ChromosomalComparative genomic hybriAllelic imbalanceTumorsChromosome imbalancesGains and lossesVariantsScreeningACGHPediatricGeneticDeletionsChromosomesAberrationsAmplificationMethodsGene expressionDetectionMutationsVariationClinicalFragmentsCNVsPTENIntegrityDataArisePatternsCommonArraysCancerMolecularInvestigateSequenceDatabasePatientsCopyCasesPersonalised medicineArrayResearchOrigin
Chromosomal11
- Genome-wide screening for chromosomal imbalances using comparative genomic hybridization (CGH) revealed a wealth of data on previously unrecognized tumor-specific genomic alterations. (edu.sy)
- Some individual imbalances were associated with increasing numbers of chromosomal changes, that were +7q in both oligodendrogliomas and astrocytomas, and -9p, -10q, +20p, and +20q in astrocytomas. (uludag.edu.tr)
- Imbalances involving large chromosomal regions or entire chromosomes were detected by aCGH in seven of the patients studied. (ox.ac.uk)
- Abstract BACKGROUND: Chromosomal abnormalities have been associated with most human malignancies, with gains and losses on some genomic regions associated with particular entities. (baudisgroup.org)
- METHODS: Of the 15429 cases collected for the Progenetix molecular-cytogenetic database, 5918 malignant epithelial neoplasias analyzed by chromosomal Comparative Genomic Hybridization (CGH) were selected for further evaluation. (baudisgroup.org)
- CONCLUSION: Although considerable case-by-case variation of genomic profiles can be found by CGH in epithelial malignancies, a limited set of variously combined chromosomal imbalances may be typical for carcinogenesis. (baudisgroup.org)
- To cover the whole genome, genome wide screening for chromosomal imbalances using microsatellite markers has been reported, 17, 18 as well as metaphase CGH. (bmj.com)
- Screening for chromosomal imbalances by array CGH, whether using cDNA 23 or BAC clones, 24 has mainly been performed on cancer samples, 25- 30 which usually contain large gene dose alterations. (bmj.com)
- 2 , 3 , 9 Indeed, the atypical B cells of NLPHL and THRLBCL share many characteristics, including expression of pan-B-cell markers, germinal center B-cell origin and common chromosomal imbalances. (haematologica.org)
- Patterns of chromosomal imbalances defines subgroups of breast cancer with distinct clinical features and prognosis. (lu.se)
- We characterized point mutations, insertions, deletions and chromosomal allelic imbalance. (tmc.edu)
Comparative genomic hybri3
- Screening for chromosome imbalances was carried out using comparative genomic hybridisation (CGH) in 14 frozen samples of tumour from a series of 13 breast cancer patients with multiploid (n = 11) and hypertetraploid (n = 2) tumours. (bmj.com)
- Comparative genomic hybridisation (CGH) was used to screen 76 vestibular schwannomas from 76 patients (66 sporadic and 10 NF2 related) to identify other chromosome regions that may harbour genes involved in the tumorigenesis. (bmj.com)
- Standard chromosome analysis by G-banding has a limited resolution, but molecular cytogenetic techniques, such as multi-subtelomeric FISH, microdeletion FISH, multicolour FISH and comparative genomic hybridisation (CGH), have played an important role for the diagnosis of MR during the past decade. (bmj.com)
Allelic imbalance2
- Hereditary breast cancers linked to germ-line mutations of BRCA1 and BRCA2 genes almost invariably show allelic imbalance (Al) at the respective loci. (lu.se)
- Furthermore, very few polymorphisms were identified among the resistant individuals suggesting allelic imbalance. (usda.gov)
Tumors4
- A study of 305 tumors by comparative genomic hybridization. (lu.se)
- The DDLPS-associated losses were much more common in tumors with increased genomic complexity. (biomedcentral.com)
- Our findings show that the application of array-CGH allows to delineate clearly the genomic profiles of WDLPS, DDLPS and MLPS that reflect biological differences between these tumors. (biomedcentral.com)
- Although CNAs varied widely, the subtypes of tumors have characteristic genomic profiles that could facilitate the differential diagnosis of LPS subtypes, especially between WDLPS and DDLPS. (biomedcentral.com)
Chromosome imbalances2
- 19- 22 Yet none of these techniques is able to offer a high resolution screening of the whole genome for chromosome imbalances. (bmj.com)
- All chromosome imbalances were size mapped using BAC and PAC clones based on clone mapping databases ( www.ensembl.org , July 2003), except for case 9, which was size mapped using a chromosome 22 specific micro-array. (bmj.com)
