Nucleotide sequence deletion. Medical search. Frequent questions

In the recombination process of the β chain, loci of the variable (V), diversity (D), and joining (J) regions are randomly spliced together with non-templated insertions and deletions occurring between each junction, resulting in up to 10 11 possible sequences ( 3 , 4 ). (biorxiv.org)
After sequencing these exomes with the Illumina HiSeq 2500, the researchers scrutinized the sequences for single nucleotide changes, small insertions and deletions, and copy number variants. (genomeweb.com)
Except for lacking exons, these pseudogenes contained several nucleotide substitutions, insertions and deletions. (yourdictionary.com)

The efficacy of pSelAct-KO was demonstrated in C. michiganensis and confirmed using whole genome sequencing. (biorxiv.org)
Landscape of somatic mutations in 560 breast cancer whole-genome sequences. (nature.com)
Tandem repeat identified in the sequence from whole genome sequencing. (cdc.gov)
Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing. (cdc.gov)
This study sought to identify SARS-CoV-2 by enrichment next-generation sequencing (NGS) from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients. (cdc.gov)
This study examined the added value of whole genome sequencing (WGS) for investigating a non-point source outbreak of Salmonella ser. (who.int)
2 Whole genome sequencing (WGS) is a high-resolution typing method that can help foodborne disease investigators distinguish outbreak cases from non-outbreak cases. (who.int)

7- 9 All reported mutations are single nucleotide alterations leading to splice site, missense, nonsense, or frameshift mutations, or intra-exonic deletions and insertions of up to four nucleotides, which have been detected through exonic PCR amplifications and sequencing. (bmj.com)
In contrast to the abundance mutations in SDHB and SDHD , only a single multiply affected family and an isolated case, containing a single nucleotide initiation codon and a splice site mutations in SDHC , respectively, have been described by Niemann et al . (bmj.com)
They found that 1,084 genes in 129 strain mice have insertions, deletions, or single-nucleotide mutations that cause them to diverge in sequence from Black 6 mice. (the-scientist.com)
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)
One hundred sixteen patients with classical and atypical RTT were studied for mutations of the MeCP2 gene by using DHPLC and direct sequencing. (neurology.org)
The authors found 17 novel mutations, including a complex gene rearrangement found in one individual involving two deletions and a duplication. (neurology.org)
However, Fleischman and colleagues did not detect mutations in the coding sequence of HOX genes known to affect radial development. (medscape.com)
Overall, these assays and approaches detect specific mutations or features such as insertions, deletions and point mutations in the SARS CoV-2 genome that are characteristic of a particular VOC/VOI using PCR. (who.int)

Insertions, deletions, and duplications can all be frameshift variants. (medlineplus.gov)
Seven novel sequence variants were described, including 5 single nucleotide substitutions, 1 insertion and 1 deletion. (llu.edu)
None of the identified sequence variants demonstrated complete segregation with the affected phenotype in the pedigree. (llu.edu)
Poxvirus adaptation can involve combinations of recombination-driven gene copy number variation and beneficial single nucleotide variants (SNVs) at the same loci. (elifesciences.org)
In order to expand our understanding of how recombination might influence virus variation during the course of adaptation, we focused on large DNA viruses, in which rapidly evolving populations can simultaneously harbor both adaptive gene copy number variation and beneficial single nucleotide variants (SNVs) at the same locus. (elifesciences.org)
Screening for single nucleotide variants, small indels and exon deletions with a next-generation sequencing based gene panel approach for Usher syndrome. (mpg.de)

A reading frame consists of groups of three nucleotides that each code for one amino acid . (medlineplus.gov)
The numbers on top organize the nucleotides into triplets, reflecting the way that the genetic code uses groups of three nucleotides to code for one amino acid. (learn-biology.com)

To address this problem in CGP, we propose a Frameshift Mutation Cartesian Genetic Programming (FMCGP), which is inspired by the DNA mutation mechanism in biology and the frameshift mutation caused by insertion or deletion of nodes is introduced to CGP. (springer.com)
The frameshift mutation changes the compiling framework of genotype to increase diversity by randomly insertion or deletion of nodes. (springer.com)
Accession A0036 Description Frameshift deletion in the exon 1 Date 11-Jan-2000 (Rel. (lu.se)

