognostic significance of genomic copy number alterations. Methods: Eight cases of cutaneous ENKTCL-NT (5 primary, 2 secondary, 1 no staging performed), including 2 patients with an unusually prolonged course of 5 and 23 years, were investigated using array comparative genomic hybridization. Results: All patients presented with typical clinicopathologic features. Epstein-Barr virus was found in neoplastic cells in all specimens. Copy number alterations were detected in all 8 cases with losses on 6q (37.5% of cases) and 7p (37.5% of cases), and gains on 7q (37.5% of cases) being the most frequent. Complexity of array comparative genomic hybridization profile did not correlate with the course of the disease. However, an increase of copy number alterations was detected in sequential biopsy specimens of 1 long-term survivor. Limitations: This was a small case series retrospective study. Conclusion: Clinicopathologic features of cutaneous ENKTCL-NT are distinctive. Lower number of copy number alterations cannot be used as predictor for prolonged survival in cutaneous ENKTCL-NT. [Copyright &y& Elsevier]

Abstract: We present our experience of array comparative genomic hybridization (aCGH) characterization of two cases of prenatally detected de novo simple and complex apparently balanced reciprocal translocations. Amniocentesis of the first case revealed a complex chromosome rearrangement and a karyotype of 46,XY,t(5;8;6)(q11.2;p23.1;q22.32)dn. aCGH of amniocytes revealed no genomic imbalance. Ultrasound findings were unremarkable. The pregnancy was carried to term, and pediatric follow-ups were normal at 3 months of age. Amniocentesis of the second case revealed a simple reciprocal translocation and a karyotype of 46,XY,t(3;11)(q14;q23)dn. aCGH of amniocytes revealed a 1.32-Mb microduplication in chromosome 2p12 [arr cgh 2p12 (75,245,747-76,563,965)×3] encompassing the genes of TACR1, FAM176A, MRPL19, and C2orf3. Ultrasound findings were unremarkable. The pregnancy was carried to term, and the pediatric follow-ups were normal at 8 months of age. In cases of prenatally detected de novo apparently balanced reciprocal translocations, cryptic intrachromosomal rearrangements may exist in addition to the cytogenetically visible structural chromosome aberrations. aCGH is useful not only in identifying the genomic imbalances at the breakpoints, but also in detecting unexpectedly complex rearrangements in other chromosomes. [Copyright &y& Elsevier]

Abstract: Background: Cancer genomes accumulate frequent and diverse chromosomal abnormalities as well as gene mutations but must maintain the ability to survive in vivo. We hypothesize that genetic selection acts to maintain tumour survival by preserving copy number of specific genes and genomic regions. Genomic regions and genes that remain unaltered in copy number and expression, respectively, may be essential for maintaining tumour survival. Methods: We analyzed copy number data of 243 previously reported breast tumours and computationally derived stable copy number regions. To identify genes in stable copy number regions with nominal changes in expression, datasets for tumour and normal samples were compared. Results were replicated by analysis of a series of independent copy number, expression and genomic sequencing studies. A subset of stable regions, including stable paralogous regions, were confirmed by quantitative PCR and fluorescence in situ hybridization (FISH) in 5 breast cancer cell lines. We deduced a comprehensive set of dually stable genes (i.e. maintaining nominal copy number and expression) which were categorized according to pathway and ontology assignments. The stability of genes encoding therapeutic drug targets was also assessed. Results and Conclusion: Tumour genome analysis revealed 766 unstable (amplified and/or deleted) and 812 stable contiguous genomic regions. Replication analysis of an independent set of 171 breast tumours confirmed copy number stability of 1.3 Gb of the genome. We found that 5804 of these genes were dually stable. The composition of this gene set remained essentially unchanged (<2% reduction) after accounting for commonly mutated breast cancer genes found by sequencing and differential expression. The stable breast cancer genome is enriched for cellular metabolism, regulation of gene expression, DNA packaging (chromatin and nucleosome assembly), and regulation of apoptosis functions. Stable genes participating in multiple essential pathways were consistently found to be targets of chemotherapies. Preservation of stable, essential genes may be related to the effectiveness of certain chemotherapeutic agents that act on multiple gene products in this set. [Copyright &y& Elsevier]

Summary: Giant cell ependymoma, a rare ependymoma subtype, was recently recognized as a separate diagnostic entity with variations both in malignant potential and course of disease. We analyzed the first supratentorial giant cell ependymoma using G-band karyotyping, DNA ploidy analysis, and array comparative genomic hybridization. The tumor was hypodiploid, and the karyotype showed multiple monosomies. This novel cytogenetic pattern seems specific for giant cell ependymoma as the only previous cytogenetic analysis of a giant cell ependymoma found similar monosomies. We were also able to analyze cytogenetically the subsequent recurrent tumor, phenotypically an anaplastic ependymoma, allowing a first insight into the genetic events involved in disease progression. [ABSTRACT FROM AUTHOR]

