PIK3CA-associated developmental disorders exhibit distinct classes of mutations with variable expression and tissue distribution

Abstract

Mosaicism is increasingly recognized as a cause of developmental disorders with the advent of next-generation sequencing (NGS). Mosaic mutations of PIK3CA have been associated with the widest spectrum of phenotypes associated with overgrowth and vascular malformations. We performed targeted NGS using 2 independent deep-coverage methods that utilize molecular inversion probes and amplicon sequencing in a cohort of 241 samples from 181 individuals with brain and/or body overgrowth. We identified PIK3CA mutations in 60 individuals. Several other individuals (n = 12) were identified separately to have mutations in PIK3CA by clinical targeted-panel testing (n = 6), whole-exome sequencing (n = 5), or Sanger sequencing (n = 1). Based on the clinical and molecular features, this cohort segregated into three distinct groups: (a) severe focal overgrowth due to low-level but highly activating (hotspot) mutations, (b) predominantly brain overgrowth and less severe somatic overgrowth due to less-activating mutations, and (c) intermediate phenotypes (capillary malformations with overgrowth) with intermediately activating mutations. Sixteen of 29 PIK3CA mutations were novel. We also identified constitutional PIK3CA mutations in 10 patients. Our molecular data, combined with review of the literature, show that PIK3CA-related overgrowth disorders comprise a discontinuous spectrum of disorders that correlate with the severity and distribution of mutations.

Molecular diagnosis of somatic overgrowth conditions: A single‐center experience

“…The maximum VAF of a P/LP variant in blood was 4.5%. These results reinforce previous findings that testing blood alone is not a suitable strategy for diagnosis of somatic overgrowth, although some exceptions have been noted (Riviere et al, , Keppler‐Noreuil et al, , Luks et al , Mirzaa et al, , Chang et al, , Kuentz et al, ). The diagnostic yield increased to 56% (36/64) after removing patients where only blood and/or saliva were submitted.…”

“…Finally, we evaluated the likely cause of negative findings in the 40 patients where a P/LP variant was not identified. As mentioned previously, 12/40 of these patients only had blood available for testing, and thus, it is likely that, for a subset of these patients, P/LP variants were present in the targeted regions but not detectable in blood (Riviere et al, , Keppler‐Noreuil et al, , Luks et al, , Mirzaa et al, , Chang et al, , Kuentz et al, ). To determine whether full PIK3CA sequencing would increase the molecular diagnostic rate, we evaluated an expanded panel which included full exonic coverage for PIK3CA in 7 patients where clearly affected tissue was submitted and the phenotype was strongly suggestive of PROS (Supporting information Table ).…”

“…It is not clear whether this high VAF is representative of a very early post‐zygotic variant or whether the variant was selected for during culture. Several cases of germline PIK3CA variants have been reported recently (Chang et al, ; Mirzaa et al, ). Ultimately, the pregnancy did not go to full‐term.…”

New insights into the generation and role of de novo mutations in health and disease

“…A common feature to these disorders is that they are caused by mutations known to lead to activation of cellular proliferation pathways and overgrowth. The mutations with the strongest effect generally result in more-severe developmental alterations [168], suggesting that the type of de novo mutation influences the expression of the phenotype. Remarkably, the mutations with the strongest effect on activation have also been observed as somatic events in cancer [168], for which constitutive activation of cellular proliferation pathways is a major hallmark [169].…”

“…The mutations with the strongest effect generally result in more-severe developmental alterations [168], suggesting that the type of de novo mutation influences the expression of the phenotype. Remarkably, the mutations with the strongest effect on activation have also been observed as somatic events in cancer [168], for which constitutive activation of cellular proliferation pathways is a major hallmark [169]. This finding supports the view that not only the type of pathogenic mutation but also the time at which the mutation occurs is crucial in defining its consequences.…”