Targeted sequencing of FH-deficient uterine leiomyomas reveals biallelic inactivating somatic fumarase variants and allows characterization of missense variants

Abstract

Uterine leiomyomas (ULs) constitute a considerable health burden in the general female population. The fumarate hydratase (FH) deficient subtype is found in up to 1.6% of cases.Identifying these individuals is important as a subset of cases is related to germline FH variants in the setting of the hereditary leiomyomatosis and renal cell carcinoma (HLRCC) syndrome which is associated with aggressive renal cell cancer.We sequenced 13 FH-deficient ULs using the TruSight Cancer Panel. In all 13 cases, we could identify biallelic FH variants. In eight cases, we found a FH point mutation (two truncating, six missense) with evidence for loss of the second allele. Variant allelefrequencies pointed to somatic variants in all cases with a point mutation. Spatial clustering of the identified missense variants in the lyase domain indicated their importance for proper fumarase oligomerization. In five tumors, we found a biallelic deletion of FH. Analysis of driver mutations of other genes revealed two truncating TP53 variants in one case. Copy number (CN) analysis found a large RB1 deletion in three tumors and enrichment for ALK CN gains. Following our recommendation, one individual presented for genetic consultation. A germlineFH variant could not be identified. Clinical examination and family history raised the suspicion of tuberous sclerosis complex, which could subsequently be confirmed due to the splice variant c.2040A>G in TSC1. This case highlights that presence of FH deficiency does not exclude other concurrent genetic syndromes.By comparing the FH mutation carrier frequency in public databases and the prevalence of FH deficient ULs, we conclude that most of these are likely sporadic and estimate 3.5 -14.3% of females with an FH deficient UL to carry a germline FH variant. Further prospective tumor/normal sequencing studies are needed to develop a reliable screening strategy for HLRCC in women with ULs.

Hereditary leiomyomatosis and renal cell carcinoma syndrome associated uterine smooth muscle tumors: Bridging morphology and clinical screening

“…Lehtonen et al, however, found two sporadic FH mutations amongst 153 uterine leiomyomas from 46 unselected women 21 . More recent data suggests that sporadic FH alterations are more common than germline and likely account for the majority of FH deficient USMT 9,22,23 . In contrast the majority of FH deficient renal cell carcinomas appear to be associated with germline FH alterations 24 .…”

“…Germline mutations in FH result in two distinct conditions: (a) homozygous or compound heterozygous mutations are referred to as fumarase deficiency syndrome resulting in death within the first decade and (b) the heterozygous state, resulting in HLRCC, in which FH acts as a tumor suppressor. HLRCC patients are born with one defective allele and develop a second hit in the tumor, frequently by loss of heterozygosity 8,9 …”

A novel syndrome caused by the constitutional gain-of-function variant p.Glu1099Lys in NSD2

“…The NSD2 germline variants were harmonized to a common reference with VariantValidator 22 (NM_001042424.2 transcript, hg19 reference). The distribution of NDD associated NDS2 variants in the linear protein representation and in the tertiary protein structure (PDB 7CRO 14 ) was compared to variants from databases as described previously 23 (details in Supplementary notes).…”

Prenatal phenotype of PNKP-related primary microcephaly associated with variants affecting both the FHA and phosphatase domain

“…In brief, reads were demultiplexed, adapters trimmed, and overrepresented sequences removed before we aligned the reads to the hg38 reference. Alignments were visualized and inspected for aberrant splicing as described previously [20]. We applied iREAD [21] to quantify observed intron retention events.…”