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Journal articles on the topic 'ACGH'

Author: Grafiati

Published: 4 June 2021

Last updated: 26 July 2025

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1

De Paz, Juan F., Rocío Benito, Javier Bajo, Ana Eugenia Rodríguez, and María Abáigar. "aCGH-MAS: Analysis of aCGH by means of Multiagent System." BioMed Research International 2015 (2015): 1–12. http://dx.doi.org/10.1155/2015/194624.

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There are currently different techniques, such as CGH arrays, to study genetic variations in patients. CGH arrays analyze gains and losses in different regions in the chromosome. Regions with gains or losses in pathologies are important for selecting relevant genes or CNVs (copy-number variations) associated with the variations detected within chromosomes. Information corresponding to mutations, genes, proteins, variations, CNVs, and diseases can be found in different databases and it would be of interest to incorporate information of different sources to extract relevant information. This wor

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2

Cordoba, Marcos, Stephanie Andriole, Shara M. Evans, David Britt, Melissa Chu Lam, and Mark I. Evans. "Integrating Microarrays into Routine Prenatal Diagnosis: Determinants of Decision Making." Fetal Diagnosis and Therapy 40, no. 2 (2016): 135–40. http://dx.doi.org/10.1159/000442197.

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Objectives: The explosion in genetic technologies, including array comparative genomic hybridization (aCGH), has increased the complexity of genetic counseling. We now offer chorionic villus sampling (CVS) and aCGH to all first-trimester patients, as this allows the prenatal diagnosis of an additional 1% of anomalies not otherwise detectable and can detect genetic copy number variants at a much higher resolution than conventional cytogenetics. Here, we explored some of the determinants of how patients are deciding to use or not use this new technology and evaluate risk-benefit analyses for tha

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3

Ribeiro, Katyanne Heringer de Oliveira, Thainá Altoé dos Santos, and Terezinha Sarquis Cintra. "AVALIAÇÃO DE ANOMALIAS CROMOSSÔMICAS POR CGH-ARRAY EM PORTADORES DE DISMORFIAS E DEFICIÊNCIA INTELECTUAL COM CARIÓTIPO NORMAL." Semina: Ciências Biológicas e da Saúde 38, no. 1supl (2018): 99. http://dx.doi.org/10.5433/1679-0367.2017v38n1suplp99.

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A deficiência intelectual é uma condição presente em 2% a 3% da população e mais da metade dos casos aindasão considerados idiopáticos. Sua etiologia é heterogênea e as anomalias cromossômicas têm importantecontribuição. A detecção de pequenas instabilidades genômicas, atualmente são apontadas como fatoretiológico. O estudo cromossômico microscópico pelo bandeamento G (cariótipo convencional) apresentalimitações para detecção de pequenas instabilidades genômicas e a Hibridização Genômica Comparativa porarray (aCGH) é capaz de identificar perdas e ganhos de material genômico com alta resolução.

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Shankar, Ganesh, Michael R. Rossi, Devin E. Mcquaid, et al. "aCGHViewer: A Generic Visualization Tool for aCGH Data." Cancer Informatics 2 (January 2006): 117693510600200. http://dx.doi.org/10.1177/117693510600200023.

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Array-Comparative Genomic Hybridization (aCGH) is a powerful high throughput technology for detecting chromosomal copy number aberrations (CNAs) in cancer, aiming at identifying related critical genes from the affected genomic regions. However, advancing from a dataset with thousands of tabular lines to a few candidate genes can be an onerous and time-consuming process. To expedite the aCGH data analysis process, we have developed a user-friendly aCGH data viewer (aCGHViewer) as a conduit between the aCGH data tables and a genome browser. The data from a given aCGH analysis are displayed in a

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Hightower, Hannah B., Nathaniel H. Robin, Fady M. Mikhail, and Namasivayam Ambalavanan. "Array comparative genomic hybridisation testing in CHD." Cardiology in the Young 25, no. 6 (2014): 1155–72. http://dx.doi.org/10.1017/s1047951114001838.

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AbstractBackground: CHD is the leading cause of mortality due to birth defects. Array comparative genomic hybridisation (aCGH) detects submicroscopic copy number changes and may improve identification of the genetic basis of CHD. Methods: This is a retrospective analysis of 1252 patients from a regional referral centre who had undergone aCGH. Of the patients, 173 had CHD. A whole-genome custom-designed oligonucleotide array with >44,000 probes was used to detect copy number changes. Results: Of the 1252 patients, 335 (26.76%) had abnormal aCGH results. Of the 173 patients with CHD, 50 (28.9

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Bystřická, Dagmar, Z. Zemanová, J. Březinová, et al. "The Assessment of Array Comparative Genomic Hybridization in Complex Karyotype Analyses." Folia Biologica 56, no. 5 (2010): 223–30. http://dx.doi.org/10.14712/fb2010056050223.

