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Prenatal Diagnostic Testing of the Noonan Syndrome Genes in Fetuses with Abnormal Ultrasound findings

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Prenatal Diagnostic Testing of the Noonan Syndrome Genes in Fetuses with Abnormal Ultrasound findings European Journal of Human Genetics (2013) 21, 936–942 & 2013 Macmillan Publishers Limited All rights reserved 1018-4813/13 www.nature.com/ejhg ARTICLE Prenatal diagnostic testing of the Noonan syndrome genes in fetuses with abnormal ultrasound findings Ellen A Croonen1, Willy M Nillesen2, Kyra E Stuurman3, Gretel Oudesluijs4, Ingrid MBM van de Laar4, Liesbeth Martens2, Charlotte Ockeloen2, Inge B Mathijssen5, Marga Schepens2, Martina Ruiterkamp-Versteeg2, Hans Scheffer2, Brigitte HW Faas2, Ineke van der Burgt2 and Helger G Yntema*,2 In recent studies on prenatal testing for Noonan syndrome (NS) in fetuses with an increased nuchal translucency (NT) and a normal karyotype, mutations have been reported in 9–16% of cases. In this study, DNA of 75 fetuses with a normal karyotype and abnormal ultrasound findings was tested in a diagnostic setting for mutations in (a subset of) the four most commonly mutated NS genes. A de novo mutation in either PTPN11, KRAS or RAF1 was detected in 13 fetuses (17.3%). Ultrasound findings were increased NT, distended jugular lymphatic sacs (JLS), hydrothorax, renal anomalies, polyhydramnios, cystic hygroma, cardiac anomalies, hydrops fetalis and ascites. A second group, consisting of anonymized DNA of 60 other fetuses with sonographic abnormalities, was tested for mutations in 10 NS genes. In this group, five possible pathogenic mutations have been identified (in PTPN11 (n ¼ 2), RAF1, BRAF and MAP2K1 (each n ¼ 1)). We recommend prenatal testing of PTPN11, KRAS and RAF1 in pregnancies with an increased NT and at least one of the following additional features: polyhydramnios, hydrops fetalis, renal anomalies, distended JLS, hydrothorax, cardiac anomalies, cystic hygroma and ascites. If possible, mutation analysis of BRAF and MAP2K1 should be considered. European Journal of Human Genetics (2013) 21, 936–942; doi:10.1038/ejhg.2012.285; published online 16 January 2013 Keywords: Noonan syndrome; nuchal translucency; prenatal testing; mutation analysis INTRODUCTION abnormalities.20–24 The first prenatal DNA diagnosis of NS in a Noonan syndrome (NS) is an autosomal dominant condition with an fetus with massive cystic hygroma, pleural effusion and ascites showed incidence of 1:1000–2500 live births. It is characterized by character- amutationinthePTPN11 gene.25 Lee et al26 performed a istic facies, short stature, congenital heart defects (CHD), skeletal retrospective review of prenatal PTPN11 testing. The two most abnormalities, cryptorchidism and variable development delay.1–3 NS common indications for testing in this study were increased NT is one of the ‘RASopathies’, a specific class of developmental disorders, (44%) and cystic hygroma (48%). PTPN11 mutations were identified caused by germline mutations in genes, encoding proteins of the RAS– in 9% of fetuses (2 and 16% of fetuses with increased NT and cystic mitogen-activated protein kinase (RAS–MAPK) pathway. This path- hygroma, respectively). In a prospective DNA diagnostic study on way has an essential role in the control of the cell cycle, differentiation, fetuses with a normal karyotype and an increased NT, we previously growth and cell senescence. Dysregulation has profound developmen- identified a de novo mutation rate of 15.8% (3/19 fetuses) by parallel tal consequences. About 50% of known NS cases have a mutation in sequencing of PTPN11 and KRAS.27 the PTPN11 gene.4,5 Heterozygous gain-of-function mutations in In the present study, we investigated the DNA of 56 additional other genes perturbing RAS–MAPK signaling have also been identified fetuses with a normal karyotype and one or more abnormal in NS patients: KRAS, SOS1, BRAF, RAF1, MAP2K1, NRAS, SHOC2 ultrasound findings for a mutation in one or more of the NS genes and CBL.6–13 Several of these genes are also involved in Cardio-Facio- in a diagnostic setting. Parallel sequencing of PTPN11, KRAS, SOS1 Cutaneous (CFC) syndrome and Costello syndrome.14–16 Because of and RAF1 was offered, as these are the most frequent mutated genes the high variability of clinical symptoms and the genetic heterogeneity in patients diagnosed with NS after birth. The actual number of genes establishing a diagnosis of one of these syndromes is often difficult. tested in each fetus depended on the amount of DNA available for Patients are most frequently diagnosed postnatally, but also prenatal testing (chorionic villi or amniotic fluid, cultured or uncultured cells). characteristic findings are described. Costello syndrome is associated In an attempt to define whether parallel sequencing of these four with polyhydramnios, fetal overgrowth, a relative macrocephaly and to genes revealed the highest mutation frequency in fetuses with an a lesser extent with nuchal thickening, hydrops, ventriculomegaly, abnormal ultrasound, we investigated in a second anonymized study pyelectasia and fetal atrial tachycardia/arrhythmia.17–19 the DNA (amplified by whole genome amplification to allow a Prenatal features of NS are increased nuchal translucency (NT), sufficient amount of DNA) of 60 other fetuses with increased NT, distended jugular lymphatic sacs (JLS), cystic hygroma, hydrops hydrops fetalis and/or CHD and a normal karyotype, for mutations in fetalis, pleural effusion, polyhydramnios, CHD and renal 10 genes of the RAS–MAPK pathway. 