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21 results for “mutation frequency”
Data and software supporting the manuscript 'The population frequency of human mitochondrial DNA variants is highly dependent upon mutational bias'
<p>Next-generation sequencing can quickly reveal genetic variation potentially linked to heritable disease. As databases encompassing human variation continue to expand, rare variants have been of high interest, since the frequency of a variant is expected to be low if the genetic change leads to a loss of fitness or fecundity. However, the use of variant frequency when seeking genomic changes linked to disease remains very challenging. Here, we explore the role of selection in controlling human variant frequency using the HelixMT database, which encompasses hundreds of thousands of mitochondrial DNA (mtDNA) samples. We find that a substantial number of synonymous substitutions, which have no effect on protein sequence, were never encountered in this large study, while many other synonymous changes are found at very low frequencies. Further analyses of human and mammalian mtDNA datasets indicate that the population frequency of synonymous variants is predominantly determined by mutational biases rather than by strong selection acting upon nucleotide choice. Our work has important implications that extend to the interpretation of variant frequency for non-synonymous substitutions. </p> <p> </p>
Low-frequency somatic mutations are heritable in tropical trees Dicorynia guianensis and Sextonia rubra
<p>Somatic mutations potentially play a role in plant evolution, but common expectations pertaining to plant somatic mutation remain insufficiently tested. Unlike in most animals, the plant germline is assumed to be set aside late in development, leading to the expectation that plants accumulate somatic mutations along growth. Therefore, several predictions were made on the fate of somatic mutations: mutations have generally low frequency in plant tissues; mutations at high frequency have a higher chance of intergenerational transmission; branching topology of the tree dictates mutation distribution; and, exposure to UV radiation increases mutagenesis. To provide new insights into mutation accumulation and transmission in plants, we produced two high-quality reference genomes and a unique dataset of 60 high-coverage whole-genome sequences of two tropical tree species, <i>Dicorynia guianensis</i> (Fabaceae) and <i>Sextonia rubra </i>(Lauraceae). We identified 15,066 <i>de novo</i> somatic mutations in <i>D. guianensis</i> and 3,208 in <i>S. rubra</i>, surprisingly almost all found at low frequency. We demonstrate that: 1) low-frequency mutations can be transmitted to the next generation; 2) mutation phylogenies deviate from the branching topology of the tree; and 3) mutation rates and mutation spectra are not demonstrably affected by differences in UV exposure. Altogether, our results suggest far more complex links between plant growth, ageing, UV exposure, and mutation rates than commonly thought.</p>
Antiviral activity of HIV-1 integrase strand-transfer inhibitors against mutants with integrase resistance-associated mutations and their frequency in treatment-naïve individuals
<p>The development of resistance to human immunodeficiency virus 1 (HIV-1) integrase strand-transfer inhibitors (INSTI) has been documented; however, knowledge of the impact of pre-existing integrase (IN) mutations on INSTI resistance (INSTI-R) is still evolving. The frequency of HIV-1 IN mutations in 2177 treatment-naïve subjects was investigated, along with the INSTI susceptibility of site-directed mutant viruses containing major and minor INSTI-R mutations. Total 6 of 39 minor INSTI-R mutations (M50I, S119P/G/T/R, and E157Q) were found in >1% of IN-treatment-naïve subjects with no impact on INSTI susceptibility. When each combined with major INSTI-R mutation, M50I, S119P, and E157Q led to decreased susceptibility to elvitegravir but remained sensitive to dolutegravir and bictegravir.</p>
