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62 results for “tandem repeats”
Supplementary datasets for: Polymorphic short tandem repeats make widespread contributions to blood and serum traits
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Data from: Phylogeny of Mycoplasma bovis isolates from Hungary based on multi locus sequence typing and multiple-locus variable-number tandem repeat analysis
Background: Mycoplasma bovis is an important pathogen causing pneumonia, mastitis and arthritis in cattle worldwide. As this agent is primarily transmitted by direct contact and spread through animal movements, efficient genotyping systems are essential for the monitoring of the disease and for epidemiological investigations. The aim of this study was to compare and evaluate the multi locus sequence typing (MLST) and the multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) through the genetic characterization of M. bovis isolates from Hungary. Results: Thirty one Hungarian M. bovis isolates grouped into two clades by MLST. Two strains had the same sequence type (ST) as reference strain PG45, while the other twenty nine Hungarian isolates formed a novel clade comprising five subclades. Isolates originating from the same herds had the same STs except for one case. The same isolates formed two main clades and several subclades and branches by MLVA. One clade contained the reference strain PG45 and three isolates, while the other main clade comprised the rest of the strains. Within-herd strain divergence was also detected by MLVA. Little congruence was found between the results of the two typing systems. Conclusions: MLST is generally considered an intermediate scale typing method and it was found to be discriminatory among the Hungarian M. bovis isolates. MLVA proved to be an appropriate fine scale typing tool for M. bovis as this method was able to distinguish closely related strains isolated from the same farm. We recommend the combined use of the two methods for the genotyping of M. bovis isolates. Strains have to be characterized first by MLST followed by the fine scale typing of identical STs with MLVA.
Phased VCF outputs for "HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing"
<p>The collection of raw and processed VCF files for the paper titled: "HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing".</p><p>Raw VCF files from DeepVariant, pbsv, and TRGT are included in the unphased subfolder. Outputs from WhatsHap and HiPhase are in their own subfolders. Three replicates of HG002 are included in all subfolders. Layout is as follows:</p><blockquote><p>hiphase_vcfs</p><p>├── all_vcfs.md5</p><p>├── hiphase</p><p>│ ├── HG002-rep1.GRCh38.deepvariant.hiphase.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.deepvariant.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep1.GRCh38.pbsv.hiphase.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.pbsv.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep1.GRCh38.trgt.hiphase.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.trgt.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.deepvariant.hiphase.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.deepvariant.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.pbsv.hiphase.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.pbsv.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.trgt.hiphase.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.trgt.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.deepvariant.hiphase.vcf.gz</p><p>│ ├── HG002-rep3.GRCh38.deepvariant.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.pbsv.hiphase.vcf.gz</p><p>│ ├── HG002-rep3.GRCh38.pbsv.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.trgt.hiphase.vcf.gz</p><p>│ └── HG002-rep3.GRCh38.trgt.hiphase.vcf.gz.tbi</p><p>├── unphased</p><p>│ ├── HG002-rep1.GRCh38.deepvariant.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.deepvariant.vcf.gz.tbi</p><p>│ ├── HG002-rep1.GRCh38.pbsv.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.pbsv.vcf.gz.tbi</p><p>│ ├── HG002-rep1.GRCh38.trgt.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.trgt.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.deepvariant.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.deepvariant.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.pbsv.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.pbsv.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.trgt.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.trgt.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.deepvariant.vcf.gz</p><p>│ ├── HG002-rep3.GRCh38.deepvariant.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.pbsv.vcf.gz</p><p>│ ├── HG002-rep3.GRCh38.pbsv.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.trgt.vcf.gz</p><p>│ └── HG002-rep3.GRCh38.trgt.vcf.gz.tbi</p><p>└── whatshap</p><p> ├── HG002-rep1.GRCh38.deepvariant.whatshap.vcf.gz</p><p> ├── HG002-rep1.GRCh38.deepvariant.whatshap.vcf.gz.tbi</p><p> ├── HG002-rep2.GRCh38.deepvariant.whatshap.vcf.gz</p><p> ├── HG002-rep2.GRCh38.deepvariant.whatshap.vcf.gz.tbi</p><p> ├── HG002-rep3.GRCh38.deepvariant.whatshap.vcf.gz</p><p> └── HG002-rep3.GRCh38.deepvariant.whatshap.vcf.gz.tbi</p><p>3 directories, 43 files</p></blockquote>
