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Is the Genomiser (or something similar) going to be the next Enlis, but for Whole Genome Sequencing (WGS)?

Discussion in 'ME/CFS research news' started by BeautifulDay, Nov 21, 2017.

  1. BeautifulDay

    BeautifulDay Established Member (Voting Rights)

    United States
    I realize some people in the CFS/ME community look down on the Jackson Laboratory. Despite the fact that JAX is a late comer and there are some politics going on here that I don't understand, JAX has received a large amount of cash money from NIH, so it's important to keep an idea on what they are doing.

    In a blog on the JAX site titled "GENOMES VERSUS EXOMES VERSUS GENOTYPES", it goes into how up until recently, the extra information in the Genome versus Exome data was seen as junk. Now researchers are finding more things in that genome (outside exome) that are relating to disease.

    Specifically, I found the below two paragraphs from the article interesting:

    "But progress is being made on the research front, where tools are being developed to analyze the potential impact of non-coding variants throughout the human genome. Last week, a group led by newly arrived JAX Professor Peter Robinson published a paper detailing a new tool called “genomiser,” which assesses the pathogenicity of known non-coding variants and finds a high rate of causal mutations in human disease. Increasing knowledge of non-coding variant effects and developing analytical tools to quickly find probable disease variants will greatly expand WGS usefulness in both clinical and research settings.

    Future thoughts
    Recent initiatives such as the U.K.’s 100,000 genomes project and the U.S.’s Precision Medicine Initiativeare driving progress in clinical genomics at a rapid pace. What seemed exotic a few years ago may quickly become standard procedure. Questions and challenges and even pessimism regarding precision medicine persist in the healthcare system, but becoming familiar with the testing and sequencing options and their pros and cons is important and relatively easy these days — and many of us will likely be mulling over our variants of uncertain significance in the near future."

    I started imagining a world where we could run our data through a Genomiser (or some similar app), just like we can through Enlis today (with our 23andme data and our VCF files from WGS or WES). With the huge data size for WGS, there are a few leaps in technology at the personal level, etc... that will have to take place first -- but I don't believe they are that far off.

    In their link "genomiser" comes up an article that states:

    "Abstract: The interpretation of non-coding variants still constitutes a major challenge in the application of whole-genome sequencing in Mendelian disease, especially for single-nucleotide and other small non-coding variants. Here we present Genomiser, an analysis framework that is able not only to score the relevance of variation in the non-coding genome, but also to associate regulatory variants to specific Mendelian diseases. Genomiser scores variants through either existing methods such as CADD or a bespoke machine learning method and combines these with allele frequency, regulatory sequences, chromosomal topological domains, and phenotypic relevance to discover variants associated to specific Mendelian disorders. Overall, Genomiser is able to identify causal regulatory variants as the top candidate in 77% of simulated whole genomes, allowing effective detection and discovery of regulatory variants in Mendelian disease."

    It's worth reading it, if you haven't already.

    I realize none of this is new to many of you and I'm just behind. But for me, I need to keep in mind that while there are researchers that I'm routing for, there are other researchers who might push research here and there too. In the end, I'm thankful for any of the researchers whose discoveries lead to help for me, my kids, and future generations.

    merylg, healthforall, sea and 7 others like this.
  2. Andy

    Andy Committee Member

    Hampshire, UK
    I wasn't aware of people being dismissive of them at all but then I can be pretty blind at times to politics of most sorts.
    Skycloud, Louie41, ahimsa and 3 others like this.
  3. Jenny TipsforME

    Jenny TipsforME Senior Member (Voting Rights)

    Thanks for sharing. I’m in the process of getting my whole genome done
    BeautifulDay, merylg and wastwater like this.
  4. wastwater

    wastwater Senior Member (Voting Rights)

    Me too, to get on the UK 100,000 genomes you need a rare genetic disorder or I think maybe cancer There’s a video on YouTube
    Think it’s ending this year around September so try get on it if you’re eligible
    Last edited: Jan 28, 2018
    BeautifulDay and merylg like this.
  5. Londinium

    Londinium Senior Member (Voting Rights)

    From what I recall, a minority were disappointed the OMF didn't get funded. Personally (as I've posted here before) I'm really pleased the Unutmaz team got funded as I think it's really valuable to get a new team into the field.

    Not that rare though - my missus+family are on it due to epilepsy.

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