Analysis of somatic mutations. Medical search. Frequent questions

To evaluate the role of mitochondrial genes, stem cell-specific genes and DNA repair genes in cancer development, their mutation frequency was determined via further analysis. (biomedcentral.com)
qBiomarker Somatic Mutation PCR Arrays are translational research tools that allow rapid and accurate profiling of the somatic mutation status for important genes related to a biological pathway or disease. (qiagen.com)
PMS2 -related SEOC is less common due to lower risks for these cancers associated with germline PMS2 mutation compared to other Lynch genes. (tempus.com)
Tumor profiling with next-generation sequencing of 648 genes identified sixteen shared somatic actionable and biologically relevant mutations. (tempus.com)
Deep sequencing studies show that 4.2% of tumours carry activating mutations in GNAS (encoding Gα s ), and that oncogenic activating mutations in genes encoding Gα q family members ( GNAQ or GNA11 ) are present in ∼ 66% and ∼ 6% of melanomas arising in the eye and skin, respectively. (nature.com)
Recently, MYH1 and MYH9 have been identified as candidate breast cancer genes in a systematic analysis of the breast cancer genome. (tuni.fi)
In the tabs below you can see any other genes that have resistance mutations to the same drug(s), and the distribution of mutations that occur in those genes. (sanger.ac.uk)
Alternative transcripts are also displayed here for genes where reported resistant mutations are not located on the canonical transcript but are on the alternative, and also where reported resistant mutations are located at the same genomic position on both the canonical and alternative transcripts or on overlapping genes and/or fusions and share a COSM id. (sanger.ac.uk)
In both univariate and multivariate analyses, mutations in all genes except MYD88 were associated with a significantly shorter TTFT. (soton.ac.uk)
The ability to generate high-quality sequence data in a public health laboratory enables the identification of pathogenic strains, the determination of relatedness among outbreak strains, and the analysis of genetic information regarding virulence and antimicrobial-resistance genes. (cdc.gov)
Weighted gene co-expression network analysis (WGCNA) was used to identify key genes for mRNA vaccines. (frontiersin.org)
In vitro experiments in endothelial cells demonstrated that the GJA4 mutation activated SGK-1 signalling that in turn upregulated key genes involved in cell hyperproliferation and the loss of arterial specification. (bmj.com)
Characteristics of Clonal Hematopoiesis (CH) Mutations - a) We identified somatic mutations in known clonal hematopoiesis of indeterminate potential (CHIP) driver genes using peripheral blood mononuclear cells isolated from 14 astronauts who flew short space Shuttle missions lasting a median of 12 days between 1998-2001. (spaceref.com)
b) Number of somatic nonsynonymous single nucleotide variants (SNVs) in CHIP-driver genes harbored per subject. (spaceref.com)
Using DNA sequencing followed by extensive bioinformatics analyses, researchers identified 34 mutations in 17 CH-driver genes. (spaceref.com)
The most frequent mutations occurred in TP53, a gene that produces a tumor-suppressing protein, and DNMT3A, one of the most frequently mutated genes in acute myeloid leukemia. (spaceref.com)
However, the frequency of the somatic mutations in the genes that the researchers assessed was less than two percent, the technical threshold for somatic mutations in hematopoietic stem cells to be considered clonal hematopoiesis of indeterminate potential (CHIP). (spaceref.com)
Hereditary breast cancers linked to germ-line mutations of BRCA1 and BRCA2 genes almost invariably show allelic imbalance (Al) at the respective loci. (lu.se)
A multidimensional bioinformatics analysis was performed to examine the relationship between NRP genes and prognostic and pathological features, tumour mutational burden (TMB), microsatellite instability (MSI), and immunological features based on public databases and find the potential prognostic value of NRPs in pancancer. (hindawi.com)
These tumors are caused by germline or somatic mutations in known susceptibility genes in up to 70% of cases. (nih.gov)
Integrated genomic analyses have shown that the mutation status of PCC/PGL susceptibility genes strongly correlates with multi-omics data. (nih.gov)
Through genomic analysis of tumor samples, the researchers identified somatic mutations in EGFR, KRAS, and other target genes. (dana-farber.org)
Using the genomic and ancestry data, the researchers assessed the associations of somatic mutations in target genes and global ancestry groups within a single admixed population. (dana-farber.org)
Meyerson and colleagues then stratified patients by their self-reported smoking status and evaluated the association between global ancestry and mutations in target genes. (dana-farber.org)

