Thrombocytopenia 5 and Predisposition for Hematologic Malignancy via the ETV6 Gene

Inherited thrombocytopenias (IT) comprise a heterogeneous group of disorders characterized by platelet counts below the lower limit of normal, below 150,000/µL (150 x 10⁹/L) in adults. Bleeding manifestations of thrombocytopenia range from mild to severe and may include excessive bruising (purpura), petechiae, prolonged bleeding from cuts or from surgical procedures, spontaneous nose bleeds, and in women, heavy menstrual flows. About half of ITs are syndromic disorders characterized by other physical and neurological anomalies, or immunodeficiencies (Balduini et al. 2013. PubMed ID: 23397552). Over 30 genes are known to be associated with ITs. Pathogenic variants in known genes are found in only about 50% of cases (Kunishima and Saito. 2006. PubMed ID: 16169642; Noris and Pecci. 2017. PubMed ID: 29222283). Noris and Pecci divide ITs into three groups: forms characterized by only platelet deficiencies, syndromic ITs with additional congenital defects, and ITs associated with increased risk of developing additional disease such as myelodysplastic syndrome (MDS) and acute leukemia (AL). For additional information regarding inherited hematologic malignancies, see Churpek et al. 2013. PubMed ID: 22691122; Furutani and Shimamura. 2017. PubMed ID: 28297620. It is important to distinguish ITs from immune/idiopathic thrombocytopenias (ITP) in order to inform clinical management and identify potential at risk family members.

Variants in ETV6 have been identified in several families with autosomal dominant thrombocytopenia (Thrombocytopenia 5) and who have mild-to-moderate bleeding tendencies and an increased risk of bone marrow failure and development of hematologic malignancies including primarily acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) (Bluteau et al. 2018. PubMed ID: 29146883; Zhang et al. 2015. PubMed ID: 25581430; Topka et al. 2015. PubMed ID: 26102509; Noetzli et al. 2015. PubMed ID: 25807284). ETV6-related thrombocytopenia accounts for about 5% of inherited thrombocytopenias, and approximately 25% of patients with ETV6-related thrombocytopenia acquire ALL and other hematologic malignancies (Noris and Pecci. 2017. PubMed ID: 29222283). In one study, ETV6 deficient platelets were shown to have a rounder shape, variable size, and decreased function compared to normal platelets (Poggi et al. 2017. PubMed ID: 27663637).

Somatic variants in ETV6 including gene fusions, deletions, and single nucleotide substitutions are frequently found in hematopoietic malignancies (Wang et al. 2014. PubMed ID: 24997145), but only recently have germline missense, nonsense, and other variants been found to segregate with hematopoietic malignancies (Zhang et al. 2015. PubMed ID: 25581430; Moriyama et al. 2015. PubMed ID: 26522332). ETV6 variants segregate completely with thrombocytopenia in affected families, but penetrance for malignancies is incomplete (Zhang et al. 2015. PubMed ID: 25581430; Topka et al. 2015. PubMed ID: 26102509; Noetzli et al. 2015. PubMed ID: 25807284). Functional studies of pathogenic ETV6 variants found in different kindreds show decreased DNA-binding and / or mislocalization of ETV6 protein suggesting that abnormal ETV6 functions in a dominant-negative manner that impairs hematopoiesis (Topka et al. 2015; Zhang et al. 2015).

ETV6 encodes a transcription repressor important for blood cell development and differentiation, in particular, platelet formation (Wang et al. 1998. PubMed ID: 9694803; Poggi et al. 2017. PubMed ID: 27663637).

Over 30 genes are known to be associated with inherited thrombocytopenias. Pathogenic variants in known genes are found in only about 50% of cases (Kunishima and Saito. 2006. PubMed ID: 16169642; Noris and Pecci. 2017. PubMed ID: 29222283). ETV6-related thrombocytopenia accounts for about 5% of inherited thrombocytopenias, and approximately 25% of patients with ETV6-related thrombocytopenia acquire ALL and other hematologic malignancies (Noris and Pecci. 2017. PubMed ID: 29222283).

Copy number variants (CNVs) are also detected from NGS data. We utilize a CNV-calling algorithm that compares mean read depth and distribution for each target in the test sample against multiple matched controls. Neighboring target read depth and distribution and zygosity of any variants within each target region are used to reinforce CNV calls. All CNVs are confirmed using another technology such as aCGH, MLPA, or PCR before they are reported.

This test provides full coverage of all coding exons of the ETV6 gene plus coverage of 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing.