Hybrid ENIGMA meeting, June, 28th-30th 2024

Riga, Latvia

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Day 1: Introductory Session - Chairs Amanda Spurdle and Maaike Vreeswijk

Welcome, thanks, housekeeping – Mandy, Maaike, Arvids, Zanda (slides – presentation)

CIMBA plus Report and discussion –  Amanda Spurdle (slides – presentation)

Integration of Protein Stability and Structural Context Scores Improves Bioinformatic Predictions for BRCA1 and TP53 Variants – Miguel de la Hoya, Nitsan Rotenberg (slidespresentation)

Update – ClinGen Hereditary Breast Ovarian Pancreatic Cancer Variant Curation Expert Panel. Progress on CHEK2 rules – Marcy Richardson (slidespresentation)

Update – ClinGen ENIGMA BRCA1/2 Variant Curation Expert Panel Progress – old classifications using new rules, priority classifications for ClinVar variants etc – Michael Parsons (slidespresentation)

ENIGMA BRCA1/2 VCEP UCSC tracks – Anna Benet-Pages (virtual), Melissa Cline (slidespresentation)

Development of an automated variant classification algorithm in Hereditary Breast and Ovarian Cancer – Ana-Lena Katzke (slidespresentation)

ClinGen ACMG/AMP V4.0 – Sean Tavtigian (slidespresentation)

 

 

Day 1: Clinical Working Group - Chairs Arcangela De Nicolo & Joanne Ngeow

Vocabulary Translation Project (VTP) – Arcangela De Nicolo (slidespresentation)

Clinical and molecular studies of BRCA1, BRCA2, PALB2 variants identified in Fanconi Anemia patients – Amanda Spurdle (slidespresentation)

BRCA2 c.8351G>A p.(Arg2784Gln): a variant with reduced penetrance? – Encarna Gomez-Garcia (slides also contributed by David Goldgar and Kyriaki Michailidou) (slidespresentations)

CHEK2 and hematological diseases (literature review and study proposal) – Encarna Gomez-Garcia (slides also contributed by Zdenek Kleibl and Petra Kleiblova) (slides – presentation)

CHEK2 Clinical Practice Resource (and PRS) – Paul James (virtual) (slidespresentation)

Gaining insights into platinum and PARPi resistance (study update and planned analyses) – Banu Arun (slidespresentation)

HRD and type of peritoneal tumor spread: two (independent?) markers for survival in ovarian cancer – Simon Schnaiter (slidespresentation)

HBOC risk population screening: results communicated via digital platform (report on a pilot study) and Management of BRCA1 and BRCA2 (L)P carriers at the Breast Unit of the Paul Stradiņš Clinical University Hospital – Arvids Irmejs (slidespresentation)

Day 2: Pathology Working Group - Chairs Melissa Southey & Mads Thomassen

Introduction to PWG Project updates: Mads Thomassen and Melissa Southey (slides – presentation)

Analytical strategies and technical points of AI studies of histopathology: application to variant classification – Nicolas Viart (slidespresentation)

HRD methods – Inge Søkilde Pedersen (slidespresentation)

ShallowHRD – Louise Adel Jensen (slidespresentation)

RAD51 assay as biomarker for functional HR: Progress update – Joanna Domenech Vivo / Sara Gutierrez-Enriquez (slidespresentation)

Resources the PWG could consider for molecular pathology studies – Melissa Southey (slidespresentation)

Day 2: Analytic Working Group - Chairs David Goldgar and Kyriaki Michailidou

Introduction – David Goldgar and Kyriaki Michailidou (slides – presentation)

CCLR update BRIDGES/CARRIERS/UKB – Maria Zanti (slidespresentation)

UK approach – Clare Turnbull, Alice Garrett (slidespresentation)

Working towards a TP53 reduced penetrance model – Cristina Fortuno (slidespresentation)

Applying current VCEP criteria to reduced penetrance variants and ClinGen low-risk group advice – Mandy Spurdle (slidespresentation)

Co-segregation for reduced penetrance – Bing Feng (slidespresentation)

Family history analysis for reduced penetrance variants/genes – David Goldgar (slidespresentation)

Case-control and functional data for reduced penetrance variants – Maria Zanti (slidespresentation)

Population data for reduced penetrance variants – Sam Cotton (slidespresentation)

Approaches to calibrate a classification model for reduced penetrance variants, project proposal – Kyriaki Michailidou (slides – presentation)

Day 2: Splicing Working Group - Chairs Logan Walker and Sara Gutiérrez-Enríquez

Welcome – Sara and Logan (slides – presentation)

Evaluating the accuracy and utility of computational splicing prediction tools – George Wiggins (slidespresentation)

BRCA1 IVS18 splicing variants: update on last results and variant classification – Joanna Domènech Vivo/Sara Gutierrez-Enriquez (slidespresentation)

Project 7 extension ATM – Ada Esteban-Sánchez (slidespresentation)

Project 7 extension – CHEK2 – a project update and call for data – Petra Kleiblova (slidespresentation)

BRCA1 Δ11q splicing variants: Update on Project – Lidia Feliubadaló / Sara Gutiérrez-Enríquez
(slidespresentation)

BRCA1 IVS11 – General overview and update – Michael Parsons (slidespresentation)

Long-read RNASeq kConfab – Mads Thomassen

  • Inge Søkilde Pedersen – PacBio long read seq analysis (slidespresentation)
  • Anna-Lena Katzke – Long read seq analysis (slidespresentation)
  • Louise Adel Jensen – Compilation of long read seq data (slides – presentation)

Functional analysis of alternative transcripts – Romy Mesman (slidespresentation)

Quantitative analysis of leaky splicing variants at the BRCA2 exon 13 donor site – Paolo Radice (slidespresentation)

ClinGen SVI Splicing subgroup – manuscript responses – Logan Walker (slidespresentation)

Admin, future meetings – Mandy, Maaike (slides – presentation)

Day 3: Functional Working Group - Chairs Maaike Vreeswijk & Zdenek Kleibl

Welcome – Maaike/Zdenek (slides – presentation)

Update Zdenek Kleibl – CHEK2gether (slides – presentation)

BRCA2 MAVE analysis and classification – Fergus Couch (please contact the presenter for more information)

Functional assay VUS in BRCA2-PALB2 binding domain – Muthiah Bose (Maria Rossing’s lab) (please contact the presenter for more information)

Site-saturation functional screens identify PALB2 missense variants associated with increased breast cancer risk – Haico van Attikum (please contact the presenter for more information)

Saturation Genome Editing of BRCA1: comparing functional effects across cell lines – Greg Findlay (slidespresentation)

ATM functional – Sean Tavtigian (slides – presentation)

Functional screen for ATM missense VUS – Paul Andreassen (University of Cincinnati) (please contact the presenter for more information)

Saturation genome editing of BRCA2 in mouse ES cells – Sounak Sahu (Sharan Shyam lab) (slidespresentation)

Day 3: MAVE session

Introductory comments – Fergus Couch (please contact the presenter for more information)

Theme 1: Cell models – Greg Findlay (slidespresentation)

Theme 2: Quantitative Validation Approaches – Clare Turnbull (slidespresentation)

Theme 3: Combining Assays – Alvaro Monteiro (slidespresentation)

Theme 4: Reduced Function/ Penetrance – Fergus Couch (please contact the presenter for more information)

Theme 5: Data “sign-off” for use in clinical variant interpretation – Clare Turnbull Sign-off comments (slidespresentation)

MAVE session – Fergus Couch Sign-off comments (please contact the presenter for more information)

Sign-off ENIGMA meeting (Mandy, Maaike)