The genomic architecture of the passerine MHC region: high repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes
<p><span>The Major Histocompatibility Complex (MHC) is of central importance to the immune system, and an optimal MHC diversity is believed to maximize pathogen elimination. Birds show substantial variation in MHC diversity, ranging from few genes in most bird orders to very many genes in passerines. Our understanding of the evolutionary trajectories of the MHC in passerines is hampered by lack of data on genomic organization. Therefore, we assemble and annotate the MHC genomic region of the great reed warbler (<em>Acrocephalus arundinaceus</em>), using long-read sequencing and optical mapping. The MHC region is large (>5.5Mb), characterized by structural changes compared to hitherto investigated bird orders and shows higher repeat content</span><span> than the genome average. These features were supported by analyses in three additional passerines. MHC genes in passerines are found in two different chromosomal arrangements, either as single copy MHC genes located among non-MHC genes, or as tandemly duplicated tightly linked MHC genes. Some single copy MHC genes are old and putative orthologs among species. In contrast tandemly duplicated MHC genes are monophyletic within species and have evolved by simultaneous gene duplication of several MHC genes. Structural differences in the MHC genomic region among bird orders seem substantial compared to mammals and have possibly been fuelled by clade-specific immune system adaptations. Our study provides methodological guidance in characterizing complex genomic regions, constitutes a resource for MHC research in birds, and calls for a revision of the general belief that avian MHC has a conserved gene order and small size compared to mammals.</span></p>
MD simulations associated to the paper "A PDZ tandem repeat folds and unfolds via different pathways"
<p>These are the MD simulation data generated for this study. The files are:</p> <p>x11_plain_simulation: training data, charmm22*+tip3p simulation of X11 PD1-PDZ2</p> <p>x11_random_coil: reference random coil data for X11 PDZ1-PDZ2</p> <p>x11_e0.21_0.335_folding_t310: 200 folding simulations</p> <p>x11_e0.21_0.335_melting_t380: 200 unfolding simulations</p> <p>x11d2_e0.21_0.33_folding_t310: 200 folding simulations for the isolated PDZ2</p> <p>x11_e0.21_0.33_folding_t310_d2open: 200 folding simulations for X11 PDZ1-PDZ2 starting with PDZ1 folded and the C-ter tail bound</p>
Platinum Tandem Repeats
<div> <div> <div> <div> <div> <div> <div> <p>Annotation of tandem repeat loci in the human genome</p> <ul> <li>~7.8 million loci: STRs and VNTRs</li> <li>Minimum locus size 10 bp</li> <li>Maximum locus size 10,000 bp</li> <li>Loci within 50 bp are merged to produce compound/complex loci</li> <li>CHM13-T2T and GRCh38 genomes</li> <li><a title="Tandem Repeat Genotyper on GitHub" href="https://github.com/PacificBiosciences/trgt">TRGT</a> locus definitions and bed files</li> <li>Generated using Tandem Repeats Finder and tr-solve</li> </ul> </div> </div> </div> </div> </div> </div> </div> <div> <div> <div> <div> </div> </div> </div> </div> <p>For more details and the code used to generate the loci, see:</p> <p><a title="PlatinumTRs on Github" href="https://github.com/dashnowlab/PlatinumTRs">https://github.com/dashnowlab/PlatinumTRs</a></p> <p>This data was used to call tandem repeat genotypes using TRGT by the <a title="Platinum Pedigree Consortium on GitHub" href="https://github.com/Platinum-Pedigree-Consortium">Platinum Pedigree Consortium</a>.</p>
Source data for manuscript "Polygenic burden of short tandem repeat expansions promote risk of Alzheimer's disease"
<p>Included are the source data and scripts used to make all plots for the mansucript "Polygenic burden of short tandem repeat expansions promote risk of Alzheimer's disease"</p>
Data from: Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing
High-throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high-throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, we detected by sequencing, only 164 alleles would have been detected by capillary electrophoresis as the remaining 130 alleles (44%) would have been hidden by length homoplasy. The ability to detect a greater number of unique alleles resulted in the ability to resolve greater population genetic structure. The primary advantages of fragment analysis by sequencing are the ability to precisely size fragments, resolve length homoplasy, multiplex many individuals and many loci into a single high-throughput run, and compare data across projects and across laboratories (present and future) with minimal technical calibration. A significant disadvantage of fragment analysis by sequencing is that the method is only practical and cost-effective when performed on batches of several hundred samples with multiple loci. Future work is needed to optimize throughput while minimizing costs and to update existing microsatellite allele calling and analysis programs to accommodate sequence-aware microsatellite data.