12 ] mapped non-synonymous somatic mutations of Breast Invasive Carcinoma and Colon Adenocarcinoma Tumor samples to their corresponding protein domains, in order to extract domains with significant mutation frequency. (biomedcentral.com)
Sequence alterations are abundant in cancer genomes but the proportion of fragments in cell-free DNA (cfDNA) that harbor tumor-specific (somatic) mutations is often low 8 , 9 , making it difficult to detect bona fide variants amidst background noise from sequence changes introduced in library construction and sequencing. (nature.com)
Here, we considered whether identifying somatic mutations genome-wide could enable the detection of an increased number of circulating tumor DNA (ctDNA) alterations and increase the detection of early stage disease. (nature.com)
In principle, if mutations could be identified in cfDNA without knowledge of alterations in the tumor, then they could be useful for early cancer detection. (nature.com)
However, this would require efficient detection of somatic changes in cfDNA, including those related to mutational signatures 24 , and the ability to effectively distinguish these from non-tumor-derived alterations. (nature.com)
Early-grade tumors are not often sent for somatic tumor profiling. (tempus.com)
We present a 39 year old SEOC patient with germline PMS2 Lynch syndrome and clinical tumor analysis leading to insight regarding the origin and cause of these tumors, with potential therapy options. (tempus.com)
A worldwide database analysis revealed that younger age, smaller tumor size, early stage, and granulosa cell tumor histologic type appear to be independent prognostic factors for improved survival in patients with malignant sex cord-stromal tumors who undergo lymph node dissection. (medscape.com)
Other spontaneous mutations found in this condition, called somatic mutations, are acquired during a person's lifetime and are present only in the tumor cells. (medlineplus.gov)
This study evaluated the TruSight Tumor 170 assay for the simultaneous detection of somatic gene mutations (SNPs and indels), gene fusions and CNVs, and its implementation into routine diagnostics. (mdpi.com)
For data analysis the TruSight Tumor 170 app, the BaseSpace Variant Interpreter (Illumina), and the Molecular Health Guide Software (Molecular Health) were used. (mdpi.com)
Mutations in KRAS, TP53, SMAD4, and others were similar in primary and metastatic tumor pairs. (genomeweb.com)
In addition, primary and metastatic tumor pairs were also likely to share somatic SNVs and small indels. (genomeweb.com)
Cancer is a genetic disease with incidence driven by inherited (germline) variation in the person and evolution driven by somatic events in the tumor. (dana-farber.org)
In general, do germline variants induce specific somatic changes or modulate the impact of somatic variation on the tumor? (dana-farber.org)
Using a new method developed by Jian Carrot-Zhang, PhD, and Alexander Gusev, PhD, the researchers also performed ancestry analyses from tumor samples in this admixed population. (dana-farber.org)
After adjusting for a variety of factors, including self-reported smoking status and sample-specific tumor mutational burden, the researchers found that global Native American ancestry was positively correlated with mutations in the EGFR gene. (dana-farber.org)
We developed subclone multiplicity allocation and somatic heterogeneity (SMASH), a new statistical method for intra-tumor heterogeneity (ITH) inference. (biomedcentral.com)
e.g., single nucleotide variants or indels) and somatic copy number alterations (SCNAs), are the underlying driving force for tumor growth. (biomedcentral.com)
Therefore, association studies between somatic mutations and clinical outcomes may provide insights into tumor biology or personalized treatment selection. (biomedcentral.com)
In this paper, we consider three such features: tumor mutation burden (TMB, i.e., the total number of SPMs), SCNA burden, and the degree of (genetic) intra-tumor heterogeneity (ITH), which refers to the fact that tumor cells can be grouped in subclones such that the cells within one subclone share similar sets of somatic mutations. (biomedcentral.com)
An alternative metric to quantify ITH is mutant-allele tumor heterogeneity (MATH) [ 13 ], which is defined as 100×MAD/median, where median is the median of the variant allele frequencies (VAFs) of all somatic point mutations within a sample, and MAD is the median absolute deviation of the VAFs. (biomedcentral.com)
Noninvasive prediction of axillary lymph node breast cancer metastasis using morphometric analysis of nodal tumor microvessels in a contrast-free ultrasound approach. (medscape.com)

