Internal tandem duplication tandem repeat sequences. Medical search. Frequent questions

FLT3 tyrosine kinase domain mutations are biologically distinct from and have a significantly more favorable prognosis than FLT3 internal tandem duplications in patients with acute myeloid leukemia. (ox.ac.uk)
This study addressed the role of DEP-1 for regulation of the acute myeloid leukemia (AML)-related mutant FLT3 internal tandem duplication (ITD) protein. (nih.gov)
Approximately 30% of the adult cases harbor an internal tandem duplication ( FLT3 -ITD) and 5- 10% a tyrosine kinase domain (TKD) amino acid substitution ( FLT3-TKD ). (dovepress.com)
Using targeted sequencing from single cells and colonies from patient samples, we demonstrate tremendous clonal diversity in the majority of acute myeloid leukemia (AML) patients with activating FLT3 internal tandem duplication mutations at the time of acquired resistance to the FLT3 inhibitor quizartinib. (bvsalud.org)
Although previous studies suggested that the expression of FMS-like tyrosine kinase 3 (Flt3) initiates downstream of mouse hematopoietic stem cells (HSCs), FLT3 internal tandem duplications (FLT3 ITDs) have recently been suggested to intrinsically suppress HSCs. (ox.ac.uk)
In acute myeloid leukemia (AML), internal tandem duplications (ITDs) of FLT3 are frequent mutations associated with unfavorable prognosis. (oncotarget.com)
At diagnosis, the FLT3- ITD status is routinely assessed by fragment analysis, providing information about the length but not the position and sequence of the ITD. (oncotarget.com)
To overcome this limitation, we performed cDNA-based high-throughput amplicon sequencing (HTAS) in 250 FLT3- ITD positive AML patients, treated on German AML Cooperative Group (AMLCG) trials. (oncotarget.com)

While whole exome sequencing (WES) remains popular and effective as a method of genetically profiling different cancers, advances in sequencing technology has enabled an increasing number of whole-genome based studies. (frontiersin.org)
Compared to whole genome sequencing (WGS), exome sequencing covers only the 1% of the genome that is translated into protein, greatly reducing the technical burden of data collection and analysis. (frontiersin.org)
performed the first whole-genome sequencing study on AML cells collected from a single patient. (frontiersin.org)
Shotgun sequencing regarding cultured bacterial isolates/individual eukaryotes (whole-genome sequencing) as well as microbe residential areas (metagenomics) has become popular inside biology. (syk-signaling.com)
Using long-insert jumping libraries at 105X mean physical coverage and linked-read whole-genome sequencing from 10X Genomics, we document seven major SV classes at ~5 kb SV resolution. (biomedcentral.com)

Several large species-specific families appear to result from multiple rounds of segmental duplications of tandem gene arrays, a novel mechanism not yet described in yeasts. (biomedcentral.com)

Le Flèche P , Hauck Y , Onteniente L , Prieur A , Denoeud F , Ramisse V , A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis . (cdc.gov)
Sequence analysis of the Daphnia pulex genome holds some surprises that could not have been anticipated from what was learned so far from other arthropod genomes. (biomedcentral.com)
Simple sequence repeats (SSRs) are highly variable features of all genomes. (biomedcentral.com)
Long terminal repeat (LTR) retroelements represent a successful group of transposable elements (TEs) that have played an important role in shaping the structure of many eukaryotic genomes. (biomedcentral.com)
In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona , and allotetraploid E. oryzicola ) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. (nature.com)
Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. (biomedcentral.com)
Both pufferfish genomes encode five tenascin genes: two tenascin-C paralogs, a tenascin-R with domain organization identical to mammalian and avian tenascin-R, a small tenascin-X with previously undescribed GK repeats, and a tenascin-W. Four tenascin genes corresponding to tenascin-C, tenascin-R, tenascin-X and tenascin-W were also identified in the X. tropicalis genome. (biomedcentral.com)
MOTIVATION: Long arrays of near-identical tandem repeats are a common feature of centromeric and subtelomeric regions in complex genomes. (bvsalud.org)

Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. (biomedcentral.com)
In birds and mammals, tenascin-R genes encode 4.5 EGF-like repeats and 9 FN type III domains. (biomedcentral.com)
This tenascin has 18.5 EGF-like repeats, and the tenascin-X genes of mouse and human encode 29 and 32 FN type III domains, respectively. (biomedcentral.com)
We present a novel approach to deal with the problem of reconstructing the duplication history of tandemly repeated genes that are supposed to have arisen from unequal recombination. (cnrs.fr)
With 914 introns within 6116 genes, A. adeninivorans is one of the most intron-rich hemiascomycetes sequenced to date. (biomedcentral.com)
10,200 protein-encoding genes were predicted based on the genome sequence. (springeropen.com)
The genes and proteins were predicted and annotated based on the genome sequence. (springeropen.com)
98.1 %) contains 22,382 protein-coding genes and 61.5 % repetitive sequences. (biomedcentral.com)
The genome sequence and annotation of L. minor protein-coding genes provide new insights in biological understanding and biomass production applications of Lemna species. (biomedcentral.com)

However, the abundance of long ITDs (≥75nt) was underestimated by HTAS, as the size of the ITD affected the mappability of the corresponding sequence reads. (oncotarget.com)

Later genomic duplication events led to the appearance of four family members in vertebrates: tenascin-C, tenascin-R, tenascin-W and tenascin-X. (biomedcentral.com)
We have used comparative genomic hybridisation to analyse 19 constitutional chromosome abnormalities detected by G band analysis, including seven deletions, five supernumerary marker chromosomes, two interstitial duplications, and five chromosomes presenting with abnormal terminal banding patterns. (bmj.com)
Full-length transcriptome sequencing further revealed several novel gene fusions within the nested genomic variants. (bvsalud.org)
These sequences present a source of repeat structure diversity that is commonly ignored by standard genomic tools. (bvsalud.org)
9] Genomic sequencing for the LAMP2 gene revealed mutations in 2 of 197 (1%) patients with HCM. (medscape.com)

B) Tandem repeat arrays were coded accordingly. (cdc.gov)
Using long sequencing reads from the Oxford Nanopore Technologies platform, we phased SNVs within large gene copy arrays for the first time. (elifesciences.org)
In addition, we found that CanSINE proliferation in Felidae frequently targeted existing CanSINE loci for insertion sites, resulting in tandem arrays. (biomedcentral.com)

Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri . (biomedcentral.com)
In addition to the annotation of gene space, a detailed annotation of repeated sequences and transposable elements (TEs) ( e.g. presence/absence, types, and location) is critical for understanding the biology of a genome, as well as an important tool for the improvement of high-quality genome assemblies. (biomedcentral.com)
The use of repeat libraries of one species to detect repeats from a related species (that diverged e.g. 10 million years ago) is highly problematic as it is known that intergenic space is rapidly evolving for the high turnover rates of transposable elements and repetitive sequence. (biomedcentral.com)
Unfortunately, high-copy number repeats and transposable elements are not well represented in most genome assemblies. (biomedcentral.com)
Illumina): highly repetitive sequences and transposable elements pose significant problems to assembly algorithms. (biomedcentral.com)
A conserved function of piRNAs across all bilateral animals is to silence sequence-complementary transposable elements (TEs) 1 , 2 , 3 , 4 . (gokcumenlab.org)

A phylogenetic tree based on the predicted amino acid sequences of the fibrinogen-related domains demonstrates that tenascin-C and tenascin-R are the most closely related vertebrate tenascins, with the most conserved repeat and domain organization. (biomedcentral.com)

All these different codes can be deduced one from the other by simple duplication and deletion events, with no need to invoke point mutations. (cdc.gov)
This study reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems. (elifesciences.org)