With the help of Sanger sequencing, the team determined that the affected woman carried two copies of this mutation, while her mother, sister, and two brothers had one copy of the altered CPE gene. (genomeweb.com)
The method is limited to around 300-500 nucleotide base pairs, compared with the greater chain lengths of over 1000 base pairs achievable using Sanger sequencing. (news-medical.net)
The results of the multi‑gene panel test were further verified by Sanger sequencing. (spandidos-publications.com)

We systematically violated canonical qPCR design principles to develop a Pan-Degenerate Amplification and Adaptation (PANDAA), a point mutation assay that mitigates the impact of sequence variation on probe-based qPCR performance. (nature.com)
DNA was obtained from affected and unaffected subjects for the performance of a genome-wide linkage analysis as well as PCR amplification and sequencing of DCN, DSPG3, FOXC1, KERA, LUM, and PITX2. (llu.edu)
DNA isolation, genotyping of simple tandem repeat polymorphisms, PCR amplification and sequencing were performed using standard techniques 2 and all simple tandem repeat polymorphisms were amplified in the presence of 10% glycerol and 5% DMSO after labelling one oligonucleotide primer with 32 P and analysed on a 6% polyacrylamide gel. (bmj.com)
Comparative genomic hybridization (CGH) has been developed to elucidate genome-wide sequence copy number variation (CNV) between different genomes, such as the differential amplification or deletion of genetic regions between tumor DNA and normal DNA from neighboring unaffected tissue [ 7-10 ]. (idtdna.com)

Estimates of evolutionary distances (numbers of substitutions that have occurred since a pair of sequences diverged from a common ancestor) are typically calculated using substitution models (evolutionary distances are used input for distance methods such as neighbor joining ). (wikipedia.org)
It is also necessary to assume a substitution model to estimate evolutionary distances for pairs of sequences (distances are the number of substitutions that have occurred since sequences had a common ancestor). (wikipedia.org)
The K a /K s ratio can be used to examine the action of natural selection on protein-coding regions, [5] [6] it provides information about the relative rates of nucleotide substitutions that change amino acids (non-synonymous substitutions) to those that do not change the encoded amino acid (synonymous substitutions). (wikipedia.org)

Fig. 5: Detecting methylated nucleotides using single-molecule sequencing. (nature.com)
Resolving the complexity of the human genome using single-molecule sequencing. (nature.com)
In an effort to track down new genes that contribute to inherited, single-gene forms of obesity, the researchers performed exome sequencing on members of a Sudanese family found through a genetic obesity clinic at a UK hospital. (genomeweb.com)
The DNA that is to be sequenced is broken up into fragments of around 100 base pairs of single-strand DNA. (news-medical.net)
One of the four types of nucleotides that make up DNA are added to the wells, which begin to be incorporated onto the single-strand DNA template by DNA polymerase at the 3' end, releasing pyrophosphate.ATP sulfurylase then converts pyrophosphate to adenosine triphosphate (ATP) in the presence of adenosine 5' phosphosulfate. (news-medical.net)
If no light is emitted upon the addition of cytosine, then the next complimentary base in the single-strand DNA template must be one of the other three nucleotides. (news-medical.net)
It is also able to detect single nucleotide polymorphisms, insertion-deletions or other sequence variations, in addition to being able to quantify DNA methylation and allele frequency. (news-medical.net)
We found 453 single nucleotide polymorphisms in protein-coding regions, which were used to assess the evolutionary relationships of these Y. pestis strains. (asm.org)
Large deletions involving entire single exons or multiple exons, large insertions and other complex genetic events have been reported in PTEN and will not be identified using this test methodology. (cincinnatichildrens.org)
While there have been impressive technical innovations demonstrating feasibility-for example, generating paired measurements of single-cell transcriptome (single-cell RNA sequencing [scRNA-seq]) and chromatin accessibility (single-cell assay for transposase-accessible chromatin using sequencing [scATAC-seq])-widespread application of joint profiling is challenging due to its experimental complexity, noise, and cost. (stanford.edu)
ReadyMade Random Hexamers can be used for various applications, including cDNA synthesis and identification of single nucleotide polymorphisms. (idtdna.com)
You can use random sequence oligonucleotides to identify single nucleotide polymorphisms (SNPs) as well as small scale chromosome events, primarily insertions or deletions [ 5,6 ]. (idtdna.com)
8 The MeCP2 protein, initially characterized by its ability to bind single methylated CG nucleotides, 9 plays a significant role in the transcriptional silencing of genes. (neurology.org)
An allele is one of two or more versions of DNA sequence (a single base or a segment of bases) at a given genomic location. (genome.gov)
It also discovered a single letter change in the genetic code, single nucleotide polymorphism (SNP). (yourdictionary.com)
[ 9 ] They discovered one low frequency single nucleotide polymorphism (SNP) in the noncoding 5' untranslated (UTR) region of the gene RBM8A in 4 of the cases and another low frequency noncoding SNP in the first intron of the same gene. (medscape.com)
This process helps identify single or multiple nucleotide variations as well as areas of insertion or deletion. (msdmanuals.com)

