Chromosomes oligonucleotide array sequence analysis. Medical search. Frequent questions

The Agilent eArray platform was used to design an M. persicae oligonucleotide microarray representing over 10,000 unique genes. (nih.gov)
These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. (nih.gov)
Linkage analysis and direct sequencing of candidate genes were used to exclude six responsible genes/loci for isolated SHFM. (ox.ac.uk)
Array comparative genomic hybridization (CGH) was performed to detect copy number variations on a genome-wide scale, and quantitative real-time polymerase chain reaction (qPCR) assays were designed to validate the identified copy number variation in the index and other family members.ResultsNo mutations were found in genes or loci linked to isolated SHFM. (ox.ac.uk)
We hope to provide a concise review of the literature and genes involved within our deletion sequence in the hope that it will contribute to creating a phenotypic profile for this patient population. (hindawi.com)
We now provide a comprehensive compendium of the genes expressed in T cells and of those regulated by IL-2 based on a combination of DNA microarrays and serial analysis of gene expression (SAGE). (torvergata.it)
BeadChip microarray and gene ontology analysis revealed that RUNX1‑RUNX1T1 and MAPK1 suppression reduced the proliferation rate of the t(8;21) cells with deregulated expression of several classical positive regulator genes that are otherwise known to enhance cell proliferation. (prinsesmaximacentrum.nl)
This gene shares high sequence identity with three other gene members and is clustered with those three genes at chromosome 10p15-p14. (cancer-genetics.org)
Through systematically enrichment analyses based on simulations and bioinformatics analyses, we revealed CNV-related genes undergo a different selective constraint from those CNV-unrelated regions, and CNVs may be associated with or affect pig health and production performance under recent selection. (biomedcentral.com)
Tumor suppressor genes located in the 5q21 region on the long arm of human chromosome 5. (edu.au)
A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. (edu.au)
A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human chromosome 13 at locus 13q12.3. (edu.au)
This test is not a chromosome microarray (CMA) test, and we will usually interpret and report copy number variants only in requested genes. (preventiongenetics.com)
Here, we present a large-scale genetic association study of intelligence (n = 269,867), identifying 205 associated genomic loci (190 new) and 1,016 genes (939 new) via positional mapping, expression quantitative trait locus (eQTL) mapping, chromatin interaction mapping, and gene-based association analysis. (scite.ai)
Gene-level association analysis reveals a role for tissue-specific expression of multiple genes in longevity. (scite.ai)
Genes Chromosomes Cancer. (uchicago.edu)
In the past ten years, improvements in massively parallel sequencing techniques have led to the development and widespread clinical use of multigene panels, which allow simultaneous testing of two to more than 150 genes. (nih.gov)
These include genes selected by a clinician for analysis by clinical sequencing. (nih.gov)
Results for each gene on the custom multigene panel are reported to the ordering clinician, whereas the results from the remaining genes sequenced (but not requested by the clinician) are not analyzed or included in the final laboratory report. (nih.gov)
Exome sequencing is a laboratory test designed to identify and analyze the sequence of all protein-coding nuclear genes in the genome. (nih.gov)
Detailed mapping suggests that haploinsufficiency of one or more genes in Xp22.3, the distal 8.3 megabases (Mb) of the X chromosome, is responsible for a TS neurocognitive phenotype. (biomedcentral.com)
The genetic abnormality in TS is determined by the absence of one copy of genes on the X chromosome. (biomedcentral.com)
Although one X chromosome undergoes inactivation in normal females during early embryogenesis, about 15% of all X chromosome genes, mostly situated on the short arm (Xp), remain active to some degree on both X chromosomes [ 17 ]. (biomedcentral.com)
Then they perform supervised analyses to identify differentially methylated or expressed genes. (scientistlive.com)
The physiological conditions experienced by a microbial community can thus be inferred using meta-transcriptomic sequencing by comparing transcription levels of specifically chosen genes. (osti.gov)
However, this analysis requires accurate reference genomes to identify the specific genes from which RNA reads originate. (osti.gov)
Subsequent differentiation allows for rear- analysis of a set of mouse B lineage cell lines rep- rangements of the Ig light-chain (IgL) genes that replace the resenting defined stages of B cell development us- surrogate light-chain genes on the surface of the B cell [8]. (lu.se)
The genes for the alpha and beta subunits have been localized to chromosome 2. (medscape.com)

