• Identification of low-penetrance alleles that occur commonly in populations may benefit from unbiased genome-wide screening. (mcw.edu)
  • Previous phylogenetic comparisons based on orthology, diversity, and expression patterns identified three plant FBX groups--Common, Lineage-Specific, and Pseudo(genized)--whose emergences are consistent with genomic drift evolution. (nih.gov)
  • Taken together, we propose that reversible epigenomic modifications helped shape FBX gene evolution by transcriptionally suppressing the adverse effects of gene dosage imbalance and harmful FBX alleles that arise during genomic drift, while simultaneously allowing innovations to emerge through epigenomic reprogramming. (nih.gov)
  • Using a statistically rigorous protocol, we investigated the genomic distribution of ASHM in hESCs, and their relationship to sites of allele-specific expression (ASE) and DNA methylation. (ed.ac.uk)
  • Genomic DNA from the patient was screened for chromosomal imbalances by array-based comparative genomic hybridisation. (bmj.com)
  • Using comparative, evolutionary and functional genomic approaches, we profiled genome-wide allelic imbalance in mammalian placental samples including marsupials, mouse, cattle, dog and interspecific equid hybrids (mules and hinnies), and characterized different forms of X chromosome inactivation and their epigenetic regulation in the placenta. (xuwang.us)
  • Genomic imprinting is an extreme form of allelic imbalance, in which the expression of imprinted genes is in a parent-of-origin dependent fashion. (xuwang.us)
  • 2013 ) . The best studied example of allele-specific methylation (ASM) is genomic imprinting. (bioconductor.org)
  • Type 2 diabetes (T2D) demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. (blogspot.com)
  • The researchers then compared the relative gene expression levels of each allele across different tissues within each individual, theorizing that if two alleles are expressed in a biallelic fashion, the overall allelic expression ratio should fit a binomial distribution, whereas randomly expressed alleles wouldn't. (the-scientist.com)
  • More subtle variation of gene expression, that is not parent-of-origin specific, termed 'allele-specific gene expression' (ASE) is more common and may give rise to milder phenotypic differences. (ox.ac.uk)
  • Corrigendum: analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. (tamu.edu)
  • RNA-sequencing (RNA-seq) is a powerful technique for the identification of genetic variants that affect gene-expression levels, either through expression quantitative trait locus (eQTL) mapping or through allele-specific expression (ASE) analysis. (biomedcentral.com)
  • for allele-specific discrimination, genotyping and gene expression analysis? (genaxxon.com)
  • Together, these data suggest that one or more breast cancer-related genes are located within the dominantly acting WKy allele at the Mcs7 locus. (mcw.edu)
  • In contrast, the Lineage-Specific and Pseudo groups are enriched in genes with basal expression and higher SNP density and more correlated with methylation marks (RNA-directed DNA methylation and histone H3K27 trimethylation) that promote transcriptional silencing. (nih.gov)
  • A study identifies nearly 3,000 genes where one allele tends to be expressed more than the other, but the findings ignited controversy in the field. (the-scientist.com)
  • E very person carries two copies of most genes, with one version, or allele, coming from each parent. (the-scientist.com)
  • Using a model that characterizes patterns in allele expression from bulk RNA sequencing data, the researchers found that both alleles of some genes were equally active throughout tissues-but for almost 3,000 genes, cells favored one allele or the other, exhibiting what the authors call random allelic expression (RAE). (the-scientist.com)
  • We] discovered that there are some genes where the two alleles are absolutely in lockstep with each other," Gregg explains. (the-scientist.com)
  • As a control, they tested whether the method could distinguish X-linked genes from autosomal genes, and indeed, the model labeled X-linked genes as RAE, validating the model's ability to discern biased expression of alleles. (the-scientist.com)
  • BACKGROUND: Imprinted genes show expression from one parental allele only and are important for development and behaviour. (ox.ac.uk)
  • This extreme mode of allelic imbalance has been described for approximately 56 human genes. (ox.ac.uk)
  • Using two allele-specific high-throughput technologies alongside bioinformatics predictions, normal term human placenta was screened to find new imprinted genes and to ascertain the extent of ASE in this tissue. (ox.ac.uk)
  • The development of targeted therapies for both germline and somatic DNA mutations has increased the need for molecular profiling assays to determine the mutational status of specific genes. (oncotarget.com)
  • We found that individuals with ASD had more genes that were up-or down-regulated in an individual-specific manner. (huji.ac.il)
