182 Matching Annotations
  1. Last 7 days
    1. Hypothes.is Gene Annotation SOP v1

      The Hypothes.is Gene Annotations SOP version 1 is located under the "Additional Supporting Materials Tab."

      This protocol outlines procedures for annotating and tagging applicable gene curation evidence and is structured to capture fields required for the ClinGen Gene curation Interface (GCI).

    2. Standard Operating Procedures

      To see Hypothes.is annotated notes on the SOP, click the hyperlink on the webpage titled "Gene-Disease Validity Standard Operating Procedures, Version 7"

    1. APPENDIX C:SEMIDOMINANT MODE OF INHERITANCE OVERVIEW

      New section that outlines examples on how to score Semidominant mode of inheritance in the GCI.

    2. PMID: 18853439

      Using these PMIDs allows a curator to score applicable evidence within the GCI that is included as part of a general, large resource database.

    3. APPENDIX A:

      This section was updated to include new useful websites, including PMIDs to use for curation purposes on websites that may house important evidence (e.g. The Human Protein Atlas, MGI, IMPC, etc). A new section entitled Case-Level databases was added to provide curators with information on well-known sites containing case-level genetic evidence that may be applicable to scoring for a given gene-disease relationship.

    4. SOP REFERENCES

      This section was updated to reflect new references

    5. RECURATION PROCEDURE

      New section that outlines the procedures for all GCEPs to follow for recuration of gene-disease relationships under their purview. A hyperlink to the full recuration document is included.

    6. Figure 10footnotes

      New section that outlines additional information to consider for the final classification summary.

    7. SUMMARY &FINAL MATRIX

      This section has been updated to reflect the current curation workflow using the GCI.

    8. General Considerations for Variant Evidence Scoring:

      Updated section that provides guidance and recommendations for upgrading and downgrading default variant scores based on several lines of evidence, including mode of inheritance, computational predictors, population frequency, disease mechanism, phenotype, and constraint metrics.

    9. Founder variants:

      New section that provides guidance and recommendations for scoring founder variants in a given gene-disease relationship.

    10. Recurrent variants:

      New section that provides examples, guidance and recommendations for the evaluation of recurrent variants, or variants that have been observed multiple times for a given gene-disease relationship.

    11. Figure 3. Genetic evidence matrix footnotes

      New section that outlines important information on the matrix including max points per variant type and category, and information on how to manually override a calculated gene-disease validity classification in the GCI (visual representation on Figure 4, p18).

    12. Scoring Genetic Evidence: Default and Range score per case

      New section that outlines the purpose of the default and range scores per case.

    13. EVIDENCE COLLECTION

      This section has been updated to include additional useful publication search engines.

    14. Mode of inheritance (MOI):

      New section that outlines the current “Mode of inheritance” (MOI) options available in the GCI and how they affect the ability to score and/or publish gene-disease validity classifications to the website. A new table visually outlines the MOIs and scoring, approving, and publishing capabilities (Table 1).

    15. ESTABLISHING THE GENE-DISEASE-MODE OF INHERITANCE

      This is a new section outlining the process of selecting a gene, disease, and mode of inheritance. Hyperlinks to supportive resources, such as the ClinGen Lumping and Splitting guidelines, GeneTracker, etc. are provided.

    16. NO KNOWN DISEASE RELATIONSHIP3

      The classification of “No reported Evidence” has been updated to “No known disease relationship” in order to align with the new terminology recommendation from the international Gene Curation Consortium (GenCC).

    17. Figure 1: GENE CURATION WORKFLOW

      This figure has been updated to reflect the current curation workflow and approval process.

    18. OVERVIEW OF GENE CURATION

      This section has been updated to reflect our current curation workflow.

    19. Optional:

      Information on Hypothes.is and a hyperlink to the Hypothes.is Annotation SOP is now included. This web-based annotation tool is used by many GCEPs, and has been shown to significantly reduce curation time.

    1. Seizures
    2. 22 mo
    3. variant id lookup result

    4. constipation
    5. hairy elbows
    6. strabismus
    7. joint laxity
    8. fetal fingerpads
    9. mild hypertelorism
    10. long eyelashes
    11. mild exophthalmos
    12. broad forehead
    13. triangular face
    14. aggressivity
    15. no eye contact,
    16. social interaction
    17. autistic
    18. yes
    19. severe
    20. no speech
    21. 122 cm (−2.7)
    22. Facial dysmorphisms
    23. sleeping difficulties
    24. Behavioral abnormalities
    25. developmental delay
    26. FBXO11
  2. Aug 2019
    1. Hypothes.is Gene Annotation SOP v1

      The Hypothes.is Gene Annotations SOP version 1 is located under the "Additional Supporting Materials Tab."

      This protocol outlines procedures for annotating and tagging applicable gene curation evidence and is structured to capture fields required for the ClinGen Gene curation Interface (GCI).

    2. Standard Operating Procedures

      To see Hypothes.is annotated notes on the SOP, click the hyperlink on the webpage titled "Gene-Disease Validity Standard Operating Procedures, Version 7"

    1. Version 7

      ClinGen Gene-Disease Validity Standard operating Procedures Version 7 was released on August 12, 2019.

    2. Table of Contents

      The Table of Contents is now interactive and “clickable.” Clicking on a section title will take the reader to the section of interest.

    1. Gene-Disease Validity Standard Operating Procedures, Version 7

      Click the following link to see SOP version 7 updates using Hypothes.is annotation. These notes will be similar to the HIGHLIGHTED version of the SOPv7.

  3. May 2019
  4. Mar 2019
  5. Feb 2019
  6. Dec 2018
    1. HNF4A
  7. Nov 2018
    1. ClinVar variant ID lookup result: https://www.ncbi.nlm.nih.gov/clinvar/variation/427942/

    2. ClinVar variant ID lookup result: https://www.ncbi.nlm.nih.gov/clinvar/variation/427941/

    3. PLAA
  8. Aug 2018
    1. PPM1D
    1. EMC1
  9. Jul 2018
  10. Jun 2018