Gains and losses3
- With the matrix-CGH protocol presented here, robust and reliable detection of genomic gains and losses is accomplished in an automated fashion, which provides the basis for widespread application in tumor and clinical genetics. (edu.sy)
- RESULTS: With large variation in overall genomic instability, recurring genomic gains and losses were prominent. (baudisgroup.org)
- Comparative genomic hybridization (aCGH) is a powerful diagnostic tool for detecting DNA copy number gains and losses associated with chromosome abnormalities. (enzolifesciences.com)
Variants3
- At the opposite site of DGV (the Database of Genomic Variants, which contains only not pathogenic variations), there is DECIPHER, a useful database to retrieve pathogenic and plausibly pathogenic structural variations in humans. (bredagenetics.com)
- Beyond this, the contribution of smaller genomic imbalances (copy number variants) or common single nucleotide variants and their impact on gene regulation in the placenta, for example through DNA methylation, remains largely unexplored. (ubc.ca)
- In this thesis, I hypothesized that placental genomic imbalances, including aneuploidy and copy number variants (CNVs), and candidate single nucleotide variants in a gene relevant to DNA methylation (DNAme) are associated with poor fetal growth and/or altered placental DNAme. (ubc.ca)
Screening1
- Rascall: Rapid (Ra) screening (Sc) of RNA-seq data for prognostically significant genomic alterations in acute lymphoblastic leukaemia (ALL). (cdc.gov)
ACGH2
- By use of aCGH, DNA derived from tumor tissue can be compared with reference DNA, e.g., normal whole blood DNA, and genomic imbalances can effectively be investigated. (biomedcentral.com)
- aCGH provides an understanding of genetic disorders, cancers and other genomic aberrations. (enzolifesciences.com)
Pediatric2
- In contrast to adult MDS, little is known about the genomic landscape of pediatric MDS. (nature.com)
- In this study we perform tumor and normal whole exome sequencing (WES) on 32 pediatric primary MDS patients and targeted sequencing on another 14 cases through a single institution study focused on defining the genomic landscape of pediatric MDS. (nature.com)
Genetic4
- Comprehensive genetic analysis identifies a pathognomonic NAB2/STAT6 fusion gene, nonrandom secondary genomic imbalances, and a characteristic gene expression profile in solitary fibrous tumor. (scilifelab.se)
- 1999). "Clinical significance of genetic imbalances revealed by comparative genomic hybridization in chondrosarcomas" . (wikidoc.org)
- Precision medicine progress relies on using high throughput technologies and integrated data analysis for detecting, measuring and assessing a wide spectrum of biomedical data, including clinical information about patients, and their genetic, genomic, metabolomics, proteomics, histopathological, behavioural and environmental characteristics. (bmj.com)
- Unlike previous population genetic methods, DeepLOF utilizes a novel deep learning framework to integrate both population and functional genomic data, allowing us to pinpoint short essential genes that can hardly be predicted from population genomic data alone. (biomedcentral.com)
Deletions1
- Other recurrent genomic imbalances in MIFS, such as homozygous loss of CDKN2A and 3p- and 13q-deletions, are shared with other sarcomas, suggesting overlapping pathogenetic pathways. (mendeley.com)
Chromosomes1
- This was in line with WGS and Cap-seq results, revealing variable breakpoints in chromosomes 1 and 10 and genomic breakpoints that should not yield functional fusion transcripts. (mendeley.com)
Aberrations1
- 31, 32 In this report we used a cDNA micro-array and two BAC clone micro-arrays on 10 previously identified cases containing 16 cryptic chromosome aberrations, to test their performance for the detection of small imbalances. (bmj.com)
Amplification2
- We show that matrix CGH is also feasible from small tissue samples requiring universal amplification of genomic DNA. (edu.sy)
- With optimized, proprietary reagents, the Enzo Life Sciences CGH Labeling Kits for oligo arrays produce high quality data using as little as 0.25 µg of genomic DNA, without a need for pre-amplification. (enzolifesciences.com)
Methods3
- However, these methods are designed to work under assumptions that may not be valid for array-CGH data when copy number imbalances are present. (biomedcentral.com)
