Homologous sequence deletion. Medical search. Frequent questions

Sequences were aligned by using ClustalW ( http://www.genome.jp/tools/clustalw/ ) and MEGA4.1 ( http://www.megasoftware.net/ ) and showed 100% identity with each other ( Figure ). (cdc.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)
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)
We used whole-genome sequencing of multiple isogenic chicken DT40 cell clones to precisely determine the consequences of BRCA1/2 loss on all types of genomic mutagenesis. (crick.ac.uk)
1 Clustered regularly interspaced palindromic repeats (CRISPR) refers to sequences in the bacterial genome. (bmj.com)
It is the latter which allows precise genome editing: the homologous section of DNA with the required sequence change may be delivered with the Cas9 nuclease and sgRNA, theoretically allowing changes as precise as a single base-pair. (bmj.com)
Similar sequences in the human genome can cross over during mitosis or meiosis, resulting in a shortened portion of the gene sequence. (wearefibro.org)
Phenotypic effects of deletions depend on the size and location of deleted sequences on the genome. (wearefibro.org)
This study obtained a genome assembly of T. hamatum T21, with a 41.4 Mb genome sequence comprising 8170 genes. (qxmd.com)
Whole exome sequencing (WES), involves sequencing of coding exons comprising approximately 2% of the whole human genome, which are estimated to contain approximately 85% of pathogenic variants associated with monogenic disease [ 6 ]. (biomedcentral.com)
For comprehensive investigation of the genetic heterogeneity of diseases with a wide range of causative genes, such as hearing loss, and to identify novel candidate genes, WES analysis overcomes the limitations of targeted analysis and is considerably more cost-effective than whole genome sequencing (WGS) analysis. (biomedcentral.com)
In this study, using a combination of Oxford Nanopore Technologies and Illumina sequencing data, we generated a highly contiguous reference genome (283 scaffolds with an N50 length of 294 kb, totaling 41.5 Mb). (bvsalud.org)
CRISPR-Cas systems are a new generation of RNA-guided microbial genome engineering tools that allow targeted genome modifications, such as insertions, deletions, and point mutations, to be introduced with greater ease than ever before. (sigmaaldrich.com)

Collapsed forks can be rescued by homologous recombination, which restarts replication. (elifesciences.org)

The pipeline includes an algorithm for detection of large (single exon-level or larger) deletions and duplications. (arupconsult.com)
Approximately 89% of pathogenic variants are sequence variants, whereas 10% are large deletion/duplications. (arupconsult.com)
As with duplications, deletions can affect gene dosage and thus the resulting phenotype. (wearefibro.org)
Sequence variants and/or copy number variants (deletions/duplications) within the CCDC148 gene will be detected with >99% sensitivity. (fulgentgenetics.com)
single exon deletions or duplications may occasionally be identified, but are not routinely detected by this test. (fulgentgenetics.com)
Identified putative deletions or duplications are confirmed by an orthogonal method (qPCR or MLPA). (fulgentgenetics.com)
Lyon hypothesis (X-inactivation) Sex chromosome abnormalities may involve aneuploidy, partial deletions or duplications of sex chromosomes, or mosaicism. (msdmanuals.com)

Once detected by the cell, blunt-ended DSBs are repaired by the non-homologous end joining (NHEJ) pathway, which is notorious for adding or removing stretches of DNA during repair. (technologynetworks.com)
The situations were caused by different DNA repair mechanisms, nonhomologous end joining (NHEJ), and homologous recombination (HR). Overall, we have successfully constructed an efficient and convenient CRISPR/Cas9 system in T. hamatum for the first time, which has important scientific significance and application value for studies on functional genomics of Trichoderma and other filamentous fungi. (qxmd.com)
These nucleases can create double strand breaks (DSBs) in the DNA sequence that can be repaired by two main mechanisms: Non-homologous end joining (NHEJ), which introduces indels to modify the DNA sequence, and Homology-directed repair (HDR), which uses a donor template for accurate genetic correction. (uc3m.es)
U2OS.EGFP cells caused by inactivating frameshift insertion/deletion (indel) mutations introduced by error prone non-homologous end-joining (NHEJ) repair of nuclease-induced double-stranded breaks (DSBs) (Fig. 1a and Methods ). (cdc.gov)

