16 Matching Annotations
  1. Jun 2022
  2. www.biorxiv.org www.biorxiv.org
    Evidence-based calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for clinical use of PP3/BP4 criteria
    4
    1. azankl 17 Jun 2022
      As with the ClinVar set, all missense variants from genes without asingle pathogenic variant of any type in ClinVar were removed.

      is this reasonable, is this different from how the tool creators did their accuracy assessments?

    2. azankl 17 Jun 2022
      the ClinVar 2019 set

      isn’t this basically just predicting pathogenicity based on being in Clinvar? and with 1 star level being considered pathogenic?

    3. azankl 17 Jun 2022
      ACMG-AMP_criteria genomics
    4. azankl 17 Jun 2022
      Among these, all VUS, variants with a zero-star reviewstatus, i.e., without any detailed review information, and those with conflicting classificationswere excluded

      dodgy labs might mark variant as pathogenic and link to assessment criteria but apply them wrongly. These might be detected if other labs post conflicting assessments. But for ultrarare variants, no other lab might have submitted that variant

      genomics ACMG-AMP_criteria
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    biorxiv.org/content/10.1101/2022.03.17.484479v1
  3. www.biorxiv.org www.biorxiv.org
    Pooled-parent exome sequencing to prioritise de novo variants in genetic disease
    1
    1. azankl 16 Jun 2022
      An average individual exome has 10,000-12,000non-synonymous variants [13], 120 protein truncating variants, and ~54 variants previouslyreported as pathogenic
      exome
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    biorxiv.org/content/10.1101/601740v1.full.pdf
  4. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    A guide to performing Polygenic Risk Score analyses
    1
    1. azankl 15 Jun 2022
      A guide to performing Polygenic Risk Score analyses

      very detailed

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    ncbi.nlm.nih.gov/pmc/articles/PMC7612115/
  5. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Post‐GWAS Polygenic Risk Score: Utility and Challenges
    3
    1. azankl 15 Jun 2022
      yield an AUC >0.80

      does this assume all variant effects are independent of each other, and if so, is that assumption reasonable? Answered below

    2. azankl 15 Jun 2022
      QUS

      quantitative ultrasound

    3. azankl 15 Jun 2022
      Another caveat of the PRS is its assumption of additive effects

      answer to my earlier question here

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    ncbi.nlm.nih.gov/pmc/articles/PMC7657393/
  6. Aug 2020
  7. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    VCV000431917.2 - ClinVar - NCBI
    1
    1. azankl 02 Aug 2020
      Last evaluated:

      last evaluated in 2015, but only submitted in 2019, does not make sense

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    ncbi.nlm.nih.gov/clinvar/variation/431917/
  8. Sep 2019
  9. www.sciencedirect.com www.sciencedirect.com
    Multicentric Carpotarsal Osteolysis Is Caused by Mutations Clustering in the Amino-Terminal Transcriptional Activation Domain of MAFB
    1
    1. azankl 05 Sep 2019
      complete destruction of carpal bones

      HP:0001495

      HPO
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    sciencedirect.com/science/article/pii/S0002929712000353
  10. Jun 2018
  11. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Multicentric carpotarsal osteolysis is caused by mutations clustering in the amino-terminal transcriptional activation domain of MAFB. - PubMed - NCBI
    2
    1. azankl 14 Jun 2018
      MAFB
      Gene:MAFB
    2. azankl 14 Jun 2018
      progressive renal failure
      Renal Failure
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    ncbi.nlm.nih.gov/pubmed/22387013
  12. Nov 2017
  13. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    The practical update for family physicians in the diagnosis and management of overactive bladder and lower urinary tract symptoms. - PubMed - NCBI
    1
    1. azankl 21 Nov 2017
      urinary urgency

      its working!

      Urinary urgency
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    ncbi.nlm.nih.gov/pubmed/29151006
  14. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Achondroplasia: Current Options and Future Perspective. - PubMed - NCBI
    2
    1. azankl 14 Nov 2017
      craniocervical junction compression

      missing HPO

      missing
    2. azankl 14 Nov 2017
      macrocephaly

      HPO:000256

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    ncbi.nlm.nih.gov/pubmed/26182483