Due to global developmental delay, he had a chromosomal microarray analysis at 28 months. (hindawi.com)
Analysis of syndromic DNA using an oligonucleotide microarray (Agilent 4 x 180K) demonstrated the characteristic deletion in 15q11.2-q13 (chromosome 15) found in patients with Prader-Willi syndrome. (enzolifesciences.com)
For M. tuberculosis , M. bovis , and the various bacillus Calmette-Guérin daughter strains, genome-wide microarray analyses have identified large sequence polymorphisms ( 4 , 8 - 10 ). (cdc.gov)
SNP array is an efficient microarray-based genotyping technique used for genome-wide screening of alterations. (geneticeducation.co.in)
SNP array or SNP Microarray is an array CGH or comparative genomic hybridization technique developed in 1998. (geneticeducation.co.in)

ChIP-seq technology is currently seen primarily as an alternative to ChIP-chip which requires a hybridization array. (wikipedia.org)
Array comparative genomic hybridization analysis of colorectal cancer cell lines and primary carcinomas. (ox.ac.uk)
Array comparative genomic hybridization, with a genome-wide resolution of approximately 1 Mb, has been used to investigate copy number changes in 48 colorectal cancer (CRC) cell lines and 37 primary CRCs. (ox.ac.uk)
Cytogenetic, fluorescence in situ hybridization (FISH), and loss-of-heterozygosity (LOH) studies have revealed that MRTs frequently contain deletions at chromosome locus 22q11.1. (medscape.com)
Array comparative genomic hybridization (aCGH) enables the detection of CNVs of single and multiple exons within a given gene (Tayeh et al. (preventiongenetics.com)
We isolated equine, cow, pig, pet, kitty, and mouse sequences orthologous towards the human being 21q interval in parallel using 14 common oligonucleotide hybridization probes (overgos) designed based on sequences conserved between human beings and mice (Thomas et al. (bioinbrief.com)
Even though these array-based methods are high-throughput, they are physically limited by probe density and suffer from noisy signals resulting from background noise due to cross hybridization and signal saturation [ 3 , 8 - 10 ]. (biomedcentral.com)
Genetic analysis included karyotyping, X inactivation studies, fluorescent in situ hybridization, microsatellite marker genotyping, and array comparative genomic hybridization. (biomedcentral.com)
Comparative genomic hybridization (aCGH) is a powerful diagnostic tool for detecting DNA copy number gains and losses associated with chromosome abnormalities. (enzolifesciences.com)
The mother carried a 3Mb deletion on one copy and a reciprocal, similar sized duplication on the other copy of chromosome 22q11.2 as shown by fluorescence in situ hybridization and array comparative genome hybridization analyses. (elsevierpure.com)
An SNP array is a hybridization-based high throughput technique used for SNP genotyping. (geneticeducation.co.in)
The SNP array relies on the principle of DNA hybridization. (geneticeducation.co.in)
Positive hybridization signals have been recorded and assessed accordingly using the sequence or genomic information. (geneticeducation.co.in)

Combined analyses including FISH, coding sequence analysis, high-density single nucleotide polymorphism-based oligonucleotide arrays, and multiplex ligation-dependent probe amplification enable the identification of biallelic, inactivating perturbations of SMARCB1 in nearly all MRTs, consistent with the 2-hit model of tumor formation. (medscape.com)

For a much more extensive list see the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer . (cancer-genetics.org)

A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes. (uams.edu)

Loss of chromosome 18q was a recurrent finding along with deletion of discrete regions such as chromosome 4q34-q35. (ox.ac.uk)
The methods used in multigene panels may include sequence analysis , deletion/duplication analysis , and/or other non-sequencing-based tests. (nih.gov)

