Li-Fraumeni syndrome: not a straightforward diagnosis anymore—the interpretation of pathogenic variants of low allele frequency and the differences between germline PVs, mosaicism, and clonal hematopoiesis

Abstract

The introduction of next-generation sequencing has resulted in testing multiple genes simultaneously to identify inherited pathogenic variants (PVs) in cancer susceptibility genes. PVs with low minor allele frequencies (MAFs) (< 25–35%) are highlighted on germline genetic test reports. In this review, we focus on the challenges of interpreting PVs with low MAF in breast cancer patients undergoing germline testing and the implications for management. The clinical implications of a germline PV are substantial. For PV carriers in high-penetrance genes like BRCA1, BRCA2, and TP53, prophylactic mastectomy is often recommended and radiation therapy avoided when possible for those with Li-Fraumeni syndrome (LFS). For germline PV carriers in more moderate-risk genes such as PALB2, ATM, and CHEK2, annual breast MRI is recommended and prophylactic mastectomies considered for those with significant family histories. Detection of PVs in cancer susceptibility genes can also lead to recommendations for other prophylactic surgeries (e.g., salpingo-oophorectomy) and increased surveillance for other cancers. Therefore, recognizing when a PV is somatic rather than germline and distinguishing somatic mosaicism from clonal hematopoiesis (CH) is essential. Mutational events that occur at a post-zygotic stage are somatic and will only be present in tissues derived from the mutated cell, characterizing classic mosaicism. Clonal hematopoiesis is a form of mosaicism restricted to the hematopoietic compartment. Among the genes in multi-gene panels used for germline testing of breast cancer patients, the detection of a PV with low MAF occurs most often in TP53, though has been reported in other breast cancer susceptibility genes. Distinguishing a germline TP53 PV (LFS) from a somatic PV (TP53 mosaicism or CH) has enormous implications for breast cancer patients and their relatives. We review how to evaluate a PV with low MAF. The identification of the PV in another tissue confirms mosaicism. Older age, exposure to chemotherapy, radiation, and tobacco are known risk factors for CH, as is the absence of a LFS-related cancer in the setting of a TP53 PV with low MAF. The ability to recognize and understand the implications of somatic PVs, including somatic mosaicism and CH, enables optimal personalized care of breast cancer patients.

Clonal hematopoiesis in cancer

“…Cancer patients are often tested for germline mutations in genes that predispose to malignancy, some of which can drive clonal hematopoiesis when somatically mutated. As the DNA used in these tests typically comes from blood, it can lead to the incidental discovery of mutations in genes like TP53, which may be enriched in this population likely to have received cytotoxic therapy [34,37]. How to appropriately counsel these patients and others in whom clonal hematopoiesis is discovered is not clear, but raises several important questions.…”

Germline TP53 Testing in Breast Cancers: Why, When and How?

“…However, there are two particular pitfalls in TP53 testing. Whilst true ‘mosaicism’ is not an infrequent occurrence in TP53 where multiple tissues have low levels of the variant, a more frequent cause of detected low allele frequency is clonal haematopoiesis of indeterminate potential (CHIP) [ 29 , 30 , 31 , 32 ]. CHIP corresponds to the expansion of a mutant hematopoietic stem and progenitor cell and is associated with increased risks of haematological neoplasms, including myelodysplastic syndromes and acute myeloid leukaemia.…”

New surveillance guidelines for Li-Fraumeni and hereditary TP53 related cancer syndrome: implications for germline TP53 testing in breast cancer

“…However, there is a particular pitfall in TP53 testing as well as for a number of other genes such as PPM1D and several oncogenes. A frequent cause of low level allele frequencies detected is clonal haematopoiesis of indeterminate potential (CHIP) [35][36][37][38][39]. CHIP has recently become apparent in lymphocyte DNA panel testing by NGS.…”

“…CHIP was first reported in patients over 70 years of age, but can be detected from 30 years of age. The frequency of CHIP increases with age, smoking and chemotherapy or radiotherapy treatments [35][36][37][38][39]. Even with an allele frequency consistent with a germline variant of 50%, clonal haematopoiesis is still possible and should be considered where a TP53 variant is found in a context not usually associated with germline TP53 [36,39].…”