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Molecular-cytogenetic methods were used to analyse and specify complex genome rearrangements in malignant cells. Twelve samples of bone marrow cells were collected from patients with myelodysplastic syndromes (MDS). The complex karyotypes were examined by multicolour fluorescence in situ hybridization (mFISH), high-resolution multicolour banding (mBAND) and array comparative genomic hybridization (aCGH). For aCGH, DNA was isolated from fixed bone marrow cells in methanol and acetic acid and amplified by whole-genome amplification. Three samples were analysed by the oligonucleotide array Nimble

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Malysheva, Olga Viktorovna, Aleksandr Nikolayevich Baranov, Anna Andreyevna Pendina, Yelena Sergeyevna Shabanova, and Vladislav Sergeyevich Baranov. "DIAGNOSTICS OF CHROMOSOMAL ABBERATIONS BY arrayCGH." Journal of obstetrics and woman disease 62, no. 2 (2013): 133–38. http://dx.doi.org/10.17816/jowd622133-138.

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ACGH is a modern and highly efficient approach for full-genomic scanning of wide spectrum of chromosomal disbalance. Here, we discuss diagnostic capabilities of aCGH and give examples of diagnostic cases.

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8

Chung, Wendy K., James Weisberger, Yi Sun, et al. "Utility of Oligonucleotide Array Comparative Genomic Hybridization to Identify Cryptic Copy Number Alterations in Myelodysplastic Syndromes." Blood 112, no. 11 (2008): 5076. http://dx.doi.org/10.1182/blood.v112.11.5076.5076.

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Abstract Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematological neoplasms characterized by peripheral cytopenias due to ineffective hematopoiesis and significant cytologic atypia in one or more of the myeloid lineages. There is a variable risk of progression to acute myeloid leukemia, which is dependent on the blast count and certain recurrent cytogenetic abnormalities. Cytogenetic characterization is important in both diagnosis and prognosis, but can be of limited value in lower-risk MDS subtypes because of the low frequency of karyotypic abnormalities detected by c

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Tulay, Pinar, Mahmut Cerkez Ergoren, Ahmet Alkaya, Eyup Yayci, Sebnem Ozemri Sag, and Sehime Gulsum Temel. "Inconsistency of Karyotyping and Array Comparative Genomic Hybridization (aCGH) in a Mosaic Turner Syndrome Case." Global Medical Genetics 07, no. 04 (2020): 128–32. http://dx.doi.org/10.1055/s-0041-1722974.

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Abstract Purpose Turner syndrome is a sex chromosomal aberration where majority of the patients have 45,X karyotype, while several patients are mosaic involving 45,X/46,XX; 46,X,i(Xq); and other variants. Cytogenetic analysis, karyotyping, is considered to be the “gold standard” to detect numerical and structural chromosomal abnormalities. In the recent years, alternative approaches, such as array comparative genomic hybridization (aCGH), have been widely used in genetic analysis to detect numerical abnormalities as well as unbalanced structural rearrangements. In this study, we report the use

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Guha, Subharup, Yuan Ji, and Veerabhadran Baladandayuthapani. "Bayesian Disease Classification Using Copy Number Data." Cancer Informatics 13s2 (January 2014): CIN.S13785. http://dx.doi.org/10.4137/cin.s13785.

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DNA copy number variations (CNVs) have been shown to be associated with cancer development and progression. The detection of these CNVs has the potential to impact the basic knowledge and treatment of many types of cancers, and can play a role in the discovery and development of molecular-based personalized cancer therapies. One of the most common types of high-resolution chromosomal microarrays is array-based comparative genomic hybridization (aCGH) methods that assay DNA CNVs across the whole genomic landscape in a single experiment. In this article we propose methods to use aCGH profiles to

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Robak, Laurie A., Renqian Du, Bo Yuan, et al. "Integrated sequencing and array comparative genomic hybridization in familial Parkinson disease." Neurology Genetics 6, no. 5 (2020): e498. http://dx.doi.org/10.1212/nxg.0000000000000498.

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ObjectiveTo determine how single nucleotide variants (SNVs) and copy number variants (CNVs) contribute to molecular diagnosis in familial Parkinson disease (PD), we integrated exome sequencing (ES) and genome-wide array-based comparative genomic hybridization (aCGH) and further probed CNV structure to reveal mutational mechanisms.MethodsWe performed ES on 110 subjects with PD and a positive family history; 99 subjects were also evaluated using genome-wide aCGH. We interrogated ES and aCGH data for pathogenic SNVs and CNVs at Mendelian PD gene loci. We confirmed SNVs via Sanger sequencing and f

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Patel, Keyur, Farhad Ravandi, Deqin Ma, et al. "Detection of Cytogenetic Abnormalities Associated with Outcome Differences in Acute Myeloid Leukemia Using Array-Based Comparative Genomic Hybridization (aCGH) Analysis." Blood 114, no. 22 (2009): 1633. http://dx.doi.org/10.1182/blood.v114.22.1633.1633.

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Abstract Abstract 1633 Poster Board I-659 Background The presence of abnormal cytogenetic findings at diagnosis is an independent indicator of the outcome in patients with acute myeloid leukemias (AML). Recent availability of high-resolution analysis by aCGH technology has facilitated rapid detection of cytogenetic abnormalities previously undetected by the conventional G-banded karyotyping. Aim: To determine whether specific cytogenetic abnormalities, as detected by the aCGH analysis, are associated with differences in clinical outcomes in a group of patients with AML treated uniformly with t

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Patel, Ankita, Rui-Yu Wang, Patricia Hixson, et al. "Clinical Evaluation of a Custom Genome Wide 44K Oligoarray for Copy Number Changes in Acute Myeloid Leukemia." Blood 112, no. 11 (2008): 4869. http://dx.doi.org/10.1182/blood.v112.11.4869.4869.