The human exome includes all coding nuclear DNA sequences, approximately 180,000 exons that are transcribed into mature RNA. (nih.gov)
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)
To detect pathogenic variants in multiple deafness genes, in addition to novel candidate genes associated with hearing loss, whole exome sequencing (WES), followed by analysis prioritizing genes categorized in four tiers, were applied. (biomedcentral.com)
Exome sequencing findings in children with annular pancreas. (cdc.gov)

Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is an autosomal recessive multisystem disorder associated with depletion, multiple deletions and site-specific point mutations of mitochondrial DNA (mtDNA). (nih.gov)
X linked Alport syndrome (ATS, OMIM 301050) is a hereditary glomerulonephritis resulting from either point mutations or intragenic deletions of the COL4A5 gene encoding the α5 chain of type IV collagen. (bmj.com)
Spontaneously arising and MMS-induced insertion/deletion mutations and large rearrangements were also more common in BRCA1/2 mutant cells compared with the wild-type control. (crick.ac.uk)
A single mutation in NEMO/IKK -gamma involving the deletion of exons 4 through 10 accounts for most (80%) incontinentia pigmenti mutations. (medscape.com)
A local high frequency of microhomologies, macrohomologies, tandem repeats, and repeat/repetitive sequences contribute to a high rate of nonallelic homologous recombination involving NEMO , resulting in the development of de novo deletion mutations. (medscape.com)
Further, many of the human diseases and functional divergence between homologous proteins are related more to the indel mutations than to the substitution mutations, even though the former occurs less often than the latter. (concordia.ca)
The mtDNA 4977 bp deletion is one of the most frequently observed mtDNA mutations in human tissues and may play a role in breast cancer (BC). (wearefibro.org)
How do deletion mutations occur? (wearefibro.org)

Allows for insertions or deletions in the sequences being aligned. (aporc.org)
From this cleavage and repair process, sequence insertions or deletions (indels) often cause errors in translation, leading to functional gene, and subsequent protein, knockdown. (technologynetworks.com)
Moreover, sequencing revealed fragment deletions between dual sgRNA target sites or GFP gene insertions presented in knockout strains. (qxmd.com)
To solve this, we have developed a novel, dual-vector Cas9-mediated recombineering system that allows researchers to create scarless insertions, deletions, and replacements with incredibly high efficiency in E. coli . (sigmaaldrich.com)

The HNPP (hereditary neuropathy with liability to pressure palsies) deletion and CMT1A (Charcot-Marie-Tooth disease type 1A) duplication are the reciprocal products of homologous recombination events between misaligned flanking CMT1A-REP repeats on chromosome 17p11. (nih.gov)
3 Selection markers can be integrated into double-stranded DNA (dsDNA) donors, but excision of these markers requires a second step and creates scar sequences 4 that can trigger unwanted recombination events. (sigmaaldrich.com)

4, 5 Until recently, the only known contiguous gene syndrome involving the COL4A5 gene was Alport syndrome and diffuse leiomyomatosis (ATS-DL, OMIM 308940), 6- 9 in which the deletion extends towards the centromere to include the first two exons of the adjacent COL4A6 gene. (bmj.com)

