Dissecting the Knowns for the Unknowns: Refining the Classification of Genomic Variations in Hematological Diseases By the Clingen Hematological Cancer Taskforce (HCT)

Abstract

Genomic variants are important diagnostic, prognostic and/or therapeutic markers in hematological malignancies. However, substantial interlaboratorydiscrepancy in interpretation and reporting of these variants creates challenges. To provide a reliable clinical reference and assist the consistent interpretation of genomic variations, the Hematological Cancer Taskforce (HCT) was formed under the ClinGen Somatic Cancer Clinical Domain Working Group in 2020 with a goal to standardize the systematic curation, evidence-based clinical interpretation and reporting of somatic genetic variations found in hematological cancers. A team of multi-disciplinary experts, including genomic scientists, oncologists, hematopathologists, molecular pathologists, clinical lab directors, and biocurators with expertise in hematological malignancies, were recruited to evaluate the genomic alterations seen in hematological malignancies according to the AMP/ASCO/CAP and/or the ClinGen/CGC/VICC guidelines (PMIDs: 27993330, 35101336). The HCT identified FLT3 variants as the highest priority for curation and clinical interpretation efforts based on the immediate and strong clinically actionable implications of FDA-approved FLT3 inhibitors. A ClinGen FLT3 Somatic Cancer Variant Curation Expert Panel (SC-VCEP) was formed to focus on curation of FLT3 tyrosine kinase domain (TKD) variants and is now developing FLT3-specific classification guidelines. FLT3-ITD (internal tandem duplication) and TKD (D835/I836) are the most frequent FLT3 variants with well-established prognostic and therapeutic significance and predict response to Midostaurin and Gilteritinib, FDA-approved drugs for newly diagnosed and relapsed/ refractory AML, respectively. The FLT3SC-VCEP classified their assertions of the FLT3-ITD and D835 variants as Tier 1 - level A in CIViC following the AMP/ASCO/CAP guideline. The interpretation of the rest of FTL3 TKD variants including D835 were less consistent. A pilot assessment to apply the ClinGen/CGC/VICC oncogenicity standards has classified the following D835 variants as oncogenic (OS2, OS3, OP1, OP4): c.2505T>A (Asp835Glu), c.2503G>T (Asp835Tyr), c.2503G>C (Asp835His), and c.2504A>T (Asp835Val); one variant as likely oncogenic: c.2028C>A (Asn676Lys) (OS2, OM4, OP4); and one variant of uncertain significance (VUS): c.2503_2504delinsAT (Asp835Ile) (OM1, OP1, OP3, OP4). Assessment of additional FLT3 variants is underway with the goal to refine FLT3-specific rules to classify FLT3 variants using the AMP/ASCO/CAP guidelines and the ClinGen/CGC/VICC oncogenicity classification standards as a framework. Published evidence using FDA-approved tests simultaneously evaluating the TKD variants in amino acids D835 or I836 often do not specify the affected codon. Due to the high prevalence of D835 variants in AML, the clinical significance of I836 variants is much less studied. In addition to curation from the literature, the FLT3 SC-VCEP is leveraging their international expertise by performing a multi-institutional deidentified data collection for I836 variants from individual laboratories to assess therapeutic response and oncogenicity. Due to the critical need for consistent and standardized interpretation of genetic test results, the HCT aims at developing gene-specific recommendations to standardize the reporting and interpretation of somatic variants and plans to expand ClinGen SC-VCEPs in additional gene-disease domains.