Identifying potential germline variants from sequencing hematopoietic malignancies

Abstract

Next-generation sequencing (NGS) of bone marrow and peripheral blood increasingly guides clinical care in hematological malignancies. NGS data may help to identify single nucleotide variants, insertions/deletions, copy number variations, and translocations at a single time point, and repeated NGS testing allows tracking of dynamic changes in variants during the course of a patient’s disease. Tumor cells used for NGS may contain germline, somatic, and clonal hematopoietic DNA alterations, and distinguishing the etiology of a variant may be challenging. We describe an approach using patient history, individual variant characteristics, and sequential NGS assays to identify potential germline variants. Our current criteria for identifying an individual likely to have a deleterious germline variant include a strong family history or multiple cancers in a single patient, diagnosis of a hematopoietic malignancy at a younger age than seen in the general population, variant allele frequency > 0.3 of a deleterious allele in a known germline predisposition gene, and variant persistence identified on clinical NGS panels, despite a change in disease state. Sequential molecular testing of hematopoietic specimens may provide insight into disease pathology, impact patient and family members’ care, and potentially identify new cancer-predisposing risk alleles. Ideally, individuals should give consent at the time of NGS testing to receive information about potential germline variants and to allow future contact as research advances.

Germline Testing Data Validate Inferences of Mutational Status for Variants Detected From Tumor-Only Sequencing

“…12 Current practices in interpreting tumor-only data for this purpose are gene-specific and are often on the basis of variant allele frequency (VAF) criteria that may need to be adjusted for different settings and tumor types. 13,14 Although such criteria could be sensitive for identifying PGV from tumor-only data, [14][15][16] their application requires extensive expert review and results in low specificity in exclusion of somatic variants and a significantly decreased overall accuracy. 12,13 To address these challenges, we examined the performance of a gene-independent, information-theoretic pipeline aimed at accurately categorizing the variants identified by tumor-only assays as somatic or germline.…”

Diagnosis of myelodysplastic syndromes in Poland: Polish Adult Leukemia Group (PALG) 2021 recommendations

“…The exact frequency of these diseases is unknown, but it is estimated that they affect 1-5% of myeloid neoplasms. MNGP/HMMS can occur in as isolated abnormality or with concomitant diseases (including other neoplasms -lymphoid or solid tumors) or as part of complex syndromes [20][21][22].…”

Genetics of Myelodysplastic Syndromes

“…Cytogenetic analysis revealed a normal karyotype and NGS showed disappearance of the ASXL1 mutation, but persistence of the DDX41 c.1496dup (p.Ala500Cysfs*9) mutation at a VAF of 49%. The persistence of the DDX41 mutation raised concern for germline predisposition [ 41 ], especially considering this specific variant is seen as a germline allele most commonly in Asian populations [ 42 ]. Importantly, her family history was significant for AML in her mother and a maternal aunt.…”