What is an example of deletion mutation? (wearefibro.org)
What is deletions mutation? (wearefibro.org)
Deletion is a type of mutation involving the loss of genetic material. (wearefibro.org)
A deletion mutation occurs when a wrinkle forms on the DNA template strand and subsequently causes a nucleotide to be omitted from the replicated strand (Figure 3). (wearefibro.org)
For instance, if just one nucleotide is deleted from the sequence, then all of the codons including and after the mutation will have a disrupted reading frame. (wearefibro.org)
Fig. 3: Haplotype and association analyses in natural populations identify the deletion in TaHRC as the likely causal mutation for Fhb1 . (nature.com)
Other sources of experimental information include X-ray diffraction, biotinylation, sequence mutation and deletion, solution binding and chemical cross-linking data. (lu.se)
The reason for the observed defective assembly in E. coli is probably not some unidentified mutation in the plasmid DNA because the same plasmid preparation complemented a B. subtilis sdhCAB deletion strain [7]. (lu.se)
Accession C0001 Systematic name Allele 1 and 2: g.20063delC, c.123delC, r.123delc, Systematic name p.Val42fsX37 Original code 22-year-old man Description Allele 1 and 2: a frame shift deletion mutation in the Description exon 5 leading to a premature stop codon in the UP/Ly6 Description domain Date 24-Aug-2004 (Rel. (lu.se)

Large deletion/duplication calls made using MPS are confirmed by an orthogonal exon-level microarray when sample quality and technical conditions allow. (arupconsult.com)
The first strategy used TALENs and showed the feasibility of an exon deletion-based approach to correct RDEB epidermal stem cells as safe clonal therapy. (uc3m.es)

Chromosomal fluorescence in situ hybridization (FISH) demonstrating the deletion of one chromosomal region 22q11 segment. (medscape.com)
A chromosomal deletion occurs when seg-ments of genetic information are missing on a particular chromosome or more. (bvsalud.org)
E. coli , one of the most commonly engineered bacteria, has an active homologous recombination (HR) system, so chromosomal integration can be achieved simply by donating DNAs with homology arms to recombine at a target site. (sigmaaldrich.com)

Five individuals also had interspersed patches of proximal or distal repeat specific DNA sequence indicating potential gene conversion during the exchange of genetic material. (nih.gov)
Deletions are responsible for an array of genetic disorders, including some cases of male infertility, two thirds of cases of Duchenne muscular dystrophy, and two thirds of cases of cystic fibrosis (those caused by ΔF508). (wearefibro.org)
Nucleotide sequences change places with the target gene during homologous recombination and are left behind as a genetic scar, undermining the effectiveness of subsequent deletions. (wearefibro.org)
Conclusion: Deletions on chromosome 6 are a very rare genetic alteration. (bvsalud.org)
This organism's appeal among genetic analysts lends itself to the organism's superior tractability when "homologous recombination between transforming DNA and target genomic sequences " takes place. (ensembl.org)
In meiosis, the genetic information inherited from a person's mother and father is recombined through crossing over (exchange between homologous chromosomes). (msdmanuals.com)

Sanger sequencing is performed as necessary to fill in regions of low coverage and in certain situations, to confirm variant calls. (arupconsult.com)
The results of the multi‑gene panel test were further verified by Sanger sequencing. (spandidos-publications.com)
Sanger sequencing is used to confirm variants with low quality scores and to meet coverage standards. (fulgentgenetics.com)

This "facilitates functional analysis by site-specific gene deletion. (ensembl.org)

Using long sequencing reads from the Oxford Nanopore Technologies platform, we phased SNVs within large gene copy arrays for the first time. (elifesciences.org)

Velocardiofacial syndrome (VCFS) is caused by a deletion (microdeletion) at the q11.2 band, which is located on the long arm (q) of chromosome 22 (see the images below). (medscape.com)
Karyotype of a patient with a deletion of chromosome region 22q11. (medscape.com)
A long range deletion map was constructed using available X chromosome YAC contigs and the DNA of the proband of family 1, hybrid 1C3 derived from the mother of family 2, and patients 3 and 4. (bmj.com)
Deletion of part of the short arm of chromosome 5 results in Cri du chat syndrome. (wearefibro.org)
For instance, deletions that span a centromere result in an acentric chromosome that will most likely be lost during cell division. (wearefibro.org)
Objective: Report the case of a child with a terminal segment deletion of 8,9 Mb on the short arm of chromosome 6 (in 6p25.3p24.3) Methods: This case report was approved by the Ethics and Research Committee of the institution. (bvsalud.org)
Twenty-two of the pairs, chromosome numbers 1 to 22, the autosomes, are normally homologous (identical in size, shape, and position and number of genes). (msdmanuals.com)

