Genetics sequences microsatellites gene contains trinucleotide repeat expansion. Medical search. Frequent questions

A trinucleotide repeat expansion, also known as a triplet repeat expansion, is the DNA mutation responsible for causing any type of disorder categorized as a trinucleotide repeat disorder. (wikipedia.org)
For instance, if you've got a mutation caused by triplet repeat expansion, for instance in the Huntington's gene, where the trinucleotide repeats a CAG, you might have 17 CAGs in a normal chromosome. (hstalks.com)
Some occur in the coding region of the gene, others occur in the five prime region and others occur in the three prime region, and these have different consequences on the function of the gene and the results of the mutation. (hstalks.com)
Indeed, mutation detection enhancement gel electrophoresis of mixed PCR products from cloned haplotypes revealed 24 distinct heteroduplex patterns for the six possible trinucleotide heterozygotes. (scite.ai)
from the mutation of a single gene. (scirp.org)
YBM12-A and YBM12-B). This mutation in leaf color is controlled by a single dominant nuclear gene. (geneticsmr.com)
Huntington's disease (HD) is an autosomal dominant progressive neurodegenerative disorder caused by a dynamic mutation due to the expansion of CAG repeats in the HTT gene (4p16.3). (geneticsmr.com)
METHOD: Mutation screening of positional candidate genes was performed in two stages. (neurotransmitter.net)
2005) identified a mutation in the APP gene (104760.0019). (findzebra.com)
This subtype is due to a mutation in the APP gene (21q21.2), encoding the beta-amyloid precursor protein. (findzebra.com)

These are labelled in dynamical genetics as dynamic mutations. (wikipedia.org)
These diseases are all caused by microsatellite mutations, where a microsatellite either has three bases, four bases, five bases, or six bases, and these mutations result in excess numbers of copy of these particular units. (hstalks.com)
What this slide shows is that these types of mutations can occur in various parts of the gene. (hstalks.com)
Short tandem repeats (STRs) compose approximately 3% of the genome, and mutations at STR loci have been linked to dozens of human diseases including amyotrophic lateral sclerosis, Friedreich ataxia, Huntington disease, and fragile X syndrome. (biomedcentral.com)
To estimate the genome-wide pattern of mutations at STR loci, we analyze blood-derived whole-genome sequencing data for 544 individuals from 29 three-generation CEPH pedigrees. (biomedcentral.com)
We hypothesize that there might be at least three types of autism susceptibility genes/mutations that can be (i) specific to an individual patient or family, (ii) in a genetically isolated sub-population and (iii) a common factor shared amongst different populations. (neurotransmitter.net)
The genes/mutations could act alone or interact with other genetic and/or epigenetic or environmental factors, causing autism or related disorders. (neurotransmitter.net)
New technologies such as next-generation sequencing (including whole exome or whole genome sequencing) are expanding testing options, discovering new mutations, and creating challenges in counseling, interpreting, and reporting results to the patient. (medlink.com)
21 allelic mutations have been discovered in the APP gene. (findzebra.com)
2003) reviewed the pathology and genetics of APP -related CAA and discussed the different neuropathologic consequences of different APP mutations. (findzebra.com)

Diversity and genetic stability in banana genotypes in a breeding program using inter simple sequence repeats (ISSR) markers. (geneticsmr.com)
We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition. (biomedcentral.com)

The number of trinucleotide repeats appears to predict the progression, severity, and age of onset of Huntington's disease and similar trinucleotide repeat disorders. (wikipedia.org)
In 1993, for Huntington's disease (HD), a longer-than-usual CAG repeat with was found in the exon 1 coding sequence. (wikipedia.org)
REVIEW-ARTICLE Intermediate alleles of Huntington's disease HTT gene in different populations worldwide: a systematic review. (geneticsmr.com)

Next-generation sequencing of the whole exome is useful for testing for multiple candidate genes simultaneously or for discovering new, rare disorders. (medlink.com)
Whole exome sequencing is not suitable for detecting polynucleotide repeat disorders or large insertion/deletions. (medlink.com)
A total of 89 tumor tissues with matched normal tissues from Chinese NSCLC patients were collected and subjected to whole exome sequencing (WES). (biomedcentral.com)
Here, we investigated DNAm profiles of a Chinese NSCLC cohort, together with whole exome sequencing (WES) data to explore their direct correlation with TMB. (biomedcentral.com)