This problem is relevant to many cancer sequencing studies, in which one aims to discover somatic variants that distinguish patients with fast-growing tumors that require aggressive treatment from patients with better prognosis [1]. (princeton.edu)
This case is a rare example of a patient with PMS2 germline Lynch syndrome with shared somatic variants that demonstrate clonality of the two tumors arising from one common site. (tempus.com)
We observe a mean of 26 somatic single-nucleotide variants per brain present in ≥4% of cells, with enrichment of mutations in coding and putative regulatory regions. (nih.gov)
This suggests that a typical individual possesses ~80 somatic single-nucleotide variants present in ≥2% of cells-comparable to the number of de novo germline mutations per generation-with about half of individuals having at least one potentially function-altering somatic mutation somewhere in the cortex. (nih.gov)
In addition, the contributions of these mosaic somatic variants to phenotype and disease aetiology remain largely unknown. (sanger.ac.uk)
We are developing single-cell genome sequencing technologies to enable the discovery of the entire spectrum of DNA mutation -including the acquisition of ploidy changes, aneuploidies, copy number variants, structural variants, retrotranspositions, indels, and single nucleotide variants. (sanger.ac.uk)
Authors are encouraged to attempt these aneuploid analyses when reporting scRNA-seq data, much like copy-number variants are commonly reported in bulk genome sequencing data. (techscience.com)
Accepted 1 August 2008 the same methodology described in the previously that somatic sequence variants occur with high published reports. (cdc.gov)
Two synonymous germline in a majority of these patients.10 13 The same sequence variants were identified in two separate investigators also found somatic sequence variants patients. (cdc.gov)
Based on the TBX5, GATA4, and HEY2, often simultaneously incidence of somatic mutations described in the within the same patient.9-13 The observation of two previously published reports, our study was adequately or more somatic sequence variants in the same powered to replicate the previous studies. (cdc.gov)
The somatic NKX2-5 sequence variants were defects. (cdc.gov)

Although diverse events like point mutations/deletions, nondisjunction, and homologous mitotic recombination might theoretically cause this loss of heterozygosity, nondisjunction processes are generally not relevant for most of the examined chemicals. (wikipedia.org)

Nearly 20% of human cancers harbour mutations in GPCRs. (nature.com)
Little evidence for a role of somatic MYH11 mutations in the formation of breast or prostate cancers was obtained in this study. (tuni.fi)
It is worth noting that the therapeutic effect of KRASG12C inhibitors on different RAS allelic mutations or even different cancers with KRASG12C varies significantly. (researchgate.net)
Besides, the pathological characteristics and treatment responses of different cancers carrying RAS mutations are listed based on clinical reports. (researchgate.net)
RNA sequences, somatic mutations, and clinicopathological features of 33 cancers were downloaded from The Cancer Genome Atlas (TCGA) database. (hindawi.com)
Aging skin contains somatic mutant clones from which such cancers develop. (cdc.gov)

The landscape of somatic mutation in normal colorectal epithelial cells. (cam.ac.uk)