Approximately 90% of pathogenic variants are detectable by sequencing and deletion/duplication analysis. (arupconsult.com)
Protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs. (ensembl.org)

Testing for a known familial sequence variant by sequencing gene of interest. (arupconsult.com)

Insertion/deletion (indel) and substitution of an amino acid are two common events that lead to the evolution of and variations in protein sequences. (concordia.ca)
Repair after the DNA cut may occur via two pathways: non-homologous end joining, typically leading to a random insertion/deletion of DNA, or homology directed repair where a homologous piece of DNA is used as a repair template. (bmj.com)

We can therefore amplify nucleotide sequences from infinitesimal amounts of DNA extract. (intechopen.com)
Nucleotide sequences can be compared with nucleotide sequences in a database using BLASTN, for example. (aporc.org)

The methods used in multigene panels may include sequence analysis , deletion/duplication analysis , and/or other non-sequencing-based tests. (nih.gov)

While direct repeats and imperfectly homologous sequences appear to mediate the formation of mtDNA deletions, the nicotinamide adenine dinucleotide dehydrogenase 5 gene is a hot-spot for these rearrangements. (nih.gov)

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)
The aim of this study was to investigate the frequency of mtDNA 4977 bp deletion in BC tissue and its association with clinical factors. (wearefibro.org)
Introduction: Deletion syndromes are rare events in clinical practice. (bvsalud.org)

The nptII gene in transgenic potato plants coding for kanamycin resistance, transforms naturally competent cells of the soil bacteria Pseudomonas stutzeri and Acinetobacter BD413 (both harboring a plasmid with an nptII gene containing a small deletion (hence nonfunctional) with the same high efficiency as nptII genes on plasmid DNA ( 3x10-5 -1x10-4) despite the presence of a more than 106 fold excess of plant DNA. (gmwatch.org)

We find that this type of non-canonical fork convergence in fission yeast is prone to trigger deletions between repetitive DNA sequences via a mechanism we call Inter-Fork Strand Annealing (IFSA) that depends on the recombination proteins Rad52, Exo1 and Mus81, and is countered by the FANCM-related DNA helicase Fml1. (elifesciences.org)
A difference in the short deletion phenotypes of BRCA1 and BRCA2 suggested distinct roles for the two proteins in the processing of DNA lesions, as BRCA2 mutants contained more short deletions, with a wider size distribution, which frequently showed microhomology near the breakpoints resembling repair by non-homologous end joining. (crick.ac.uk)
Several proteins were affected post-translationally by the bldA deletion. (biomedcentral.com)
The first and most important step in studying a newly discovered protein sequence is to search protein databases for proteins that are similar or closely-related to the new protein, and then to align the new protein sequence to these proteins. (concordia.ca)
Cell 75:495, 1993), and a series of unique E6-AP homologous proteins have been identified (Huibregtse et al. (justia.com)
Although, the number of omic techniques is ever expanding, the most developed omics technologies are high throughput DNA sequencing, transcriptomics (focused on gene expression), epigenomics (focused on epigenetic regulation of gene expression), proteomics (focused on large sets of proteins, the proteome) and metabolomics (focused on large sets of metabolites, the metabolome). (who.int)

A novel aspect of the mtDNA deletions in MNGIE is the presence of microdeletions at the imperfectly homologous breakpoints. (nih.gov)

We have now identified five major forms of mtDNA deletions in the skeletal muscle of MNGIE patients. (nih.gov)

The guide RNA complexes with the Cas endonuclease, is transported to the nucleus, and creates a DNA double-strand break (DSB) at a site pre-programmed in the targeting sequence of the guide RNA. (technologynetworks.com)

Each gene has a specific location (locus), which is typically the same on each of the 2 homologous chromosomes. (msdmanuals.com)