A single sequencing run can scan for genome-wide associations with high resolution, meaning that features can be located precisely on the chromosomes. (wikipedia.org)
Whole-transcriptome sequencing (RNA-seq) technology has emerged as a revolutionary platform for genome-wide quantification of mRNA transcripts. (biomedcentral.com)
Recent genome-wide meta-analyses have identified 24 genomic loci linked to variation in intelligence, but much about its genetic underpinnings remains to be discovered. (scite.ai)

The primary focus of our report is to compare our case with the few others in the literature describing interstitial deletions at the long arm of chromosome 7. (hindawi.com)
Terminal deletions at the long arm of chromosome 7 have been described more frequently in the medical literature [ 1 , 2 ] compared to interstitial deletions at the distal 7q region. (hindawi.com)
The aim of this case report is to further understand the phenotypic features associated with interstitial deletions at the long arm of chromosome 7 and offer a basis for the development of a possible syndromic profile for these deletions in the future. (hindawi.com)

This epigenetic information is complementary to genotype and expression analysis. (wikipedia.org)
Methodology: This was a hospital-based, analytical cross-sectional study carried out on 226 symptomatic women wherein cervico-vaginal samples were obtained during gynaecological examination for Pap smears, HPV-DNA and genotype detection with linear array HPV strip, conducted from November 2019 to January 2021. (bvsalud.org)

This introduces some bias, as an array is restricted to a fixed number of probes. (wikipedia.org)
Recognition and Evaluation of Evolutionarily Conserved Human being Sequences To recognize sequences which are evolutionarily conserved between human beings and mice, DNA isolated through the group of minimally overlapping mouse BAC clones was pooled, labeled fluorescently, and hybridized to high-density oligonucleotide arrays including probes for the initial sequences within the period on human being 21q (Frazer et al. (bioinbrief.com)
This set of tracks shows the genomic positions of probes and targets from a full suite of in-solution-capture target enrichment exome kits for Next Generation Sequencing (NGS) applications. (ucsc.edu)
Here, millions of known sequence probes have been immobilized on the solid surface on which the sample DNA is allowed to hybridize. (geneticeducation.co.in)
Probes are smaller, single-stranded and known DNA oligonucleotide sequences that have been immobilized on a solid glass slide. (geneticeducation.co.in)
Millions of oligonucleotide probes are designed to target various genomic loci being investigated. (geneticeducation.co.in)
Chemical spry, micro-mechanical printing and in situ synthesis are three common methods used to prepare SNP array probes. (geneticeducation.co.in)
Around 1 cm * 1 cm area of the glass slide contains 4,00,000 oligonucleotide probes. (geneticeducation.co.in)
The slide already contains various sequence-specific probes that represent the SNP of specific loci. (geneticeducation.co.in)
In addition, oligonucleotide probes are used to analyse gene expression. (scientistlive.com)

Genetic analyses suggest recent divergence of M. ulcerans from M. marinum , a well-known fish pathogen that can cause limited granulomatous skin infections in humans ( 14 ). (cdc.gov)

Here, we perform two meta-analyses of GWA studies of a rigorous longevity phenotype definition including 11,262/3484 cases surviving at or beyond the age corresponding to the 90th/99th survival percentile, respectively, and 25,483 controls whose age at death or at last contact was at or below the age corresponding to the 60th survival percentile. (scite.ai)
Prior to the development of massively parallel sequencing (also known as next-generation sequencing ), the only cost-effective way to test more than one gene was serial single-gene testing (i.e., complete testing of one gene that might account for the phenotype before proceeding to testing of the next gene) ‒ an expensive and time-consuming approach with a potentially low yield. (nih.gov)
The neurocognitive phenotype was measured as a quantitative trait, the Turner Syndrome Cognitive Summary (TSCS) score, derived from discriminant function analysis. (biomedcentral.com)