Data from: Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing
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Data from: Phylogeny of Mycoplasma bovis isolates from Hungary based on multi locus sequence typing and multiple-locus variable-number tandem repeat analysis
Open the record for dataset details and reuse information.
The genomic architecture of the passerine MHC region: high repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes
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Data from: RUNX2 tandem repeats and the evolution of facial length in placental mammals
BACKGROUND: When simple sequence repeats are integrated into functional genes, they can potentially act as evolutionary 'tuning knobs', supplying abundant genetic variation with minimal risk of pleiotropic deleterious effects. The genetic basis of variation in facial shape and length represents a possible example of this phenomenon. Runt-related transcription factor 2 (RUNX2) which is involved in osteoblast differentiation, contains a functionally-important tandem repeat of glutamine and alanine amino acids. The ratio of glutamines to alanines (the QA ratio) in this protein seemingly influences the regulation of bone development. Notably, in domestic breeds of dog, and in carnivorans in general, the ratio of glutamines to alanines is strongly correlated with facial length. RESULTS: In this study we examine whether this correlation holds true across placental mammals, particularly those mammals for which facial length is highly variable and related to adaptive behavior and lifestyle (e.g., primates, afrotherians, xenarthrans). We obtained relative facial length measurements and RUNX2 sequences for 41 mammalian species representing 12 orders. Using both a phylogenetic generalized least squares model and recently-developed Bayesian comparative method, we tested for a correlation between genetic and morphometric data while controlling for phylogeny, evolutionary rates, and divergence times. Non-carnivoran taxa generally had substantially lower glutamine-alanine ratios than carnivorans (primates and xenarthrans with means of 1.34 and 1.25, respectively, compared to a mean of 3.1 for carnivorans), and we found no correlation between RUNX2 sequence and face length across placental mammals. CONCLUSIONS: Results of our diverse comparative phylogenetic analyses indicate that QA ratio does not consistently correlate with face length across the 41 mammalian taxa considered. Thus, although RUNX2 might function as a 'tuning knob' modifying face length in carnivorans, this relationship is not conserved across mammals in general.
Selection and exploitation of prevalent, tandemly repeated genomic targets for improved real-time PCR-based detection of Wuchereria bancrofti and Plasmodium falciparum in mosquitoes
<p><b>Background</b></p> <p>Optimization of polymerase chain reaction (PCR)-based diagnostics requires the careful selection of molecular targets that are both highly repetitive and pathogen-specific. Advances in both next-generation sequencing (NGS) technologies and bioinformatics-based analysis tools are facilitating this selection process, informing target choices and reducing labor. Once developed, such assays provide disease control and elimination programs with an additional set of tools capable of evaluating and monitoring intervention successes. The importance of such tools is heightened as intervention efforts approach their endpoints, as accurate and complete information is an essential component of the informed decision-making process. As global efforts for the control and elimination of both lymphatic filariasis and malaria continue to make significant gains, the benefits of diagnostics with improved analytical and clinical/field-based sensitivities and specificities will become increasingly apparent.</p> <p><b>Methodology/Principal Findings </b></p> <p>Coupling Illumina-based NGS with informatics approaches, we have successfully identified the tandemly repeated elements in both the <i>Wuchereria bancrofti </i>and <i>Plasmodium falciparum </i>genomes of putatively greatest copy number. Utilizing these sequences as quantitative real-time PCR (qPCR)-based targets, we have developed assays capable of exploiting the most abundant tandem repeats for both organisms. For the detection of <i>P. falciparum</i>, analysis and development resulted in an assay with improved analytical and field-based sensitivity vs. an established ribosomal sequence-targeting assay. Surprisingly, analysis of the <i>W. bancrofti </i>genome predicted a ribosomal sequence to be the genome's most abundant tandem repeat. While resulting cycle quantification values comparing a qPCR assay targeting this