Association between susceptibility of Thrips palmi to spinetoram and frequency of G275E mutation provides basis for molecular diagnostics of field-evolved resistance
<p><b><span>Background</span></b><span>: Spinosyn resistance is an increasing problem in field control of targeted pests. While putative mechanisms underlying spinosyn resistance have been identified in controlled studies on many species, mechanisms underlying field-evolved resistance and the development of a molecular diagnostic method for monitoring field resistance have lagged behind. Here, we examined levels of resistance of melon thrips, <i>Thrips palmi,</i> to spinetoram as well as target site mutations in field populations across China to identify potential mechanisms and useful molecular markers for diagnostic purposes.</span></p> <p><b><span>Results</span></b><span>: LC<sub>50</sub> </span><span>of 16 field-collected populations to the spinetoram varied from 0.12 to 759.34 </span>mg L<sup>-1</sup><span>. In resistant populations, we identified the G275E mutation, which has previously been linked to spinosyns resistance, as well as another nonsynonymous mutation, F314V, both located in the <i>α</i>6 subunit of the nicotinic acetylcholine receptor. There was a strong correlation between levels of spinetoram resistance and allele frequency of G275E mutation in field-collected populations (<i>r<sup>2</sup></i> = 0.84) and those reared under laboratory conditions for two to five generations (<i>r<sup>2</sup></i> = 0.91). LC<sub>50</sub> ranged from 0.12 to 0.66 </span>mg L<sup>-1</sup><span> in populations without </span><span>G275E mutation, while it ranged from </span>33.12<span> to 39.91</span> mg L<sup>-1</sup><span> in most populations with a </span><span>G275E mutation frequency > 90%, with the exception of one field-collected population which had an G275E frequency of 92% and a very high LC<sub>50</sub> value of 759.34</span> mg L<sup>-1</sup><span>, suggesting additional mechanisms.</span></p> <p><b><span>Conclusions: </span></b><span>Our results indicate that field-evolved resistance of <i>T. palmi</i> to spinetoram in China is mainly conferred by the G275E mutation, with other mechanisms contributing to a higher level of resistance. The frequency of the G275E mutation provides a useful diagnostic for quantifying resistance levels in field populations of <i>T. palmi</i>.</span></p>
Mutation frequency and copy number alterations determine prognosis and metastatic tropism in 60.000 clinical cancer samples
<p>The intricate interplay between somatic mutations and copy number alterations critically influences tumour evolution and patient prognosis. Traditional genomic studies often overlook this interplay by analysing these two biomarker types in isolation. We developed INCOMMON, a computational method to detect allele-specific copy number alterations from clinical targeted panels without matched normal, discover recurrent tumour-specific patterns of co-existing mutations and copy-number alterations, and stratify patients based on these composite genotypes for downstream analyses of survival, metastatic propensity and organotropism. The tool can be used as an open-source R package available at <a href="https://github.com/caravagnalab/INCOMMON">https://github.com/caravagnalab/INCOMMON</a>, and a shiny application available at <a href="https://ncalonaci.shinyapps.io/incommon/" target="_blank" rel="noopener">https://ncalonaci.shinyapps.io/incommon/</a>. This repository contains all the scripts that we used to analyse PCAWG, TCGA, MSK-MetTropism and AACR GENIE-Dfci data, and all the relevant results in the form of data tables.<strong></strong></p>
Association between susceptibility of Thrips palmi to spinetoram and frequency of G275E mutation provides basis for molecular diagnostics of field-evolved resistance
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Frequency of EGFR Mutations in Latinos/Hispanics With Non-Small Cell Lung Cancer
ClinicalTrials.gov study NCT01255150. IPD Sharing: Not stated. Countries: 5. Publications: 3.
IDH1/IDH2 Mutation Frequency in Acute Myeloblastic Patients
ClinicalTrials.gov study NCT03204838. IPD Sharing: NO. Countries: 1. Publications: 4.