These results are consistent with the hypothesis that minimum efficient processing segments, which have been characterized in Escherichia coli, yeast, and cultured mammalian cells, may be required for efficient homologous meiotic recombination in humans. (nih.gov)
In addition, embryonic stem cells may be modified by homologous recombination for use in producing chimeric or transgenic mammalian hosts, which may be used as source of universal donor organs. (justia.com)

In this article, we present an application of our novel E. coli CRISPR/Cas-mediated Lambda-Red (λ-Red) homologous recombination (HR) vector system, which facilitates gene editing through the homology-directed repair (HDR) of double-stranded DNA breaks (DSBs) created by Cas9 endonuclease, using either ssDNA or dsDNA as an editing template. (sigmaaldrich.com)

The recruitment of this machinery results in the production of viroid-derived small RNAs (vd-sRNAs) that mediate RNA degradation and DNA methylation of cognate sequences. (degruyter.com)

The bla gene originates from the cloning vector PUC18 and is not expressed in maize, but has bacterial regulatory sequences that would allow it to become functional were it to be transferred back into bacteria. (gmwatch.org)

Although next generation sequencing technologies and our bioinformatics analysis significantly reduce the contribution of pseudogene sequences or other highly-homologous sequences, these may still occasionally interfere with the technical ability of the assay to identify pathogenic variant alleles in both sequencing and deletion/duplication analyses. (fulgentgenetics.com)
2 alleles may have slight differences or the same DNA sequences. (msdmanuals.com)

also known as next generation sequencing [NGS]) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline. (arupconsult.com)
afterwards, this variant sequence may have significantly expanded to cultivated groups, thereby improving adaptation during the domestication process. (biomedcentral.com)

NF1 whole gene deletions are associated with more severe cognitive issues, somatic overgrowth, large numbers of cutaneous neurofibromas, and dysmorphic facial features. (arupconsult.com)

Thus, the alignment of multiple protein sequences is one of the most commonly performed tasks in bioinformatics analyses, and has been used in many applications, including sequence annotation, phylogenetic tree estimation, evolutionary analysis, secondary structure prediction and protein database search. (concordia.ca)
Identical sequences of the TaHRC-R allele in diverse accessions indicate that Fhb1 had a single origin, and phylogenetic and haplotype analyses suggest that the TaHRC-R allele most likely originated from a line carrying the Dahongpao haplotype. (nature.com)

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)
Owing to their function in homologous recombination repair, much research has focused on the unstable genomic phenotype of BRCA1/2 mutant cells manifest mainly as large-scale rearrangements. (crick.ac.uk)

This method can generate tens of billions of copies of a particular DNA fragment (the sequence of interest, DNA of interest, or target DNA) from a DNA extract (DNA template). (intechopen.com)

A 1.7-kb hotspot for homologous recombination was previously identified wherein the relative risk of an exchange event is 50 times higher than in the surrounding 98.7% identical sequence shared by the CMT1A-REPs. To refine the region of exchange further, we designed a PCR strategy to amplify the recombinant CMT1A-REP from HNPP patients as well as the proximal and distal CMT1A-REPs from control individuals. (nih.gov)
By comparing the sequences across recombinant CMT1A-REPs to that of the proximal and distal CMT1A-REPs, the exchange was mapped to a 557-bp region within the previously identified 1.7-kb hotspot in 21 of 23 unrelated HNPP deletion patients. (nih.gov)
Two patients had recombined sequences suggesting an exchange event closer to the mariner-like element previously identified near the hotspot. (nih.gov)

A first assembly was previously obtained for the Tift 23D2B1-P1-P5 cultivar genotype using short-read sequencing technologies. (bvsalud.org)

Sequences were grouped with VACV group 2 isolates. (cdc.gov)
We examined the distribution of the pilus islet, using the presence of the rlrA gene as a marker for the locus, among a collection of invasive isolates recovered in Portugal and analyzed its association with capsular serotypes, clusters defined by the pulsed-field gel electrophoretic profiles (PFGE) and multilocus sequence types. (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)