Nucleotide sequences of partial Kex gene exons of Lacazia loboi (Ll) and Paracoccidioides brasiliensis (Pb), including pathogen DNA sequences isolated from bottlenose dolphins, Indian River Lagoon, Florida, USA, and P. lutzii (Pl) containing mismatches (bold) and unique gaps. (cdc.gov)

Approximately 80% of patients with CS, 60% patients with BRRS, 20% of patients with PS/PSL syndrome will have a PTEN mutation identifiable by sequencing. (cincinnatichildrens.org)
Deletion/duplication analysis of PTEN will detect a mutation in about 10% of individuals with Bannayan-Riley-Ruvalcaba syndrome. (cincinnatichildrens.org)

Small deletions remove one or a few nucleotides within a gene, while larger deletions can remove an entire gene or several neighboring genes. (medlineplus.gov)
Cloning and sequencing of the phn (psiD) genes involved in alkylphosphonate uptake and C-P lyase activity in Escherichia coli B. (embl-heidelberg.de)
The ARX and CDKL5 genes, both of which are located within the Xp22 region, were sequenced in the affected family members, and a deletion of nucleotide 183 of the coding sequence (c.183delT) was identified in CDKL5 in the affected family members. (nih.gov)
We, therefore constructed an in frame deletion mutant of dltX , without affecting the expression of the other genes of the operon. (frontiersin.org)
Current diagnostic PCR assays target a variety of SARS CoV-2 genes and the vast majority target sequences in regions of the SARS CoV-2 genome that are highly conserved. (who.int)

is a type of substitution in which the nucleotide change results in the replacement of one protein building block (amino acid) with another in the protein made from the gene. (medlineplus.gov)
Instead of causing a change in one amino acid, however, the altered DNA sequence results in a stop signal that prematurely signals the cell to stop building a protein. (medlineplus.gov)
The Human Genome Variation Society (HGVS) has established a sequence variant nomenclature , an international standard used to report variation in genomic, transcript and protein sequences. (ucsc.edu)
Sequence homology searches identify PhnC, PhnK, PhnL, and, possibly, PhnN proteins as members of nucleotide-binding proteins of the binding protein-dependent transport systems. (embl-heidelberg.de)
The regulation of expression of X-box-binding protein-1 (XBP1), a transcriptional factor, involves an unconventional mRNA splicing that removes the 26 nucleotides intron. (mdpi.com)
Most of the work on substitution models has focused on DNA/ RNA and protein sequence evolution. (wikipedia.org)
the alphabet is the 20 proteinogenic amino acids for proteins and the sense codons (i.e., the 61 codons that encode amino acids in the standard genetic code ) for aligned protein-coding gene sequences. (wikipedia.org)
In fact, substitution models can be developed for any biological characters that can be encoded using a specific alphabet (e.g., amino acid sequences combined with information about the conformation of those amino acids in three-dimensional protein structures [7] [8] ). (wikipedia.org)
The Ghent researchers looked through the sequences for differences between Black 6 mice and the 129 strains that would affect protein production. (the-scientist.com)
or the transmembrane protein gene cassettes of some pathogenic bacteria ( Santoyo and Romero, 2005 ), gene conversion can also generate sequence diversity. (elifesciences.org)
When this conversion occurs in the coding region of mRNA, it results in an altered nucleotide codon and, therefore, can change the amino acid sequence of the coded protein in what is referred to as a re-coding editing event. (biomedcentral.com)
A protein consists of one or more chains of amino acids (called polypeptides) whose sequence is encoded in a gene. (genome.gov)
The full-length sequence exhibits little overall homology to any other known protein at either the nucleotide or the amino acid level. (yourdictionary.com)
The investigators found coinheritance of the 1q21.1 deletion with either SNP, causing significant decreases in the level of Y14, a protein encoded by RBM8A . (medscape.com)