  • A number of genetic studies led to the identification of genes and/or copy number variants whose alterations are associated with autism, but no specific factor has been found so far to be responsible for a substantial proportion of cases. (biomedcentral.com)
  • Nonetheless, quantitative whole-genome analyses promise to identify one or a few autism-specific copy number variants (CNVs) harboring genes whose dosage alterations could be critical in causing ASD. (biomedcentral.com)
  • Following up on their findings, they examined a subset of genes more closely, directly visualized imbalances between gene copies at the cellular level in the mouse and human brain. (utah.edu)
  • Imprinted genes and X-linked genes are specific gene categories that differentially activate their maternal and paternal gene copies. (utah.edu)
  • His lab previously found widespread evidence of allelic imbalances in the brains of mice and in cultured cells. (the-scientist.com)
  • The shift in b-allele frequency is calculated relative to the expected heterozygous frequency 0.5, and minor allele frequencies are "mirrored" above and below 0.5 so that it does not matter which allele is considered the reference - the relative shift from 0.5 will be the same either way. (readthedocs.io)
  • It demonstrates high analytic sensitivity and broad reportable range and it provides simultaneous detection of concomitant mutations and a quantitative measurement of mutant allele frequencies to predict tumor heterogeneity and mutant allele-specific imbalance. (ecologicalsgardens.com)
  • Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. (blogspot.com)
  • To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. (blogspot.com)
  • We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. (blogspot.com)
  • Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. (blogspot.com)
  • Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed disparity in T2D incidence rates across ethnic populations. (blogspot.com)
  • Tumor multiplicity was significantly higher ( approximately 50%) in DMBA-treated congenics homozygous and heterozygous for the WKy allele at the Mcs7 locus, compared to controls. (mcw.edu)
  • We also investigated allelic imbalance (AI) in mammary carcinomas from (WKy x WF)F1 rats and Mcs7 heterozygous congenics. (mcw.edu)
  • In this context, the "B" allele is the non-reference allele observed in a germline heterozygous SNP, i.e. in the normal/control sample. (readthedocs.io)
  • From a biological point of view, you might want to run this mode if you are interested in loss or gain of allele-specificity linked to somatic or germline heterozygous SNPs (sequence-dependent ASM). (bioconductor.org)
  • Expression allelic imbalance is characterized by a deviation from the Mendelian expected 1:1 expression ratio and is an important source of allele-specific heterogeneity. (researchgate.net)
  • Burst-Like Transcription of Mutant and Wildtype MYH7-Alleles as Possible Origin of Cell-to-Cell Contractile Imbalance in Hypertrophic Cardiomyopathy. (crossref.org)
  • Study finds allele-specific open chromatin variants are likely to be linked to several neuropsychiatric traits and illnesses, including schizophrenia and bipolar disorder. (brainscientists.com)
  • eQTL mapping on individual tissues revealed that a limited number of samples already suffice to identify tissue-specific eQTLs for known disease-associated genetic variants. (biomedcentral.com)
  • Given the exponential growth of the number of publicly available RNA-seq samples, we expect this approach will become especially relevant for studying the effects of tissue-specific and rare pathogenic genetic variants to aid clinical interpretation of exome and genome sequencing. (biomedcentral.com)
  • Our results reveal that there is a considerably higher than expected prevalence of putative disease alleles and variants associated with VWD and suggest that a large number of VWD patients are undiagnosed. (cdc.gov)
  • Here, we performed a genome-wide survey of allele expression imbalance (AEI) in the human brain using single-nucleotide polymorphisms (SNPs), in 18 individuals with ASD and 15 controls. (huji.ac.il)
  • But due to allele-specific copy number alterations, loss of heterozygosity or allelic imbalance, the allelic frequency of these SNPs may be different in the tumor, and that's evidence that one (or both) of the germline copies was gained or lost during tumor evolution. (readthedocs.io)
  • While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. (blogspot.com)
  • Human genetic variation, DNA methylation, and disease have been intensely studied, uncovering many sites of allele-specific DNA methylation (ASM). (ed.ac.uk)
  • The main focus is allele-specific expression (ASE), allele-specific DNA methylation (ASM) and allele-specific histone modifications. (xuwang.us)
  • 1.1 What is allele-specific methylation? (bioconductor.org)
  • The phenomenon occurs when there is an asymmetry in methylation between one specific allele and the alternative allele (Hu et al. (bioconductor.org)
  • We focus on any case of ASM in which there is an imbalance in the methylation level between two alleles, regardless of the allele of origin. (bioconductor.org)