Discriminating driver mutations from the ones that play no role in cancer is a severe bottleneck in elucidating molecular mechanisms underlying cancer development. (biomedcentral.com)
This article presents a comprehensive study to map mutations from 29 cancer types to both sequence- and structure-based domains. (biomedcentral.com)
Besides, performing interactome analysis on specific proteins of each cancer type showed high levels of interconnectivity among them, which implies their functional relationship. (biomedcentral.com)
Only some of the mutations in coding regions, and not all of them lead to cancer. (biomedcentral.com)
To this aim, some efforts have been made to study cancer mutations at the protein domain level. (biomedcentral.com)
Regions with high numbers of mutation for each cancer type were called hotspot. (biomedcentral.com)
It's worth noting that measuring mitotic recombination in somatic cells is important for genotoxicity screening since abnormal recombination activity is frequently linked to cancer. (wikipedia.org)
Somatic mutations are a hallmark of tumorigenesis and may be useful for non-invasive diagnosis of cancer. (nature.com)
We analyzed whole-genome sequencing data from 2,511 individuals in the Pan-Cancer Analysis of Whole Genomes (PCAWG) study as well as 489 individuals from four prospective cohorts and found distinct regional mutation type-specific frequencies in tissue and cell-free DNA from patients with cancer that were associated with replication timing and other chromatin features. (nature.com)
This approach lays the groundwork for non-invasive cancer detection using genome-wide mutation features that may facilitate cancer screening and monitoring. (nature.com)
To address these challenges, we developed an approach, called GEnome-wide Mutational Incidence for Non-Invasive detection of cancer (GEMINI), that can identify a much larger number of somatic alterations in cfDNA (Fig. 1 ). (nature.com)
Recent cancer genome deep sequencing efforts have revealed an unanticipated high frequency of mutations in G proteins and G-protein-coupled receptors (GPCRs) in most tumour types. (nature.com)
Transforming mutations in GNAS have been well documented in human thyroid and pituitary tumours, and recent sequencing efforts have shown these mutations to be present in a wide variety of additional tumour types, including colon cancer, hepatocellular carcinoma, and parathyroid, ovarian, endometrial, biliary tract and pancreatic tumours. (nature.com)
Many GPCR mutations are still uncharacterized with respect to their potential contribution to tumorigenesis and cancer progression. (nature.com)
Detailed three dimensional structures of GPCRs in various activation states can now help to explain the functional impact of cancer-associated GPCR mutations, and guide the rational design of signalling-selective GPCR agonists, antagonists and allosteric modulators. (nature.com)
We have previously shown that MYH11 mutations occur in human colorectal cancer, and may also be associated with Peutz-Jeghers syndrome. (tuni.fi)
A total of 155 breast cancer and 71 prostate cancer samples were analyzed for those regions in MYH11 (altogether 8 exons out of 42 coding exons) that harboured mutations in colorectal cancer in our previous study. (tuni.fi)
One prostate cancer sample harbored a frameshift mutation c.5798delC, which we have previously shown to result in a protein with unregulated motor activity. (tuni.fi)
Oncogenic mutations in KRAS or BRAF are frequent in colorectal cancer and activate the ERK kinase. (researchgate.net)
Here, we find graded ERK phosphorylation correlating with cell differentiation in patient-derived colorectal cancer organoids with and without KRAS mutations. (researchgate.net)
In this study, we performed Reverse Protein Phase Array (RPPA) analysis of murine lung cancer, which suggests that VEGFR2 protein is strongly positively regulated by MSI2. (researchgate.net)
A central theme of this Cancer Policy Framework is the use of risk analysis as an organizing construct based on sound biomedical and other scientific judgment to define plausible exposure ranges of concern rather than single numerical conclusions that may convey an artificial sense of precision. (cdc.gov)
A central theme of ATSDR's Cancer Policy Framework is the use of risk analysis as an organizing construct to promote optimal decisions in the Agency's human health assessment programs. (cdc.gov)
however, typical sequencing methods are error-prone , and there is vast heterogeneity of somatic mutations between individual patients and different cancer types. (aacr.org)
Astronauts are at higher risk for developing mutations-possibly linked to spaceflight-that can increase the risk of developing cancer and heart disease during their lifetimes, according to a first-of-its kind study from the Icahn School of Medicine at Mount Sinai. (spaceref.com)
The mutations identified in this study were characterized by the overrepresentation of blood cells derived from a single clone, a process called clonal hematopoiesis (CH). Such mutations are frequently caused by environmental factors, such as exposure to ultraviolet radiation or certain chemicals, and may be a result of cancer chemo- or radiotherapy. (spaceref.com)
The presence of these mutations does not necessarily mean that the astronauts will develop cardiovascular disease or cancer, but there is the risk that, over time, this could happen through ongoing and prolonged exposure to the extreme environment of deep space," Dr. Goukassian said. (spaceref.com)
In conclusion, the high prevalence of Al at BRCA1 in BRCA2 mutation tumours and vice versa suggests that somatic events occurring at the other breast cancer susceptibility gene locus may be selected in the cancer development. (lu.se)
2) Understanding the relationship between heritable/germline and somatic variation in cancer. (dana-farber.org)
We seek to learn the interactions between germline and somatic events as well as their impact on cancer progression and response to treatment. (dana-farber.org)
Somatic mutations are important determinants of cancer behaviour and response to therapy. (bmj.com)
Recent global analyses of gene transcripts revealed that specific transcription factors (TFs) and their networking systems physiologically correspond to the onset of human diseases, including cancer. (intechopen.com)
Integrated Analysis of Genetic Abnormalities of the Histone Lysine Methyltransferases in Prostate Cancer. (cancerindex.org)
posttranslational modifications, amino acid variations, computational mutation analysis, protein PTM predictor, network biology Introduction Protein PTMs are biochemical alterations of amino acids that change the physicochemical properties of target proteins, leading to structural changes and therefore regulating protein-protein interactions and cellular signal transduction in developmental and cancer pathways [1]. (deepdyve.com)
11] indicated that acetylation and ubiquitination site mutations are enriched in cancer. (deepdyve.com)
In a pan-cancer study of 14 cancer types, we studied the associations between survival time and ITH quantified by SMASH, together with other features of somatic mutations. (biomedcentral.com)
Our results show that ITH is associated with survival time in several cancer types and its effect can be modified by other covariates, such as mutation burden. (biomedcentral.com)
Age-adjusted mutation load and burden correlate with the corresponding cancer incidence and precede it on average by 15 years, pointing to pre-clinical cancer development times. (who.int)
Behaviour of mutation load also exhibits gender differences and late-life reversals, explaining some gender-specific and late-life patterns in cancer incidence rates. (who.int)
Somatic mutations in facial skin from countries of contrasting skin cancer risk. (cdc.gov)
Correction: A prospective case-cohort analysis of plasma metabolites and breast cancer risk. (medscape.com)
Human cancer genome sequencing studies have generated ample, publicly available data, and analyses of these data have substantially broadened the knowledge of somatic mutations accumulating in tumours. (who.int)
Analysis of mutational signatures focuses on how characteristic somatic DNA mutation patterns reflect the contributions of particular mutagenic processes to cancer development, and it is thus of key importance for cancer etiology and carcinogen exposure studies. (who.int)
PCAWG, Pan-Cancer Analysis of Whole Genomes. (who.int)

