• Trinucleotide repeat disorders, also known as microsatellite expansion diseases, are a set of over 50 genetic disorders caused by trinucleotide repeat expansion, a kind of mutation in which repeats of three nucleotides (trinucleotide repeats) increase in copy numbers until they cross a threshold above which they cause developmental, neurological or neuromuscular disorders. (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)
  • 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)
  • Many regions of the genome (exons, introns, intergenic regions) normally contain trinucleotide sequences, or repeated sequences of one particular nucleotide, or sequences of 2, 4, 5 or 6 nucleotides. (wikipedia.org)
  • 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)
  • 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)
  • Short tandem repeats (STRs) are widely present in the human genome. (researchsquare.com)
  • Short tandem repeats (STRs), also known as microsatellites, are repetitive DNA sequences consisting of 1-6-bp motifs present in a genome. (researchsquare.com)
  • 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)
  • The advent of massively parallel sequencing technologies [ 8 ] allowed cheap and efficient evaluation of the somatic mutations in a cancer genome. (biomedcentral.com)
  • This provided an unprecedented opportunity to examine somatic mutational patterns by sequencing multiple cancer-associated genes, by sequencing all coding regions of the human genome (i.e., usually referred to as whole-exome sequencing), or even by interrogating the complete sequence of a cancer genome (i.e., an approach known as whole-genome sequencing). (biomedcentral.com)
  • In addition to confirming prior observations, whole-exome and whole-genome sequencing data provided a unique opportunity for identifying all of the mutational processes that have been active in the lineage of a cancer cell [ 12 ]. (biomedcentral.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)
  • In this paper we report the complete chloroplast genome sequences of the angiosperms Nuphar advena (Nymphaeaceae) and Ranunculus macranthus (Ranunculaceae). (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)
  • The discovery that trinucleotide repeats could expand during intergenerational transmission and could cause disease was the first evidence that not all disease-causing mutations are stably transmitted from parent to offspring. (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)
  • 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)
  • 21 allelic mutations have been discovered in the APP gene. (findzebra.com)
  • 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)
  • 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)
  • 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)
  • An increase number of repeats of a genomic, tandemly repeated DNA sequence from one generation to the next. (uams.edu)
  • 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)
  • The particularity of the FCGS coding resides in exploiting the statistical properties of the genomic sequence itself. (springeropen.com)
  • However, the search for relevant information along the genomic sequences is not an easy task. (springeropen.com)
  • In order to better understand the genomic sequence role and structure, several signal processing approaches have been investigated. (springeropen.com)
  • The specificity of our coding consists on exploiting the statistical properties of the genomic sequence itself, which may serve in detecting interesting structures within the DNA sequences. (springeropen.com)
  • Diversity and genetic stability in banana genotypes in a breeding program using inter simple sequence repeats (ISSR) markers. (geneticsmr.com)
  • The chromosomal instability resulting from this trinucleotide expansion presents clinically as intellectual disability, distinctive facial features, and macroorchidism in males. (wikipedia.org)
  • Short tandem repeats (STRs), or microsatellites, are 1-6 base pair (bp) motifs of repeating units of DNA. (biomedcentral.com)
  • of tandem repeats within their genomes [6, 17]. (scirp.org)
  • Trinucleotide repeats are a subset of a larger class of unstable microsatellite repeats that occur throughout all genomes. (wikipedia.org)
  • Genomes of individuals strains typically incorporate 45-55 recombinations between parental chromosomes. (nervenet.org)
  • 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 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)
  • 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)
  • 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)
  • Genetic correlations between loci on different chromosomes can be high and can generate false positive linkage. (nervenet.org)
  • Such repetitive sequences occur at a low level that can be regarded as "normal. (wikipedia.org)
  • repetitive sequences. (scirp.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)
  • Today I'm going to tell you about microsatellites, and trinucleotide repeat expansions diseases. (hstalks.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 used the two sequence characterized amplified region (SCAR) markers (CRF-SCAR and CMS-SCAR) in CMS pepper, to identify the genotype. (geneticsmr.com)
  • In this second type of disorder, large repeat expansions in DNA are transcribed into pathogenic RNAs that form nuclear RNA foci. (wikipedia.org)
  • The third main category of trinucleotide repeat disorders and related microsatellite disorders is due to the translation of repeat sequenced into pathogenic proteins containing a stretch of repeated amino acids. (wikipedia.org)
  • 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)
  • 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)
  • 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)
  • Yet, next-generation sequencing does not detect many neurogenetic disorders. (medlink.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)