Fig. 2: Structural variant detection with long-read sequencing. (nature.com)
The sensitivity of DNA sequencing is over 99% for the detection of nucleotide changes, small deletions and insertions in the regions analyzed. (cincinnatichildrens.org)
The objective of this document is to outline the available methods and tools for screening and sequencing patient specimens for the detection of VOC or VOI, with a focus on those that offer a rapid turn-around time so as to support rapid implementation of public health actions for COVID 19 control. (who.int)

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing. (nature.com)
To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. (asm.org)
We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis . (asm.org)

Albers and colleagues applied high-throughput sequencing in 5 unrelated patients with TAR syndrome and the chromosome 1q21.1 deletion. (medscape.com)

As they reported online yesterday in PLOS One , the researchers did exome sequencing on members of a consanguineous family affected by a condition characterized by extreme obesity, type 2 diabetes, intellectual disability, and other features. (genomeweb.com)
This technology involves breaking the entire genome into small segments, sequencing the segments, and then reassembling the sequences using intensive computational techniques to provide the base-by-base sequence of the entire genome or more limited regions, such as the expressed portion of the genome known as the exome. (msdmanuals.com)
However, the sheer volume of information generated by sequencing the exome or genome results in a variety of interpretive problems that complicate understanding of the results. (msdmanuals.com)

The unique sequence tags allow strains to be analyzed in parallel. (the-scientist.com)

ReadyMade Random Hexamers (randomers) are oligonucleotides composed of all possible sequences for a given length. (idtdna.com)

A later application was the use of random sequence primers to detect random amplified polymorphisms (RAPDs) [ 3,4 ]. (idtdna.com)

Adenine (A) is one of the four nucleotide bases in DNA, with the other three being cytosine (C), guanine (G) and thymine (T). Within a double-stranded DNA molecule, adenine bases on one strand pair with thymine bases on the opposite strand. (genome.gov)
The first three have apparently evolved from the adenine nucleotide carrier. (yourdictionary.com)

For example, if three cytosine nucleotides are added sequentially to the same fragment of DNA, the light emitted will be three times more intense than fragments of DNA with only one cytosine nucleotide added. (news-medical.net)

This is facilitated by directing primer and probe design to evolutionarily conserved regions identified through multiple sequence alignments that portray geographical and temporal genomic variability. (nature.com)
It contains corresponding amino acid and nucleotide sequence alignments, with trees inferred from each alignment. (yourdictionary.com)

Inventoried oligos comprising all possible sequences for a given length. (idtdna.com)

Substitution models are used to calculate the likelihood of phylogenetic trees using multiple sequence alignment data. (wikipedia.org)

qPCR probe design is more averse to similar modifications because increasing probe T m through nucleotide degeneracy or sequence lengthening may lead to high T m variations that reduce specific target discrimination. (nature.com)
In addition, no pathogenic sequence variations were found in DCN, DSPG3, LUM, PITX2 and FOXC1, which have also been implicated in corneal and anterior segment dysgenesis. (llu.edu)

