Array based comparative genomic. Medical search. Frequent questions

To detect CNVs, we used a set of NimbleGen whole-genome comparative genomic hybridization arrays containing 718,256 oligonucleotide probes with a median probe spacing of 500 bp. (biomedcentral.com)
We detected CNVs in rice by array-based comparative genomic hybridization. (biomedcentral.com)
CNVs can be detected using cytogenetic techniques such as fluorescent in situ hybridization, array-based comparative genomic hybridization, and SNP genotyping arrays. (biomedcentral.com)
Array-based comparative genomic hybridization characterization of cytogenetically polyclonal myeloid malignancies. (lu.se)
Microarray-based comparative genomic hybridization is a method of molecular analysis that identifies chromosomal anomalies (or copy number variants) that correlate with clinical phenotypes. (nih.gov)
Another goal was to test the association between a positive microarray-based comparative genomic hybridization result and the severity of intellectual disability/developmental delay. (nih.gov)
Microarray-based comparative genomic hybridization identified structural chromosomal alterations responsible for the intellectual disability/developmental delay phenotype in 16% of our sample. (nih.gov)
We want to emphasize the need to conduct microarray-based comparative genomic hybridization on all individuals with intellectual disability/developmental delay, regardless of the severity, because the degree of intellectual disability/developmental delay does not predict the diagnostic yield of microarray-based comparative genomic hybridization. (nih.gov)
Recently, we developed our own array-based comparative genomic hybridization (array CGH) with an average resolution of 1.3 Mb. (elsevierpure.com)
Copy number variation can be detected with various types of tests such as fluorescent in situ hybridization, comparative genomic hybridization and with high-resolution array-based tests based on array comparative genomic hybridization (or aCGH), SNP array technologies and high resolution microarrays that include copy number probes as well an SNPs. (wikipedia.org)
For generating a comparable rhesus macaque CNV dataset, we designed a rhesus macaque-specific array comparative genomic hybridization (aCGH) platform containing 950,843 unique 60-mer oligonucleotide probes. (biomedcentral.com)
Using the 270 K Nimblegen comparative genomic hybridization (CGH) array on a set of cv. (usda.gov)
Genomic complexity (GC) and del(17p) status were assessed by array comparative genomic hybridization. (confex.com)
Routine G-banded karyotype, array-based comparative genomic hybridization, and fluorescence in situ hybridization analyses were used to characterize the cytogenetic abnormality in the patient's bone marrow. (hindawi.com)
This case study reports a rare double minute chromosome via FLT3 amplification in CMML by using array-based comparative genomic hybridization and fluorescence in situ hybridization analyses. (hindawi.com)
Array comparative genomic hybridization (CGH) was performed following the standard protocol provided by Agilent Technologies (Agilent Technologies, Santa Clara, CA, United States). (hindawi.com)
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)
To identify the deletion, we conducted gene dosage analysis and array-based comparative genomic hybridization (aCGH) analysis. (neurology.org)
Background Microarray-based comparative genomic hybridization (aCGH) is certainly a robust diagnostic tool for the detection of DNA copy number benefits and losses connected with chromosome abnormalities, a lot of that are below the resolution of regular chromosome analysis. (bibf1120.com)
Intro Molecular cytogenetic methods such as for example array-based comparative genomic hybridization (aCGH) possess revolutionized cytogenetic diagnostics and, subsequently, the medical management of individuals with developmental delays and multiple congenital anomalies [1,2]. (bibf1120.com)
The change from fluorescence in situ hybridization to array-based technology. (marketdataforecast.com)
Using array-based comparative genomic hybridization (CGH), we determined the normal range of variation in CGH signals using normal controls. (endometriosi.it)
Additionally, comparative genomic hybridization was employed to compare genomic alterations between the CAISMOV24 cell line and its primary malignant cells. (biomedcentral.com)
In this concern, methods such as comparative genomic hybridization allow the detection of deletions and duplications of genomic segments, known as copy number variation (CNV). (biomedcentral.com)
We performed array-based comparative genomic hybridization (aCGH) and whole exome sequencing (WES) to analyze paired samples from ET and sAML phases. (elsevierpure.com)
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)
utilizes a combination of high-resolution comparative genomic hybridization, short hairpin RNA inhibition of target genes at the locations of focal genomic deletions, and a primed cell mosaic mouse model to identify novel tumor suppressors in hepatocellular carcinoma. (biomedcentral.com)
Margriet von Kogelenberg (Wellcome Trust Sanger Institute) described the UK-based Deciphering Developmental Disorders (DDD) project, which is currently recruiting 12,000 patients with developmental delay for array comparative genomic hybridization analysis and exome sequencing. (biomedcentral.com)
Hidden Markov Models (HMM) are often used for analyzing Comparative Genomic Hybridization (CGH) data to identify chromosomal aberrations or copy number variations by segmenting observation sequences. (biomedcentral.com)
Array-based comparative genomic hybridization in early-stage mycosis fungoides: recurrent deletion of tumor suppressor genes BCL7A, SMAC/DIABLO, and RHOF. (medscape.com)
However, the availability of DNA studies (eg, sequencing and oligonucleotide-based array comparative genomic hybridization [CGH]) may supersede the need to start with fatty acid oxidation studies in cultured fibroblasts. (medscape.com)