Summary: Increased expression of cyclin D1 is notoriously associated with mantle cell lymphoma because of translocation t(11;14)(q13;q32) or variants involving the cyclin D1 gene. We present an unusual case of CD5-negative diffuse large B-cell lymphoma expressing cyclin D1 in the absence of translocation by fluorescence in situ hybridization analysis. Using array-comparative genomic hybridization, we found a complex karyotype without the characteristic chromosomal aberrations accompanying cyclin D1 translocation in mantle cell lymphoma; instead, there was monoallelic deletion of AKT interacting protein and glycogen synthase kinase-3 β genes, both involved in the AKT/glycogen synthase kinase-3 β cascade-controlling nuclear levels of cyclin D1. These findings suggest that posttranslational events regulating cyclin D1 activity may take place also in a subset of diffuse large B-cell lymphomas and contribute to lymphomagenesis. As a consequence, the sole cyclin D1 positivity by immunohistochemistry may not be enough to distinguish pleomorphic/blastoid mantle cell lymphoma from diffuse large B-cell lymphoma. Search for t(11;14) with fluorescence in situ hybridization probes should always be performed in doubtful cases. [Copyright &y& Elsevier]

Summary: Hypotonia in infants in the first year of life is a common diagnostic and management challenge for pediatricians and neonatologists. Several published clinical studies have shown that a substantial proportion of cases are accounted for by genetic disorders. Rapid advances in biotechnology, bioinformatics, and molecular genetic testing have made it possible to offer specific genetic diagnoses in a timely manner. The value of clinical examination in the localization of hypotonia within the nervous system as the first step towards a diagnosis cannot be overemphasized. Due importance should be given to specific features on examination and in the selection of appropriate laboratory tests to minimize laboratory costs. Inborn errors of metabolism, although infrequently encountered, are of importance. Based on clinical evidence from published studies, an algorithm is suggested that would incorporate the clinical features and testing modalities in providing a high diagnostic yield for the clinician. [ABSTRACT FROM AUTHOR]

Summary: Array technology, here termed molecular karyotyping, is an attractive alternative to conventional karyotyping for prenatal diagnosis given the increase in resolution as well as faster report times. We review the benefits and limitations of this technique for the detection of pathogenic genomic imbalances, address the challenges raised in the interpretation of copy number variations, discuss practical considerations for the routine implementation of molecular karyotyping in prenatal diagnosis, and identify areas where more research is desired to enable large scale introduction of the technique(s). [ABSTRACT FROM AUTHOR]

Array-based comparative genomic hybridization is rapidly becoming a standard assay for research and clinical cytogenetics laboratories. Certain automated workflows are used to achieve economies in running this relatively expensive assay. Here, we describe the ways in which our medium throughput laboratory has investigated automation at various points in our workflow to achieve economies and improve the resulting data for our investigators. We investigate an automated hybridization station to improve microarray hybridization, an autoloading scanner to facilitate the rapid scanning of multiple arrays, and a software package that allows for quick and easy access to many external resources to extend the analysis. [Copyright &y& Elsevier]

Summary: According to the new World Health Organization classification system, there are 2 types of enteropathy-associated T-cell lymphoma. Type 1 is associated with celiac disease and accounts for the majority of cases in Western countries, whereas type 2 is not associated with celiac disease. To characterize enteropathy-associated T-cell lymphoma types in Korea, we carried out clinicopathologic and immunophenotypic analyses of 8 Koreans with enteropathy-associated T-cell lymphoma and investigated genomic profile using array comparative genomic hybridization. The tumors involved the small intestine in 5 patients and the colorectum in 3 patients. Two patients carried an HLA DQB1⁎0302 allele that corresponds to HLA DQ8. None of the patients had gluten-sensitive malabsorption syndrome. Intraepithelial lymphocytosis was observed in all patients. The sizes of the tumor cells were small or small-to-medium in 7 cases and medium-to-large in 1 case. The immunophenotypes of the tumor cells were CD4−CD8+CD56+ in 4 cases, CD4−CD8+CD56− in 1 case, CD4−CD8−CD56+ in 2 cases, and CD4−CD8−CD56− in 1 case. Array comparative genomic hybridization analysis showed that chromosome 9q33-q34.1 gain was present in 4 (80%) of the 5 cases examined. Other recurrent genomic alterations were gain of 6p21.1-21.31 (3/5, 60%), gain of 19q (2/5), and the loss of 3p12.1-p12.2 (2/5) and 3q26.31 (2/5). These results suggest that the most prevalent type of enteropathy-associated T-cell lymphoma in this geographic region is type 2, and the genetic changes associated with it are similar to those in Western countries. [ABSTRACT FROM AUTHOR]