At least in plants, DNA regions that become de novo methylated can be defined by homologous RNA molecules in a process termed RNA-directed DNA methylation (RdDM). (degruyter.com)

1- 3 Contiguous gene syndromes are phenotypically complex disorders associated with the deletion of multiple adjacent genes. (bmj.com)

This allowed us to focus on the effects of bldA deletion on metabolism and overall cell physiology without the complication of the unsynchronised morphological differentiation observed with surface-grown S. coelicolor cultures. (biomedcentral.com)

by transgenic plant DNA strictly depends on homologous sequences in the recipient cells. (gmwatch.org)

Why does deletion occur? (wearefibro.org)
Deletions occur when there is homologous but unequal recombination between gene sequences. (wearefibro.org)

The discipline of obtaining information about genomic or protein sequence data. (aporc.org)
The BLASTP program is used to search a protein database for a match against a query protein sequence. (aporc.org)
The objectives of this thesis are to develop a novel scheme to predict indel flanking regions (IndelFRs) in a protein sequence and to develop an efficient algorithm for the alignment of multiple protein sequences incorporating the information on the predicted IndelFRs. (concordia.ca)
In the first part of the thesis, a variable-order Markov model-based scheme to predict indel flanking regions in a protein sequence for a given protein fold is proposed. (concordia.ca)
We are also interested in understanding how oligomerization specificity is encoded in protein sequence and structure, in particular in coiled-coils. (lu.se)

In order to cut, a specific sequence of DNA of between 2 and 5 nucleotides (the exact sequence depends upon the bacteria which produces the Cas9) must lie at the 3' end of the guide RNA: this is called the protospacer adjacent motif (PAM). (bmj.com)

Small deletions remove one or a few nucleotides within a gene, while larger deletions can remove an entire gene or several neighboring genes. (wearefibro.org)

Homologous recombination is employed to inactivate genes, particularly genes associated with MHC antigens. (justia.com)

An alternative to PAM tables, BLOSUM tables were derived using local multiple alignments of more distantly related sequences than were used for the PAM matrix. (aporc.org)
For example, the validity of the branch arrangement in a predicted phylogenetic tree can be tested by resampling columns in a multiple sequence alignment to create many new alignments. (aporc.org)
In spite of considerable research and efforts that have been recently deployed for improving the performance of multiple sequence alignment (MSA) algorithms, finding a highly accurate alignment between multiple protein sequences still remains a challenging problem. (concordia.ca)
In the second part of the thesis, a novel and efficient algorithm incorporating the information on the predicted IndelFRs for the alignment of multiple protein sequences is proposed. (concordia.ca)

The cutaneous manifestations usually appear in a characteristic, chronologic sequence. (medscape.com)

Anatomy6

Organisms5

Diseases2

Chemicals and Drugs32

Analytical, Diagnostic and Therapeutic Techniques and Equipment19

Phenomena and Processes74

Disciplines and Occupations2

Information Science9

Genome13

Rescued by homologous recombination1

Duplications7

NHEJ4

Exome5

Mutations8

Insertions4

Recombination events2

Exons1

Mutation9

Exon2

Chromosomal3

Genetic6

Sanger3

Gene Deletion1

Oxford Nanopore Technologies1

Chromosome7

Variants2

Familial sequence variant1

Insertion2

Nucleotide sequences2

Duplication analysis1

Repeats1

Clinical4

Plasmid1

Proteins6

Breakpoints1

MtDNA1

Strand1

Chromosomes1

Mammalian2

CRISPR1

Mediate1

Functional1

Alleles2

Variant2

Somatic1

Analyses2

Phenotype2

Fragment1

Previously identified3

Genotype1

Isolates2

Pathogenic1

Novo1

Syndromes1

Metabolism1

Transgenic1

Occur2

Protein sequence5

Depends1

Nucleotides1

Genes associated1

Multiple4

Manifestations1