Due to the repetitive structure of STRs and their high mutability, sequencing and genotyping these loci is difficult, especially using short-read sequencing data. (biomedcentral.com)
Some of these tools are designed to detect STR expansions at disease-related loci, while others detect expansions and contractions of STRs genome-wide but are constrained by sequencing read length and the STR motif size. (biomedcentral.com)
Although NanoSTR needs further optimization and development, it is useful as an analytical method for the detection of STR loci by nanopore sequencing. (researchsquare.com)
These highly individual-specific number of repeats and the abundance of motifs have contributed to the polymorphism of STR loci. (researchsquare.com)
The final consensus maps are based on 1578 microsatellite loci and these maps have a cumulative length of approximately 1400 cM after adjustment for recombination frequencies of RI strains. (nervenet.org)

Nanopore sequencing is an evolving third/fourth generation sequencing technology for direct detection of nucleotide sequences with kb or even Mb base pairs (7)(8) . (researchsquare.com)
The analysis of the nucleotide sequences showed that the 77 accessions of A. thaliana were partitioned into two major differentiated haplotype classes (MDHCs). (biomedcentral.com)

Sequencing of their polymerase chain reaction (PCR) products revealed a G-->A transition immediately preceding the trinucleotide repeats, hence defining 8 distinct haplotypes and 36 possible genotypes. (scite.ai)
In another study, the trnL - trnF cpDNA intergenic spacer region of 475 individuals from 167 A. thaliana populations in its native range was sequenced and 16 haplotypes were identified [ 8 ]. (biomedcentral.com)

Due to the repetitive nature of the DNA sequence in these regions, 'loop out' structures may form during DNA replication while maintaining complementary base pairing between the parent strand and daughter strand being synthesized. (wikipedia.org)
repetitive sequences. (scirp.org)
Short tandem repeats (STRs), also known as microsatellites, are repetitive DNA sequences consisting of 1-6-bp motifs present in a genome. (researchsquare.com)

The Web site "www.artichokegenome.unito.it" hosts all the available genomic sequences, together with their structural/functional annotations and project information are presented to users via the open-source tool JBrowse, allowing the analysis of collinearity and the discovery of genomic variants, thus representing a one-stop resource for Cynara cardunculus genomics. (researchgate.net)
In this study, we identified abundant genomic SVs in the Panax genus that are hypothesized to have occurred through during the repeated polyploidizations/(re)diploidizations. (bvsalud.org)
Hello, my name is Professor Eamonn Maher, I'm professor of medical genetics and genomic medicine at the University of Cambridge. (hstalks.com)
The mechanisms by which genetic variants result in loss of protein function are many and variable, and include large-scale genomic deletions that can involve multiple genes, down to smaller single-exon deletions that may result in the protein reading frame being shifted and a truncated protein, or an in-frame loss of protein sequence. (hstalks.com)
SSRs occur less frequently than predicted and, although the majority of the repeat motifs do include A and T nucleotides, the A+T bias in SSRs is less than that predicted from the underlying genomic nucleotide composition. (biomedcentral.com)

Short tandem repeats (STRs), or microsatellites, are 1-6 base pair (bp) motifs of repeating units of DNA. (biomedcentral.com)
A total of 4,761 perfect and 6,583 imperfect SSRs were present in 3,781 genes (14.11% of the total), corresponding to an overall density across the gene space of 32,5 and 44,9 SSRs/Mbp for perfect and imperfect motifs, respectively. (researchgate.net)
In broader comparisons, SSRs vary among genomes in terms of abundance and length and most contain repeat motifs based on A and T nucleotides. (biomedcentral.com)

Other human diseases in which triplet repeat expansion occurs are fragile X syndrome, several spinocerebellar ataxias, myotonic dystrophy and Friedreich's ataxia. (wikipedia.org)

