Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • david.tamborero
    replied
    thanks for the answer!

    I think that I am going to score as 'highly deleterious' those mutations in 2 last/ 2 initial bases of introns in canonical splice sites, as I am currently doing with mutations in exons introducing a stop codon or a frameshift indel. For those mutations in other splice regions of the intron, for the moment I will consider them as having unknown effect, since I am not able to find a reliable score to classify their deleterious potential, and actually they should be not well catalogued -I guess- since I am dealing with exome seq data.

    Now I will move towards the assessment of how mutations in exons can create cryptic splice junctions. Absolutely, I will check skippy, it looks very nice!

    thanks again,
    best
    David

    Leave a comment:


  • m_two
    replied
    If you are interested in de novo splice site potential you might be interested in this:
    SKIPPY_-_Exonic_Splice_Modulator_Scoring

    Web query:
    A collection of online resources developed by NHGRI Division of Intramural Research investigators, including specialized genomic databases and novel software tools for use in genomic analysis


    Home:
    A collection of online resources developed by NHGRI Division of Intramural Research investigators, including specialized genomic databases and novel software tools for use in genomic analysis


    Pub:
    Woolfe, A., Mullikin, J., and Elnitski, L. 2009. Genomic features defining exonic variants that modulate splicing. Genome Biology. 11:R20 [PubMed]



    See: Table S1 – List of 87 Synonymous and Missense variants that cause exon skipping ,used for analysis in this study. The variants are located in 40 genes and 47 individual ,exons. Variant locations are from human genome assembly hg18. References can be ,found in the main text of the paper.

    Additional file 1. List of 87 synonymous and missense splice-affecting genome variants (SAVs) that cause exon skipping used for analysis in this study. The variants are derived from [12,13,37,41,44,47,48,54-56,65-103].

    Format: PDF Size: 117KB Download file

    Leave a comment:


  • m_two
    replied
    Ensembl VEP annotates mutations affecting the 5' and 3' and last two bases of the annotated introns as splice_donor_variant / splice_acceptor_variant, it does not predict de novo splice sites.

    To further filter the annotation you can try these four things:

    Eliminate variants exclusive to transcripts that are known pseudogenes or undergo NMD.

    Grab the nucleotide conservation scores from UCSC, real splice sites should have very high conservation scores.

    Eliminate splice variants that affect noncanonical GT AG splice sites.

    Filter common dbSNPs identified in 1000 Genomes data and NHLBI GO Exomes

    Leave a comment:


  • david.tamborero
    started a topic impact of mutations in splicing sites

    impact of mutations in splicing sites

    hi,

    I would like to score the impact of mutations occurring in gene regions that the variant effect predictor state as 'splice_variant'. Note that at this moment I do not want to predict whether the mutations create a cryptic splice site.

    I guess that there are some consensus sequences for both donor and acceptors, but I assume that it is more complicated that to construct the weight matrix by myself and check how it fits the wild type vs the mutant.

    Actually, I'm a bit lost. I found the Human Splice Finder and the MaxEntScan, but I am not sure of how to interpret their results, and -mainly- I would need some tool that can be run by script, since them are only available via manual entering of the data in the web.

    many thanks,
    david

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
26 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 09:45 AM
0 responses
201 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 08:54 AM
0 responses
212 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-02-2024, 03:00 PM
0 responses
193 views
0 likes
Last Post seqadmin  
Working...
X