title: Next-generation sequencing identifies rare variants associated with Noonan syndrome.
abstract: Noonan syndrome (NS) is a relatively common genetic disorder, characterized by typical facies, short stature, developmental delay, and cardiac abnormalities. Known causative genes account for 70-80% of clinically diagnosed NS patients, but the genetic basis for the remaining 20-30% of cases is unknown. We performed next-generation sequencing on germ-line DNA from 27 NS patients lacking a mutation in the known NS genes. We identified gain-of-function alleles in Ras-like without CAAX 1 (RIT1) and mitogen-activated protein kinase kinase 1 (MAP2K1) and previously unseen loss-of-function variants in RAS p21 protein activator 2 (RASA2) that are likely to cause NS in these patients. Expression of the mutant RASA2, MAP2K1, or RIT1 alleles in heterologous cells increased RAS-ERK pathway activation, supporting a causative role in NS pathogenesis. Two patients had more than one disease-associated variant. Moreover, the diagnosis of an individual initially thought to have NS was revised to neurofibromatosis type 1 based on an NF1 nonsense mutation detected in this patient. Another patient harbored a missense mutation in NF1 that resulted in decreased protein stability and impaired ability to suppress RAS-ERK activation; however, this patient continues to exhibit a NS-like phenotype. In addition, a nonsense mutation in RPS6KA3 was found in one patient initially diagnosed with NS whose diagnosis was later revised to Coffin-Lowry syndrome. Finally, we identified other potential candidates for new NS genes, as well as potential carrier alleles for unrelated syndromes. Taken together, our data suggest that next-generation sequencing can provide a useful adjunct to RASopathy diagnosis and emphasize that the standard clinical categories for RASopathies might not be adequate to describe all patients.
authors: Department of Genetics, Harvard Medical School, Boston, MA 02115;Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115;Institute of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70457, Taiwan;
authors: Peng-Chieh
authors: PC
authors: Chen
authors: Princess Margaret Cancer Center, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 1L7;
authors: Jiani
authors: J
authors: Yin
authors: Institute of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70457, Taiwan;
authors: Hui-Wen
authors: HW
authors: Yu
authors: Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115;
authors: Tao
authors: T
authors: Yuan
authors: Princess Margaret Cancer Center, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 1L7;
authors: Minerva
authors: M
authors: Fernandez
authors: Ontario Institute for Cancer Research, Toronto, ON, Canada M5G 0A3;
authors: Christina K
authors: CK
authors: Yung
authors: Ontario Institute for Cancer Research, Toronto, ON, Canada M5G 0A3;
authors: Quang M
authors: QM
authors: Trinh
authors: Ontario Institute for Cancer Research, Toronto, ON, Canada M5G 0A3;
authors: Vanya D
authors: VD
authors: Peltekova
authors: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030; and.
authors: Jeffrey G
authors: JG
authors: Reid
authors: Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115;
authors: Erica
authors: E
authors: Tworog-Dube
authors: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030; and.
authors: Margaret B
authors: MB
authors: Morgan
authors: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030; and.
authors: Donna M
authors: DM
authors: Muzny
authors: Ontario Institute for Cancer Research, Toronto, ON, Canada M5G 0A3;
authors: Lincoln
authors: L
authors: Stein
authors: Ontario Institute for Cancer Research, Toronto, ON, Canada M5G 0A3;
authors: John D
authors: JD
authors: McPherson
authors: Department of Cardiology and Division of Genetics, Department of Medicine, Boston Children's Hospital Boston, Boston, MA 02115.
authors: Amy E
authors: AE
authors: Roberts
authors: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030; and.
authors: Richard A
authors: RA
authors: Gibbs
authors: Princess Margaret Cancer Center, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 1L7; bneel@uhnresearch.ca rkucherlapati@partners.org.
authors: Benjamin G
authors: BG
authors: Neel
authors: Department of Genetics, Harvard Medical School, Boston, MA 02115;Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115; bneel@uhnresearch.ca rkucherlapati@partners.org.
authors: Raju
authors: R
authors: Kucherlapati
mesh_terms: D000483:Alleles; D056726:Genetic Association Studies; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D048369:MAP Kinase Kinase 1 / Q000235:genetics; D020935:MAP Kinase Signaling System / Q000235:genetics; D009154:Mutation / Q000235:genetics*; D025542:Neurofibromin 1 / Q000235:genetics; D009634:Noonan Syndrome / Q000235:genetics*; D018631:ras Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D025542:Neurofibromin 1; D048369:MAP Kinase Kinase 1; C482125:MAP2K1 protein, human; C486776:RIT1 protein, human; D018631:ras Proteins
keywords: PTPN11; RAS; developmental diseases; human genetics; whole exome sequencing