Maternal germinal mosaicism for <i>SCN1A</i> in sibs with a mild form of Dravet syndrome

BackgroundDravet syndrome is a severe genetic encephalopathy, caused by pathogenic variants in SCN1A. Low-grade parental mosaicism occurs in a substantial proportion of families (7%–13%) and has important implications for recurrence risks. However, parental mosaicism can remain undetected by methods regularly used in diagnostics. In this study, we use single-molecule molecular inversion probes (smMIP), a technique with high sensitivity for detecting low-grade mosaic variants and high cost-effectiveness, to investigate the incidence of parental mosaicism of SCN1A variants in a cohort of 90 families and assess the feasibility of this technique.MethodsDeep sequencing of SCN1A was performed using smMIPs. False positive rates for each of the proband’s pathogenic variants were determined in 145 unrelated samples. If parents showed corresponding variant alleles at a significantly higher rate than the established noise ratio, mosaicism was confirmed by droplet digital PCR (ddPCR).ResultsSequence coverage of at least 100× at the location of the corresponding pathogenic variant was reached for 80 parent couples. The variant ratio was significantly higher than the established noise ratio in eight parent couples, of which four (5%) were regarded as true mosaics, based on ddPCR results. The false positive rate of smMIP analysis without ddPCR was therefore 50%. Three of these variants had previously been considered de novo in the proband by Sanger sequencing.ConclusionsmMIP technology combined withnext generation sequencing (NGS) performs better than Sanger sequencing in the detection of parental mosaicism. Because parental mosaicism has important implications for genetic counselling and recurrence risks, we stress the importance of implementing high-sensitivity NGS-based assays in standard diagnostics.

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Parental germline mosaicism in genome-wide phased de novo variants: recurrence risk assessment and implications for precision genetic counselling

Lecoquierre,

Drouot,

Coutant

et al. 2024

Preprint

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Background: De novo mutations (DNMs) significantly impact health, particularly through developmental disorders. DNMs occur in both paternal and maternal germlines via diverse mechanisms including parental early embryonic mosaicism, which increases recurrence risk for future pregnancies through germline mosaicism. Embryonic mosaicism is divided based on primordial germ cell specification (PGCS): pre-PGCS events may affect both germline and somatic tissues, while post-PGCS events are only found in the germline. The specific contribution of germline mosaicism to DNMs across the genome is not well defined. We aimed at categorizing DNMs and their recurrence risk by detecting a large set of DNMs followed by systematic deep sequencing of parental blood and sperm DNA. Methods: We performed trio-based short-read genome sequencing for initial DNM detection and long-read genome sequencing for phasing, followed by high-depth targeted sequencing of parental blood and paternal sperm to detect germline mosaicism. Results: We detected a total of 428 DNMs (on average 85.6 per trio, n = 5 trios), with an expected paternal bias of 80%. Targeted resequencing of parental blood and sperm (depth > 5000x) unveiled 20/334 parental germline mosaics (2–5 per trio) with variant allele fractions (VAFs) ranging from 0.24–14.7%, including 7 that were detected in paternal sperm exclusively (1–2 per trio). We estimate that individual genomes harbour about 2 paternal and 2 maternal pre-PGCS DNMs and 2 paternal post-PGCS DNMs (detectable in sperm only). Due to paternal bias, maternally phased variants appear 3.4x more likely to be mosaic in blood. By using average VAFs in sperm as a direct indicator, we estimate recurrence risk of genome -wide paternally phased de novo variants to be 0.3%, prior to any sperm sequencing assessment. This estimate is an average between a majority of variants with a null recurrence risk and a handful of variants with a high recurrence risk. Conclusions: Genetic counselling of DNM may not rely anymore on empirical estimates of recurrence risk. Sperm sequencing may be an effective method to reliably specify the recurrence risk of most individual DNMs. Long-read sequencing, allowing the phasing of DNMs, may also become critical in this process.

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Maternal germinal mosaicism for SCN1A in sibs with a mild form of Dravet syndrome

Cited by 3 publications

References 10 publications

Dravet syndrome with autism inherited from a paternal mosaic heterozygous mutation on SCN1A

Dravet syndrome with autism inherited from a paternal mosaic heterozygous mutation on SCN1A

Assessment of parental mosaicism in SCN1A-related epilepsy by single-molecule molecular inversion probes and next-generation sequencing

Parental germline mosaicism in genome-wide phased de novo variants: recurrence risk assessment and implications for precision genetic counselling

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