To prove somatic mutations and SNPs of ATAD5 identified indeed affect the function of ATAD5 and promote tumorigenesis in human, we made 34 ATAD5 expression constructs with a mutation or SNP in ATAD5 that were collected from publically available databases and our studies. (nih.gov)

The colorectal adenoma-carcinoma sequence has provided a paradigmatic framework for understanding the successive somatic genetic changes and consequent clonal expansions that lead to cancer1. (cam.ac.uk)
Astronauts work in an extreme environment where many factors can result in somatic mutations, most importantly space radiation, which means there is a risk that these mutations could develop into clonal hematopoiesis. (spaceref.com)
Although the clonal hematopoiesis we observed was of a relatively small size, the fact that we observed these mutations was surprising given the relatively young age and health of these astronauts. (spaceref.com)
Most of the liver and all of the brain metastases harbored many private clonal somatic SNVs, but no subclonal ones. (genomeweb.com)
Somatic mutations are now recognized to contribute to clonal heterogeneity within otherwise normal, aged tissue. (techscience.com)
Aneuploidy, the loss or gain of chromosome arms, appears less prevalent in normal tissue in these clonal mutant next-generation sequencing analyses. (techscience.com)
De novo activating mutations drive clonal evolution and enhances clonal fitness in KMT2A -rearranged leukemia. (lu.se)

Mutually exclusive activating mutations in GNAQ or GNA11 (encoding Gα q family members) occur in 5.6% of tumours, and they are present in ∼ 66% and ∼ 6% of melanomas arising in the eye and skin, respectively, where they can act as driver oncogenes. (nature.com)
We carried out Al and fluorescence in situ hybridization (FISH) analyses of BRCA2 in breast tumours from germline BRCA1 mutation carriers and vice versa. (lu.se)
8 of the 11 (73%) informative BRCA1 mutation tumours showed Al at the BRCA2 focus. (lu.se)
5 of the 6 (83%) informative BRCA2 mutation tumours showed Al at the BRCA1 locus. (lu.se)

An activating NLRC4 inflammasome mutation causes autoinflammation with recurrent macrophage activation syndrome. (nih.gov)
The project is fully computational and composed of three main parts in which the skills of the student will be developed: identification of somatic alterations, design of algorithms for tumour evolution, and statistical analysis of recurrent mutations. (ucl.ac.uk)

Some spontaneous mutations associated with this condition occur during the formation of reproductive cells (eggs or sperm) or just after fertilization and are called de novo mutations. (medlineplus.gov)
Standard methods sequence DNA that has been extracted from a population of cells, such that not only the genetic composition of individual cells is lost, but also de novo mutations in cell(s) are effectively concealed by the bulk signal. (sanger.ac.uk)

By combining allele-specific amplification and hydrolysis probe detection, qBiomarker Somatic Mutation real-time PCR assays have been developed which can detect as few as 1% somatic mutations in the background of wild-type genomic DNA. (qiagen.com)
In both never smokers and smokers, global Native American ancestry was associated with mutations in the EGFR gene, suggesting that the genomic differences associated with Native American ancestry are independent of smoking status. (dana-farber.org)

PMID:18786442 mutations and the risk of esophageal squamous cell carcinoma. (who.int)
PMID:19064517 intraepithelial neoplasia: meta-analysis. (who.int)