  • 1756-8935-5-6-s1.xls: Read counts for each allele and each histone modification at the sites of ASHM identified in this study. (ed.ac.uk)
  • However, little is known about the genome-wide occurrence of sites of allele-specific histone modification (ASHM) and their relationship to human disease. (ed.ac.uk)
  • And scientists have described cases of random monoallelic expression, wherein cells only express one allele and suppress the other, but experts disagree about the phenomenon's prevalence. (the-scientist.com)
  • Chromatin structure at a given site can differ between chromosome copies in a cell, and such imbalances in chromatin structure have been shown to be important in understanding the molecular mechanisms controlling several disease loci. (ed.ac.uk)
  • The maternal PLZF allele harbours a recessive missense mutation (c.1849A→G), which leads to the substitution of a highly conserved methionine by valine (p.Met617Val) within a zinc-finger motif. (bmj.com)
  • Taking into account specific alpha-helical propensities of Val and Met, this mutation is likely to destabilise the alpha helix of the zinc finger that forms the contact with the DNA duplex, thus affecting the biological function as shown by reporter-gene assays. (bmj.com)
  • This study has investigated whether the same gene is responsible for grade I invasive ductal carcinoma (IDC), using allele imbalance analysis, mutation screening, and immunohistochemistry (IHC). (ox.ac.uk)
  • Furthermore, negative early experiences interact with specific gene alleles to produce long-lasting effects on the body and brain over the course of a lifetime via epigenetic mechanisms. (alliedacademies.org)
  • This null allele was PCR amplified by redesign of one of the original primers and multiple individuals homozygous for null as well as for nonnull alleles were sequenced using the new primer. (escholarship.org)
  • In two cases that were studied in detail, the monoallelic expression was confined to specific brain region or cell type. (huji.ac.il)
  • The "digital era" has revolutionized both the generation and the interpretation of the data, thus supporting-if not replacing completely, for specific analyses-functional studies to understand physiology and pathology of the cells. (mdpi.com)
  • The Mcs7 quantitative trait locus is associated with an increased susceptibility to mammary cancer in congenic rats and an allele-specific imbalance. (mcw.edu)
  • ZNF331 is imprinted in human term placenta and might be a new ubiquitously imprinted gene, part of a primate-specific locus. (ox.ac.uk)
  • One locus exhibited a high-frequency nonamplifying allele localized to a single population. (escholarship.org)
  • These molecular dissections revealed that the original failure to amplify some alleles from this microsatellite locus was due to a 4 bp deletion in one of the original PCR priming sites. (escholarship.org)
  • Traditional methods for tumor characterization are tumor-type specific and include assays such as immunohistochemistry (IHC), in situ hybridization (ISH), quantitative PCR (qPCR), Sanger sequencing and gene signature microarrays [ 1 - 8 ]. (oncotarget.com)
  • Even though these copies tend to be functionally redundant, conventional genetic theory dictates that biallelic expression, wherein both alleles are transcribed equally when the gene is expressed, is nearly universal. (the-scientist.com)
  • Biased allele expression is a known genetic phenomenon, but it's thought to be rare. (the-scientist.com)
  • None of the bioinformatically predicted candidates tested showed imprinting except for a skewed allelic expression in a parent-specific manner observed for PHACTR2, a neighbour of the imprinted PLAGL1 gene. (ox.ac.uk)
  • He highlighted various approaches for tapping the genetic potential in crops such as using environmental genome-wide association studies (GWAS) to identify useful alleles from diverse landraces, sequencing many closely related species to predict the most deleterious alleles, and using machine learning to model TF binding preferences and to predict allele-specific expression within and across species. (biomedcentral.com)
  • When a gene is imprinted, one of the parental alleles is hyper-methylated compared to the other allele, which leads to parent-allele-specific expression. (bioconductor.org)
  • Because of this complexity, decades of experimental work, even with the aid of sophisticated molecular genetic tools (such as high resolution total genome quantitative analysis, array expression analysis or high resolution single nucleotide polymorphism (SNP) array platforms) have failed to identify specific causes in any substantial proportion of cases [ 4 , 5 ]. (biomedcentral.com)
  • From this data, Kravitz calculated the abundance of each allele across tissues. (the-scientist.com)
  • 2012) Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases. (blogspot.com)
  • Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. (blogspot.com)
  • Specific factors relating to cardiovascular disease are listed below. (medscape.com)
  • In health, specific microbes exist in a symbiotic relationship with their human host, where they contribute essential vitamins and nutrients, prime the human immune system to recognize "non-self" antigens, and produce useful anti-inflammatory compounds that deter disease-causing microbes. (genaxxon.com)