The resulting high density array of template clusters on the flow cell surface is sequenced by a genome analyzing program. (wikipedia.org)
The conserved components are shown in accordance with their position within the human being reference series (horizontal axis), and their percent conformances (vertical … Likewise, to recognize conserved components (30 nt size and 60% conformance) between human beings and horses, cows, pigs, canines, and cats within the period, we hybridized the BAC clones chosen for each of the varieties towards the human being 21q high-density arrays. (bioinbrief.com)

Amount 2 Evolutionarily TNFSF8 conserved bottom pairs within a 365-kb RETRA hydrochloride IC50 area on individual chromosome 21 filled with the locus. (bioinbrief.com)

ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. (wikipedia.org)
Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications. (wikipedia.org)
Oligonucleotide adaptors are then added to the small stretches of DNA that were bound to the protein of interest to enable massively parallel sequencing. (wikipedia.org)

Some technologies that analyze the sequences can use cluster amplification of adapter-ligated ChIP DNA fragments on a solid flow cell substrate to create clusters of approximately 1000 clonal copies each. (wikipedia.org)
Consistent copy number changes were identified, including gain of chromosomes 20, 13, and 8q and smaller regions of amplification such as chromosome 17q11.2-q12. (ox.ac.uk)
In addition, the target of amplification on chromosome 8q appeared to differ, with 8q24.21 amplified frequently in CIN+ samples but 8q24.3 amplification a common finding in MSI+ samples. (ox.ac.uk)
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)
Widely used RNA-seq methods start with adapter ligation and cDNA synthesis of biological RNA samples followed by PCR amplification to generate sequencing libraries1. (cdc.gov)

Analysis of the frequency of the most common mutation (G1528C) revealed a carrier frequency of 1:240 in Finland. (medscape.com)

In addition, 300 bp of flanking intronic sequence on either side of targeted exons has enriched probe coverage. (preventiongenetics.com)
The human exome includes all coding nuclear DNA sequences, approximately 180,000 exons that are transcribed into mature RNA. (nih.gov)
The gene encoding Sec31B is located on chromosome 10q24 and contains 29 exons. (biologists.com)
PCR analysis of exon utilization reveals massive alternative mRNA splicing of Sec31B, with just 16 exons being constitutively utilized in all transcripts. (biologists.com)

Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). (nih.gov)
Despite its biological importance, transfer RNA (tRNA) could not be adequately sequenced by Author Manuscript standard methods due to abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. (cdc.gov)
Significant obstacles for the sequencing of tRNA include the presence of numerous post-transcriptional modifications and its stable and extensive secondary structure, which interfere with cDNA synthesis and adapter ligation. (cdc.gov)

PGxome and exome-based sequencing panels, including custom panels, include copy number variant (CNV) analysis via NextGen sequencing (NGS) data at no additional cost. (preventiongenetics.com)
Approximately 95% of the exome can be sequenced with currently available techniques. (nih.gov)
The diagnostic utility of exome sequencing has consistently been 20%-30% (i.e., a diagnosis is identified in 20%-30% of individuals who were previously undiagnosed but had features suggestive of a genetic condition) [ Gahl et al 2012 , Lazaridis et al 2016 ]. (nih.gov)
Additionally, 207 donors were assessed for rare known and novel coding region variants via whole exome sequencing (WES). (nature.com)
c ) To detect rare or novel variants, whole exome sequencing (WES) was performed on DNA from nPOD donors (modified from Roche NimbleGen SeqCap EZ Exome Library workflow 68 ). (nature.com)

Cross-species DNA series assessment is a simple way for identifying essential components biologically, because functional sequences are conserved evolutionarily, wheres non-functional sequences drift. (bioinbrief.com)

1996). In cases where the majority of the reported pathogenic variant in a gene can be detected by DNA sequencing, PreventionGenetics' aCGH is an excellent complementary test when DNA sequencing fails to identify the causative pathogenic variant(s). (preventiongenetics.com)
The availability of both DNA sequencing and PreventionGenetics' HDGC custom aCGH significantly improves the sensitivity of molecular clinical testing at PreventionGenetics. (preventiongenetics.com)