Size variation was readily detected, with four common alleles containing 12-15 repeats. (scite.ai)
One individual was found to carry a 12 kb deletion in one copy of the ASPA gene on 17p13, which when mutated in both alleles leads to Canavan disease. (biomedcentral.com)
The considered normal alleles have less than 27 CAG repeats. (geneticsmr.com)
Intermediate alleles (IAs) show 27 to 35 CAG repeats and expanded alleles have more than 35 repeats. (geneticsmr.com)

the detection of various repeats within these diseases demonstrated this relationship. (wikipedia.org)
During the decade after evidence that linked TNR to onset of disease was found, focus was placed on studying repeat length and dynamics on diseases, as well as investigating the mechanism behind parent-child disease inheritance. (wikipedia.org)
Currently, CAG repeat length is considered the biggest onset age modifier for TNR diseases. (wikipedia.org)
Today I'm going to tell you about microsatellites, and trinucleotide repeat expansions diseases. (hstalks.com)
The focus of my talk is going to be on the genetics of these diseases, and I'll talk very little about the functional biology of these conditions. (hstalks.com)
Long expansions of transcribed trinucleotide microsatellites have been etiologically associated with some neurological diseases. (scite.ai)

Our genome-wide comparisons demonstrated that although these polyploidization-derived SVs have evolved at distinct evolutionary stages, a large number of SV-intersecting genes showed enrichment in functionally important pathways related to secondary metabolites, photosynthesis and basic cellular activities. (bvsalud.org)
The uniparentally inherited chloroplast genome has been utilized in many studies in plant population and evolutionary genetics. (biomedcentral.com)

The first stage involved identifying, in unrelated subjects showing linkage to 2q24-q33, genetic variants in exons and flanking sequence within candidate genes and comparing the frequency of the variants between autistic and unrelated nonautistic subjects. (neurotransmitter.net)

We searched the expressed sequence tag databank for reiterated trinucleotides and selected EST00493 (D2S196E) with 14 tandem ACA triplets as a potentially polymorphic locus. (scite.ai)
of tandem repeats within their genomes [6, 17]. (scirp.org)
Short tandem repeats (STRs) are widely present in the human genome. (researchsquare.com)
NanoSTR can be used for STR detection and genotyping based on long-read data from nanopore sequencing with improved accuracy and efficiency compared with other existing methods, such as Tandem-Genotypes and TRiCoLOR. (researchsquare.com)
There are a few methods for STR identification based on nanopore sequencing, and the representative software are Tandem-Genotypes (11) , NanoSatellite (12) , STRique (13) ， etc. (researchsquare.com)

We used the two sequence characterized amplified region (SCAR) markers (CRF-SCAR and CMS-SCAR) in CMS pepper, to identify the genotype. (geneticsmr.com)

The observation of heteroduplex patterns in non-denaturing polyacrylamide gel electrophoresis (instead of the more commonly used denaturing gels) can thus be utilized to increase the informativeness of microsatellite polymorphisms by unraveling otherwise cryptic sequence variation. (scite.ai)
The number of repeat units differs between individuals, resulting in highly complex allele polymorphisms. (researchsquare.com)
In practice, however, the high error rate and special data characteristics of long-read sequencing have limited the efficient identification of STR polymorphisms, and therefore, further evaluation of the analytical methods is required (9)(10) . (researchsquare.com)
Two single nucleotide polymorphisms (SNPs) that showed evidence for divergent distribution between autistic and nonautistic subjects were identified, both within SLC25A12, a gene encoding the mitochondrial aspartate/glutamate carrier (AGC1). (neurotransmitter.net)

These authors found considerable variation existed among the non-coding single-copy sequences in the chloroplast genome of A. thaliana . (biomedcentral.com)
In this paper we report the complete chloroplast genome sequences of the angiosperms Nuphar advena (Nymphaeaceae) and Ranunculus macranthus (Ranunculaceae). (biomedcentral.com)

But in a diseased chromosome, you might have 40 successive copies of CAG trinucleotides in the gene. (hstalks.com)

For example, NanoSatellite directly analyzes STRs based on electric current distribution, and the accuracy of analysis depends heavily on the stability of the sequencing current and the precision of the basecalling model. (researchsquare.com)
We therefore developed NanoSTR as a method for detecting target STRs based on nanopore sequencing. (researchsquare.com)