1Department of Paediatrics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands; 2Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands; 3Department of Clinical Genetics, VU University Medical Centre, Amsterdam, The Netherlands; 4Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands; 5Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands *Correspondence: Dr HG Yntema, Department of Human Genetics, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands. Tel: +31 24 361 3799; Fax: +31 24 361 6658; E-mail: [email protected] Received 25 June 2012; revised 28 November 2012; accepted 28 November 2012; published online 16 January 2013 Prenatal testing for Noonan syndrome genes EA Croonen et al 937 The aim of this study is to provide a protocol for prenatal NS Rouen, France) was used to assess the effect of the mutation. Parameters used testing, to serve as a useful aid to facilitate parental counseling and in this program include the Grantham score, SIFT and PolyPhen analysis, targeted DNA testing. PhyloP score and analysis of frequency of the mutation in the population. MATERIALS AND METHODS Statistical analysis Patients The data were collected in SPSS 16.0. For statistical analysis we used the The first, diagnostic, study group consisted of 75 fetuses with a normal Student’s t-test and the Fischer’s Exact test. A statistically significant two-sided karyotype and one or more abnormal ultrasound findings. This group contains threshold was set at Po0.05. Because of the small number of fetuses also all fetuses sent to our laboratory from different clinical genetics centers in the descriptive analysis was performed. Netherlands for a period of 2 years. Part of the positive cases have been described in case reports.24,27 Ultrasound findings considered as indication for prenatal sequencing were increased NT (greater than the 95th percentile RESULTS (p95)), cystic hygroma, distended JLS, ascites, hydrops fetalis, pleural effusion, Diagnostic study group polyhydramnios, CHD and renal abnormalities. The diagnostic study group included 75 fetuses with a normal From all mutation-negative cases the ultrasound findings provided by the karyotype and abnormal ultrasound findings, described in NS. referring physician were marked, and ultrasound findings that were not Table 1 shows the prenatal ultrasound findings in the total group mentioned were regarded not to be present. From all the mutation-positive and classified by the presence or absence of a mutation. The most cases the applicants were asked to deliver detailed information about frequently identified prenatal characteristics are increased NT (n ¼ 50; gestational age (GA) and corresponding ultrasound findings. Blood of both 66.7%), cystic hygroma (n ¼ 17; 22.7%), cardiac anomalies and parents was available for testing of detected mutations and variants. hydrops fetalis (each n ¼ 15; 20.0%), distended JLS (n ¼ 12; 16.0%), The second, anonymized, study group consisted of 60 other fetuses with increased NT, hydrops fetalis and/or CHD and a normal karyotype. Medical hydrothorax (n ¼ 9; 12.0%), renal anomalies (n ¼ 7; 9.3%), polyhy- records of these cases were reviewed before anonymizing the samples. Because dramnios (n ¼ 3; 4.0%) and ascites (n ¼ 1; 1.3%). No postnatal of the anonymous design of the study, parents could not be tested and results information of the mutation-negative cases is present. However, we were not communicated to the parents. never received a request for testing of the remaining NS genes once the baby was born, suggesting that no NS-specific features were Sequence analysis present. However, it cannot be excluded that part of the pregnancies In the diagnostic study group, parallel sequencing of the coding regions and have been terminated because of the abnormalities seen on the splice sites of PTPN11, KRAS, SOS1 and RAF1 was performed. The number of ultrasound. genes tested depended on the amount of DNA available for testing (chorionic In 13/75 (17.3%) fetuses a mutation was detected. Table 2 shows villi or amniotic fluid, cultured or uncultured cells) and the GA of the their pre- and postnatal clinical characteristics. The mutations and pregnancy. In 15 fetuses only PTPN11 was tested, 9 fetuses were tested for clinical features of four of these fetuses have also been described PTPN11 and KRAS, 11 fetuses were tested for PTPN11, KRAS,andSOS1.In40 elsewhere; case 1 has been described by Bakker et al24 and cases 9, 12 fetuses all four genes were analyzed. The order of genes tested in case not and 13 have been described by Houweling et al.27 Nine fetuses had a enough DNA was available (PTPN11, KRAS, SOS1, RAF1) is based on the de novo mutation in PTPN11, three in RAF1 and one in KRAS.
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