Development of a Diagnostic Service for Extended Characterisation of Apparently De Novo Disease Associated Variants

Abstract

Developmental disorders caused by de novo variation are a significant burden on human health, with estimates in the United Kingdom placing live-born incidence at between 1 in 213 and 1 in 448. Such disorders also cause unique difficulties for reproductive genetic counselling due to the risk of mosaicism within the germline in one of the parents. Indeed, recent work using high read depth next generation sequencing has demonstrated that ~4% of all apparently de novo variants are detectable as low level mosaics in the leucocyte DNA of parents. Historically, parents of children with apparently de novo pathogenic variants have been assigned an arbitrary recurrence risk of 1% in future pregnancies; it is clear that this figure over-estimates the risk for many families while simultaneously downplaying it in others. In this study, technologies and techniques readily available within the established genetics laboratories of the NHS have been used to further characterise 12 de novo variants across 11 families in terms of low level parental mosaicism and parent-of-origin, with an aim to stratify families into one of five recurrence risk groups: 1) Post-zygotic mutation, no risk of recurrence; 2) Paternally derived variant not detectable in a paternal semen sample, very low risk of recurrence; 3) Paternally derived variant detectable in paternal semen, defined risk of recurrence; 4) Maternally derived variant not detectable in maternal blood, unknown risk but raised above groups 1 and 2; 5) Maternally derived variant detectable in maternal blood, unknown risk but raised above group 4. Complete characterisation was obtained for 8 of the studied variants, with one tentatively placed into group 1, one each into groups 3 and 5, and five into group 2. Estimated costs for the service were ~£900, roughly equivalent to the per pregnancy test costs for non-invasive prenatal diagnosis from a UK laboratory. In an expansion of the initial aims of the project, the techniques used were also adapted to elucidate mosaicism and offspring risk in a case of unilateral vestibular schwannoma in which three pathogenic variants in NF2 had previously been detected on tumour analysis. Natural history of tumour development with respect to the three variants was inferred, with offspring risk minimised, offering reassurance to the patient.

Date of Award	23 Apr 2021
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Miriam Smith (Main Supervisor)