This thematic series of companion papers constitutes the initial exploration of the genome biology of the waterflea (Daphnia) building on the first complete crustacean genome sequence. (biomedcentral.com)

Identity between most parsimonious duplication trees and most parsimonious phylogenies for the same data, combined with the agreement with additional knowledge about the sequences, such as the presence of polymorphisms, shows strong evidence that our reconstruction procedure providesgood insights into the duplication histories of these loci. (cnrs.fr)
However, mammalian piRNA sequences and piRNA-producing loci evolve more rapidly than the rest of the genome for unknown reasons. (gokcumenlab.org)
Our results indicate that genetic instability at pachytene piRNA loci, while producing certain pathogenic SVs, also protects genome integrity against TE mobilization by driving the formation of rapid-evolving piRNA sequences. (gokcumenlab.org)
While most pachytene piRNAs lack obvious targets, neither the copy numbers nor nucleotide sequences of pachytene piRNA loci are conserved 5 , 6 , 7 , and many of them are not found in syntenic regions even in closely related mammals 8 , 9 . (gokcumenlab.org)

Conversely, de novo methods such as Piler [ 3 ] and RepeatModeler ( http://www.repeatmasker.org/RepeatModeler.html ) have been developed to identify repeats in genome assemblies based on the number of times a sequence motif appears in an input file. (biomedcentral.com)
Resolving multi-copy duplications de novo using polyploid phasing. (stanford.edu)

Eight spacers are used in the report, 7 of which contain tandem repeats, and the sequence variability used to produce the typing data and the strain clustering result from variation in the number of tandem repeats (and incorrect data analysis produces a dendrogram with 34 branches from only 19 different isolate types). (cdc.gov)
This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. (biomedcentral.com)

1 ) report the development of an original genotyping system for Yersinia pestis based on intergenic spacer sequencing. (cdc.gov)

Our results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone. (biomedcentral.com)
Theoretically, whenever repeats longer than the reads are present, assemblies are limited within the boundaries of repetitive elements. (biomedcentral.com)
Unlike reads shorter than the underlying repeat structure that rely on indirect inference methods, e.g. assembly, long reads allow direct inference of satellite higher order repeat structure. (bvsalud.org)

Sequence analyses separated Feliform CanSINEs into two subfamilies, each characterized by distinct RNA polymerase binding motifs and phylogenetic associations. (biomedcentral.com)
Direct phenotypic variation is possible by altering gene expression via insertion into coding regions or interference from the internal RNA polymerase promoters in SINEs [ 29 ]. (biomedcentral.com)

Our assemblies also identify novel gene region duplications. (biomedcentral.com)

However, the approach appears to rely upon the characterization of polymorphisms due to tandem repeat variation. (cdc.gov)

CGH has been widely applied to detect gains and losses of DNA sequences on specific chromosomes in the study of solid tumours, 1 but has not been extensively used to study unbalanced constitutional karyotypes. (bmj.com)
The sequencing of strain LS3 revealed that the nuclear genome of A. adeninivorans is 11.8 Mb long and consists of four chromosomes with regional centromeres. (biomedcentral.com)

CV-N has a complex fold composed of a duplication of a tandem repeat of two homologous motifs comprising three-stranded beta-sheet and beta-hairpins. (wikipedia.org)
Following duplication events, the resulting stretches of homologous sequence can promote recombination between gene copies. (elifesciences.org)

We have designed a multiplex ligation-dependent probe amplification (MLPA) technique for genotyping and CNV determination in one single assay and validated the results by next-generation sequencing and with a KIR gene-specific short tandem repeat assay. (amsterdamumc.org)

