Sentences with phrase «exon with»

Besides being much easier and more efficient than replacing the dysfunctional exon with a working copy, simply snipping out the weak link is a strategy that would be effective in a larger swath of the patient population.

a Distribution of the number of exons with significant differential inclusion across the different tissues; inset: number of exons with differential inclusion occurring in multiple tissues.

b, c Examples of two exons with PMI - correlated inclusion levels.

Exons with PSI values following the three criteria defined in the previous section in Blood samples were selected for differential expression analysis.

Not exact matches

Sarepta Therapeutics, which won a pioneering Food and Drug Administration approval for its Duchenne muscular dystrophy drug last year, has settled a patent dispute with rival BioMarin over the «exon - skipping» technology at heart of the companies» muscular dystrophy treatments.

The biotech specialist said that its updated phase 2 data in a study of its poziotinib candidate treatment for non-small cell lung cancer resulted in a preliminary confirmed objective response rate and potential progression - free survival benefit in patients with the EGFR Exon 20 Mutant form of the disease.

In the study, researchers worked with a mouse model that has a debilitating mutation on one of the exons of the dystrophin gene.

The human UFD1L gene was deleted in all 182 patients studied with 22q11 deletion, and a smaller deletion of approximately 20 kilobases that removed exons 1 to 3 ofUFD1L was found in one individual with features typical of 22q11 deletion syndrome.

CAPRI - GOIM is a non-profit, academic, phase II trial enrolling 340 patients with mCRC and KRAS exon 2 wild - type tumours, according to local molecular pathology laboratory assessment.

The researchers found abnormal fusion - circular RNAs (f - circRNAs), corresponding to different exons associated with the PML - RARα gene fusion as well as the MLL - AF9 gene fusion.

«Previous studies utilizing similar techniques have focused primarily on slowly evolving regions, such as exons, due to concerns with capture success,» explains Folk.

Results for different genomic partitions, methods, and data types are consistent with or contradict clades in our TENT ExaML, TENT MP - EST *, and exon - only trees and previous studies of morphology (15), DNA - DNA hybridization (24), mitochondrial genes (14), and nuclear genes (17).

Like many genes, Dscam consists of protein - coding regions called exons interspersed with noncoding regions.

Trees created from analysis of the first and second codon positions (exon c12) of the TENT data also had lower levels of BS (~ 39 to 64 %) but with more topological differences on the deep branches (Figs. 2, 4C, and 5A), yet all but one of the fully resolved relationships (local difference in egret + ibis + pelican) were congruent with the TENT (Fig. 5B).

We further investigated the source of the conflict in the protein - coding genes (SM11) and found that trees using all codon positions from the 10 % most compositionally homogeneous (low - variance) exons (n = 830) were most congruent with the c12 tree and, thus, more similar to the TENT than to the c123 tree (Figs. 2 and 6A; cladograms in fig.

Conversely, trees using all codon positions from the 10 % most compositionally heterogeneous (high - variance) genes (n = 830) were more congruent with the exon c123 and c3 trees (Figs. 2 and 6B and fig.

To estimate the avian timetree with genomic - scale data, we used first and second codon positions from 1156 clock - like exon genes (which do not strongly exhibit the above protein - coding compositional bias), calibrated with 19 conservatively chosen avian fossils (plus nonavian outgroups) as minimum bounds for lineage ages (with a maximum - bound age constraint of 99.6 Ma for Neornithes), in a Bayesian autocorrelated relaxed clock method using MCMCTREE (77) on the fixed ExaML TENT topology (SM12).

These differences are not merely due to shorter alignments of the exon and UCE sequences, because each accounted for ~ 25 % of the TENT data, similar in sequence length to the random 25 % subset of the TENT with introns (table S3) that produced a tree with a higher average BS and a topology closer to the full TENT (Fig. 5A and fig.

From these efforts, we identified a high - quality orthologous gene set across avian species, consisting of exons from 8251 syntenic protein - coding genes (~ 40 % of the proteome), introns from 2516 of these genes, and a nonoverlapping set of 3769 ultraconserved elements (UCEs) with ~ 1000 bp of flanking sequences.

The branch lengths of the high - variance exon tree showed a strong positive correlation with GC content and a negative correlation with the average body mass of species, seen at a much lesser magnitude in the low - variance exon tree (Fig. 6, A to D).

«Most often when material from introns is improperly included with exons, the result is nonsense proteins that go on to quickly degrade, meaning that cancer may use this strategy to downregulate the production of certain anti-cancer proteins,» Tan says.

Unfortunately, if SF3B1 is mutated, this cutting and pasting can go awry in ways that introduce unintended bits of introns along with the intended bits of exons into the blueprint.

In order to reach maturation and be sent to the cellular «machine» that deals with protein synthesis, the non-coding fragments contained in the mRNA, the introns, need to be removed, whereas the coding sequences, the exons, have to be linked together.

The research, which appears online Aug. 1 in the journal Annals of Neurology, is the first study from a double - blind controlled randomized trial of an exon - skipping agent to provide conclusive proof based on the standard six - minute walk test used to measure muscle function in patients with Duchenne muscular dystrophy (DMD), the most common form of muscular dystrophy in children.