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)

Natural killer (NK) cell lymphomas/leukemias are highly aggressive lymphoid malignancies, but little is known about their genomic alterations, and thus there is an urgent need for identification and analysis of NK cell lymphomas/leukemias. (elsevierpure.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)
Although array CGH has provided a higher resolution compared to conventional CGH, it has not yet become a widely applied method for the analysis of gene dose alterations in individuals with idiopathic mental retardation. (bmj.com)
Genomic alterations in the endometrium may be a proximate cause for endometriosis. (endometriosi.it)
Objective: To test the hypothesis that endometriosis may originate from genomic alterations in the endometrium by genomic analysis of endometrial tissues in patients with endometriosis and compare them with those from normal controls. (endometriosi.it)
Results: We identified several regions of genomic alterations in all five patients. (endometriosi.it)
For select markers, the genomic alterations were confirmed by real-time PCR and LOH analyses. (endometriosi.it)
Conclusions: There is evidence that the endometrium in women with endometriosis has genomic alterations. (endometriosi.it)
Although the cell line had developed alongside the accumulation of genomic alterations (28 CNV in primary cells and 37 CNV in CAISMOV24), most of them were related to CNVs already present in primary malignant cells. (biomedcentral.com)
Our results corroborate with the idea that genomic alterations, depicted by CNVs, can be used for subtyping epithelial ovarian carcinomas. (biomedcentral.com)
Moreover, the potential of off-label prescription of targeted therapies favors classifying tumors based on DNA alterations rather than traditional tissue pathology. (oncotarget.com)

More recently, the technique of comparative genomic hybridisation (CGH) using metaphase chromosomes has been applied to this clinical problem. (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)
I am looking at the results for survival analysis for leukaemia patients, categorised based on Copy Number Variation (CNV) levels using array comparative genomic hybridisation. (stackexchange.com)
It initially entails Whole Genome Amplification (WGA) and thereafter fluorescent labelling of the DNA and its hybridisation on BAC arrays . (girofiv.com)

Currently, specialized high-density arrays with oligonucleotide probes or probes derived from BAC clones are predominately used. (biomedcentral.com)

Background: Genomic gains and losses are a result of genomic instability in many types of cancers. (tudelft.nl)
Senescent hepatocytes lose the telomeric repeats that protect chromosomal ends from inter- and intra-chromosomal fusion, deletion, rearrangement, and transposition events that contribute to genomic instability. (biomedcentral.com)
Genomic instability is a hallmark of the cancer phenotype, and cancer is considered to be a disease of the cell's disordered genome. (biomedcentral.com)

Genomic amplification of FLT3 has been reported in solid tumors including colorectal cancer, breast cancer, and gastric cancer [ 9 ]. (hindawi.com)
Patterns of genomic aberrations in primary colorectal tumors may reveal a chromosomal signature for organ specific metastases. (tudelft.nl)
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)

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)
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)
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)
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)

Copy number variants (CNVs), defined as losses and gains of segments of genomic DNA, are a major source of genomic variation. (biomedcentral.com)

In addition, the growing incidence of cancer disease, which necessitates better cancer diagnostics such as genomic imaging, epigenetics, and cytology for chromosomal abnormalities, is expected to promote the market's growth rate in this region. (marketdataforecast.com)

Our method of genotyping deletions on chromosome 7B relied on a model-based clustering algorithm (Mclust) to accurately predict the presence or absence of a given genomic sequence in a deletion line. (usda.gov)
The methods used in multigene panels may include sequence analysis , deletion/duplication analysis , and/or other non-sequencing-based tests. (nih.gov)
AS is a classic example of genomic imprinting in that it is usually caused by deletion or inactivation of genes on the maternally inherited chromosome 15 while the paternal copy, which may be of normal sequence, is imprinted and therefore silenced. (medicalmarijuana.com)
Extent of the deletion/duplication should be specified using the genomic description (g.). "-" indicates the variant described on genomic level does not affect the coding DNA reference sequence. (lovd.nl)

