Genotype-phenotype associations in a large PTEN Hamartoma Tumor Syndrome (PHTS) patient cohort

Background: Pathogenic PTEN germline variants cause PTEN Hamartoma Tumor Syndrome (PHTS), a rare disease with a variable genotype and phenotype. Knowledge about these spectra and genotype-phenotype associations could help diagnostics and potentially lead to personalized care. Therefore, we assessed...

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Authors: Hendricks, Linda A.J.; Hoogerbrugge, Nicoline; Venselaar, Hanka; Aretz, Stefan; Spier, Isabel; Legius, Eric; Brems, Hilde; De Putter, Robin; Claes, Kathleen B.M.; Evans, D. Gareth; Woodward, Emma R.; Genuardi, Maurizio; Brugnoletti, Fulvia; Van Ierland, Yvette; Dijke, Kim; Tham, Emma; Tesi, Bianca; Schuurs Hoeijmakers, Janneke H.M.; Branchaud, Maud; Salvador, Héctor; Jahn, Arne; Schnaiter, Simon; Anastasiadou, Violetta C.; Brunet, Joan; Oliveira, Carla; Roht, Laura; Blatnik, Ana; Irmejs, Arvids; Mensenkamp, Arjen R.; Vos, Janet R.; Duijkers, Floor; Giltay, Jacques C.; Van Hest, Liselotte P.; Kleefstra, Tjitske; Leter, Edward M.; Nielsen, Maartje; Nijmeijer, Sebastiaan W.R.; Olderode-Berends, Maran J. W.
Format: Article
Status:Published version
Publication date:2022
Country:España
Institution:Universidad de Barcelona
Repository:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/191809
Online Access:https://hdl.handle.net/2445/191809
Access Level:Open access
Keyword:Oncologia
Genètica humana
Fenotip
Oncology
Human genetics
Phenotype
Summary:Background: Pathogenic PTEN germline variants cause PTEN Hamartoma Tumor Syndrome (PHTS), a rare disease with a variable genotype and phenotype. Knowledge about these spectra and genotype-phenotype associations could help diagnostics and potentially lead to personalized care. Therefore, we assessed the PHTS genotype and phenotype spectrum in a large cohort study. Methods: Information was collected of 510 index patients with pathogenic or likely pathogenic (LP/P) PTEN variants (n = 467) or variants of uncertain significance. Genotype-phenotype associations were assessed using logistic regression analyses adjusted for sex and age.Results: At time of genetic testing, the majority of children (n = 229) had macrocephaly (81%) or developmental delay (DD, 61%), and about half of the adults (n = 238) had cancer (51%), macrocephaly (61%), or cutaneous pathology (49%). Across PTEN, 268 LP/P variants were identified, with exon 5 as hotspot. Missense variants (n = 161) were mainly located in the phosphatase domain (PD, 90%) and truncating variants (n = 306) across all domains. A trend towards 2 times more often truncating variants was observed in adults (OR = 2.3, 95%CI = 1.5-3.4) and patients with cutaneous pathology (OR = 1.6, 95%CI = 1.1-2.5) or benign thyroid pathology (OR = 2.0, 95%CI = 1.1-3.5), with trends up to 2-4 times more variants in PD. Whereas patients with DD (OR = 0.5, 95%CI = 0.3-0.9) or macrocephaly (OR = 0.6, 95%CI = 0.4-0.9) had about 2 times less often truncating variants compared to missense variants. In DD patients these missense variants were often located in domain C2.Conclusion: The PHTS phenotypic diversity may partly be explained by the PTEN variant coding effect and the combination of coding effect and domain. PHTS patients with early-onset disease often had missense variants, and those with later-onset disease often truncating variants.

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