  • An imbalance in the human microflora, or dysbiosis, features in many disease states. (genaxxon.com)
  • What the genetic imbalance could mean for our health remains to be determined, but preliminary results suggest that it could shape vulnerabilities to disease, explains Gregg. (utah.edu)
  • There are various limitations in susceptibility, how host susceptibility ies may focus only on specific tumour epidemiological studies (e.g. statis- factors may modulate the impact of outcomes or may not be designed to tical power, exposure assessment, mechanistic events leading to tumour detect some types of tumours). (who.int)
  • Thus, host susceptibil- of carcinogens: (1) is electrophilic by Hill and Ul rich), as well as other ity may determine how and wheth- or can be metabolical y activated to host susceptibility factors from this er specific individual sites or target electrophiles, (2) is genotoxic, (3) al- large and rich database. (who.int)
  • Grade I invasive ductal breast carcinomas have a specific pattern of genetic aberrations, namely gain of 1q and loss of 16q. (ox.ac.uk)
  • These null alleles did not overlap in length with the nonnull alleles, and they also differed consistently by a linked nucleotide substitution. (escholarship.org)
  • CNVpytor workflow 1.1 for CNV/CNA detection and analysis based on read depth and allele imbalance in WGS. (sevenbridges.com)
  • FACETS workflow 0.6.1 for allele-specific copy number analysis (ASCN). (sevenbridges.com)
  • Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution. (tamu.edu)
  • Species-specific PCR revealed an enrichment of potentially harmful species (Escherichia coli and Eubacterium biforme), and a reduction in beneficial species (Faecalibacterium prausnitzii, Bifidobacterium spp. (genaxxon.com)
  • Type two diabetes is the adult onset form that is strongly associated with obesity and other particular dietary imbalances. (blogspot.com)
  • Results suggest that the original null allele (as well as the nonnull class) has diversified considerably since its origin and has not recombined frequently with the nonnull class of alleles. (escholarship.org)
  • Despite extensive genetic and biological research, significant controversy surrounds our understanding of the specific mechanisms of their pathogenesis. (mdpi.com)
  • Such forces are especially obvious within the F-Box (FBX) superfamily, one of the largest and most polymorphic gene families in land plants, where its frequent lineage-specific expansions and contractions provide an excellent model to assess how genetic variation impacted gene function before and after speciation. (nih.gov)
  • DNMT3A and TET2 compete and cooperate to repress lineage-specific transcription factors in hematopoietic stem cells. (tamu.edu)
  • In the present study, our aim was to establish an in vitro cell model based on patient-specific human neurons to study the pathomechanism of sporadic AD. (biomedcentral.com)
  • There is also an association between the dosage of NOD2 risk alleles (rs104895467, rs2066844, rs2066845, rs5743277 and rs5743293) and increases in the relative abundance of Enterobacteriaceae, which is independent of the effect of antibiotics on dysbiosis [7, 2, 14, 6]. (genaxxon.com)
  • Data table showing topics related to specific cancers and associated disorders. (cancerindex.org)
  • Activating a gene copy that is mutated and silencing the healthy copy - even temporarily - could be disruptive enough to cause trouble in specific cells. (utah.edu)
  • The results from this study, however, suggests that silencing one gene copy may be a way in which cells fine tune their genetic program at specific times during the lifecycle of the animal, or in discrete places. (utah.edu)
  • But a study published in Cell Reports in January posits something different: that it might be somewhat common for cells to preferentially express only one of a gene's alleles. (the-scientist.com)
  • S1P is generated intracellularly by two sphingosine kinases (SphK1, SphK2) and is exported out of cells by Spinster 2 (Spns2) to exert its effects through activation of five specific cell surface S1PRs in autocrine or paracrine manners. (sphingolipidclub.com)
  • Here, psychosine's effect was cell-type specific. (sphingolipidclub.com)
  • The sensory experience is produced by stimulation of specific receptors in the oral cavity. (medscape.com)
  • In one study of the effect of host genetics on specific gut microbes related to MetS status, individuals with MetS exhibited reduced gut microbial diversity, with an enrichment of Sutterella, Methanobrevibacter and Lactobacillus, while healthy individuals were enriched in Akkermansia, Odoribacter and Bifidobacterium. (genaxxon.com)
  • There is a fairly strong genetic background to pemphigus vulgaris with linkage to HLA class II alleles. (bvsalud.org)
  • Stress leads to an imbalance in the neural circuitry that supports cognition, judgment, anxiety, and mood, which can change how these behaviours and behavioural states are expressed. (alliedacademies.org)