False negatives arise due to repeat/TE sequence diversification across taxa which can hamper the identification of distinctive repeat features ( i.e. lineage specific sequences) of the species. (biomedcentral.com)
Unfortunately, this method loses power when the target genome is distantly related to the species used to develop the repeat library. (biomedcentral.com)
The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. (biomedcentral.com)
To date, mtDNA sequences have been generated for hundreds of thousands of specimens in many vertebrate species [ 8 ]. (biomedcentral.com)
In contrast to the well-delimitated species boundary inferred from the nuclear ITS sequence variations, three of the four species are non-monophyletic in the plastome trees, which is consistent with previous studies based on a few chloroplast markers. (biomedcentral.com)
Previous study failed to discern the four Ostrya species based on four chloroplast (cp) fragments ( rps16 , trnG (UCC) intron, trnH-psbA , and trnL-trnF ) while the ITS sequence variations did [ 5 ]. (biomedcentral.com)
Thus, sequencing of the Blastobotrys (Arxula) adeninivorans genome was of interest in order to generate an additional landmark in the basal portion of the hemiascomycete tree and possibly resolve phylogenetic relationships among basal species. (biomedcentral.com)

The first cancer exomes were sequenced soon after the completion of the Human Genome Project in 2001. (frontiersin.org)

Instead, the Figure shows how internal variation within the array can be coded to facilitate interpretation. (cdc.gov)

Pachytene piRNAs have been proposed to either regulate mRNAs 10 , 11 , 12 , 13 , 14 or stabilize PIWI proteins for a function that does not require piRNA-guided sequence specificity 15 . (gokcumenlab.org)

The adoption of exhaustive repeat libraries developed directly from the genome under investigation is important for minimizing false negatives in the annotation. (biomedcentral.com)
As a result, repeat annotation of most SGS assemblies leads to skewed representations of the actual native repeat content. (biomedcentral.com)
In order to clarify the biological and pharmacological mechanisms of O. sinensis , we carried out the genome sequencing of H. sinensis, anamorph of O. sinensis , for the first time, described the annotation and gene expression, and analyzed the complete sequencing data (Li et al. (springeropen.com)

This article will review recent impact of massively parallel next-generation sequencing (NGS) in our understanding and treatment of cancer. (frontiersin.org)
First, this article summarizes the history of massively parallel next-generation sequencing (NGS) in the context of cancer genomics and reviews recent research and clinical applications. (frontiersin.org)
In both scenarios, overlaps between sequences (Sanger or next-generation sequencing, NGS) have been used to assemble full-length mitogenomes. (biomedcentral.com)

Pourcel C , Andre-Mazeaud F , Neubauer H , Ramisse F , Vergnaud G . Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis . (cdc.gov)

Concerted evolution refers to the pattern in which copies of multigene families show high intraspecific sequence homogeneity but high interspecific sequence diversity. (biomedcentral.com)
Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity. (biomedcentral.com)
or the transmembrane protein gene cassettes of some pathogenic bacteria ( Santoyo and Romero, 2005 ), gene conversion can also generate sequence diversity. (elifesciences.org)

The sequences are compared to modern sequences by BLAST analysis, which is not relevant for tandem repeats. (cdc.gov)
They did not invent a new genotyping method but used the well-known multiple locus variable analysis (MLVA) number of tandem repeats approach. (cdc.gov)
another proposed identification of Y. pestis strains by using variable numbers of tandem repeats analysis (VNTR) ( 4 ). (cdc.gov)
Combining long-read genome and transcriptome sequencing enables an in-depth analysis of how SVs disrupt the genome and sheds new light on the complex mechanisms involved in cancer genome evolution. (bvsalud.org)

Multiple sequence alignment reveals that differences in the size of tenascin-W from various vertebrate classes can be explained by duplications of specific fibronectin type III domains. (biomedcentral.com)

Therefore the use of software tools such as ReAS and RE can lead to a more accurate and complete representation of the repeat content of a given genome. (biomedcentral.com)
As the integration of NGS in the study and treatment of cancer continues to mature, we believe that the field of cancer genomics will need to move toward more complete 100% genome sequencing. (frontiersin.org)
Second, we highlight the importance and potential of complete or 100% genome sequencing, i.e., the ability to sequence highly repetitive non-coding sequences beyond the reach of current NGS technologies. (frontiersin.org)
Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. (bvsalud.org)