Mixed cultures can be grown and sampled and the abundance of each deletion strain determined by hybridization of genomic DNA to an oligonucleotide microarray of the complementary bar-code sequences. (the-scientist.com)
Array comparative genomic hybridization in patient one and patient two revealed copy-number variant (CNV) deletions, respectively, ~ 1.45 Mb in size involving FOXF1 and an ~ 0.7 Mb in size involving FOXF1 enhancer and leaving FOXF1 intact. (researchgate.net)
Array comparative genomic hybridization (aCGH) is a type of microarray now routinely used to identify deleted or duplicated regions of DNA sequence in specific chromosomes on a genome-wide basis. (msdmanuals.com)

deleted each gene, from start to stop codon, by replacing it with a deletion cassette incorporating the KanMX gene flanked by two distinct 20-nucleotide sequences that serve as unique 'molecular bar codes' for identification. (the-scientist.com)
A codon is a DNA or RNA sequence of three nucleotides (a trinucleotide) that forms a unit of genetic information encoding a particular amino acid. (genome.gov)
An anticodon is a trinucleotide sequence located at one end of a transfer RNA (tRNA) molecule, which is complementary to a corresponding codon in a messenger RNA (mRNA) sequence. (genome.gov)

Deletion analysis demonstrated that at least 13 kilobases of DNA information is required for E. coli to express the phosphonate utilization phenotype (Phn+). (embl-heidelberg.de)
Deletion of rpoX in the Tr background resulted in a higher ability to resist ethanol challenges and to survive hyperosmolarity challenges, and in the Op background the opposite phenotype was observed. (hindawi.com)

Goodwin, S., McPherson, J. D. & McCombie, W. R. Coming of age: ten years of next-generation sequencing technologies. (nature.com)
Through this new partnership we are pleased to offer you comprehensive next generation sequencing solutions. (idtdna.com)
You can view Archer assays alongside IDT's xGen™ NGS portfolio to find the best next generation sequencing solution for your lab. (idtdna.com)
For this, miRNA-based next-generation sequencing was performed in adrenal tissues taken from patients with ACTH-independent cortisol-producing adrenocortical adenomas (CPA), from patients with ACTH-dependent pituitary Cushing's disease (CD) after bilateral adrenalectomy, and from control subjects. (bvsalud.org)
Next-generation sequencing technologies have dramatically changed the approach to genetic diagnosis. (msdmanuals.com)
This revolutionary and rapidly evolving technology has moved a significant portion of the technical aspects of genetic diagnosis to next-generation sequencing and has become the mainstay of genetic diagnosis. (msdmanuals.com)

Sigma factors are a class of proteins constituting essential dissociable subunits that confer sequence-specific DNA binding properties to RNA polymerase (RNAP). (hindawi.com)

This type of variant replaces one DNA building block (nucleotide) with another. (medlineplus.gov)
This variant occurs when a deletion and insertion happen at the same time in the same location in the gene. (medlineplus.gov)
In a deletion-insertion variant, at least one nucleotide is removed and at least one nucleotide is inserted. (medlineplus.gov)
A deletion-insertion (delins) variant may also be known as an insertion-deletion (indel) variant. (medlineplus.gov)
is a variant that increases the number of times that the short DNA sequence is repeated. (medlineplus.gov)

Following duplication events, the resulting stretches of homologous sequence can promote recombination between gene copies. (elifesciences.org)

RNA editing refers to post-transcriptional processes that alter the nucleotide sequence of an RNA transcript by insertion, deletion or nucleotide conversion. (biomedcentral.com)

Intraspecific and interspecific pairwise distances (K2P) were 0-0.5% and 4.9-5.2%, respectively, and each species was recovered as a distinct, well supported group of sequences (i.e., species) in the ML analysis. (bioone.org)

The nucleotide and deduced amino acid sequences of the phnA gene showed no significant homology with any data bank accessions. (embl-heidelberg.de)

Here, we present a suite of tools for genetic manipulation in the tomato pathogen C. michiganensis including a markerless deletion system, an integrative plasmid, and an R package for identification of permissive sites for plasmid integration. (biorxiv.org)

