Page 72 - Haematologica Vol. 109 - July 2024

ARTICLE - Familial germline pathogenic alleles and hematologic malignancies Q. Feng et al.
with a family history identified in a population-based registry. Concerning the elevated familial risk of lymphoid malignan- cies other than leukemia that our group has observed in California,7 previous studies have reported similar results: that first-degree relatives of patients with non-Hodgkin lymphoma (NHL), Hodgkin lymphoma (HL), or chronic lym- phocytic leukemia/small lymphocytic lymphoma (CLL/SLL) among European origin populations have approximately 1.7 times, 3.1 times, and 8.5 times higher risk of developing these malignancies, respectively.12-17 Rare variants associated with familial-associated lymphoma risk, however, have not been studied extensively.18
The risk of hematologic cancers varies by ancestral/ethnic group. In California, Latino individuals have a higher incidence of ALL compared to those of other ancestral/ethnic groups across all ages;19 however, the highest familial risk (identified by families with 2 or more independent sibling cancers) was found among non-Latino Asian/Pacific Islanders (NLAPI).7 For lymphomas diagnosed under 19 years of age, the incidence among non-Latino White (NLW) subjects is higher than sub- jects of other ancestral/ethnic groups.7 However, the variation in germline predisposition that may drive this difference in risk by ancestral/ethnic group has not been formally addressed. Standard US state-based population registries may be useful to study rare genetic predispositions in an objective, “real world” population-based manner when biological samples are available. Here, we utilize linked cancer population registries in California along with the California Biobank to identify the nature and ancestral origin of rare P/LP germline variants that may explain this variation in cancer risk.
Methods
Our study methods were reviewed and approved by the Com- mittee for Protection of Human Subjects (IRB) of the State of California. Cancer patients were derived from linked popula- tion-based registries in California, as previously described.7 Briefly, the dataset was created by linking information from the California Cancer Registry (CCR) and California Birth Statistical Master File. The linked dataset encompassed all cancer cases comprehensively diagnosed in individuals aged 0-26 years old (since 26 is the oldest age for which it was possible to perform this linkage at the time of this work), and their sibling’s and their mother’s cancers also captured within this registry. To study the rare genetic predispositions in association with hematologic cancers, we first identified all sibling pairs with cancer in the database. For all individ- uals with hematologic cancers (leukemia or lymphoma) and a sibling with cancer (of any type, excluding any iatrogenic cancers), we processed the pair for sequencing. Overall, 70 patients from 35 families were eligible for inclusion.
DNA preparation and sequencing, and mapping and variant identification were performed as explained in the Online Supplementary Methods. The GATK pipeline for germline
short variant calling was performed, with variant filter- ing as appropriate. Presence of Down syndrome (DS) was assessed by chromosome 21 copy number normalized to all other chromosomes. Pathogenicity of variants in 1,172 genes (Online Supplementary Table S1) was initially assessed using informatic tools (Varsome, PeCanPie), followed by strict manual curation of all identified alleles by ACMG/ AMP guidelines.
The ancestral identity of each individual was assessed by matching local haplotypes with one of 5 Earth superpopula- tions: Latino (LAT), European (EUR), East Asian (EAS), African (AFR), South Asian (SAS). The informatic tool RFMix was used for this purpose, and the global ancestry of each individual was calculated by summing up the ancestral components of each of the haplotypes for the entire genome.
Results
Demographics of study participants
Among the 70 patients eligible for inclusion, 67 samples had adequate DNA for genotyping, and 64 of the 67 samples were sibling pairs from the same family and were included in the genetic analyses. The 64 subjects were from 32 families, among which 12 (38%) were LAT and 10 (31%) were non-Lati- no White (NLW) families (Table 1). Including parents and all healthy or diseased children, the average size of each LAT family was 4.92 people/family and the average size of NLW families was 6.10 people/family. One out of the 32 families had a mother diagnosed with cancer (desmoplastic small round cell tumor) in her twenties; we note that given the recruitment period of 1989-2015 we have a limited available follow-up time to track adult cancer in parents. We do not report age of onset of any cancer case to protect confiden- tiality of the families evaluated in this study. One subject (#534, family #2) was identified to have DS (# chr21 reads= 917228; population mean and Standard Deviation [SD] of chr21 = 651691+/-128812).
Pathogenic/likely pathogenic and variants of uncertain significance
The mean sequencing coverage across subjects was 69.1 (range: 37.2-98.7) (Online Supplementary Table S2). Our initial software-guided curation yielded 14 unique P/LP variants. Upon further refined manual curation, 5 P/LP variants were reclassified as variants of uncertain significance (VUS), leaving 9 rare P/LP variants shared between siblings among 8 sibling pairs (Online Supplementary Table S3), and 105 rare VUS that are shared between siblings among the 32 families (Online Supplementary Table S4). Notably, along with demoting 5 LP variants to VUS, manual curation rescued one VUS to be LP (HABP2), and reclassified another 23 VUS to be LB (likely benign; Online Supplementary Table S4). Among the P/LP variants, one (11%) was found in LAT families, 2 (22%) were found in NLW families, 2 (22%) were found in non-Latino
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