Content Comparison

Interpretation and Workflow SOPs

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Current version (Policy Stat)

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Please tag the SOP owner in the Google Doc draft for any potential updates

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https://docs.google.com/document/d/1R0YpB18hIW0pvw86fMM7c1mMLtXV60YvbAmGEslGmQ0/edit#heading=h.guh6a7zg753q

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Nurture Clinical Interpretation https://broadinstitute.policystat.com/policy/15614704/latest/

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Fabric Genomics SOPs

• GEM Workflow

• Panel SOP

• Variant Classification

• CNV Curation

• MtDNA interpretation

Variant Interpretation

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Links / Resources

• https://docs.google.com/spreadsheets/d/1M9a74RyVOjUAUCQIlUXFyFAaNANkdwPJEHT0FYxH9-4/edit#gid=487083693

• Segregation calculator

• Splice AI lookup

  • Demo version with new features

• https://liftover.broadinstitute.org/

• Other helpful resources:

  • ACMG / AMP Guidelines, Richards 2015

    • https://docs.google.com/presentation/d/15LyMNNcODtNMjU4pa1PkhywChSWX1Um3CVx4HjX0L-0/edit#slide=id.p

    • https://docs.google.com/presentation/d/1lUZcHfwopn-Bo7k67hgRWe-CREVEZTo0xMFN-wqb0vU/edit#slide=id.g2827f193e86_0_1

  • PVS1 paper - Tayoun et al. 2018 https://drive.google.com/open?id=18DLSzEt5iUDVNYqGZYpcZK6lrSP3Y6Uz&usp=drive_fs

  • Splice consensus sequence

  • TGG Variant Curation SOP

  • ACMG SF v3.2 (2023)

• CNVs

  • Nomenclature in Fabric (notes from 01.08.24). Both examples in CASE D-061109681-BH-4009-P-A

    • INTERGENIC variants: Chr#:g.####-####del

      • Example: chr17:g.29517928-31373373del

    • INTRAGENIC variants: NM_###(GENE):c.###_###del

      • Example: NM_001165963.4(SCN1A):c.3430-816_4003-790del

  • Editing parental origin, size, number of genes:

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  • https://search.clinicalgenome.org/kb/gene-dosage?page=1&size=25&search=

  • https://cnvcalc.clinicalgenome.org/redmine/projects/cnvcalc/cnv_calculator/cnv-loss

  • https://docs.google.com/document/d/1m4oLaScW88S5p5YUxBAfNZqK8bNOBAQEDQfyXiZycKc/edit#heading=h.ftj7oc7qj5cy

Gene Curation

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• Curation template

• https://docs.google.com/spreadsheets/d/1X71XG1qz3YqJWFM6iaJY7tcAUaFyeF3UIj3mC7EVmUs/edit#gid=0 - please add your summaries that are reported out here

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