Title: Clonal Hematopoiesis and Germline Predisposition in High-Risk Leukemia Pedigrees
Authors: Osman Afaf , Feusier Julie , Avery Brian , Stephens Deborah M. , Madsen Michael , Williams Justin , Pomicter Tony , Jones Brandt , Clayton Adam , Szankasi Philippe , Patel Jay , Garzon Ramiro , Camp Nicola J 
Published: December 2024

CLL is one of the most heritable human cancers. First-degree relatives of patients with CLL have an 8-fold increase in the risk of developing CLL, and family history of CLL is among the strongest risk factor for developing CLL. In addition to the known germline predisposition to CLL, clonal hematopoiesis (CH)has been shown to predispose to CLL. Initial CH studies focused on CH predisposing to myeloid malignancies, but more recent work showed that specific single nucleotide variants (SNV) and copy number variants (CNVs) are associated with risk of developing CLL (lymphoid-CH). How the germline genetic CLL risk interacts with lymphoid-CH to produce CLL remains unknown.

The extensive Utah Population Database (UPDB) contains 50 years of cancer data from a statewide registry, a 4.5-million-person genealogy and is an excellent resource to study inherited and somatic CLL risk. We defined high-risk CLL pedigrees as those containing a statistical excess of CLL (p &lt; 0.05), compared with sex-, birth cohort-, and birthplace-matched rates from the full UPDB dataset. We ascertained 23 high-risk CLL pedigrees and collected and banked biospecimens for the CLL cases and their relatives. We screened whole blood DNA from 80 unaffected first-degree relatives in these high-risk CLL pedigrees along with 24 age- and sex-matched local controls for the presence of SNV-driven CH. SNV-driven CH was observed in 11% of the unaffected relatives with an average age of 54 years compared to 8% in age-matched controls. SNV-driven CH in the CLL relatives involved distinct genes, including BCR, PLEC1 and SMARCA2. Additionally, the variant allele frequencies (VAF) of the CH clones in the relatives was significantly higher than in controls (13% vs 4.7% p=0.048), indicating further expansion of these clones. We also found overlap between CH and monoclonal B-cell lymphocytosis (MBL) for 2 of the 3 relatives with MBL. The CH mutation was detectable in DNA extracted from sorted lymphocytes and monocytes. A subset of CLL relatives (n=45) were screened for CNV-driven CH, which appears more prevalent than SNV-driven CH (15% vs 11%, respectively) with a complex clonal architecture consistent with prior lymphoid CH studies.

To investigate the underlying germline CLL susceptibility variant in our large pedigrees we used the novel Shared Genetic Segment (SGS) analysis. SGS is a unique statistical tool developed specifically for discovery of germline susceptibility in the large pedigrees available at UPDB. SGS analysis can produce genome-wide significance using only a single large UPDB pedigree. SGS analysis was used on pedigree 6233, which contains 27974 members. SGS analysis identified a 0.9 Mb CLL risk locus on chromosome 2 containing two genes: CXCR4 and THSD7B. The identified segment overlaps with and narrows a previously identified CLL risk locus on chromosome 2. Several relatives in this pedigree have MBL and CH. Ongoing work will establish any other relatives with MBL and/or CH and whether they also inherited the 2q22 susceptibility locus.

In conclusion, our large Utah high-risk CLL pedigrees represent an exciting opportunity to study both somatic and germline CLL risk in a familial context. CH in CLL families may involve a unique set of genes/SNVs/CNVs which may be influenced by germline genetics. The novel SGS analysis successfully narrowed down the CLL risk locus on chromosome 2 to 0.9 Mb region using one large high-risk CLL pedigree.