PF238 TUMOR NGS‐PANEL UTILITY IN THE IDENTIFICATION OF GERMLINE VARIANTS IN MYELOID MALIGNANCIES
Authors: Palomino‐Echeverria S. , Vazquez I. , Alfonso‐Pierola A. , Ariceta B. , Blasco‐Iturri Z. , Aguilera‐Diaz A. , Larrayoz M.J. , Mañu A. , Bernal del Castillo T. , Olivares Salaverri M. , Olave Rubio M. , Rifon‐Roca J. , Prosper F. , Fernandez‐Mercado M. , Calasanz M.J. 
Published: June 2019

Background:

Myeloid neoplasms (MN) are heterogeneous clonal diseases arising in hematopoietic cells. Although MN are usually sporadic late‐onset cancers, growing evidence suggests that an important number of cases could emerge as a consequence of inherited predisposition. Since many of the genes associated with hereditary myeloid malignancies (HMM) are also affected by somatic mutations in sporadic MN, there is a chance of identifying variants of germline nature when performing Next Generation Sequencing (NGS) tumor testing. Given the clinical relevance of the issue, it is important to correctly classify those suspicious variants as somatic or germline.

Aims:

We intended to identify hematological patients with potentially inherited variants in a myeloid cohort with tumor‐only NGS data.

Methods:

We reviewed 332 NGS clinical reports of samples from 299 myeloid patients tested with tumor‐only sequencing during 2018 in our lab. We considered variants detected in BM sample at a 40–60% VAF classified as pathogenic, likely pathogenic or of uncertain significance variants as potentially inherited.

On the one hand, for patients with available follow‐up data, we considered as suggestive of inherited origin variants with stable VAF. On the other hand, for patients with available non‐myeloid tissue we sequenced 20 samples including DNA derived from cultured skin fibroblasts (n = 3), cultured bone marrow (BM) fibroblasts (n = 1), hair follicles (n = 5), purified CD3+ T cells (n = 6) and buccal swab (n = 5). Libraries were sequenced using our custom Pan‐Myeloid Panel, which includes 22 genes related to HMM (PMP, 48 genes, capture‐based, SOPHiA GENETICS). All patients signed a written informed consent form for genetic testing, research and tissue banking (Biobank of the University of Navarra). Samples were processed following Standard Operating Procedures approved by the Ethical and Scientific Committee of the University.

Results:

In total, 130 suspicious variants in HMM‐related genes were identified in tumor sample from 100 patients. Follow‐up data was available for 8 patients harboring a total of 9 variants. Six variants from 5 patients presented stable VAFs and clearance of accompanying variants during follow‐up; this might be due to an inherited event, although germline tissue testing is required for confirmation. Suspicious germline variants were found in ASXL1, DDX41, RUNX1 and IKZF1. Additionally, non‐myeloid tissue was available for 7 patients harboring a total of 8 variants. All 8 (100%) variants were confirmed of inherited origin. Germline variants were detected in ASXL1, DDX41, SH2B3, TET2 and NF1 (Figure 1).

Summary/Conclusion:

This study shows that NGS panels may incidentally detect inherited variants related to predisposition to MN despite not having been designed for that purpose. Our data supports the importance of considering variants incidentally found upon tumor‐only sequencing as potentially of germline origin. Indeed, one third of our cohort was suspicious of carrying a germline variant. We could confirm as inherited 100% of tested variants from patients with non‐myeloid tissue available. For patients with follow‐up data, VAF may help in discriminating ambiguous variants, but ultimately germline tissue sequencing is needed to determine the nature of the variant.

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These findings suggest that there is an increasing need for germline tissue testing along with the appropriate genetic counseling associated to it.