A report on the Genomic Disorders 2012: Genomics of Rare Diseases meeting, Hinxton, UK, 21-23 March 2012. (biomedcentral.com)

Microarray-based techniques for genome-wide investigation of copy number aberrations (CNAs) have recently gained much attention. (biomedcentral.com)
It's been presumed that whole-genome oligonucleotide arrays, because they possess higher resolutions, would identify more duplicate quantity aberrations than whole-genome BAC arrays. (bibf1120.com)

Analysis results of 579 cases of genomic copy number variation sequencing of pregnant women in prenatal diagnosis. (cdc.gov)

Our analyses of IDH1 mutations in for R132C mutations in astrocytes or glioblastomas from a population- precursor cel s that already carry a based study (407 cases) showed that germline TP53 mutation. (who.int)

Sequencing refers to determining the order of base pairs that make up the genome. (nature.com)
The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed using computational tools. (researchgate.net)
datasets coming from high-density arrays and next generation sequencing amplify these problems. (biomedcentral.com)

Array-based methods have been accepted as the most efficient in terms of their resolution and high-throughput nature and the highest coverage (choose an array with over 2 million probes) and they are also referred to as virtual karyotype. (wikipedia.org)

In recent years, the application of high-resolution methods, such as array-CGH, results in a significant progress in the whole-genome analysis. (biomedcentral.com)

We identified the differences in the genomic alteration patterns of the two groups. (elsevierpure.com)
Strikingly, unbiased computational analysis of genomic alteration data correctly classified nearly all progressing low grade dysplasia cases. (biomedcentral.com)

In both cases, DNA from two samples are differentially labeled with fluorescent dyes and co-hybridized to immobilized genomic capture probes. (biomedcentral.com)
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)

Microarrays remain an invaluable tool for omics-based research not only in drug discovery, but in the life sciences, in clinical research, and for diagnostic applications worldwide. (routledge.com)
imbalance of potential medical significance detectable from the whole-genome BAC array, and 73 (15.6%) had a copy-number imbalance of potential clinical significance detectable from the whole-genome oligo array. (bibf1120.com)
Of these complete instances examined for the BAC array, 17.6% were found to truly have a copy-number abnormality of potential clinical significance, whereas the recognition rate risen to 22.5% for the cases tested by oligo array. (bibf1120.com)
The central theme of this year's meeting was very clear: genomic technologies are now entering clinical laboratories across the world on a scale that would have seemed unimaginable even a year ago. (biomedcentral.com)
The task of assembling systems for translating genomic data into clinical interpretation was thus a key topic of discussion. (biomedcentral.com)
Clinical diagnosis of genetic disorders at both single-nucleotide and chromosomal levels based on BGISEQ-500 platform. (cdc.gov)

a) PCR-based amplification of randomly selected bin mapped sequences (b) comparison with previously mapped ESTs and (c) comparison with a 7B genetic map developed in the present study. (usda.gov)
Genomic amplification of FLT3 has not been reported in hematological disease. (hindawi.com)

Previously, Matson was involved in the research and development of microarray technologies, detection chemistries, as well as point-of-care devices for more than 17 years while at Beckman Coulter, Inc. He participated in the National Institute of Standards and Technology's (NIST) Advanced Technology Program sponsored Genosensor Consortium and collaborated with Sir Edwin Southern on the development of an in situ oligonucleotide array synthesis platform for the corporation. (routledge.com)
Furthermore, we evaluated 3 prospectively,443 individuals from the whole-genome BAC array and 3,096 individuals from the whole-genome oligo array and likened the detection prices of medically significant abnormalities and the ones of unclear medical significance. (bibf1120.com)
We also describe the validation of the Affymetrix OncoScan platform, an array technology for high resolution copy number variant detection for use in parallel with the NGS panel that can detect single copy amplifications and hemizygous deletions. (oncotarget.com)

Array CGH analyzes all chromosomes. (sdfertility.com)

Chromosome specific micro-arrays have however been used in a few cases to determine the critical regions in microdeletion disorders. (bmj.com)

One of the other key factors propelling the market for Molecular Cytogenetics is the capacity to scan and analyze the entire genomic organization. (marketdataforecast.com)