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Abstract Oligonucleotide-based array CGH (aCGH) technique enables detection of submicroscopic copy number changes in cancer. This technique offers the flexibility to increase robustness by selecting best performing probes maximize the gene coverage while excluding repetitive sequences through a combination of bioinformatics and computation and increased resolution that allows for detection of smaller region of change. We designed a high resolution (44,000 probes) custom array using an Agilent platform and specifically targeted ~500 genes implicated in leukemogenesis. The disease gene regions h

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Abáigar, María, Eva Lumbreras, Irene Rodríguez, et al. "Array CGH As a Complementary Tool in the Diagnosis of Myelodysplastic Syndromes." Blood 120, no. 21 (2012): 3827. http://dx.doi.org/10.1182/blood.v120.21.3827.3827.

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Abstract Abstract 3827 Background: Myelodysplastic syndromes (MDS) are a heterogeneous group of hematological disorders in which diagnosis, risk stratification, and treatment selection are based on morphological and cytogenetic studies in bone marrow (BM) samples. MDS are characterized by several recurrent chromosomal abnormalities, most of them unbalanced, with a widely variable prognosis. The assessment of these genomic defects is essential for a correct risk stratification of these patients. However, conventional cytogenetic (CC) techniques are not sufficient for the study of all MDS patien

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Amado-Puentes, Alfonso, Alfredo Reparaz-Andrade, Aida Del Campo-García, et al. "Neurodevelopmental Disorders and Array-Based Comparative Genomic Hybridization: Sensitivity and Specificity using a Criteria Checklist for Genetic Test Performance." Neuropediatrics 50, no. 03 (2019): 164–69. http://dx.doi.org/10.1055/s-0039-1685216.

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Background Array-based comparative genomic hybridization (aCGH) is a molecular analysis method for identifying chromosomal anomalies or copy number variants (CNVs) correlating with clinical phenotypes. The aim of our study was to identify the most significant clinical variables associated with a positive outcome of aCGH analyses to develop a simple predictive clinical score. Methods We conducted a cross-sectional study in a tertiary center comparing the genotype and phenotype of the cases. A score was developed using multivariate logistic regression. The best score cutoff point, sensitivity, s

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O'Malley, Dennis P., Christina Giudice, Averee S. Chang, et al. "Comparison of Array Comparative Genomic Hybridization (aCGH) to FISH and Cytogenetics in Prognostic Evaluation of CLL." Blood 114, no. 22 (2009): 4393. http://dx.doi.org/10.1182/blood.v114.22.4393.4393.

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Abstract Abstract 4393 INTRODUCTION Chronic lymphocytic leukemia (CLL) is a commonly encountered hematologic neoplasm. Evaluation of prognosis in CLL is strongly based on genetic findings and the most commonly used studies are classical cytogenetics and targeted interphase fluorescence in situ hybridization (FISH). High resolution array comparative genomic hybridization (aCGH) is a relatively new and robust method of evaluating chromosomal alterations over the entire genome. We compared aCGH with routine cytogenetics and FISH in detecting genetic alterations in newly-diagnosed CLL cases. MATER

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Bahamat, Abeer A., Mourad Assidi, Sahira A. Lary, et al. "Use of Array Comparative Genomic Hybridization for the Diagnosis of DiGeorge Syndrome in Saudi Arabian Population." Cytogenetic and Genome Research 154, no. 1 (2018): 20–29. http://dx.doi.org/10.1159/000487094.

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DiGeorge syndrome (DGS) is a genetic disorder known as a clinically variable syndrome with over 180 associated phenotypic features. It is caused by a common human deletion in the 22q11.2 chromosomal region and currently is affecting approximately 1 in 4,000 individuals. Despite the prevalence of inherited diseases mainly due to consanguineous marriages, the current diagnosis of DGS in Saudi Arabia is mainly based on conventional high-resolution chromosome banding (karyotyping) and FISH techniques. However, advanced genome-wide studies for detecting microdeletions or duplications across the who

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Cameron, F., J. Xu, J. Jung, and C. Prasad. "Array CGH Analysis and Developmental Delay: A Diagnostic Tool for Neurologists." Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques 40, no. 6 (2013): 777–82. http://dx.doi.org/10.1017/s0317167100015882.

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Developmental delay occurs in 1–3% of the population, with unknown etiology in approximately 50% of cases. Initial genetic work up for developmental delay previously included chromosome analysis and subtelomeric FISH (fluorescent in situ hybridization). Array Comparative Genomic Hybridization (aCGH) has emerged as a tool to detect genetic copy number changes and uniparental disomy and is the most sensitive test in providing etiological diagnosis in developmental delay. aCGH allows for the provision of prognosis and recurrence risks, improves access to resources, helps limit further investigati

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Van Wieringen, Wessel N., Mark A. Van De Wiel, and Bauke Ylstra. "Normalized, Segmented or Called aCGH Data?" Cancer Informatics 3 (January 2007): 117693510700300. http://dx.doi.org/10.1177/117693510700300030.