We characterize the landscape of somatic mutations-mutations occurring after fertilization-in the human brain using ultra-deep (~250×) whole-genome sequencing of prefrontal cortex from 59 donors with autism spectrum disorder (ASD) and 15 control donors. (nih.gov)
However, the analysis of whole-genome sequence data depends on bioinformatic analysis tools and processes. (cdc.gov)
The goal of this perspective is to provide a guide for laboratories to understand the bioinformatic analyses that are needed to interpret whole-genome sequence data and how these in silico analyses can be implemented in a public health laboratory setting easily, affordably, and, in some cases, without the need for intensive computing resources and infrastructure. (cdc.gov)
Our knowledge on the nature and rate of genome mutation in a developing organism is rudimentary. (sanger.ac.uk)
Single-cell genome analyses overcome these issues. (sanger.ac.uk)
Genome-wide association analysis revealed that the NRP1 expression was strongly associated with kidney renal clear cell carcinoma (KIRC), whereas the NRP2 expression was closely associated with BLCA. (hindawi.com)
Global ancestry analysis was performed to measure proportions of African, European, and Native American ancestry across the genome. (dana-farber.org)
Because local ancestry only evaluates a small portion of the genome, there is less potential for observed associations to be confounded by environmental exposures or socioeconomic status, which may be seen in global ancestry analyses, Meyerson explained. (dana-farber.org)
The researchers next developed a local Native American ancestry risk score to evaluate the association of ancestry with EGFR mutation frequency across multiple distinct sites in the genome. (dana-farber.org)
They found that the correlation between ancestry and increased mutation frequency in the EGFR gene was stronger at the local genome level than the global genome level. (dana-farber.org)
The MUTSPEC 2.0 project was developed to accommodate a highly integrated design to identify mutational (and other toxicogenomic) signatures of carcinogens derived by genome-scale sequencing analysis of mutually complementary and cross-validating systems. (who.int)

A striking 4.2% of all tumour sequences deposited to date show activating mutations in GNAS (a complex locus that encodes Gα s ). (nature.com)
ASD brains show an excess of somatic mutations in neural enhancer sequences compared with controls, suggesting that mosaic enhancer mutations may contribute to ASD risk. (nih.gov)

We also reported that haplo-insufficiency of ATAD5 in mice developed tumors and high incidences of somatic mutations of ATAD5 in human tumors. (nih.gov)
Mutations in the VHL gene increase the risk of developing tumors of the nervous system called paragangliomas or pheochromocytomas (a type of paraganglioma). (medlineplus.gov)
Through a phylogenetic analysis, the researchers traced the origins of these metastatic tumors. (genomeweb.com)

While SF3B1 and XPO1 mutations were independent prognostic variables in both U-CLL and M-CLL, TP53, BIRC3 and EGR2 aberrations were significant predictors only in U-CLL, and NOTCH1 and NFKBIE only in M-CLL. (soton.ac.uk)

d Quantification of ERK phosphorylation in organoids, 24 h after induction of control, BRAF or KRAS transgenes, using a capillary protein analysis. (researchgate.net)

Under this is shown the amino acid sequence and the Pfam protein structures, followed by complex mutations and insertions and deletions. (sanger.ac.uk)

Further, the researchers found that Native American ancestry was predominantly associated with oncogenic mutations in the EGFR gene, but not with non-oncogenic mutations. (dana-farber.org)

Some of the obstacles preventing PHLs from implementing the bioinformatic-dependent analysis are the requirements for large-scale computational capabilities, complex molecular evolutionary analyses, and dedicated bioinformatics staff to perform these analyses. (cdc.gov)

qBiomarker Somatic Mutation PCR Arrays are intended for molecular biology applications. (qiagen.com)
Can molecular data help us efficiently identify the specific causal mutations? (dana-farber.org)
An integrative analysis of the transcriptome, epigenome and proteome of distinct TEC subpopulations will be used to attain an unparalleled systems-level understanding of the molecular conditions that select a tolerant T cell repertoire under normal physiological conditions. (sanger.ac.uk)
Cross-platform analysis reveals cellular and molecular landscape of glioblastoma invasion. (yale.edu)

Genetic factors include, but are not limited to inherited germline mutations, changing DNA methylation rate and microRNA modifications. (biomedcentral.com)

In multivariate analysis of Binet stage A patients, performed separately for IGHV-mutated (M-CLL) and unmutated CLL (U-CLL), a different spectrum of gene alterations independently predicted short TTFT within the two subgroups. (soton.ac.uk)
Given that OKSM (Yamanaka) factors convert somatic cells into induced pluripotent stem (iPS) cells, alterations in transcriptional state could affect destiny of the cells. (intechopen.com)
Firstly, the student will learn to apply standard and existing computational methods to identify different types of somatic genetic alterations (e.g. (ucl.ac.uk)