  • The authors recently mapped a susceptibility locus for autism to chromosome region 2q24-q33 (MIM number 606053). (neurotransmitter.net)
  • This results in, variously, a toxic gain of function, a loss of function, a dominant negative effect and/or a mix of these mechanisms for the protein hosting the expansion. (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)
  • A plethora of prior research has focused on examining mutational signatures and mutational patterns from single base substitutions and their immediate sequencing context. (biomedcentral.com)
  • By utilizing mathematical modelling and computational analysis, we previously created the concept of mutational signatures and provided tools for deciphering mutational signatures from massively parallel sequencing data [ 13 ]. (biomedcentral.com)
  • The DNA of Uromastyx hardwickii was amplified and sequenced using 16S rRNA primer set. (bvsalud.org)
  • After trimming ambiguous bases, the obtained 16S rRNA fragment was 520 bp while 16S rRNA fragments aligned with closely matched sequence from NCBI comprised of 510 bp. (bvsalud.org)
  • Trinucleotide repeat disorders and the related microsatellite repeat disorders affect about 1 in 3,000 people worldwide. (wikipedia.org)
  • Three categories of trinucleotide repeat disorders and related microsatellite (4, 5, or 6 repeats) disorders are described by Boivin and Charlet-Berguerand. (wikipedia.org)
  • The second main category of trinucleotide repeat disorders and related microsatellite disorders involves a toxic RNA gain of function mechanism. (wikipedia.org)
  • Sometimes, a person may have more than the usual number of copies of a repeat sequence associated with a gene, but not enough to alter the function of that gene. (wikipedia.org)
  • But in a diseased chromosome, you might have 40 successive copies of CAG trinucleotides in the gene. (hstalks.com)
  • However, the frequency of occurrence of any one particular repeat sequence disorder varies greatly by ethnic group and geographic location. (wikipedia.org)
  • The FCGS approach relies on the frequency value of each sub-pattern assignment, which gives us the opportunity to produce several signals for the same input sequence, depending on the size of the considered sub-patterns. (springeropen.com)
  • A partial duplication in the ASMT gene, located in the pseudoautosomal region 1 (PAR1) of the sex chromosomes and previously suggested to be involved in ASD susceptibility, was observed in 6-7% of the cases but in only 2% of controls (P = 0.003). (biomedcentral.com)
  • In the present study, genes across the 2q24-q33 interval were analyzed to identify an autism susceptibility gene in this region. (neurotransmitter.net)
  • Almost every chromosome is affected by numeric or structural aberrations. (neurotransmitter.net)
  • Thus, revealing the structural and organizational features in DNA sequences is a very interesting topic. (springeropen.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)
  • 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)
  • An abnormal congenital condition, associated with defects in the LAMIN TYPE A gene, which is characterized by premature aging in children, where all the changes of cell senescence occur. (lookformedical.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)
  • In fact, these regions show no evidence of sequence conservation beyond what is normal for non-coding regions of the IR. (biomedcentral.com)
  • 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)
  • The occurrence of breakpoints conforms to a Poisson distribution with a mean of 1.9 to 3.5 recombinations per chromosome. (nervenet.org)
  • However, Bayesian and maximum likelihood from sequencing data demonstrated the occurrence of a single species, Cichla kelberi. (bvsalud.org)
  • Patients carry from 230 to 4000 CGG repeats in the gene that causes fragile X syndrome, while unaffected individuals have up to 50 repeats and carriers of the disease have 60 to 230 repeats. (wikipedia.org)
  • 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 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)
  • Linkage and association of the mitochondrial aspartate/glutamate carrier SLC25A12 gene with autism. (neurotransmitter.net)
  • CONCLUSIONS: A strong association of autism with SNPs within the SLC25A12 gene was demonstrated. (neurotransmitter.net)
  • Our studies also identify some limitations of MLPA, where single base changes in probe binding sequences alter results. (biomedcentral.com)
  • There is often increased methylation at CpG islands near the repeat region, resulting in a closed chromatin state, causing gene downregulation. (wikipedia.org)
  • 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)
  • These repeats are able to promote localized DNA epigenetic changes such as methylation of cytosines. (wikipedia.org)
  • In contrast, interactions between genes and the environment cannot usually be studied using conventional mapping populations in which each animal is unique. (nervenet.org)
  • 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 number of repeat units differs between individuals, resulting in highly complex allele polymorphisms. (researchsquare.com)
  • The epigenetic alterations and their effects are described more fully by Barbé and Finkbeiner These authors cite evidence that the age at which an individual begins to experience symptoms, as well as the severity of disease, is determined both by the size of the repeat and the epigenetic state within the repeat and around the repeat. (wikipedia.org)
  • Translation of these repeat expansions occurs mostly through two mechanisms. (wikipedia.org)
  • Scalograms that relate to the organism Caenorhabditis elegans (C. elegans) exhibit a multitude of periodic organization of specific DNA sequences. (springeropen.com)
  • In general, the larger the expansion the faster the onset of disease, and the more severe the disease becomes. (wikipedia.org)
  • 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)