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Array comparative genomic hybridization (aCGH) is a high-throughput lab technique to measure genome-wide chromosomal copy numbers. Data from aCGH experiments require extensive pre-processing, which consists of three steps: normalization, segmentation and calling. Each of these pre-processing steps yields a different data set: normalized data, segmented data, and called data. Publications using aCGH base their findings on data from all stages of the pre-processing. Hence, there is no consensus on which should be used for further down-stream analysis. This consensus is however important for corr

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Patel, Ankita, Patricia Hixson, Weimin Bi, et al. "Is It Time for Arraycgh to Be the First Line Test for Detection of Chromosome Abnormalities in Hematological Disorders-Example Multiple Myeloma." Blood 118, no. 21 (2011): 2543. http://dx.doi.org/10.1182/blood.v118.21.2543.2543.

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Abstract Abstract 2543 aCGH has become the state-of art tool for assaying copy number changes of the entire genome in recent years. It offers a high resolution, high throughput and an unbiased view of detecting copy number changes in a genome compared to standard cytogenetics. In fact, aCGH has become the standard of care for detection of genomic/cytogenetic abnormalities in a postnatal setting recently (PMID # 20466091). In contrast, the application of aCGH in a clinical setting is lagging behind for acquired disease such as cancer, although aCGH has contributed greatly in our understanding o

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Garabedian, Matthew J., Donna Wallerstein, Nubia Medina, James Byrne, and Robert J. Wallerstein. "Prenatal Diagnosis of Cystic Hygroma related to a Deletion of 16q24.1 with Haploinsufficiency of FOXF1 and FOXC2 Genes." Case Reports in Genetics 2012 (2012): 1–4. http://dx.doi.org/10.1155/2012/490408.

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We report the prenatal diagnosis of cystic hygroma that was subsequently identified to have haploinsufficiency of the FOXF1 and FOXC2 genes via array comparative genomic hybridization (aCGH). Deletion o f these genes has previously neither been associated with cystic hygroma nor prenatally diagnosed. The FOX gene cluster is involved in cardiopulmonary development. This case expands the phenotypic spectrum o f abnormalities of the FOXF1 and FOXC2 genes, as it seems within the spectrum of function that disruption of the FOX gene cluster would lead to include abnormalities of prenatal onset. Iden

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Preising, Gabriel A., Joshua J. Faber-Hammond, and Suzy C. P. Renn. "Correspondence of aCGH and long-read genome assembly for detection of copy number differences: A proof-of-concept with cichlid genomes." PLOS ONE 16, no. 10 (2021): e0258193. http://dx.doi.org/10.1371/journal.pone.0258193.

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Copy number variation is an important source of genetic variation, yet data are often lacking due to technical limitations for detection given the current genome assemblies. Our goal is to demonstrate the extent to which an array-based platform (aCGH) can identify genomic loci that are collapsed in genome assemblies that were built with short-read technology. Taking advantage of two cichlid species for which genome assemblies based on Illumina and PacBio are available, we show that inter-species aCGH log2 hybridization ratios correlate more strongly with inferred copy number differences based

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Di Gregorio, Eleonora, Giorgia Gai, Giovanni Botta, et al. "Array-Comparative Genomic Hybridization Analysis in Fetuses with Major Congenital Malformations Reveals that 24% of Cases Have Pathogenic Deletions/Duplications." Cytogenetic and Genome Research 147, no. 1 (2015): 10–16. http://dx.doi.org/10.1159/000442308.

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Karyotyping and aCGH are routinely used to identify genetic determinants of major congenital malformations (MCMs) in fetal deaths or terminations of pregnancy after prenatal diagnosis. Pathogenic rearrangements are found with a variable rate of 9-39% for aCGH. We collected 33 fetuses, 9 with a single MCM and 24 with MCMs involving 2-4 organ systems. aCGH revealed copy number variants in 14 out of 33 cases (42%). Eight were classified as pathogenic which account for a detection rate of 24% (8/33) considering fetuses with 1 or more MCMs and 33% (8/24) taking into account fetuses with multiple ma

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Misra, Shibalik, Greg Peters, Elizabeth Barnes, et al. "Yield of comparative genomic hybridization microarray in pediatric neurology practice." Neurology Genetics 5, no. 6 (2019): e367. http://dx.doi.org/10.1212/nxg.0000000000000367.

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ObjectiveThe present study investigated the diagnostic yield of array comparative genomic hybridization (aCGH) in a large cohort of children with diverse neurologic disorders as seen in child neurology practice to test whether pathogenic copy number variants (CNVs) were more likely to be detected in specific neurologic phenotypes.MethodsA retrospective cross-sectional analysis was performed on 555 children in whom a genetic etiology was suspected and who underwent whole-genome aCGH testing between 2006 and 2012. Neurologic phenotyping was performed using hospital medical records. An assessment

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Кашеварова, А. А., and И. Н. Лебедев. "Molecular cytogenetic diagnostic algorithm for patients with a ring chromosome." Nauchno-prakticheskii zhurnal «Medicinskaia genetika», no. 3() (March 30, 2020): 28–29. http://dx.doi.org/10.25557/2073-7998.2020.03.28-29.

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Для обследования пациентов с кольцевыми хромосомами разработан и апробирован алгоритм молекулярно-цитогенетической диагностики, включающий дополнительно к уже проведенному стандартному кариотипированию микрочиповое исследование (aCGH), ПЦР в реальном времени и флуоресцентную in situ гибридизацию (FISH). We developed and applied for patients with ring chromosomes an algorithm for molecular cytogenetic diagnostics which includes, in addition to the standard karyotyping, array comparative genomic hybridization (aCGH), real-time PCR, and fluorescence in situ hybridization (FISH).