2001). Sequences within the 365-kb 21q period were categorized as evolutionarily conserved based on the analysis from the comparative array data using an algorithm referred to previously (Frazer et al. (bioinbrief.com)
2003). We determined 72 conserved humanCmouse components (100 nt size and 80% identification) by series alignments within RETRA hydrochloride IC50 the 365-kb interval, which 86% overlap conserved humanCmouse components (30 nt size and 60% conformance) within the comparative humanCmouse array data. (bioinbrief.com)
For many five mammalian varieties (equine/cow/pig/pet/kitty), the comparative array data recognized >93% from the 72 conserved human being components determined by humanCmouse series alignments. (bioinbrief.com)

Scholars@Duke publication: Meiotic chromosome segregation in triploid strains of Saccharomyces cerevisiae. (duke.edu)
Using DNA microarrays and other physical approaches, we examined meiotic chromosome segregation in triploid strains of Saccharomyces cerevisiae. (duke.edu)

article{, title = {Microarrays as cancer keys: an array of possibilities}, author = { S. Mohr and G. D. Leikauf and G. Keith and B. H. Rihn}, year = {2002}, date = {2002-01-01}, journal = {J Clin Oncol}, volume = {20}, number = {14}, pages = {3165-75}, abstract = {Malignant transformation results from accumulation of genetic and epigenetic events. (cnrs.fr)
However, the complete genome sequence of an organism is required for the design of synthetic oligonucleotide or PCR product-based microarrays. (cdc.gov)
SNP array, much like other microarrays, is a simple process. (geneticeducation.co.in)

Nevertheless, together with benchmarking analyses, we show here that the diametric ratio approach can be applied for evaluating the physiological conditions experienced by microbes in situ. (osti.gov)

Each template cluster undergoes sequencing-by-synthesis in parallel using novel fluorescently labelled reversible terminator nucleotides. (wikipedia.org)

Patients with autosomal recessive disorders with one or no pathogenic variants identified by DNA sequencing. (preventiongenetics.com)
Female patients with X-linked disorders with one or no pathogenic variants have been identified by DNA sequencing. (preventiongenetics.com)

The t(8;21) translocation is one of the most frequent chromosome abnormalities associated with acute myeloid leukaemia (AML). (prinsesmaximacentrum.nl)

Standard molecular typing methods such as multilocus sequence typing, restriction fragment length polymorphism, and fingerprinting using variable number of tandem repeats have shown an apparent lack of genetic diversity of M. ulcerans within individual geographic regions, which is indicative of a clonal population structure. (cdc.gov)

Using whole-genome assembly comparison (WGAC) and whole-genome shotgun sequence detection (WSSD) approaches by next generation sequencing (NGS), we probed formation signatures of both segmental duplications (SDs) and individualized CNVs in an integrated fashion, building the finest resolution CNV and SD maps of pigs so far. (biomedcentral.com)

Shape 1 Conserved human being RETRA hydrochloride IC50 sequences within the 10-kb period surrounding the very first exon of (yellowish rectangle). (bioinbrief.com)
Expression and mutational analysis of MET in human solid cancers. (uchicago.edu)
We used this method for the differential genomic analysis of M. ulcerans, a human pathogen for which the fully assembled and annotated genome sequence was not available at the time of the study. (cdc.gov)

ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. (wikipedia.org)
ChIP is a powerful method to selectively enrich for DNA sequences bound by a particular protein in living cells. (wikipedia.org)
Through the analysis, the sequences can then be identified and interpreted by the gene or region to where the protein was bound. (wikipedia.org)
lyrata (Lyre-leaved rock-cress) hypothetical protein (at5g25770) , arath-C7A10.830 Arabidopsis thaliana DNA chromosome 4,gene C7A10.830 No. 2 AT4G36530 , arath-F1N18.12 Arabidopsis thaliana (Mouse-ear cress) f1n18.12 AT1G29840 protein , arath-F1P2.110 Arabidopsis thaliana (Mouse-ear cress). (inrae.fr)