- Here we demonstrate that copy number imbalances correlate with intensity in array-CGH data thereby causing problems for conventional normalization methods. (biomedcentral.com)
- Recently, there have been numerous computational methods developed to predict human essential genes from population genomic data. (biomedcentral.com)
Gene expression1
- At the genomic level, it is rather difficult to analyze the disease, especially sporadic PD, from a single gene mutation, and it is more the imbalance in gene expression and phenotypic changes were caused by a variety of regulatory mechanisms which act as mediators between genotype and phenotype. (frontiersin.org)
Detection4
- CGH to microarrays of DNA, an approach termed matrix-CGH, allows detection of genomic imbalances at a much higher resolution. (edu.sy)
- Detection of genomic imbalances by comparative genomic hybridization in Chinese fetuses with malformations. (nel.edu)
- Wang Y, Meng J, Wang X, Zhao Y, Wang L, Simpson J, Chen Z. Detection of genomic imbalances by comparative genomic hybridization in Chinese fetuses with malformations. (nel.edu)
- 1 Discovering genomic and environmental determinants of health and disease and their interplay is essential for predicting personal susceptibility to various pathologies and individualised risk assessment, early disease detection, personalised treatment for better patient outcomes, and customising disease prevention strategies. (bmj.com)
Mutations1
- Indeed, in colons of mice carrying mutations in Apc (ApcMin/+) or exposed to the carcinogen azoxymethane, elimination of GCC increased tumor initiation by corrupting genomic integrity in the context of disabled compensatory apoptosis. (jefferson.edu)
Variation1
Clinical2
Fragments1
- A chip consisting of 188 different genomic DNA fragments, cloned in bacterial artificial chromosome (BAC) or P1-derived artificial chromosome (PAC) vectors and immobilized in replicas of 10, was used to assess the performance of the automated protocol in determining the gene dosage variations in tumor cell lines COLO320-HSR, HL60, and NGP. (edu.sy)
CNVs1
- sig-nificant burden of rare exonic (that is, affecting coding regions) CNVs and were enriched for known genomic disorders (GD). (123dok.org)
PTEN2
- Herein, we report on comparative genomic hybridization (CGH) and immunohistochemical (IHC) assessment of EGFR, PTEN, p53, and MIB-1 expression in 13 oligodendrogliomas (10 WHO grade II, 3 WHO grade III), one oligoastrocytoma (WHO grade III) and 23 high-grade astrocytomas Q WHO grade III, 20 glioblastoma multiforme). (uludag.edu.tr)
- Imbalance of genes B-RAF, K-RAS, e PTEN were evaluated. (fapesp.br)
Integrity3
- BRCA1 and BRCA2 are believed to take part in a common pathway in maintenance of genomic integrity in cells. (lu.se)
- This novel role in restricting the proliferating compartment and organizing the crypt-villus axis suggests that dysregulation of GCC, reflecting loss of endogenous ligands, might contribute to tumorigenesis by potentiating hyperproliferation which, in turn, may amplify disruption of genomic integrity. (jefferson.edu)
- This previously unrecognized role of GCC as a tumor suppressor by restricting proliferation and maintaining genomic integrity suggests that receptor dysregulation reflecting ligand insufficiency is a key event during early colorectal tumorigenesis. (jefferson.edu)
Data7
- Strikingly, unbiased computational analysis of genomic alteration data correctly classified nearly all progressing low grade dysplasia cases. (biomedcentral.com)
- Our data demonstrate that high resolution genomic analysis can be used to evaluate progression risk in low grade OPLs, a marked improvement over present histopathological approaches which cannot delineate progression risk. (biomedcentral.com)
- For the 22 clinico-pathological entities with more than 50 cases, summary profiles for genomic imbalances were generated from case specific data and analyzed. (baudisgroup.org)
- We propose a strategy to circumvent these problems by taking copy number imbalances into account during normalization, and we test the proposed strategy using several data sets from the analysis of cancer genomes. (biomedcentral.com)
- We highlight the importance of considering copy number imbalances during normalization of array-CGH data, and show how failure to do so can deleteriously affect data and hamper interpretation. (biomedcentral.com)
- Siwo and his team in South Africa were interested in data driven genomic healthcare. (cnn.com)
