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Lrg and mane 16 oct 2018

Presentation on the LRG project by Joanella Morales at GRC/GIAB workshop at ASHG 2018 meeting

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How does it relate to MANE and GRC?
The Locus Reference Genomic (LRG) project
Joannella Morales, PhD
Project Manager
EMBL-EBI
jmorales@ebi.ac.uk
• Joint effort between the NCBI and EMBL-EBI since 2008
• Recurrent requests from clinical community for tools to ensure efficient and
consistent variant reporting
• Challenges:
• Keeping track of clinically-relevant variants over time
• Changes to genome assembly
• Changes to genes and transcripts
• Inconsistent reporting of variants due to lack of approved/standardized sequences
• Multiple genomic haplotypes
• Multiple transcript sets
• Multiple versioned sequences
The LRG Project
For example, PAX6 (eye)
11 NMs
81 ENSTs
Which sequence to use??
LRG records
• Manually curated
• Contain stable reference sequences (do not version)
• Sequences selected by curators in collaboration with locus-specific
experts
• Used for reporting of clinically-relevant variants – HGVS compatible
• Genomic - LRG_1:g.15178G>A
• Transcript - LRG_1t1:c.2156G>A
• Protein - LRG_1p1:p.Gly719Asp
LRG Records
LRG and MANE convergence
• LRG Project not scalable since it is 100% manual and there are thousands of clinical genes
• Automation useful, but manual oversight required to ensure meaningful in the clinical
context
• Evolution of LRG -> MANE Plus?
• Same methodology as MANE project
• Extended to cover transcripts that are well-supported, tissue-specific or relevant to specific user
groups; a cut of the highest value representing most exons with well-expressed splice forms
• LRG Team
• Manual effort to review transcripts for MANE Plus? set
• Engage with locus-specific experts
• Continue to support existing LRG records
LRG and GRC
• LRGs are independent of GRCh38
• Many LRG users require or prefer alternate sequences
• Issues in GRCh38 (e.g. ABO)
• GRCh38 represents a minor allele (e.g. HTT, EIF2AK3)
• Vast majority of LRGs match GRCh38, but several LRGs contain non-GRCh38
sequences

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Lrg and mane 16 oct 2018

  • 1. How does it relate to MANE and GRC? The Locus Reference Genomic (LRG) project Joannella Morales, PhD Project Manager EMBL-EBI jmorales@ebi.ac.uk
  • 2. • Joint effort between the NCBI and EMBL-EBI since 2008 • Recurrent requests from clinical community for tools to ensure efficient and consistent variant reporting • Challenges: • Keeping track of clinically-relevant variants over time • Changes to genome assembly • Changes to genes and transcripts • Inconsistent reporting of variants due to lack of approved/standardized sequences • Multiple genomic haplotypes • Multiple transcript sets • Multiple versioned sequences The LRG Project For example, PAX6 (eye) 11 NMs 81 ENSTs Which sequence to use??
  • 3. LRG records • Manually curated • Contain stable reference sequences (do not version) • Sequences selected by curators in collaboration with locus-specific experts • Used for reporting of clinically-relevant variants – HGVS compatible • Genomic - LRG_1:g.15178G>A • Transcript - LRG_1t1:c.2156G>A • Protein - LRG_1p1:p.Gly719Asp
  • 5. LRG and MANE convergence • LRG Project not scalable since it is 100% manual and there are thousands of clinical genes • Automation useful, but manual oversight required to ensure meaningful in the clinical context • Evolution of LRG -> MANE Plus? • Same methodology as MANE project • Extended to cover transcripts that are well-supported, tissue-specific or relevant to specific user groups; a cut of the highest value representing most exons with well-expressed splice forms • LRG Team • Manual effort to review transcripts for MANE Plus? set • Engage with locus-specific experts • Continue to support existing LRG records
  • 6. LRG and GRC • LRGs are independent of GRCh38 • Many LRG users require or prefer alternate sequences • Issues in GRCh38 (e.g. ABO) • GRCh38 represents a minor allele (e.g. HTT, EIF2AK3) • Vast majority of LRGs match GRCh38, but several LRGs contain non-GRCh38 sequences
  • 7. Annotation about mismatches When the GRCh38 allele is not the preferred allele
  • 8. LRG and GRC • This user group cannot be served by MANE project (due to GRCh38 dependency) • LRG project will continue to create records for genes where an alternate genomic sequence is required • LRG project will continue to work with GRC to create Novel patches, when possible

Editor's Notes

  1. Describe rationale for LRG project, why it started
  2. Show LRG records
  3. Discuss how LRG relates to MANE