Genomic copy number variations (CNVs) are a major form of variation in the human genome and play an etiologic role in several neuropsychiatric diseases. Tandem repeats, particularly with long (>50 bp) repeat units, are a relatively common yet underexplored type of CNV that may significantly contribute to human genomic variation and disease risk. We therefore carried out a pilot experiment to explore the potential role of long tandem repeats as risk factors in psychiatric disorders.A bacterial artificial chromosome-based array comparative genomic hybridization (aCGH) platform was used to examine CNVs in genomic DNA from 34 probands with schizophrenia or schizoaffective disorder.The aCGH screen detected an apparent deletion on 5p15.1 in two probands, caused by the presence in each proband of two low copy number (short) alleles of a tandem repeat that ranges in length from fewer than 10 to greater than 50 3.4 kb units in the population examined. Short alleles partially segregate with schizophrenia in a small number of families, though linkage was not significant. An association study showed no significant difference in repeat length between 406 schizophrenia cases and 392 controls.Although we did not demonstrate a relationship between the 5p15.1 repeat and schizophrenia, our results illustrate that long tandem repeats represent an intriguing type of genetic variation that have not been studied in earlier connection with psychiatric illness. aCGH can detect a small subset of these repeats, but systematic investigation will require the development of specific arrays and improved analytical methods. [ABSTRACT FROM AUTHOR]

Abstract: We aimed to use array comparative genomic hybridization (CGH) to identify chromosomal loci that contribute to the pathogenesis of ruptured intracranial aneurysms (IAs) in a Korean population and to confirm the results using real-time polymerase chain reaction (PCR). Twenty-three patients with ruptured IAs were enrolled in this study. Array CGH revealed copy number aberrations in 19 chromosomal regions. Chromosomal gains were identified at a high frequency in regions 1p12, 4q24, 5p15.31, 5p15.33, 6p12.2, 6q22.33, 7p21.1, 9q22.1, 10q24.32, 10q26.3, 12q13.13, 17p12, 18q12.3, 18q23, 19p13.3, 20q13.33, 21q11.2, and 21q22.3, whereas chromosomal losses were identified at 15q11.2 and 22q11.21. Real-time PCR confirmed the results of the array CGH studies of the COL6A2, GRIN3B, MUC17, and PRODH genes. This is the first study to identify candidate regions by array CGH in patients with IAs. The identification of genes that may predispose an individual to the development of IAs may lead to a better understanding of the mechanism of IA formation. Multicenter studies comparing cohorts of patients of different ethnicities are needed to better understand the mechanism of IA formation. [Copyright &y& Elsevier]

Abstract: Histiocytic disorders have been noted to have evidence of transdifferentiation; examples of cases with combinations of different lineages have been shown. In our index case, we identified interdigitating dendritic cell (IDC) differentiation in a case of Langerhans cell histiocytosis (LCH). Little is currently known about the genetics of IDC sarcoma (IDCS) because they are exceedingly rare. Using array comparative genomic hybridization (aCGH), we evaluated 4 cases of IDCS and compared them with our index case, as well as genetic abnormalities previously found in LCH. Four cases of paraffin-embedded samples of IDCS and 1 case of LCH with IDC differentiation were evaluated using aCGH. Array CGH results showed no abnormalities in a case of LCH with interdigitating cell differentiation. In 3 of 4 cases of IDCS, genetic abnormalities were identified; 1 case had no identifiable abnormalities. Interdigitating dendritic cell sarcoma case 1 had gains of 3q and 13q; IDCS case 2 had trisomy 12; IDCS case 3 had deletions of 7p, 12p, 16p, 18q, 19q, and 22q; and IDCS case 4 had no detectable abnormalities. Our index case, LCH with IDC differentiation, showed no abnormalities by aCGH. A number of LCH cases do not have detectable genetic abnormalities. In contrast, 3 of 4 cases of IDCS evaluated had identifiable abnormalities by aCGH. Furthermore, 2 of these shared abnormalities, albeit of large genetic regions, with published abnormalities seen in LCH. No recurrent abnormalities were identified in the IDCS cases. However, the possibility of a relationship between IDCS and LCH cannot be entirely excluded by these results. [Copyright &y& Elsevier]