Page 43 - Haematologica April 2020

RUNX1 variant curation
determining the functional effect of a given variant change, despite methods of engineering variants for func- tional assessment.72-74 Early studies in Speck’s laboratory on RUNX1 showed the significance of key residues in the RHD of RUNX1 by performing alanine scanning mutage- nesis.75,76 However, these early approaches are limited in that not every combination of nucleotide change was explored. By contrast, recent high-throughput functional genomic methods,77 known as deep mutational scanning, utilize large-scale approaches to mutate every nucleotide of a gene, permitting one to test the functional conse- quence of all single nucleotide variations. This has, for example, been recently demonstrated for BRCA1.78 Additionally, systematic mutagenesis of PTEN has pro- vided a wealth of functional data to inform the classifica- tion of PTEN variants,79 in conjunction with published rules developed by the PTEN-VCEP.80 In the future, focused functional assays targeting specific VUS16 and deep mutational scanning of genes should contribute to variant curation to resolve VUS.
Fifth, while functional testing of every given genomic variant is possible, it can be costly and difficult to do for every clinically significant gene. In this regard, family studies can aid in the classification of VUS. By systemat- ically evaluating disease segregation in family members with paired genotyping for a known variant, accurate classification of a given variant can be achieved. For example, a recent study showed that this family-based method for variant classification can resolve a VUS classi- fication more frequently than other traditional approach- es can.7,81 For rare diseases, such as FPD/AML, detailed pedigree and segregation analyses can be incredibly informative, and clinicians should be encouraged to test family members when possible, seeking help from local genetic counselors and/or geneticists as needed.81 Hematologists and oncologists need to consistently take a detailed family and genetic history.
Summary
RUNX1 germline mutations associated with FPD/AML are key events in myeloid neoplasms, thrombocytopenia and leukemogenesis and represent a model of a germline gene disorder with pathogenic variants predisposing to myeloid and (to a lesser extent) lymphoid malignancies.36 Providing an accurate clinical and pathologic variant inter- pretation for genomic variants detected in routine laborato- ry testing will remain critical for the provision of appropri- ate clinical care, including genetic counseling for the index patient and their at-risk relatives and donor-selection, in some cases benefiting from stem cell transplantation.
The ClinGen MM-VCEP variant interpretation process requires a detailed understanding of the biological and functional properties of RUNX1 and disease phenotype. Here, we demonstrate the process for sequence variant
interpretation of six variant examples. By introducing and thus standardizing genomic variant interpretation, we hope to improve patients’ care, identify VUS that may benefit from directed research and encourage sharing of internal laboratory data to resolve uncertainty. In doing so, the MM-VCEP rules may ensure optimal insurance coverage for appropriate genomic testing and screening of family members, and ensure appropriate reimbursement for clinical laboratories. Overall, the ASH/ClinGen collab- oration resulting in the first set of modified criteria for germline RUNX1 variants should improve clinical care and recommendations for FPD/AML patients.
Acknowledgments
The Variant Curation Expert Panel (VCEP) thanks the Clinical Genome Resource (ClinGen) Sequence Variation Interpretation Working Group as well as the Executive Committee of the Hereditary Cancer Clinical Domain Working Group. The variant curation rules discussed in this publication were generated by the American Society of Hematology (ASH) in collaboration with Baylor College of Medicine and the University of North Carolina, National Institutes of Health (NIH)-funded ClinGen grant award recipients. The NIH sup- ported this work through: U41HG009649 (to XL, and SEP) and U41HG009650 (to SM and JER), and the 2018 NIH/NCI Leukemia SPORE DRP award (P50CA100632-16, project 00007529) (C.D.D.).
The ASH-ClinGen Myeloid Malignancy MM-VCEP collab- orative group includes co-authors (DW and LAG as co-chairs; XL, SF, SM, CK and DEP), and others, as follows:18 Christopher Porter (Emory University, USA), Sarah Jackson (GeneDx, USA), Sioban Keel (University of Washington, USA), Michael Chicka (Prevention Genetics, USA), Anna Brown (Center for Cancer Biology, Australia), Anupriya Agarwal (Oregon Health & Science University, The Knight Cancer Institute, USA), Minjie Luo (Children's Hospital of Philadelphia, USA), Zejuan Li (Houston Methodist Institute for Academic Medicine, USA), Justyne E. Ross (University of North Carolina, USA), Panagiotis Baliakas (Uppsala University, Sweden), Courtney D. DiNardo (UT MD Anderson Cancer Center, USA), Alison Bertuch (Baylor College of Medicine, USA), Nikita Mehta (Mayo Clinic, USA), Thomas Vulliamy (Queen Mary University of London, UK), Ying Wang (BioReference, USA), Kim Nichols (St Jude Children's Research Hospital, USA), Luca Malcovati (University of Pavia & S. Matteo Hospital, Italy), Michael Walsh (Memorial Sloan Kettering Cancer Center, USA), Lesley Rawlings (Centre for Cancer Biology, Australia), Shannon McWeeney (Oregon Health & Science University, USA), Jean Soulier (Hopital Saint-Louis and University de Paris, France), Anna Raimbault (INSERM U1016, Institut Cochin, France), Mark Routbort (UT MD Anderson Cancer Center, USA), Liying Zhang (Memorial Sloan Kettering Cancer Center, USA), Gabriella Ryan (American Society of Hematology, USA), Nancy Speck (Abramson Family Cancer Research Institute, USA), and Sharon E. Plon (Baylor College of Medicine, USA).
haematologica | 2020; 105(4)
885