Mutation analysis and functional genomics through Next Generation Sequencing and computational tools development. (nih.gov)

We identify a mutation (D262N) in the erythroid-affliated transcriptional repressor GFI1B, in an acute myeloid leukemia (AML) patient with antecedent myelodysplastic syndrome (MDS). (lu.se)

Our findings reveal that NRPs may be a potential prognostic marker associated with immune infiltration, tumour mutations, and tumour microenvironment, particularly in bladder urothelial carcinoma (BLCA). (hindawi.com)

Apart from wet-lab approaches, we also develop the computational means for the analysis of single cells. (sanger.ac.uk)
Computational mutation analysis can greatly narrow down the efforts on experimental work. (deepdyve.com)
To increase the utilization of current computational resources, we 﫿rst provide an overview of computational prediction of amino acid variations that influence protein PTMs and their functional analysis. (deepdyve.com)

Since protein domains are representatives of functional regions within proteins, mutations on them may disturb the protein functionality. (biomedcentral.com)
Therefore, distinguishing mutations with drastic impacts on protein functionality may help discriminate driver mutations from less significant ones. (biomedcentral.com)
This study represents a method to explore protein domains with significant mutation frequencies, using whole exome sequencing data. (biomedcentral.com)
The VHL gene mutations found in nonsyndromic paraganglioma or pheochromocytoma change single amino acids in the VHL protein or create an abnormally short protein. (medlineplus.gov)
The mutation changes a single protein building block (amino acid) in the VHL protein, replacing the amino acid arginine with the amino acid tryptophan at position 200 (written as Arg200Trp or R200W). (medlineplus.gov)
This mutation disrupts the function of the VHL protein, particularly its ability to target HIF-2α to be broken down. (medlineplus.gov)
The other VHL gene mutations that can cause familial erythrocytosis also change single amino acids in the VHL protein. (medlineplus.gov)
These genetic changes are thought to have similar effects on protein function to those of the Arg200Trp mutation. (medlineplus.gov)
Scope includes mutations and abnormal protein expression. (cancerindex.org)
Proteomic analysis and prediction of amino acid variations that influence protein. (deepdyve.com)
The development of better methods for mutation analysis-related protein PTMs will help to facilitate the development of personalized precision medicine. (deepdyve.com)
7] analyzed amino acid variations of 15 different PTMs and indicated that about 4.5% of amino acid variations may affect protein function through disruption of PTMs, and the mutation of 238 PTMs sites in human proteins was causative of disease. (deepdyve.com)
Most type II PNH cells (total lack of GPI-linked protein) are due to a frame shift mutation occurring in the early hematopoietic progenitor cells, resulting in same mutation in all blood cell lines. (medscape.com)

They discovered DNA mutations, known as somatic mutations, in the blood-forming system (hematopoietic stem cells) in all 14 astronauts studied. (spaceref.com)
Paroxysmal nocturnal hemoglobinuria (PNH) was previously classified as purely an acquired hemolytic anemia due to a hematopoietic stem cell mutation defect. (medscape.com)

The mutation impact filters are derived from the FATHMM-MKL algorithm ( Functional Analysis through Hidden Markov Models ). (sanger.ac.uk)

These mutations are displayed at the amino acid level across the full length of the gene by default. (sanger.ac.uk)

Extensive efforts have been made to detect low-frequency mutations in cfDNA. (nature.com)

Probable driver mutations were present in around 1% of normal colorectal crypts in middle-aged individuals, indicating that adenomas and carcinomas are rare outcomes of a pervasive process of neoplastic change across morphologically normal colorectal epithelium. (cam.ac.uk)

The first VHL gene mutation related to familial erythrocytosis was identified in the Chuvash population of Russia. (medlineplus.gov)

PNH is caused by somatic mutations in PIGA (which encodes phosphatidylinositol N-acetylglucosaminyltransferase subunit A) in one or more HSC clones. (medscape.com)

Real-time PCR is the most sensitive and reliable method for the detection of DNA mutations. (qiagen.com)

Survival analysis revealed that a low NRP1 expression in adrenocortical carcinoma (ACC), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), low-grade glioma (LGG), and stomach adenocarcinoma (STAD) was associated with poor prognosis. (hindawi.com)

