Diagnostic value of exome and whole genome sequencing in craniosynostosis

Abstract

BackgroundCraniosynostosis, the premature fusion of one or more cranial sutures, occurs in ∼1 in 2250 births, either in isolation or as part of a syndrome. Mutations in at least 57 genes have been associated with craniosynostosis, but only a minority of these are included in routine laboratory genetic testing.MethodsWe used exome or whole genome sequencing to seek a genetic cause in a cohort of 40 subjects with craniosynostosis, selected by clinical or molecular geneticists as being high-priority cases, and in whom prior clinically driven genetic testing had been negative.ResultsWe identified likely associated mutations in 15 patients (37.5%), involving 14 different genes. All genes were mutated in single families, except for IL11RA (two families). We classified the other positive diagnoses as follows: commonly mutated craniosynostosis genes with atypical presentation (EFNB1, TWIST1); other core craniosynostosis genes (CDC45, MSX2, ZIC1); genes for which mutations are only rarely associated with craniosynostosis (FBN1, HUWE1, KRAS, STAT3); and known disease genes for which a causal relationship with craniosynostosis is currently unknown (AHDC1, NTRK2). In two further families, likely novel disease genes are currently undergoing functional validation. In 5 of the 15 positive cases, the (previously unanticipated) molecular diagnosis had immediate, actionable consequences for either genetic or medical management (mutations in EFNB1, FBN1, KRAS, NTRK2, STAT3).ConclusionsThis substantial genetic heterogeneity, and the multiple actionable mutations identified, emphasises the benefits of exome/whole genome sequencing to identify causal mutations in craniosynostosis cases for which routine clinical testing has yielded negative results.

Structural Genome Variations Related to Craniosynostosis

“…Subsequently, genes of the WNT signaling pathway, e.g., ZIC1 , govern lineage commitment at the supraorbital center. A de novo loss of ZIC1 has been observed in a patient with bilambdoid and sagittal craniosynostosis and gain-of-function mutations in ZIC1 in 5 unrelated patients with coronal craniosynostosis and learning disability Miller et al, 2017]. Thereupon, the EFBN1 , TWIST1 , and TCF12 genes drive suture boundary formation.…”

“…, and NTRK2 genes have been documented [Roscioli et al, 2013;Miller et al, 2017]. In cases with nonsyndromic midline craniosynostosis, a digenic mechanism, involving concurrent presence of risk alleles of BMP2 and SMAD6 , has also been discovered [Timberlake, et al, 2016].…”

“…Also concomitant de-repression of GLI3 and activation of IHH targets has been demonstrated [Veistinen et al, 2017]. Thus, molecular diagnosis of craniosynostosis beyond Saethre-Chotzen, Crouzon, Pfeiffer, Apert, and Jackson-Weiss syndromes based on mutations in the TWIST1 , FGFR1 and FGFR2 genes has been complemented with a widening spectrum of loci and genes ( Table 1 ) [Jabs et al, 1993[Jabs et al, , 1994Muenke et al, 1994;Reardon et al, 1994;Park et al, 1995;Rutland et al, 1995;Wilkie et al, 1995;Wieland et al, 2004;Roscioli et al, 2013;Twigg and Wilkie, 2015;Miller et al, 2017;Timberlake et al, 2017;Timberlake and Persing, 2018].…”

“…This strategy should be used with caution since some of the databases contain SNVs that occur as somatic mosaics [Carlston et al, 2017]. By WES and WGS of large cohorts of patients with specific forms of craniosynostosis, be it as an isolated phenotype or as part of a syndrome, a considerable number of novel candidate genes and mutations have been uncovered [Roscioli et al, 2013;Miller et al, 2017;Timberlake et al, 2017;Timberlake and Persing, 2018]. Thus, de novo mutations in inhibitors of the WNT, BMP, and Ras/ERK signaling pathways in patients with nonsyndromic midline craniosynostosis and in the…”

Current Approaches in the Development of Molecular and Pharmacological Therapies in Craniosynostosis Utilizing Animal Models

“…These single-gene mutations are represented in over three-quarters of monogenic diagnoses among which Crouzon, Pfeiffer, Apert, Muenke, and Saerthre-Chotzen syndromes are the most frequently encountered [Wilkie et al, 2010]. With the recent implementation of next-generation sequencing technologies, over 52 genes have been associated with craniosynostosis [Laue et al, 2011;Keupp et al, 2013;Ehmke et al, 2017;Miller et al, 2017]. While treatment of nonsyndromic and mutation-negative patients in most cases does not necessitate more than one operation, this is not the case for mutation-positive patients.…”