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You Make the Call: Would you refer patients whose bone marrow samples came back with mutations for genetic counseling and germline testing?

November 2, 2023

November 2023

Abhay Singh, MD, MPH Associate Staff, Leukemia & Myeloid Disorders Program Cleveland Clinic Taussig Cancer Center Assistant Professor of Medicine, Cleveland Clinic Lerner College of MedicineAbhay Singh, MD, MPH
Associate Staff, Leukemia & Myeloid Disorders Program
Cleveland Clinic Taussig Cancer Center
Assistant Professor of Medicine, Cleveland Clinic Lerner College of Medicine




I have two patients whose testing of their bone marrow samples came back with abnormal next-generation sequencing (NGS) results:

  • One patient has a TET2 mutation with an allele frequency close to 50%, raising the possibility of germline origin.
  • The second patient has an unexplained normocytic anemia (hemoglobin was 11.2 g/dL with a mean corpuscular volume of 88 fL). Flow cytometry identified a clonal B-cell population with a non-specific phenotype (CD5-, CD10-, CD20+), representing 1% (< 5,000/uL) of the leukocytes. There was also a monoclonal paraproteinemia (IgA lambda on serum immunofixation) with 3-5% plasma cells in the bone marrow biopsy. The NGS panel was positive for unclear variant in EGFR with an allele frequency close to 50%, again raising possibility of germline origin.

Because these mutations may be germline, should I refer these patients for genetic counseling and germline testing? If they are germline, then it’s something that they were born with – presumably inherited – and can be passed on? I’m not clear about the clinical significance, and maybe I don’t need to do anything?


In the past, hematologic neoplasms (HNs) were mainly seen as sporadic; however, recent progress in genomic sequencing has unveiled numerous underlying hereditary predispositions to HNs. These swift advancements in NGS techniques have enabled us to associate a sizable portion of HNs with hereditary factors. These genomic advancements help guide overall management, but sometimes treating clinicians find themselves perplexed when mutations are reported at variant allele frequencies (VAF) around 50% or as variants of uncertain significance (VUS).* Generally, when VAF exceeds 30% (although it may not always surpass this threshold) on a somatic NGS panel, it should raise suspicion for a heterozygous germline variant; in homozygous or hemizygous variants, the VAF can reach close to 100%. For any such cases, if accessible, input from genetic counselors (GCs) is always helpful. If access to genetic counseling is delayed or not available, the following strategies might help in specific situations or disease states:

  • High VAF mutation identified while evaluating for unexplained mild cytopenia with no concomitant hematologic malignancy. It would be unusual for that large of a hematopoietic clone (VAF > 30%) to only cause mild change in blood counts. A genetic evaluation might help identify HN predisposition.
  • For treatment-necessitating disorders like acute myeloid leukemia (AML). If these high VAF mutations remain present in remission samples despite extensive cytotoxic treatments, it should raise suspicion for a germline variant and warrant genetic counseling or testing.
  • Putative variants. The National Comprehensive Cancer Network AML panel strongly recommends that patients with AML and VAF (>40%) with genes associated with predisposition syndromes as per the “Familial Genetic Alterations in AML” algorithm1 be referred for germline testing. Patterns of variants can either raise or lower the probability of harboring hereditary HNs. For instance, the detection of two variants within the same gene, such as DDX41 or CEBPA, significantly elevates the likelihood that one of these variants is of germline origin.
  • TET2 and germline evaluation. In the specific context of TET2 in the case above, the likelihood for germline occurrence is generally lower, because it often represents an acquired variant. If observed in the context of overt myeloid malignancy such as AML, and if after extensive treatment the VAF decreases considerably, germline evaluation likely is avoidable. However, if observed in the context of clonal hematopoiesis of indeterminate potential (CHIP) and clonal cytopenia of unknown significance (CCUS), TET2 remains under suspicion for associations with HN predisposition,2 and GC evaluation might be helpful. Specifically, I obtain germline testing in some cases of high VAF TET2 mutations, if such determination would change CHIP or CCUS prognostication based on the recently released clonal hematopoiesis risk score.3
  • The high VAF mutations are determined to be pathogenic or likely pathogenic germline variants. If this is the case, it is imperative to discuss testing for all at-risk family members, including asymptomatic individuals. These are often inheritable but may demonstrate variable expressivity and penetrance. Similarly, for suspected germline EGFR mutations, an evaluation by a GC would be important, not particularly in the context of hematologic cancers but as a possible predisposition to lung cancer.4

*Note: A VUS is a genetic variant for which insufficient data exist to determine if it is associated with disease (deleterious mutation) or is a normal genetic variant that can occur in the population without disease (benign polymorphism).


  1. Pollyea DA, Bixby D, Perl A, et al. NCCN guidelines insights: acute myeloid leukemia, version 2.2021. J Natl Compr Canc Netw. 2021;19(1):16-27.
  2. Stremenova Spegarova J, Lawless D, Mohamad SMB, et al. Germline TET2 loss of function causes childhood immunodeficiency and lymphoma. Blood. 2020;136(9):1055-1066.
  3. Weeks LD, Niroula A, Neuberg D, et al. Prediction of risk for myeloid malignancy in clonal hematopoiesis. NEJM Evid. 2023;2(5):10.1056/evidoa2200310.
  4. Yu HA, Arcila ME, Harlan Fleischut M, et al. Germline EGFR T790M mutation found in multiple members of a familial cohort. J Thorac Oncol. 2014;9(4):554-558.


I have a 27-year-old female patient who presented with a left cerebrovascular accident (CVA). A CT scan of the head did not show any evidence of acute intracranial abnormality. A cerebral perfusion CT scan did not show any evidence of abnormal perfusion; however, an MRI of the brain with and without contrast revealed a 7 mm focus of restricted diffusion in the left side of the medulla, likely representing acute infarct. Upon admission, the patient was started on aspirin, clopidogrel, and a statin. Although she had no prior history of elevated blood pressure, she was hypertensive during hospitalization and started on losartan. A transthoracic echocardiogram with a bubble study was normal. The patient was on an oral contraceptive (norethindrone and ethinyl estradiol tablets, 0.4 mg/0.035 mg) before her CVA, which was discontinued as this was felt to be a potential cause.

Three months later, neurology performed a partial hypercoagulable workup to further evaluate her CVA. The workup found her homozygous for MTHFR C677T polymorphism but with a normal homocysteine level. Her anti-β2 glycoprotein-1 antibody (β2GP1) IgG was elevated at 66 SGU U/mL and on repeat testing one month later (63 SGU U/mL). Other components of the hypercoagulable workup, including anticardiolipin and lupus anticoagulant studies, were normal. She has no other personal history of thrombosis and no significant personal or family history for strokes or myocardial infarctions at an early age.

I will repeat β2GP1 testing in three months but suspect it will be elevated again. Would you start her on anticoagulation given the homozygous MTHFR C677T polymorphism or elevation in β2GP1 and, if so, would the anticoagulant of choice be warfarin? Would you also empirically start folic acid, cyanocobalamin, and pyridoxine? She is concerned about the risks associated with lifelong anticoagulation and, though it could have been provoked by her oral contraceptive, I am most concerned about her stroke risk going forward.

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Disclaimer: ASH does not recommend or endorse any specific tests, physicians, products, procedures, or opinions, and disclaims any representation, warranty, or guaranty as to the same. Reliance on any information provided in this article is solely at your own risk.

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