Krystle Standen¹, Rebecca Walsh¹, George Elaksis¹, Bianca Rodgrigues¹

¹ Department of Genomics, NSW Health Pathology, Randwick, NSW, 2031

 

Background: Gonadal mosaicism can present diagnostic challenges. Deep sequencing approaches have proven useful in identifying mosaic pathogenic variants in conditions such as Tuberous sclerosis complex and Neurofibromatosis 1 where gonadal/gonosomal mosaicism has been reported. Identification of familial variants is necessary for access to therapy and reproductive options.

 

Methodology and results: Samples were processed using a TWIST 79-gene custom probe set kit with deep massively parallel sequencing. Libraries were sequenced on an Illumina NextSeq 500 and data processed using the Dragen server and an in house pipeline.

Case 1 showed a maternally inherited mosaic variant in TSC2. The variant was not detected in peripheral blood but was detected in an angiomyolipoma biopsy at 57% VAF.

Case 2 showed a paternally inherited mosaic variant in TSC2 in peripheral blood at 4.2% VAF. On review, they had clinical features consistent with Tuberous sclerosis.

Case 3 showed two pathogenic variants in NF1; variant 1 was detected in both left (21% VAF) and right (26% VAF) cutaneous neurofibromas biopsies, as well as in peripheral blood (2.5% VAF).

 

Conclusion: Deep sequencing can identify mosaic pathogenic variants below the limit of detection of standard sequencing assays. This, along with testing an appropriate tissue type can be used to infer gonadal mosaicism and guide appropriate genetic counselling.

 

1. Chung CWT, Bournazos AM, Chan LCD, et al. Deep Sequencing and Phenotyping in an Australian Tuberous Sclerosis Complex "No Mutations Identified" Cohort. Mol Genet Genomic Med. 2024;12(10):e70017. doi:10.1002/mgg3.70017

2. Chen JL, Miller DT, Schmidt LS, et al. Mosaicism in Tumor Suppressor Gene Syndromes: Prevalence, Diagnostic Strategies, and Transmission Risk. Annu Rev Genomics Hum Genet. 2022;23:331-361. doi:10.1146/annurev-genom-120121-105450

3. Klonowska K, Giannikou K, Grevelink JM, et al. Comprehensive genetic and phenotype analysis of 95 individuals with mosaic tuberous sclerosis complex. Am J Hum Genet. 2023;110(6):979-988. doi:10.1016/j.ajhg.2023.04.002