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. 2024 Oct;12(10):e70017.
doi: 10.1002/mgg3.70017.

Deep Sequencing and Phenotyping in an Australian Tuberous Sclerosis Complex "No Mutations Identified" Cohort

Clara W T Chung  1   2   3 , Adam M Bournazos  4   5   6 , Lok Chi Denise Chan  2   3 , Vanessa Sarkozy  2   3 , John Lawson  2 , Sean E Kennedy  2   3 , Sandra T Cooper  4   5   6 , Edwin P Kirk  1   3   7 , David Mowat  1   2   3
Affiliations

Deep Sequencing and Phenotyping in an Australian Tuberous Sclerosis Complex "No Mutations Identified" Cohort

Clara W T Chung et al. Mol Genet Genomic Med. 2024 Oct.

Abstract

Tuberous sclerosis complex (TSC) is a variable multisystem disorder. The "no mutations identified" (NMI) group are reportedly phenotypically milder than those with an identified molecular cause, and often have mosaic or intronic variants not detected by standard sequencing methods.

Methods: We describe the phenotypes in an Australian TSC NMI group (n = 18) and a molecular testing strategy implementable in a diagnostic laboratory. Massively parallel sequencing (MPS) of the whole genomic regions of TSC1 and TSC2 was performed using DNA extracted from multiple tissue samples per participant.

Results: Our study showed that the phenotype in TSC NMI individuals can be similar to those with heterozygous, particularly TSC1, variants. Although neurodevelopmental outcomes can be less severe, the number of organ systems involved was similar to the non-mosaic groups. A diagnostic yield of 72% (13/18) was achieved, with the majority (10/13) being mosaic variants and the remainder heterozygous variants missed on previous testing.

Conclusion: Testing DNA from multiple tissue samples allowed for validation of otherwise discarded low-level mosaic variants and detection of mosaic variants by MPS without excessive cost or the need for specialised techniques. Implementing this approach in a diagnostic setting is viable and allows optimal clinical care of patients with NMI TSC.

Keywords: deep sequencing; genotype/phenotype comparison; mosaicism; tuberous sclerosis complex.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

FIGURE 1
FIGURE 1
Type of variant found. 13/18 (72%) participants had a disease‐causing variant found on testing. There were 3 previously missed heterozygous variants (16.5%), consisting of 2 TSC1 and 1 TSC2 variant. There were 10 mosaic variants (55.5%), consisting of 1 TSC1 and 9 TSC2 variants. 5 individuals (28%) had no disease‐causing variants found. Het, heterozygous; NMI, no mutations identified.
FIGURE 2
FIGURE 2
Samples in which a variant was detected arranged in order of total number of reads at location of variant. Number of variant reads in black bars and wildtype reads in white bars. Most (22/33, 66%) variants were detected at 800 reads or fewer (shaded area).
See this image and copyright information in PMC

References

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