Using this approach, WGS-based diagnostic testing yields results that are not different from diagnostic testing with existing methods, such as DNA chips. (nature.com)
For normalization of array-CGH data, methods initially developed for gene expression microarray analysis have, in general, been directly adopted and used. (biomedcentral.com)
METHODS: We performed a multi-model comparative assessment of probabilistic forecasts submitted by 15 teams for annual WNND cases in US counties for 2020 and assessed forecast accuracy, calibration, and discriminatory power. (cdc.gov)

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)

Data analysis for an array-based DNA copy number test can be very challenging though due to very high volume of data that come out of an array platform. (wikipedia.org)
Even a single data point can be declared an indication of a copy number gain or a copy number loss in BAC arrays. (wikipedia.org)
These genomic regions appear to have an elevated likelihood of positive selection, based on nucleotide level conservation and transcriptional data. (biomedcentral.com)
We found at least 2 sources of cholera in Pakistan Nubra, and the Hunza, converging in the northern region during the 2010 epidemic and illustrate the value of a global and flowing through the provinces of Ladakh, Baltistan, genomic data bank in contextualizing cholera outbreaks. (cdc.gov)

The presence of subtle DNA copy number changes was investigated by array-CGH in 50 patients with learning disability and dysmorphism, employing a DNA microarray constructed from large insert clones spaced at approximately 1 Mb intervals across the genome. (bmj.com)
BAC (Bacterial Artificial Chromosome) arrays were historically the first microarray platform to be used for DNA copy number analysis. (wikipedia.org)

We test our approximate sampling method on simulated and biological ArrayCGH datasets and high-density SNP arrays, and demonstrate a speed-up of 10 to 60 respectively 90 while achieving competitive results with the state-of-the art Bayesian approaches. (biomedcentral.com)
These studies demonstrate the feasibility of machine learning-based molecular cancer classification. (lu.se)

We performed an array CGH analysis for 27 NK-cell lymphoma/leukemia cases that were classified into two disease groups based on the World Health Organization Classification (10 aggressive NK-cell leukemia cases and 17 extranodal NK/T-cell [NK/T] lymphomas, nasal type). (elsevierpure.com)
Subsequent analysis of the array yields information on excesses or deficiencies in the DNA present. (girofiv.com)

Diagnosis is typically based on blood tests finding high numbers of mature lymphocytes and smudge cells. (wikipedia.org)
At present, risk of progression in oral premalignant lesions (OPLs) is typically determined based on histopathological evaluation of biopsied material. (biomedcentral.com)

Genome profiles were generated by tiling-path array CGH for a panel of 86 oral lesions with longitudinal follow-up that included 24 invasive oral squamous cell carcinomas (OSCCs) and 62 OPLs. (biomedcentral.com)

The massive efforts to systematically find and catalog single nucleotide polymorphisms (SNPs) bear witness to the conviction that small genomic changes may provide clues to the origins of such things as heart problems, obesity, and pharmacologic responses. (the-scientist.com)

Here we describe the analytical validation of a custom probe-based NGS tumor panel, TumorNext, which can detect single nucleotide variants, small insertions and deletions in 142 genes that are frequently mutated in somatic and/or germline cancers. (oncotarget.com)

On the basis of these results, we anticipate that array-CGH will become a routine method of genome-wide screening for imbalanced rearrangements in children with learning disability. (bmj.com)
Whole-genome screening creates a personal genomic database (personal genome) that can subsequently be used to deliver 'personalised medicine' to individual patients. (nature.com)
Committee opinion no. 690: Carrier Screening in the age of genomic medicine. (msdmanuals.com)

RESULTS: Simple models based on historical WNND cases generally scored better than more complex models and combined higher discriminatory power with better calibration of uncertainty. (cdc.gov)

Anatomy34

Organisms14

Diseases26

Chemicals and Drugs24

Analytical, Diagnostic and Therapeutic Techniques and Equipment49

Psychiatry and Psychology2

Phenomena and Processes138

Disciplines and Occupations7

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture1

Information Science14

Health Care8

Hybridization31

ACGH1

Alterations11

Hybridisation4

Oligonucleotide probes1

Instability3

Tumors5

Imbalances5

CNVs1

Chromosomal abnormalities1

Deletion4

Genomics1

Aberrations2

Prenatal Diagnosis1

Mutations1

Sequencing3

Karyotype1

Whole genome analysis1

Alteration2

Fluorescent2

Clinical6

Amplification2

Detection3

Chromosomes1

Disorders1

Analyze1

Methods3

High resolution1

Data4

Copy2

Demonstrate2

Analysis2

Typically2

Lesions1

SNPs1

Genes1

Screening3

Results1