ribosomal sequence and a commonly targeted repetitive DNA sequence from the literature supported our finding that this ribosomal sequence was the most prevalent tandemly repeated target in the <i>W. bancrofti </i>genome, the resulting assay did not significantly improve detection sensitivity in conjunction with field sample testing. </p> <p><b>Conclusions/Significance </b></p> <p>Examination of pathogen genomes facilitates the development of PCR-based diagnostics targeting the most abundant and specific genomic elements. While in some instances currently available tools may deliver equal or superior performance, systematic analysis of potential targets provides confidence that the selected assays represent the most advantageous options available and that informed assay selection is occurring in the context of a particular study's objectives.</p>
Data from: Deep phylogenomics of a tandem-repeat galectin regulating appendicular skeletal pattern formation
Background: A multiscale network of two galectins Galectin-1 (Gal-1) and Galectin-8 (Gal-8) patterns the avian limb skeleton. Among vertebrates with paired appendages, chondrichthyan fins typically have one or more cartilage plates and many repeating parallel endoskeletal elements, actinopterygian fins have more varied patterns of nodules, bars and plates, while tetrapod limbs exhibit tandem arrays of few, proximodistally increasing numbers of elements. We applied a comparative genomic and protein evolution approach to understand the origin of the galectin patterning network. Having previously observed a phylogenetic constraint on Gal-1 structure across vertebrates, we asked whether evolutionary changes of Gal-8 could have critically contributed to the origin of the tetrapod pattern. Results: Translocations, duplications, and losses of Gal-8 genes in Actinopterygii established them in different genomic locations from those that the Sarcopterygii (including the tetrapods) share with chondrichthyans. The sarcopterygian Gal-8 genes acquired a potentially regulatory non-coding motif and underwent purifying selection. The actinopterygian Gal-8 genes, in contrast, did not acquire the non-coding motif and underwent positive selection. Conclusion: These observations interpreted through the lens of a reaction-diffusion-adhesion model based on avian experimental findings can account for the distinct endoskeletal patterns of cartilaginous, ray-finned, and lobe-finned fishes, and the stereotypical limb skeletons of tetrapods.
Data from: Association between the dopamine D4 receptor gene exon III variable number of tandem repeats and political attitudes in female Han Chinese
Twin and family studies suggest that political attitudes are partially determined by an individual's genotype. The dopamine D4 receptor gene (DRD4) exon III repeat region that has been extensively studied in connection with human behaviour, is a plausible candidate to contribute to individual differences in political attitudes. A first United States study provisionally identified this gene with political attitude along a liberal–conservative axis albeit contingent upon number of friends. In a large sample of 1771 Han Chinese university students in Singapore, we observed a significant main effect of association between the DRD4 exon III variable number of tandem repeats and political attitude. Subjects with two copies of the 4-repeat allele (4R/4R) were significantly more conservative. Our results provided evidence for a role of the DRD4 gene variants in contributing to individual differences in political attitude particularly in females and more generally suggested that associations between individual genes, and neurochemical pathways, contributing to traits relevant to the social sciences can be provisionally identified.
Data from: Association between the dopamine D4 receptor gene exon III variable number of tandem repeats and political attitudes in female Han Chinese
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Selection and exploitation of prevalent, tandemly repeated genomic targets for improved real-time PCR-based detection of Wuchereria bancrofti and Plasmodium falciparum in mosquitoes
Open the record for dataset details and reuse information.
Data from: RUNX2 tandem repeats and the evolution of facial length in placental mammals
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Data from: Forensic efficiency estimate and phylogenetic analysis for Chinese Kyrgyz ethnic group revealed by a panel of 21 short tandem repeats
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Data from: Deep phylogenomics of a tandem-repeat galectin regulating appendicular skeletal pattern formation
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