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Arneson, Nona, Juan Moreno, Vladimir Iakovlev, et al. "Comparison of Whole Genome Amplification Methods for Analysis of DNA Extracted from Microdissected Early Breast Lesions in Formalin-Fixed Paraffin-Embedded Tissue." ISRN Oncology 2012 (March 14, 2012): 1–10. http://dx.doi.org/10.5402/2012/710692.

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To understand cancer progression, it is desirable to study the earliest stages of its development, which are often microscopic lesions. Array comparative genomic hybridization (aCGH) is a valuable high-throughput molecular approach for discovering DNA copy number changes; however, it requires a relatively large amount of DNA, which is difficult to obtain from microdissected lesions. Whole genome amplification (WGA) methods were developed to increase DNA quantity; however their reproducibility, fidelity, and suitability for formalin-fixed paraffin-embedded (FFPE) samples are questioned. Using a

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Braunstein, Marc J., Daniel R. Carrasco, David Kahn, et al. "Clonotypic Bone Marrow-Derived Endothelial Progenitor Cells in Multiple Myeloma." Blood 108, no. 11 (2006): 3497. http://dx.doi.org/10.1182/blood.v108.11.3497.3497.

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Abstract In multiple myeloma (MM), bone marrow-derived endothelial progenitor cells (EPCs) contribute to tumor neoangiogenesis and their levels covary with tumor mass and prognosis. Recent X-chromosome inactivation studies in female patients showed that, similar to tumor cells, EPCs are clonally restricted in MM. Genomic profiling of MM using high-resolution array comparative genomic hybridization (aCGH) has been previously utilized to mine the genome and find clinical correlates in MM patients. In this study, clonotypic aspects of bone marrow-derived EPCs and MM cells were investigated using

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Forero-Castro, Maribel, Adrián Montaño, Cristina Robledo, et al. "Integrated Genomic Analysis of Chromosomal Alterations and Mutations in B-Cell Acute Lymphoblastic Leukemia Reveals Distinct Genetic Profiles at Relapse." Diagnostics 10, no. 7 (2020): 455. http://dx.doi.org/10.3390/diagnostics10070455.

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The clonal basis of relapse in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is complex and not fully understood. Next-generation sequencing (NGS), array comparative genomic hybridization (aCGH), and multiplex ligation-dependent probe amplification (MLPA) were carried out in matched diagnosis–relapse samples from 13 BCP-ALL patients to identify patterns of genetic evolution that could account for the phenotypic changes associated with disease relapse. The integrative genomic analysis of aCGH, MLPA and NGS revealed that 100% of the BCP-ALL patients showed at least one genetic alterati

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Smetana, Jan, Jan Frohlich, Romana Zaoralova, et al. "Genome-Wide Screening of Cytogenetic Abnormalities in Multiple Myeloma Patients Using Array-CGH Technique: A Czech Multicenter Experience." BioMed Research International 2014 (2014): 1–9. http://dx.doi.org/10.1155/2014/209670.

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Characteristic recurrent copy number aberrations (CNAs) play a key role in multiple myeloma (MM) pathogenesis and have important prognostic significance for MM patients. Array-based comparative genomic hybridization (aCGH) provides a powerful tool for genome-wide classification of CNAs and thus should be implemented into MM routine diagnostics. We demonstrate the possibility of effective utilization of oligonucleotide-based aCGH in 91 MM patients. Chromosomal aberrations associated with effect on the prognosis of MM were initially evaluated by I-FISH and were found in 93.4% (85/91). Incidence

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Leon, Annette, Deborah Sevilla, Joseph M. Marino, et al. "Array Comparative Genomic Hybridization: A Better Alternative for Genomic Profiling and Prognosis of Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma." Blood 120, no. 21 (2012): 4572. http://dx.doi.org/10.1182/blood.v120.21.4572.4572.

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Abstract Abstract 4572 Traditional cytogenetic techniques such as chromosome analysis and fluorescence in situ hybridization (FISH) have provided valuable genetic information in the evaluation of chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL). However, many genomic abnormalities remain undetected due to the limitations intrinsic to these techniques. We designed, validated, and clinically applied a combined targeted-whole genome custom oligonucleotide microarray for the evaluation of hematological malignancies. Incorporation of array comparative genomic hybridization (aCGH) a

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Kucharík, Marcel, Jaroslav Budiš, Michaela Hýblová, Gabriel Minárik, and Tomáš Szemes. "Copy Number Variant Detection with Low-Coverage Whole-Genome Sequencing Represents a Viable Alternative to the Conventional Array-CGH." Diagnostics 11, no. 4 (2021): 708. http://dx.doi.org/10.3390/diagnostics11040708.

