Case Review Document Library

Interpretation and Workflow SOPs

• Current version (Policy Stat)

• Version 2 (Draft)

• Clinical Interpretation of the Actionable Screening Panel (ACMG78 gene list) SOP https://broadinstitute.policystat.com/policy/13631371/latest

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

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

• BQMS deviation - ACE failure with >5000 variants BQMS-83813

Fabric Genomics SOPs

• GEM Workflow

• Panel SOP

• Variant Classification

• CNV Curation

• MtDNA interpretation

Variant Interpretation

• BCL Variant Interpretation SOP

• 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:

    • 

  • 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

• SOP

• Curation template

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

SIDR Variant Analyst Review

https://docs.google.com/document/d/1b0R11y3TSdOTtPb0xV36eEjR4BzzcawrocvF5QwweG8/edit#heading=h.e5alw54qlezf

Fabric Report Formatting https://docs.google.com/document/d/1FIMve2clZ-Mc0U9GMhqGFZcRXU_DQajcGzRhy0aMB-U/edit?usp=drive_link

CNVs: https://docs.google.com/document/d/1X38c78W0u8hopMGud7ljOAv-dIpQonCCxXTxDH2DSH4/edit https://docs.google.com/spreadsheets/d/1TlQBG3ocJNIu7v9p6mPEv0ylzAT4AqvIytUvHYIlHx8/edit#gid=0 , requests to variant summary header https://docs.google.com/spreadsheets/d/1CJo4p341-bk4uKBrPJM41x4f7TbXGuZ4mblpuq10k1U/edit#gid=0

Clinician Contact Procedure: https://docs.google.com/document/d/1G8xNzZQLpnU02Cr1skVTQHyfQL59_C0hmVlOfe63rLY/edit