In order to do this, Meléndez and her team are using Qlucore Omics Explorer to perform gene expression and methylation analyses of brain tumour samples and then validating them with data from other databases. (scientistlive.com)
Supervised analyses have allowed us to identify gene expression profiles associated with more aggressive tumours - findings that have been confirmed by analysing the methylation data with Qlucore,' she concludes. (scientistlive.com)

Then, the data collection and analysis software aligns sample sequences to a known genomic sequence to identify the ChIP-DNA fragments. (wikipedia.org)
Therefore, analysis from the array data for these additional mammals identifies a lot more conserved components (Supplemental Dining tables 2C7 and Supplemental Fig. 2), as well as the false-negative price is likely to end up being lower. (bioinbrief.com)
subsequent to the submission of this sample and the establishment of the cell line, a detailed analysis of HapMap data has shown that the sample is from an unreported relative of another member or members of this panel, as described in Nature 437:1299-1320 (2005). (coriell.org)
Taking advantage of Qlucore Omics Explorer's powerful data analysis capabilities, its speed, and its ability to work on any PC, Dr Bárbara Meléndez and her colleagues in the Unidad de Investigación de Patología Molecular (Molecular Pathology Research Unit) at Hospital Virgen de la Salud in Toledo, Spain, are investigating how such generally benign meningiomas can start to exhibit the sort of histology and recurrence usually associated with more aggressive tumours. (scientistlive.com)
The GEO accession number for the sequencing data reported in this paper is GSE66550. (cdc.gov)

The number of sequencing reads that map to each transcript is used to infer the abundance of mRNA molecules. (biomedcentral.com)
In addition, such an analysis should avoid biases in transcript counts related to differences in organism abundance. (osti.gov)

The overall pattern of copy number change was strikingly similar between cell lines and primary cancers with a few obvious exceptions such as loss of chromosome 6 and gain of chromosomes 15 and 12p in the former. (ox.ac.uk)
For example, loss of chromosome 8p was a common event in CIN+ cell lines and cancers but was often found to be gained in MSI+ cancers. (ox.ac.uk)

ClinPharmSeq: A targeted sequencing panel for clinical pharmacogenetics implementation. (coriell.org)

For more information about CNV detection via NGS, please refer to the specific sequencing test descriptions of interest on our website. (preventiongenetics.com)

Many of these contain duplications that vary in the number of times and ways they are repeated: tandemly, at distal parts of the same chromosome, or even on other chromosomes. (the-scientist.com)

Strains derived from some of the aneuploid spore colonies had very high frequencies of mitotic chromosome loss, resulting in genetically diverse populations of cells. (duke.edu)

The genotyping technique that has shown the highest discriminatory power so far is based on the use of outward-directed primers specific for the insertion sequence (IS) IS 2404 , in combination with an oligonucleotide that targets a repeated GC-rich motif ( 16 ). (cdc.gov)

Anatomy57

Organisms5

Diseases16

Chemicals and Drugs43

Analytical, Diagnostic and Therapeutic Techniques and Equipment40

Phenomena and Processes154

Disciplines and Occupations2

Technology, Industry, Agriculture2

Information Science9

Health Care6

Genes28

Microarray5

Hybridization13

Tumor1

Aberrations1

Nucleic acid sequences1

Deletion2

Genome-wide3

Long arm of chromosome3

Genotype2

Probes10

Humans1

Phenotype3

High density2

Locus1

Massively parallel3

Amplification5

Mutation1

Exons4

CDNA3

Exome5

Biologically1

ACGH2

Comparative3

Segregation2

Microarrays3

Situ1

Undergoes1

Variants2

Abnormalities1

Polymorphism1

Whole-genome1

Human3

Protein4

Methylation2

Data5

Transcript2

Cancers2

Clinical1

Detection1

Distal1

Strains1

Primers1