A Pho box-like promoter sequence is also found upstream of the gene cluster starting at phnA, which is consistent with the observation of phosphate regulation of the Phn+ response. (embl-heidelberg.de)

Nucleotide sequence analysis of five representative isolates confirmed that all isolates possessed one type of amino acid motif (R-S-S-R/GL) at cleavage site of HA, Deduced amino acid sequences showed the presence of L226 (234 in H9 numbering) in all five Iranian isolates which indicates a preference to binding of α (2-6) sialic acid receptors. (scialert.net)

occurs when there is an addition or loss of nucleotides that shifts the grouping and changes the code for all downstream amino acids. (medlineplus.gov)

For example, a trinucleotide repeat is made up of sequences of three nucleotides, and a tetranucleotide repeat is made up of sequences of four nucleotides. (medlineplus.gov)

The vector pSelAct-KO is a recombination based, markerless knockout system that uses dual selection to engineer seamless deletions of a region of interest, providing opportunities for repeated higher-order genetic knockouts. (biorxiv.org)

The complete nucleotide sequence of 15,611 bases has been determined, and the gene structures were examined. (embl-heidelberg.de)
As the coupling efficiency for each individual phosphoramidite is slightly different, a special blend of all 4 bases at different molar ratios is used to achieve an even nucleotide representation. (idtdna.com)
The As, Ts, Cs, and Gs on the row labeled "DNA nucleotides" represent the nitrogenous bases that carry genetic information in DNA. (learn-biology.com)
The sequence of the four nucleotide bases encodes DNA's information. (genome.gov)

Pyrosequencing is a method of DNA sequencing that detects light emitted during the sequential addition of nucleotides during the synthesis of a complementary strand of DNA. (news-medical.net)
This process is repeated, adding each nucleotide one after the other until the synthesis is complete. (news-medical.net)

Ultra-degenerate primers with 3' termini overlapping the probe-binding site adapt the target through site-directed mutagenesis during qPCR to replace DRM-proximal sequence variation. (nature.com)

Gene reduction analysis revealed that the gene deletion processes are under selective pressure, and many of the inactivations are probably related to the organism's interaction with its host environment. (asm.org)

Despite the reliance of clinical virology on qPCR, technical challenges persist that compromise their reliability for sustainable epidemic containment as sequence instability in probe-binding regions produces false-negative results. (nature.com)
Some regions of DNA contain short sequences of nucleotides that are repeated a number of times in a row. (medlineplus.gov)
The neuraminidase stalks regions in these viruses had no deletion as compared to that A/Dk/HK/ Y280/97 lineage (Ck/Bei-like viruses) and the 2 human isolates A/HK/1073/99, A/HK/1074/99. (scialert.net)

Several new genomics technologies have become available that offer long-read sequencing or long-range mapping with higher throughput and higher resolution analysis than ever before. (nature.com)
Here we present the first DNA sequences for Neotropical Eccopsis and use these data in a maximum likelihood (ML) analysis to evaluate the monophyly of the genus, and to examine the utility of DNA barcodes in separating the South American E. galapagana Razowski & Landry, 2008 and E. razowskii Vargas, 2011 . (bioone.org)

Anatomy8

Organisms25

Diseases2

Chemicals and Drugs84

Analytical, Diagnostic and Therapeutic Techniques and Equipment25

Phenomena and Processes100

Information Science6

Health Care1

Insertions and deletions3

Whole genome7

Mutations8

Variants6

Groups of three nucleotides2

Frameshift3

Sanger3

Amplification4

Substitutions3

Single17

Exons1

Mutation2

Genes5

Protein14

Detection3

Genomes3

Chromosome1

Exome3

Strains1

Oligonucleotides1

Detect1

Adenine2

Cytosine1

Alignments2

Possible sequences1

Phylogenetic1

Variations2

Hybridization3

Codon3

Phenotype2

Next-generation6

Proteins1

Variant5

Duplication1

Transcript1

Distinct1

Homology1

Pathogen1

Promoter1

Cleavage1

Amino acids1

Trinucleotide1

Recombination1

Bases4

Synthesis2

Variation1

Processes1

Regions3

Analysis2