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Copy number variations (CNVs) represent a type of structural variant involving alterations in the number of copies of specific regions of DNA that can either be deleted or duplicated. CNVs contribute substantially to normal population variability, however, abnormal CNVs cause numerous genetic disorders. At present, several methods for CNV detection are applied, ranging from the conventional cytogenetic analysis, through microarray-based methods (aCGH), to next-generation sequencing (NGS). In this paper, we present GenomeScreen, an NGS-based CNV detection method for low-coverage, whole-genome s

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Türkyılmaz, A., BB Geckinli, E. Tekin, et al. "Array-Based Comparative Genomic Hybridization Analysis in Children with Developmental Delay/Intellectual Disability." Balkan Journal of Medical Genetics 24, no. 2 (2021): 15–24. http://dx.doi.org/10.2478/bjmg-2021-0020.

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Abstract Developmental delay (DD) is a condition wherein developmental milestones and learning skills do not occur at the expected age range for patients under 5 years of age. Intellectual disability (ID) is characterized by limited or insufficient development of mental abilities, including intellectual functioning impairments, such as learning and cause–effect relationships. Isolated and syndromic DD/ID cases show extreme genetic heterogeneity. Array-based comparative genomic hybridization aCGH) can detect copy number variations (CNVs) on the whole genome at higher resolution than conventiona

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Ou, Zhishuo, Maureen Sherer, Jane Casey, et al. "The Genomic Landscape of PAX5, IKZF1, and CDKN2A/B Alterations in B-Cell Precursor Acute Lymphoblastic Leukemia." Cytogenetic and Genome Research 150, no. 3-4 (2016): 242–52. http://dx.doi.org/10.1159/000456572.

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We present a comprehensive comparison of PAX5,IKZF1, and CDKN2A/B abnormalities in 21 B-cell precursor acute lymphoblastic leukemia (B-ALL) patients studied by aCGH and gene-specific FISH assays. In our cohort of B-ALL patients, alterations of IKZF1, PAX5, and CDKN2A/B were detected by aCGH analysis in 43, 52, and 57% of samples, respectively. Deletions of IKZF1 were present in 9 samples, including 5 cases positive for both PAX5 and IKZF1 deletions, implying digenic impairment. Furthermore, all cases with IKZF1 deletions also had additional genomic alterations, including BCR-ABL1 gene fusions,

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Tripodi, Joseph, Ronald Hoffman, Douglas Tremblay, et al. "Conventional Cytogenetic Analysis and Array CGH+SNP Identify Essential Thrombocythemia (ET)/Prefibrotic Primary Myelofibrosis (pre-PMF) Patients Who Are at Risk for Disease Progression." Blood 142, Supplement 1 (2023): 1832. http://dx.doi.org/10.1182/blood-2023-181092.

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ET and pre-PMF are myeloproliferative neoplasms (MPNs) that are each characterized by thrombocytosis but are difficult to distinguish by clinical and histopathological criteria. Moreover, each has the propensity to progress at variable rates to more advanced forms of the disease. The cause of progression to more overt forms of myelofibrosis (MF) or accelerated /blast phase (AP/BP) has yet to be fully understood, making prognostication difficult. To identify patients (pts) who are at risk for disease progression, we retrospectively reviewed the karyotypes from conventional cytogenetics (CC) and

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Leon, Annette, Deborah Sevilla, Joseph M. Marino, et al. "Array Comparative Genomic Hybridization: Impact in the Assessment of Plasma Cell Myeloma Genetic Profile and Prognosis." Blood 120, no. 21 (2012): 4965. http://dx.doi.org/10.1182/blood.v120.21.4965.4965.

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Abstract Abstract 4965 Identification of specific chromosomal alterations in plasma cell myeloma (PCM) is essential for the prognosis and treatment of this disease. Although cytogenetic chromosome and fluorescence in situ hybridization (FISH) analyses are techniques currently used for this purpose, incorporation of array comparative genomic hybridization (aCGH) analysis as described in this study, demonstrates the insufficient power of traditional techniques in characterizing the complex and heterogeneous genetic profile of this group of hematological malignancies. In our cohort, aCGH study of

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Schreiner, Yannick, Teresa Stoll, Oliver Nowak, et al. "aCGH Analysis Reveals Novel Mutations Associated with Congenital Diaphragmatic Hernia Plus (CDH+)." Journal of Clinical Medicine 12, no. 19 (2023): 6111. http://dx.doi.org/10.3390/jcm12196111.

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Congenital diaphragmatic hernia (CDH) is a major birth anomaly that often occurs with additional non-hernia-related malformations, and is then referred to as CDH+. While the impact of genetic alterations does not play a major role in isolated CDH, patients with CDH+ display mutations that are usually determined via array-based comparative genomic hybridization (aCGH). We analyzed 43 patients with CDH+ between 2012 and 2021 to identify novel specific mutations via aCGH associated with CDH+ and its outcome. Deletions (n = 32) and duplications (n = 29) classified as either pathological or variant

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Hartmann, Luise, Christine F. Stephenson, Stephanie R. Verkamp, et al. "Detection of Clonal Evolution in Hematopoietic Malignancies by Combining Comparative Genomic Hybridization and Single Nucleotide Polymorphism Arrays." Clinical Chemistry 60, no. 12 (2014): 1558–68. http://dx.doi.org/10.1373/clinchem.2014.227785.

