• 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)
  • human whole-genome. (scirp.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)
  • Short tandem repeats (STRs), or microsatellites, are 1-6 base pair (bp) motifs of repeating units of DNA. (biomedcentral.com)
  • STRs are distributed throughout the genome and are located in both coding and non-coding regions [ 2 ]. (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)
  • Short tandem repeats (STRs), also known as microsatellites, are repetitive DNA sequences consisting of 1-6-bp motifs present in a genome. (researchsquare.com)
  • Within DNA trinucleotide repeat sequences, the repair of DNA damage by the processes of homologous recombination, non-homologous end joining, DNA mismatch repair or base excision repair may involve strand slippage mispairing leading to trinucleotide repeat expansion when the repair is completed. (wikipedia.org)
  • Genomic regions with a high proportion of repeated DNA sequences (tandem repeats, microsatellites) are prone to strand slippage during DNA replication and DNA repair. (wikipedia.org)
  • These include spinal and bulbar muscular atrophy ( trinucleotide expansion in the AR gene), dentatorubral-pallidoluysian atrophy ( trinucleotide expansion in the DRPLA gene), spinocerebellar ataxia type 1 ( trinucleotide expansion in the SCA1gene), Machado-Joseph disease ( trinucleotide expansion in the SCA3 gene), myotonic dystrophy ( trinucleotide expansion in the DMPK gene), and Friedreich's ataxia ( a trinuncleotide expansion in the X25 gene). (wikipedia.org)
  • Myotonic dystrophy type 1 is a dominantly inherited multisystemic disease caused by CTG tandem repeat expansions in the DMPK 3' untranslated region. (bvsalud.org)
  • To address the molecular and cellular events that lead to these pathological outcomes, we recently generated a mouse Dmpk CTG expansion knock-in model and identified choroid plexus epithelial cells as particularly affected by the expression of toxic CUG expansion RNAs. (bvsalud.org)
  • A slippage event normally occurs when a sequence of repetitive nucleotides (tandem repeats) are found at the site of replication. (wikipedia.org)
  • Improving our understanding of these mutations would increase our knowledge of the mutational dynamics of the genome and may uncover additional loci that contribute to disease. (biomedcentral.com)
  • Approximately 30% of new STR mutations occur within Alu elements, which compose only 11% of the genome, but only 10% are found in LINE-1 insertions, which compose 17% of the genome. (biomedcentral.com)
  • We estimate the average number of de novo genome-wide STR mutations per individual to be approximately 85, which is similar to the average number of observed de novo single nucleotide variants. (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)
  • in contrast to simple family structures reported for a variety of angiosperm nsltp genes, the putative pine nsltp gene is a member of a complex family. (liverpool.ac.uk)
  • Tandem repeats are unstable regions of the genome where frequent insertions and deletions of nucleotides can take place, resulting in genome rearrangements. (wikipedia.org)
  • Insertions are thought to be self-accelerating: as repeats grow longer, the probability of subsequent mispairing events increases. (wikipedia.org)
  • Insertions can expand simple tandem repeats by one or more units. (wikipedia.org)
  • These highly individual-specific number of repeats and the abundance of motifs have contributed to the polymorphism of STR loci. (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)
  • 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)
  • 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)
  • The expansion of the HD locus results in a dysfunctional protein leading to Huntington's disease. (wikipedia.org)
  • Therefore, replication slippage leads to a form of trinucleotide expansion which results in serious changes to protein structure. (wikipedia.org)
  • lipid transfer protein genes of loblolly pine are members of a complex gene family. (liverpool.ac.uk)
  • An individual who is not affected by Huntington's disease will have 6-35 tandem repeats at the HD locus. (wikipedia.org)
  • In long repeats, expansions may involve two or more units. (wikipedia.org)
  • control of cad gene expression could involve either differential regulation of more than one cad gene or, alternatively combinatorial regulation of a single cad gene. (liverpool.ac.uk)
  • If these repeats are found in coding regions then the variations to the polynucleotide sequence can result in the formation of abnormal proteins in eukaryotes. (wikipedia.org)
  • For example, insertion of a single repeat unit in GAGAGA expands the sequence to GAGAGAGA, while insertion of two repeat units in [GA]6 would produce [GA]8. (wikipedia.org)
  • genetic analysis of cinnamyl alcohol dehydrogenase in loblolly pine: single gene inheritance, molecular characterization and evolution. (liverpool.ac.uk)
  • Tandem repeats (the main influence for slippage replication) can be found in coding and non-coding regions. (wikipedia.org)
  • However, an affected individual will have 36- 121 repeats present. (wikipedia.org)
  • In the present study, genes across the 2q24-q33 interval were analyzed to identify an autism susceptibility gene in this region. (neurotransmitter.net)
  • This results in some repeats found in the template strand being replicated twice into the daughter strand. (wikipedia.org)
  • The HD gene is found in all human genomes. (wikipedia.org)
  • 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)
  • the gene encoding the monolignol biosynthetic enzyme cinnamyl alcohol dehydrogenase (cad, e.c. 1.1.1.195) can be expressed in response to different developmental and environmental cues. (liverpool.ac.uk)
  • In the event that a slippage event occurs there can be a large expansion in the tandem repeats of the HD gene. (wikipedia.org)
  • 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)
  • Many human diseases have been reported to be associated with trinucleotide repeat expansions including Huntington's disease. (wikipedia.org)
  • ease or are within disease genes. (scirp.org)
  • The number of repeat units differs between individuals, resulting in highly complex allele polymorphisms. (researchsquare.com)
  • Slippage occurs through five main stages: In the first step, DNA polymerase encounters the direct repeat during the replication process. (wikipedia.org)
  • DNA polymerase reassembles its position on the template strand and resumes normal replication, but during the course of reassembling, the polymerase complex backtracks and repeats the insertion of deoxyribonucleotides that were previously added. (wikipedia.org)
  • 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)
  • These expanded repeats are transcribed and produce toxic CUG RNAs that sequester and inhibit activities of the MBNL family of developmental RNA processing factors. (bvsalud.org)
  • 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)