Purpose
Noonan syndrome and related disorders are genetic conditions affecting 1:1000–2000 individuals. Variants causing hyperactivation of the RAS/MAPK pathway lead to phenotypic overlap between syndromes, in addition to an increased risk of pediatric tumors. DNA sequencing methods have been optimized to provide a molecular diagnosis for clinical and genetic heterogeneity conditions. This work aimed to investigate the genetic basis in RASopathy patients through Next Generation Sequencing in a Reference Center for Rare Diseases (IFF/Fiocruz) and implement the precision medicine at a public health institute in Brazil.
Patients and Methods
This study comprises 26 cases with clinical suspicion of RASopathies. Sanger sequencing was used to screen variants in exons usually affected in the
PTPN11
and
HRAS
genes for cases with clinical features of Noonan and Costello syndrome, respectively. Posteriorly, negative and new cases with clinical suspicion of RASopathy were analyzed by clinical or whole-exome sequencing.
Results
Molecular analysis revealed recurrent variants and a novel
LZTR1
missense variant: 24 unrelated individuals with pathogenic variants [
PTPN11
(11),
NF1
(2),
SOS1
(2),
SHOC2
(2),
HRAS
(1),
BRAF
(1),
LZTR
(1),
RAF1
(1),
KRAS
(1),
RIT1
(1), a patient with co-occurrence of
PTPN11
and
NF1
mutations (1)]; familial cases carrying a known pathogenic variant in
PTPN11
(mother-two children), and a previously undescribed paternally inherited variant in
LZTR1
. The comparative modeling analysis of the novel
LZTR1
variant p.Pro225Leu showed local and global changes in the secondary and tertiary structures, showing a decrease of about 1% in the β-sheet content. Furthermore, evolutionary conservation indicated that Pro225 is in a highly conserved region, as observed for known dominant pathogenic variants in this protein.
Conclusion
Bringing precision medicine through NGS towards congenital syndromes promotes a better understanding of complex clinical and/or undiagnosed cases. The National Policy for Rare Diseases in Brazil emphasizes the importance of incorporating and optimizing diagnostic methodologies in the Unified Brazilian Health System (SUS). Therefore, this work is an important step for the NGS inclusion in diagnostic genetic routine in the public health system.