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Abstract BACKGROUND Array comparative genomic hybridization (aCGH) has become a powerful tool for analyzing hematopoietic neoplasms and identifying genome-wide copy number changes in a single assay. aCGH also has superior resolution compared with fluorescence in situ hybridization (FISH) or conventional cytogenetics. Integration of single nucleotide polymorphism (SNP) probes with microarray analysis allows additional identification of acquired uniparental disomy, a copy neutral aberration with known potential to contribute to tumor pathogenesis. However, a limitation of microarray analysis has

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Ciabatti, Elena, Maria Immacolata Ferreri, Angelo Valetto, et al. "Myelodysplastic Syndromes: A Multidisciplinary Integrated Diagnostic Work-up for Patients' Risk Stratification." Blood 124, no. 21 (2014): 5579. http://dx.doi.org/10.1182/blood.v124.21.5579.5579.

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Abstract Conventional cytogenetics continues to have a fundamental role in the classification and risk scoring of myelodysplastic syndromes (MDS). Nevertheless, non-informative karyotypes represent up to 20% of cases. Some different molecular methods, not included in the routinary diagnostic workup, such as aCGH or mutational analysis, could be able to detect new abnormalities and improve the subtyping of MDS. The aim of this study was to propose a new diagnostic workup to determine the eventual adjunctive value offered by FISH, aCGH, and somatic mutation assays in respect of the the conventio

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DePalma,, Angelo. "aCGH Opens Up Novel Avenues of Study." Genetic Engineering & Biotechnology News 31, no. 14 (2011): 34–36. http://dx.doi.org/10.1089/gen.31.14.16.

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Nacheva, Elisabeth P., Diana Brazma, Letizia Foroni, and Colin Grace. "O23: Genomic profile of CML by aCGH." European Journal of Medical Genetics 48, no. 4 (2005): 490–91. http://dx.doi.org/10.1016/j.ejmg.2005.10.062.

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Hicks, Melissa A., Salah Ebrahim, and Bernard Gonik. "Prenatal Lethal Diagnosis of 8p23.1 Duplication Syndrome Associated with Omphalocele and Encephalocele." Case Reports in Genetics 2023 (February 25, 2023): 1–4. http://dx.doi.org/10.1155/2023/5958223.

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Despite increased prenatal and postnatal use of array comparative genomic hybridization (aCGH), isolated 8p23.1 duplication remains rare and has been associated with a widely variable phenotype. Here, we report an isolated 8p23.1 duplication in a fetus with an omphalocele and encephalocele that were incompatible with life. Prenatal aCGH demonstrated a 3.75 Mb de novo duplication of 8p23.1. This region encompassed 54 genes, 21 of which are described in OMIM, including SOX7 and GATA4. The summarized case demonstrates phenotypic features not previously described in 8p23.1 duplication syndrome and

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Gowrishankar, Banumathy, Manickam Janakiraman, Raghavendra Padmanabhan, et al. "Clinical utility of a custom next-generation sequencing panel in the diagnosis of needle biopsies from renal masses." Journal of Clinical Oncology 34, no. 2_suppl (2016): 528. http://dx.doi.org/10.1200/jco.2016.34.2_suppl.528.

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528 Background: Image-guided core-needle biopsies are increasingly being utilized to assist in the management of patients with renal masses, where only limited material is available for analysis. In this study, the performance of a custom next-generation sequencing (NGS) panel was evaluated for diagnostic and prognostic utility in this setting. Methods: DNA was available for NGS from 41 of 48 core-needle biopsies from renal masses previously submitted to array-CGH (aCGH) in this IRB-approved study. The targeted NGS panel comprised genes mutated in renal cancer, prognostic SNPs, and a 3Mbp SNP

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Small, Eric Jay, Jack Youngren, Tomasz M. Beer, et al. "The molecular and pathway characterization of patients with metastatic castration resistant prostate cancer (mCRPC) refractory to therapy with abiraterone acetate or enzalutamide: Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT)." Journal of Clinical Oncology 32, no. 4_suppl (2014): 79. http://dx.doi.org/10.1200/jco.2014.32.4_suppl.79.

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79 Background: Progressive metastatic castration resistant prostate cancer (mCRPC) has historically been challenging to biopsy and characterize on a molecular basis because of its bone tropism. Since mechanisms of resistance to androgen signaling inhibitors such as enzalutamide or abiraterone are not fully understood, both an unbiased and a targeted assessment of the molecular landscape of these patients is required. Methods: Patients (pts) with mCRPC undergo biopsy at one of five West Coast Prostate Cancer Dream Team (WCDT) clinical sites, using a uniform biopsy protocol, following central ra

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Sekulic, A., A. Miller, M. Barrett, et al. "Identification of targetable cellular subsets within melanoma tumors." Journal of Clinical Oncology 27, no. 15_suppl (2009): 9082. http://dx.doi.org/10.1200/jco.2009.27.15_suppl.9082.

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9082 Background: Human tumors, including melanoma, are complex mixtures of individual, molecularly distinct subpopulations, or clones of cancer cells. Effective cancer therapy will likely require targeting of all tumor subsets within a given cancer. Understanding the tumor complexity and the ability to identify points of therapeutic vulnerability within the individual tumor subsets will be essential for development of effective personalized cancer therapies. Methods: We have developed an approach that combines identification of individual tumor subsets using a multiparameter nuclear flow cytom

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Magadeeva, Svetlana, Xueqian Qian, Nadine Korff, et al. "Assessing the Phenotype of a Homologous Recombination Deficiency Using High Resolution Array-Based Comparative Genome Hybridization in Ovarian Cancer." International Journal of Molecular Sciences 24, no. 24 (2023): 17467. http://dx.doi.org/10.3390/ijms242417467.