Using whole exome sequencing (a next generation test to analyze the exons or coding regions of thousands of genes simultaneously) conducted at the Baylor College of Medicine Human Genome Sequencing Center, the researchers identified CLP1 mutations in two unrelated families with the disorder.

«The repair mechanism ensures that mutations do not accumulate in the genome, particularly in exons,» explains Joan Frigola, PhD student and first author of the article together with postdoc Sabarinathan Radhakrishnan.

These findings in murine muscle, coupled with a significant association between a SNP in exon 3 of the IL15RA gene and human endurance athletes, support our hypothesis whereby IL - 15Rα has a role in defining the phenotype of fast skeletal muscles.

In BRCA1, exon 11 mutations were associated with earlier ages at breast and ovarian cancer diagnosis.

Exon - Based Transcriptome Profiling Reveals Genes That Have Prognostic Impact on the Survival of Young High Risk Diffuse Large B - Cell / Follicular Grade 3 Lymphoma Patients Treated with Dose - Dense Chemoimmuno - therapy and CNS Prophylaxis.

In the current study, the genotype and allele frequency of a SNP in exon 3 of the IL15RA gene were associated with elite human endurance athletes stratified by sport.

A Phase II Single - Arm Trial to Investigate Tepotinib in advanced (Stage IIIB / IV) Non-Small Cell Lung Cancer with MET Exon 14 (METex14) Skipping Alterations After Failure of at Least One Prior Active Therapy, Including a Platinum - Doublet - Containing Regimen

The source of this «functional enrichment» likely has to do with sequence context: mutations often occur at CpG dinucleotides, which are themselves more prevalent in exons and DHSs.

Chicken β - globin exons 2 and 3 including the 3 ′ UTR are indicated as black boxes with corresponding Roman numerals followed by the β - globin polyadenylation signal (PolyA *).

7004.1 is an extension of 790.1 with 5 extra residues at the N - terminus.7004.2 is truncated 10 amino acids short of the end exon 1 of tat.

A transcribed genomic sequence that gives rise to one or more proteins with shared exons was scored as one transcription unit, and its length was taken from the position of RNA initiation to that of the site of polyadenylation, as measured on the underlying genomic sequence.

A 50 % reduction in HDAC4 restored these and other electrophysiological changes in both the R6 / 2 model, a transgenic over-expresser of Exon 1 HTT with an expanded polyglutamine repeat, and heterozygous Q175 knock - in mice (Q175 + / --RRB-, which carry one normal and one mutant HTT allele with an expanded repeat of ~ 190 polyglutamines, in addition to reversing behavioral alterations in R6 / 2 mice (Mielcarek et al, 2013; PLOS Biology, in press).

[66,67] Although responses were highly variable, patients with mutations more frequently achieved a clinical response than did those with amplifications, and patients with tumor mutations affecting exons 11 and 13 were able to achieve significant radiographic responses in over 40 % of cases.

We considered genes with at least 5 reads mapping in exons and from all biotypes in the annotation.

From this subset of selected exons we have then performed correlation analysis of the PSI value with the PMI value for each tissue.

Novel short exons (shorter than the read length) were predicted using reads with more than one split with canonical GT / AG splicing nucleotides and minimum entropy of at least 1.5 bits for each splice junction.

We report here a significant improvement in the resolution of array CGH, with the development of an array platform that utilizes single - stranded DNA array elements to accurately measure copy - number changes of individual exons in the human genome.

Next, differential exon inclusion was tested with Wilcoxon Sum Rank test, with multiple testing adjustments by Benjamini - Hochberg method44, and the median of the PSI values in each group calculated.

The percent - spliced - in (PSI) metric was computed as in Wang et al. 33 by using inclusion and exclusion reads with the minimum total count of 5 reads; that is, exons for which the combined number of inclusion and exclusion reads was less than 5 were excluded.

Dr. Mazires and colleagues retrospectively studied a group of patients in France, Spain, and Switzerland with NSCLC who carried a HER2 mutation in exon 20.

Functional analysis of genes with recurrent exons (i.e., with association with PMI in more than two tissues) shows a noteworthy enrichment on RNA binding and RNA splicing genes (Supplementary Fig. 18b, c).

In contrast to gene expression, there is a substantial sharing of exons among the top affected tissues (those with ≥ 20 significant exons), with the tissue pairwise overlap ranging from 43 % to 82 %, representing 22 to 76 shared exons.

Sequences for 54 nuclear genes were taken from Perelman et al.'s [12] nexus file with modifications to eliminate problems with probable contaminants and misidentified sequences (Table S2); sequences for 15 additional nuclear genes (ABO, CXCR4, CXCR5, Epsilon globin, FGA, IRBP intron 1, IRBP intron 3, MC1R, NRAMP, PRNP, VWF intron 11) were obtained from GenBank; and new sequences (JX856181 - JX856283, JX869897 - JX869930) for exons of four nuclear genes (GHR, IRBP, VWF, TTN) were combined with previously published GenBank sequences for these loci.

We've put it off as long as we can, but now we're faced with the daunting task of identifying and interpreting biologically - relevant variants outside of protein - coding exons.

With exome sequencing, this was commonly done on a per - gene or per - exon basis.

The coding portion of the first CCHa2 - R coding exon was replaced with sequence encoding the strong GAL4:: p65 transcriptional activator (Fig 2E; CCHa2 - R - GAL4:: p65).