Data from: Frequency and characteristics of MODY 1 (HNF4A mutation) and MODY 5 (HNF1B mutation) - Analysis from the DPV database
Objective. To characterize initial presentation and clinical course of patients with hepatocyte nuclear factor (HNF) 4A- and HNF1B-MODY in a multinational registry. Design, setting and participants. Within the Diabetes Patienten Verlaufsdokumentation (DPV) registry, 44 patients with HNF4A- and 35 patients with HNF1B-MODY were characterized and compared with patients < 20years old with type 1 diabetes (T1D)/type 2 diabetes (T2D). Main outcome measure. Clinical and laboratory parameters, therapy, metabolic control, and extrapancreatic symptoms in patients with HNF1B-MODY. Results. Patients with both MODY types were significantly older than T1D patients at diagnosis (HNF4A, 13.8 years and HNF1B, 13.5 years, vs. T1D, 8.8 years, P<0.0001). Mean C-peptide at diagnosis was higher for HNF4A-MODY than for T1D (1.8 vs. 0.9 ng/ml, P <0.01). 36.4% of patients with HNF4A-MODY and 65.7% of patients with HNF1B-MODY were treated with insulin, 20.5% and 8.6% received oral antidiabetics only (p<0.05 and p<0.01 vs. T2D). At the most recent visit, glycated hemoglobin levels were lower in HNF4A- and HNF1B-MODY compared to T1D (mean, 6.5% and 6.1%) than in T1D. In 40% of patients with HNF1B-MODY, extrapancreatic symptoms were reported. Several clinical predictors previously described to differentiate between MODY and T1D or T2D could be revalidated by logistic regression analyses in this cohort.Conclusion The DPV registry enabled us to precisely characterize phenotype and treatment in these two rare MODY types. Although phenotype of HNF4A-and HNF1B-MODY shows distinct differences to T1D and T2D, 38% of patients were initially misclassified as having T1D or T2D.
Data from: Frequency and fitness consequences of bacteriophage φ6 host range mutations
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Data from: Frequency and characteristics of MODY 1 (HNF4A mutation) and MODY 5 (HNF1B mutation) - Analysis from the DPV database
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A specific missense mutation in GTF2I occurs at high frequency in thymic epithelial tumors
GEO Series GSE57892. Homo sapiens. 25 samples. Type: Expression profiling by high throughput sequencing.
Data from: Benefits and challenges with applying unique molecular identifiers in next generation sequencing to detect low frequency mutations
Indexing individual template molecules with a unique identifier (UID) before PCR and deep sequencing is promising for detecting low frequency mutations, as true mutations could be distinguished from PCR errors or sequencing errors based on consensus among reads sharing same index. In an effort to develop a robust assay to detect from urine low-abundant bladder cancer cells carrying well-documented mutations, we have tested the idea first on a set of mock templates, with wild type and known mutants mixed at defined ratios. We have measured the combined error rate for PCR and Illumina sequencing at each nucleotide position of three exons, and demonstrated the power of a UID in distinguishing and correcting errors. In addition, we have demonstrated that PCR sampling bias, rather than PCR errors, challenges the UID-deep sequencing method in faithfully detecting low frequency mutation.
Frequency of EGFR and KRAS Mutations and Clinical-prognostic Correlation in Brazilian Lung Cancer Patients
ClinicalTrials.gov study NCT03171636. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Optimal Anti-EGFR Treatment of mCRC Patients With Low-Frequency RAS Mutation
ClinicalTrials.gov study NCT04034173. IPD Sharing: NO. Countries: 1. Publications: 0.
Frequency of SOD1 and C9orf72 Gene Mutations in French ALS
ClinicalTrials.gov study NCT04819555. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
High frequency of β-catenin mutations in mouse HCCs induced by a non-genotoxic CAR agonist
GEO Series GSE113708. Mus musculus. 22 samples. Type: Expression profiling by array.
Data from: Benefits and challenges with applying unique molecular identifiers in next generation sequencing to detect low frequency mutations
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De novo mutation in ELOVL1 causes ichthyosis, acanthosis nigricans, and hypomyelination with lower extremity spastic paraplegia, high frequency deafness, and tunnel vision.
GEO Series GSE116986. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
High Frequency of CNV Mutations in Combined Schizophrenia and Epilepsy
GEO Series GSE23703. Homo sapiens. 506 samples. Type: Genome variation profiling by genome tiling array.
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Allen Brain Atlas
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International Brain Laboratory public data
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