- Motivated by the premise that population and functional genomic data may provide complementary evidence for gene essentiality, here we present an evolution-based deep learning model, DeepLOF, to predict essential genes in an unsupervised manner. (biomedcentral.com)
Arise1
- Taken together, we propose that reversible epigenomic modifications helped shape FBX gene evolution by transcriptionally suppressing the adverse effects of gene dosage imbalance and harmful FBX alleles that arise during genomic drift, while simultaneously allowing innovations to emerge through epigenomic reprogramming. (nih.gov)
Patterns2
- Related average imbalance patterns were found for clinically distinct entities, e.g. hepatocellular carcinomas (ca.) and ductal breast ca., as well as for histologically related entities (squamous cell ca. of different sites). (baudisgroup.org)
- Previous phylogenetic comparisons based on orthology, diversity, and expression patterns identified three plant FBX groups--Common, Lineage-Specific, and Pseudo(genized)--whose emergences are consistent with genomic drift evolution. (nih.gov)
Common1
- Some of the more common symptoms women with a hormonal imbalance may experience include the following. (wakeup-world.com)
Arrays1
- We here used a combination of deep sequencing of the genome (WGS), captured sequences (Cap-seq), and transcriptome (RNA-seq) and genomic arrays to investigate the molecular outcome of the t(1;10) and the VGLL3 amplicon, as well as to assess the spectrum of other recurrent genomic features in MIFS. (mendeley.com)
Cancer1
- High-resolution microarray-based comparative genomic hybridization (CGH) techniques have successfully been applied to study copy number imbalances in a number of settings such as the analysis of cancer genomes. (biomedcentral.com)
Molecular2
- In this type of melanoma, few molecular studies are found, though it has been found that genomic amplifications of chromosome 11q13, 22q11-13 e 5p15, inactivation of the p16 signaling pathway, as well as different expressions of pRb, cyclin D1 e p16. (fapesp.br)
- of Genomic Medicine and Translational Molecular Pathology. (mdanderson.org)
Investigate1
- We therefore sought to investigate the effect on normalization imposed by copy number imbalances. (biomedcentral.com)
Sequence1
- Comparisons within expanding sequence databases have revealed a dynamic interplay among genomic and epigenomic forces in driving plant evolution. (nih.gov)
Database2
- The current microbial genome database has an obvious species imbalance. (pacb.com)
- Our goal is to create a genomic database that covers a much broader array of microbial diversity, including pathogenic microorganisms, food safety microbes, marine microbes, and terrestrial resource microbes. (pacb.com)
Patients3
- Genomic imbalances are confined to non-proliferating cells in paediatric patients with acute myeloid leukaemia and a normal or incomplete karyotype. (ox.ac.uk)
- Building a biobank network in developing countries is essential to foster genomic research and precision medicine for patients' benefit. (bmj.com)
- Une étude a été menée dans des unités de soins intensifs en chirurgie pour adultes de l'hôpital universitaire de Zagazig, (Égypte) auprès de 25 patients atteints de septicémie, de 27 patients atteints d'une septicémie sévère et de 28 témoins. (who.int)
Copy1
- In essence, relative ratios of copy number between two DNA samples are obtained by comparing the two fluorescent signal intensities for each probe under the assumption that intensities reflect the amount of corresponding genomic DNA in the respective sample. (biomedcentral.com)
Cases1
- In both cases, DNA from two samples are differentially labeled with fluorescent dyes and co-hybridized to immobilized genomic capture probes. (biomedcentral.com)
Personalised medicine1
- Here, we outline key barriers and essential milestones for the successful expansion of biobanks, genomic research and personalised medicine in Ukraine, drawing from the experience of other LMICs. (bmj.com)
Array1
- In order to identify and compare the genomic profiles, we analyzed array-based comparative genomic hybridization (array-CGH) profiles of 66 liposarcomas, including well-differentiated (WDLPS), dedifferentiated (DDLPS) and myxoid (MLPS) subtypes. (biomedcentral.com)
Research1
- Intensive efforts are being made in medical research to discover the genomic causes of undiagnosed hereditary diseases. (lu.se)
Origin1
- Burst-Like Transcription of Mutant and Wildtype MYH7-Alleles as Possible Origin of Cell-to-Cell Contractile Imbalance in Hypertrophic Cardiomyopathy. (crossref.org)