• 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)
  • As the technology evolves and test costs decline, whole genome sequencing (WGS), which can assess genetic sequences of nuclear and mitochondrial DNA and copy number variants (CNVs), or whole exome sequencing (WES), which can assess genetic sequences of the coding region of nuclear genes, but usually does not cover mitochondrial DNA and does not consistently identify CNVs, in combination with CMA, may become first-line testing for these conditions. (arupconsult.com)
  • Based on the genome sequences available from public databases, we designed eight pairs of universal PCR primers covering the entire RVFV genome. (bvsalud.org)
  • Sequencing confirmed that the products covered the entire genome of the RVFV strains tested. (bvsalud.org)
  • The entire RVFV genome was successfully amplified and sequenced at a viral concentration of 108 copies/mL. (bvsalud.org)
  • However, development of microhaplotype panels is hindered by a lack of methods for estimating microhaplotype allele frequency from low-coverage whole genome sequencing or pooled sequencing (pool-seq) data. (bvsalud.org)
  • RESULTS: We developed new methods for estimating microhaplotype allele frequency from low-coverage whole genome sequence and pool-seq data. (bvsalud.org)
  • Exome sequencing is a laboratory test designed to identify and analyze the sequence of all protein-coding nuclear genes in the genome. (nih.gov)
  • 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)
  • We used whole-genome sequencing to compare these isolates with a worldwide collection of current and historical clinical strains for characterizing population structures. (cdc.gov)
  • Clonal expansion of macrolide resistance occurred mostly within subtype 1 strains, of which clade T1-2 showed the highest recombination rate and genome diversity. (cdc.gov)
  • During the past several years, hundreds of new variations in repetitive regions of DNA have been identified, leading researchers to believe that copy number variations (CNVs) are as important a component of genomic diversity as single nucleotide polymorphisms (SNPs). (nature.com)
  • Primer specificity was confirmed via in silico comparison against all non-redundant nucleotide sequences using the BLASTn alignment tool in the NCBI database. (bvsalud.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 availability of the complete nucleotide sequences of several MTB genomes allows to use the comparative genomics as a tool to study the relationships of strains and differences in their evolutionary history including acquisition of drug-resistance. (ijpsr.com)
  • Short tandem repeats (STRs), or microsatellites, are 1-6 base pair (bp) motifs of repeating units of DNA. (biomedcentral.com)
  • Long expansions of transcribed trinucleotide microsatellites have been etiologically associated with some neurological diseases. (scite.ai)
  • An increase number of repeats of a genomic, tandemly repeated DNA sequence from one generation to the next. (uams.edu)
  • 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)
  • Results for each gene on the custom multigene panel are reported to the ordering clinician, whereas the results from the remaining genes sequenced (but not requested by the clinician) are not analyzed or included in the final laboratory report. (nih.gov)
  • 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)
  • Multiple system atrophy and CAG repeat length: A genetic screening of polyglutamine disease genes in Italian patients. (cdc.gov)
  • two genes preferentially expressed in differentiating xylem of loblolly pine (pinus taeda l.) were cloned from cdna and genomic libraries and designated ptx3h6 and ptx14a9. (liverpool.ac.uk)
  • Although not typically included in guidelines or billing algorithms, whole exome sequencing (WES) is gaining traction as a test for DD/ID/ASD. (arupconsult.com)
  • 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)
  • 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)
  • A study of Huntington disease-like syndromes in black South African patients reveals a single SCA2 mutation and a unique distribution of normal alleles across five repeat loci. (cdc.gov)
  • of tandem repeats within their genomes [6, 17]. (scirp.org)
  • 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)
  • Pol IV is needed to produce the small RNA trigger for methylation whereas Pol V acts downstream of small RNA biogenesis to facilitate de novo methylation of genomic DNA at the small RNA-targeted site. (biomedcentral.com)
  • Size variation was readily detected, with four common alleles containing 12-15 repeats. (scite.ai)
  • 2006). Perhaps the best-defined and most widely known CNVs are the trinucleotide repeats (TNRs), which consist of three nucleotides repeating in tandem. (nature.com)
  • 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)
  • 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)
  • shares 94% mitochondrial cytochrome C oxidase subunit I gene (COI) sequence identity with Heterorhabditis bacteriophora and Heterorhabditis ruandica, and 93% with Heterorhabditis zacatecana. (bvsalud.org)
  • 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)
  • 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)
  • Tandem-Genotypes requires data preprocessing steps such as LAST alignment and establishment of a genomic background database, and histograms are needed to assist STR genotyping. (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 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)
  • A phylogenetic tree for 284 strains showed that all sequenced strains consisted of 5 clades: T1-1 (sequence type [ST]1), T1-2 (mainly ST3), T1-3 (ST17), T2-1 (mainly ST2), and T2-2 (mainly ST14). (cdc.gov)
  • The methods used in multigene panels may include sequence analysis , deletion/duplication analysis , and/or other non-sequencing-based tests. (nih.gov)
  • 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)
  • RNA-directed DNA methylation results in a characteristic modification pattern that is typified by methylation of cytosines in all sequence contexts (CG, CHG and CHH, where H is A, T or C) within the region of small RNA-DNA sequence homology [ 4 ]. (biomedcentral.com)
  • These methods allowed estimation of allele frequency and expected heterozygosity at depths routinely achieved from pooled sequencing. (bvsalud.org)
  • C9orf72 Repeat Expansion Frequency among Patients with Huntington Disease Genetic Testing. (cdc.gov)
  • TNRs exhibit dynamic expansion and contraction in a number of disease states, such as fragile X syndrome and Huntington's disease, with the number of repeats varying in both normal and afflicted individuals. (nature.com)
  • The usual cause of the fragile X syndrome is an expanded (CGG)n repeat in the 5-prime noncoding region of the FMR1 gene. (coriell.org)
  • 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)
  • Upscaling techniques, such as homogenization via multiple-scale expansions, provide a framework to connect these two scale. (escholarship.org)
  • This graph shows the total number of publications written about "DNA Repeat Expansion" by people in UAMS Profiles by year, and whether "DNA Repeat Expansion" was a major or minor topic of these publications. (uams.edu)