When a DNA trinucleotide repeat sequence is damaged, it may be repaired by processes such as homologous recombination, non-homologous end joining, mismatch repair or base excision repair. (wikipedia.org)
Onwards from 1995, it was also possible to observe the formation of hairpins in triplet repeats, which consisted of repeating CG pairs and a mismatch. (wikipedia.org)

Fluorescence in situ hybridization (FISH), quantitative polymerase chain reaction (Q-PCR) and/or direct DNA sequencing were used to validate potential microdeletions and microduplications. (biomedcentral.com)

Perfect repeats mutate about 2 × more often than imperfect repeats. (biomedcentral.com)

Two subjects showed partial duplication of the TM4SF2 gene on Xp11.4, previously implicated in X-linked non-specific mental retardation, but in our subsequent analyses such variants were also found in controls. (biomedcentral.com)
Looking at loss-of-function variants and their role in human disease, in fact the majority of rare genetic disorders described to date result from loss-of-function pathogenic variants, that may partially or completely inactivate the gene product. (hstalks.com)

The number of completely sequenced plastid genomes available is growing rapidly. (biomedcentral.com)
The Nuphar [GenBank:NC_008788] and Ranunculus [GenBank:NC_008796] plastid genomes share characteristics of gene content and organization with many other chloroplast genomes. (biomedcentral.com)
Like other plastid genomes, these genomes are A+T-rich, except for rRNA and tRNA genes. (biomedcentral.com)
Detailed comparisons of Nuphar with Nymphaea , another Nymphaeaceae, show that more than two-thirds of these genomes exhibit at least 95% sequence identity and that most SSRs are shared. (biomedcentral.com)
In the majority of angiosperm chloroplast genomes two copies of a large inverted repeat (IR) of about 25 kb separate the remainder of the genome into two regions of unique DNA, the large (about 90 kb) and small (about 20 kb) single copy regions (LSC and SSC, respectively). (biomedcentral.com)

Yet, next-generation sequencing does not detect many neurogenetic disorders. (medlink.com)

These populations originated from a common ancestor, and a rapid demographic expansion began approximately 90,000 years ago. (biomedcentral.com)
The natural populations from China with specific genetic characteristics enriched the gene pools of global A. thaliana collections. (biomedcentral.com)
In contrast, interactions between genes and the environment cannot usually be studied using conventional mapping populations in which each animal is unique. (nervenet.org)

Triplet expansion is caused by slippage during DNA replication, also known as "copy choice" DNA replication. (wikipedia.org)
In addition to occurring during DNA replication, trinucleotide repeat expansion can also occur during DNA repair. (wikipedia.org)

A putative function has been assigned, using the gene ontology approach, to the set of genes harboring at least one SSR. (researchgate.net)

Pseudomolecules as well as unmapped scaffolds were used for the bulk mining of SSR markers and for the construction of the first globe artichoke microsatellite marker database. (researchgate.net)
scolymus) has been used to catalog the genome's content of simple sequence repeat (SSR) markers. (researchgate.net)
In this study we have increased the density of microsatellite markers 2- to 5-fold in each of several major RI sets that share C57BL/6 as a parental strain (AXB, BXA, BXD, BXH, and CXB). (nervenet.org)

In 1992, for myotonic dystrophy type 1 (DM1), CTG expansion was found in the myotonic dystrophy protein kinase (DMPK) 3' UTR. (wikipedia.org)
These disorders have in common that the associated genetic alterations result, in most cases, in altered expression or function of the protein product of the relevant gene, which then directly or indirectly leads to pathophysiological changes that result in disease. (hstalks.com)
It is structurally different from TELOMERIC REPEAT BINDING PROTEIN 1 in that it contains basic N-terminal amino acid residues. (lookformedical.com)
The pattern of evolution in the sequences identified as ycf15 and ycf68 is not consistent with them being protein-coding genes. (biomedcentral.com)

