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.

Technical Validation and Clinical Utility of an NGS Targeted Panel to Improve Molecular Characterization of Pediatric Acute Leukemia

“…Both ALL and AML patients had a rate of around 10% of possible germline alterations requiring additional confirmation and possible follow-up with the cancer predisposition unit. In our cohort, the somatic mutations confirmed to be of germline origin, by testing them in an MRD-negative remission sample were in TP53 and MSH6 genes, in line with the previous reports ( Kraft and Godley, 2020 ; Klco and Mullighan, 2021 ). However, it is important to keep in mind that this panel is not designed for this purpose, missing some important genes related to cancer predisposition ( Desai et al, 2017 ).…”

Oncomine™ Comprehensive Assay v3 vs. Oncomine™ Comprehensive Assay Plus

“…Moreover, the filter also removed variants such as common SNPs, synonymous mutations and potential germline. For the latter, variants were annotated if the allele ratio of the variant identified was equal to 1, assuming an ideal germline variant allele frequency when homozygous [23,24]. The population allele frequency defining common SNP was ≥1% in minor allele frequency.…”

“…Hence, cytosine deamination artifacts have been reported to cause baseline noise among low-frequency variants [14,24], we investigated if there was a clear indication of deamination artifacts among variants below the first quartile. The use of the Chisquare test revealed no statistical difference in C > T (p = 0.54) and G > A (p = 0.53) between OCAv3 and OCA-Plus in variants above the first quartile (Figure 2A), nor did the remaining base substitutions show statistical differences.…”

Incidence of Hereditary Gastric Cancer May Be Much Higher than Reported

“…Considering this argument, the number of expected mutations should be much higher among older than younger people, since the rate of somatic mutations increases with aging. Additionally, regarding the non-cancer control group, blood samples were similarly collected in adulthood, validating these comparisons [ 49 ].…”