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Ovarian cancer (OC) cells with homologous recombination deficiency (HRD) accumulate genomic scars (LST, TAI, and LOH) over a value of 42 in sum. PARP inhibitors can treat OC with HRD. The detection of HRD can be done directly by imaging these genomic scars, or indirectly by detecting mutations in the genes involved in HR. We show that HRD detection is also possible using high-resolution aCGH. A total of 30 OCs were analyzed retrospectively with high-resolution arrays as a test set and 19 OCs prospectively as a validation set. Mutation analysis was performed by HBOC TruRisk V2 panel to detect H

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Starczynowski, Daniel T., Suzanne Vercauteren, Adele Telenius, et al. "High-resolution whole genome tiling path array CGH analysis of CD34+ cells from patients with low-risk myelodysplastic syndromes reveals cryptic copy number alterations and predicts overall and leukemia-free survival." Blood 112, no. 8 (2008): 3412–24. http://dx.doi.org/10.1182/blood-2007-11-122028.

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Abstract Myelodysplastic syndromes (MDSs) pose an important diagnostic and treatment challenge because of the genetic heterogeneity and poorly understood biology of the disease. To investigate initiating genomic alterations and the potential prognostic significance of cryptic genomic changes in low-risk MDS, we performed whole genome tiling path array comparative genomic hybridization (aCGH) on CD34+ cells from 44 patients with an International Prognostic Scoring System score less than or equal to 1.0. Clonal copy number differences were detected in cells from 36 of 44 patients. In contrast, c

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Veneruso, Iolanda, Annaluisa Ranieri, Noemi Falcone, et al. "The Potential Usefulness of the Expanded Carrier Screening to Identify Hereditary Genetic Diseases: A Case Report from Real-World Data." Genes 14, no. 8 (2023): 1651. http://dx.doi.org/10.3390/genes14081651.

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Expanded carrier screening (ECS) means a comprehensive genetic analysis to evaluate an individual’s carrier status. ECS is becoming more frequently used, thanks to the availability of techniques such as next generation sequencing (NGS) and array comparative genomic hybridization (aCGH), allowing for extensive genome-scale analyses. Here, we report the case of a couple who underwent ECS for a case of autism spectrum disorder in the male partner family. aCGH and whole-exome sequencing (WES) were performed in the couple. aCGH analysis identified in the female partner two deletions involving genes

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Walter, Matthew J., R. Ries, X. Li, et al. "High Resolution Array-Based CGH and SNP Studies of AML Genomes." Blood 110, no. 11 (2007): 107. http://dx.doi.org/10.1182/blood.v110.11.107.107.

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Abstract To test if small deletions or amplifications (ie. below the resolution of cytogenetics) exist in bone marrow-derived tumor DNA from acute myeloid leukemia (AML) patients (pts), we used a dense tiling path array comparative genomic hybridization (aCGH) platform consisting of 386,165 unique oligomers spaced evenly at ∼6Kb intervals across the genome. We analyzed 144 adult de novo AML pts; 64 had normal karyotypes, and 80 had 1 or 2 clonal aberrations. Similar numbers of FAB M0/1, M2, M3, and M4 pts were included, and all samples had >30% blasts (median=72%). To generate a cancer-free

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Yoshikawa, Yoshie, Mitsuru Emi, Tomoko Hashimoto-Tamaoki, et al. "High-density array-CGH with targeted NGS unmask multiple noncontiguous minute deletions on chromosome 3p21 in mesothelioma." Proceedings of the National Academy of Sciences 113, no. 47 (2016): 13432–37. http://dx.doi.org/10.1073/pnas.1612074113.

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We used a custom-made comparative genomic hybridization array (aCGH; average probe interval 254 bp) to screen 33 malignant mesothelioma (MM) biopsies for somatic copy number loss throughout the 3p21 region (10.7 Mb) that harbors 251 genes, including BRCA1 (breast cancer 1)-associated protein 1 (BAP1), the most commonly mutated gene in MM. We identified frequent minute biallelic deletions (<3 kb) in 46 of 251 genes: four were cancer-associated genes: SETD2 (SET domain-containing protein 2) (7 of 33), BAP1 (8 of 33), PBRM1 (polybromo 1) (3 of 33), and SMARCC1 (switch/sucrose nonfermentable- S

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Kowalczyk, Katarzyna, Magdalena Bartnik-Głaska, Marta Smyk, et al. "Comparative Genomic Hybridization to Microarrays in Fetuses with High-Risk Prenatal Indications: Polish Experience with 7400 Pregnancies." Genes 13, no. 4 (2022): 690. http://dx.doi.org/10.3390/genes13040690.

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The aim of this study was to determine the suitability of the comparative genomic hybridization to microarray (aCGH) technique for prenatal diagnosis, but also to assess the frequency of chromosomal aberrations that may lead to fetal malformations but are not included in the diagnostic report. We present the results of the aCGH in a cohort of 7400 prenatal cases, indicated for invasive testing due to ultrasound abnormalities, high-risk for serum screening, thickened nuchal translucency, family history of genetic abnormalities or congenital abnormalities, and advanced maternal age (AMA). The ov

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