Methods Whole-exome sequencing was performed on ECH lesions from 12 patients (discovery cohort) and droplet digital polymerase-chain-reaction (ddPCR) was used to confirm the identified mutation in 46 additional cases (validation cohort). (bmj.com)
Given that aneuploidy is (a) known to contribute to cell biology and (b) is present at some detectable level in many cell types, it is valuable for single-cell sequencing studies to include aneuploidy information in their analyses. (techscience.com)
Recent studies have demonstrated that multi-site DNA sequencing allows us to investigate this process and reconstruct metastatic migration patterns by analysing somatic single-nucleotide mutations. (ucl.ac.uk)

Compared to somatic mutation analysis, this method has higher sensitivity due to the presence of multiple methylation sites within a single gene. (aacr.org)
10] reported that the K36M mutation of H3 impairs the differentiation of mesenchymal progenitor cells and promotes undifferentiated sarcoma through altered histone methylation landscape. (deepdyve.com)

Consensus clustering analysis was performed to identify immune subtypes using the ConsensusClusterPlus package. (frontiersin.org)

qBiomarker Somatic Mutation PCR Arrays are available in 96-well and 384-well plates and are used to detect mutations related to a disease state or pathway, plus gene copy number controls for normalization. (qiagen.com)

Statistical analysis was performed to identify candidate domains in which mutations occur with high statistical significance. (biomedcentral.com)

Grants awarded through this request for applications are intended to advance the understanding of autism spectrum disorder through analyses of human postmortem brain tissue donated to the Autism BrainNet collection. (sfari.org)

Germline gain-of-function myeloid differentiation primary response gene-88 (MYD88) mutation in a child with severe arthritis. (nih.gov)

Clinical manifestations of PNH occur when a HSC clone carrying somatic PIGA mutations acquires a growth advantage and differentiates, generating mature blood cells that are deficient of GPI-anchored proteins. (medscape.com)
An alternative to a mutation-by-mutation or gene-by-gene association study is to summarize mutation information by certain features and then associate such features with clinical outcomes. (biomedcentral.com)

The wing-spot test determines for the induction of mutant spots that represent the loss of heterozygozity due to point mutation, deletion, nondisjunction, or mitotic recombination using the recessive genetic markers multiple wing hair (mwh) and flare-3 (flr3), located on chromosome number 3. (wikipedia.org)

After that we will examine the methods of data analysis from the row data to final report after logistic regression analysis for reports and publication. (edu.sa)
This work involves methods related to QTL analyses, genetic prediction, and making the most of summary-level GWAS data. (dana-farber.org)

Recent evidence suggests that the prognostic impact of gene mutations in patients with chronic lymphocytic leukemia (CLL) may differ depending on the immunoglobulin heavy variable (IGHV) gene somatic hypermutation (SHM) status. (soton.ac.uk)

Mutations were detected in 1588 (34.7%) patients at frequencies ranging from 2.3-9.8% with mutations in NOTCH1 being the most frequent. (soton.ac.uk)

Univariate cox regression analysis, LASSO-penalized Cox regression analysis, and multivariate Cox regression analysis were applied to construct a prognostic risk model. (frontiersin.org)
Univariate and multivariate Cox regression analysis revealed that AAMRG-related signature was an independent risk factor for COAD. (frontiersin.org)

Hotspot mutations in Gα s (R201 and Q227) as well as Gα q and Gα 11 (R183 and Q209) disrupt the GTPase activity, thereby leading to constitutive activity and persistent signalling. (nature.com)

Anatomy13

Organisms7

Diseases33

Chemicals and Drugs64

Analytical, Diagnostic and Therapeutic Techniques and Equipment28

Phenomena and Processes116

Disciplines and Occupations2

Information Science4

Named Groups2

Health Care5

Genes24

Tumor23

Variants11

Point mutations1

Cancers6

Landscape of somatic mutation1

Cancer44

SNPs1

Clonal7

Tumours4

Recurrent2

Novo2

Genomic2

PMID2

Genome11

Sequences2

Tumors3

TP531

KRAS1

Deletions1

Oncogenic1

Bioinformatics1

Molecular4

Germline mutations1

Alterations3

Genomics1

Acute myeloid1

Tumour microenvironment1

Computational3

Protein13

Hematopoietic2

Functional analysis1

Amino acid1

Frequency1

Colorectal1

Gene mutation1

Encodes1

Detection1

Survival1

Sequencing3

Methylation2

Subtypes1

Detect1

Occur with high1

Tissue1

MYD881

Clinical2

Deletion1

Methods2

Suggests1

Frequencies1

Univariate2

Hotspot1