In the GT-1 and SH4 subfamilies, the trihelix domains each have a tryptophan residue in the internal hydrophobic region of the tandem repeat. (biomedcentral.com)

The copy-number tree mixture deconvolution problem and applications to multi-sample bulk sequencing tumor data. (stanford.edu)

This "mitogenome" generally has short repetitive non-coding sequences, normally within a single control region (CR). (biomedcentral.com)
Addressing this, we sequenced SK-BR-3 using long-read single molecule sequencing from Pacific Biosciences and develop one of the most detailed maps of structural variations (SVs) in a cancer genome available, with nearly 20,000 variants present, most of which were missed by short-read sequencing. (bvsalud.org)
Progressive calibration and averaging for tandem mass spectrometry statistical confidence estimation: Why settle for a single decoy. (stanford.edu)

Open in a Rabbit Polyclonal to GRAK separate window Figure?1 (A) Clinical photograph showing gigantic enlargement of bilateral breasts reaching up to bilateral iliac regions, (B) sonography with high-rate of recurrence transducer showing circumscribed hypoechoic mass component ((E) MR angiography showing bilateral lateral thoracic arteries ( em white arrowheads /em ) and dilated bilateral internal mammary arteries ( em black arrowheads /em ) and their branches. (columbiagypsy.net)

To gain deeper insight into the biological and pharmacological mechanisms, we sequenced the genome of H. sinensis . (springeropen.com)

Since the advent of second generation sequencing (SGS) technologies, the scientific community has been inundated with hundreds of genome assemblies of varying quality. (biomedcentral.com)
The rapid development of DNA sequencing technologies has driven a revolution in our understanding of this highly complex and diverse group of diseases ( Devita and Rosenberg, 2012 ). (frontiersin.org)

Klevytska AM , Price LB , Schupp JM , Worsham PL , Wong J , Keim P . Identification and characterization of variable-number tandem repeats in the Yersinia pestis genome. (cdc.gov)
Application of our MLPA assay in segregation analyses of families from the Centre d'Etude du Polymorphisme Humaine, previously KIR-genotyped by classical techniques, confirmed an earlier reported duplication and resulted in the identification of a novel duplication event in one of these families. (amsterdamumc.org)

We then provide a simple recursive algorithm which determines whether or not a given rooted phylogeny can be a duplication history and another algorithm that simulates the unequal recombination process and searches for the best duplication trees according to the maximum parsimony criterion. (cnrs.fr)

Cyanovirin-N is a lengthy, mostly beta-sheet protein that displays internal two-fold pseudosymmetry. (wikipedia.org)

Differences from repeat unit "e" are shown. (cdc.gov)

Surrounding the important ERBB2 oncogene (also known as HER2), we discover a complex sequence of nested duplications and translocations, suggesting a punctuated progression. (bvsalud.org)

Anatomy1

Diseases7

Chemicals and Drugs17

Analytical, Diagnostic and Therapeutic Techniques and Equipment12

Phenomena and Processes23

Information Science4

Health Care1

FLT38

Whole-genome5

Segmental duplications1

Genomes8

Genes9

ITDs1

Genomic5

Arrays3

Transposable elements6

Amino acid sequences1

Mutations2

Genome sequence1

Loci4

Novo2

Variability2

Intergenic1

Reads3

Polymerase2

Novel gene1

Polymorphisms1

Chromosomes2

Homologous2

Amplification1

Species7

20011

Variation1

Proteins1

Annotation3

Next-generation3

Phylogenetic1

Diversity3

Analysis4

Reveals1

Complete4

Subfamilies1

Data1

Single3

Bilateral1

Biological1

Technologies2

Identification2

Recombination1

Fold1

Differences1

Complex1