These guarantee onset of early-onset familial Alzheimer disease and all occur in the region of the APP gene that encodes the Aβ domain. (findzebra.com)
The Bloom syndrome gene (BLM) encodes a RecQ-like DNA helicase. (lookformedical.com)

Epigenetics broadly is a heritable genetic characteristic that is a cell-specific gene expression and regulation achieved by the interaction between DNA and transcriptional factors. (geneticeducation.co.in)

The same search parameters were applied to reveal the SSR content of 14 other plant species for which genome sequence is available. (researchgate.net)
CRISPR-CAS9 is a system of gene editing (precisely, the precise/specific gene-editing tool) having lucrative applications in medical research, diagnostics, animal research, plant and agriculture science. (geneticeducation.co.in)

This method adds to the toolbox for nanopore-based STR analysis and expands the applications of nanopore sequencing in scientific research and clinical scenarios. (researchsquare.com)

However, there are few methods for STR detection based on nanopore sequencing due to the challenges posed by the sequencing principles and the data characteristics of nanopore sequencing. (researchsquare.com)
In terms of data characteristics, NanoSTR effectively avoids the non-random sequencing errors and unexpected insertions-deletions (indels) associated with nanopore sequencing (8)(9) and thus improves the efficiency of sequencing data utilization, the detection rate of STR genotypes, and the accuracy of STR profiling. (researchsquare.com)

The results in PAR1/PAR2 are the first large-scale studies of gene dosage in these regions, and the findings at the ASMT locus indicate that further studies of the duplication of the ASMT gene are needed in order to gain insight into its potential involvement in ASD. (biomedcentral.com)
Negative association findings and research involving the serotonin transporter gene, FMR1, RELN, WNT2, HOXA1, and HOXB1 genes may be found elsewhere on this site . (neurotransmitter.net)

at the time, debate centered around whether disease was brought on by smaller amounts of short expansions or a small amount of long expansions. (wikipedia.org)

Our studies also identify some limitations of MLPA, where single base changes in probe binding sequences alter results. (biomedcentral.com)
RESULTS: In total, 487 no-repeat targets corresponding to the bioactive components of ZGW were screened, and 175 target genes in the intersection of ZGW and osteogenesis were obtained. (bvsalud.org)

SMBA is the first "CAG / polygutamine" disease, which is a subcategory of repeat disorders. (wikipedia.org)

Apolipoprotein E (ApoE) is one of the most extensively studied genes in the context of aging, but there are few population-based studies on ApoE polymorphism in the elderly in developing countries. (scite.ai)

The SSRs were categorized for the numbers of repeats present, their overall length and were allocated to their linkage group. (researchgate.net)

Other proposed mechanisms for expansion and reduction involve the interaction of RNA and DNA molecules. (wikipedia.org)

In 1991, for fragile X syndrome, the fragile X mental retardation 1 (FMR-1) gene was found to contain a CGG expansion in its 5' untranslated region (UTR). (wikipedia.org)

In fact, these regions show no evidence of sequence conservation beyond what is normal for non-coding regions of the IR. (biomedcentral.com)
In addition, 437 genes show DNAm aberrance status in high TMB patient group and 99 have been reported as its association with lung cancer. (biomedcentral.com)

Repeat composition and location are used to determine the mechanism of a given expansion. (wikipedia.org)

Anatomy2

Organisms2

Diseases19

Chemicals and Drugs18

Analytical, Diagnostic and Therapeutic Techniques and Equipment8

Psychiatry and Psychology2

Phenomena and Processes41

Disciplines and Occupations2

Information Science4

Health Care2

Mutation10

Mutations10

Simple sequenc2

Huntington's3

Whole exome4

Loci5

Nucleotide sequences2

Haplotypes2

Repetitive3

Genomic5

Motifs3

Triplet repeat expansion1

Alleles4

Diseases6

Evolutionary2

Candidate genes1

Tandem5

Genotype1

Polymorphisms4

Chloroplast genome2

Chromosome1

STRs2

Mismatch2

Polymerase1

Imperfect1

Variants2

Genomes5

Detect1

Populations3

Replication2

Putative1

Markers3

Protein4

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Plant2

Clinical1

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SSRs1

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Untranslated region1

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