Noonan Spectrum Panel

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Background

Genes:

  • PTPN11 at 12q24.1
  • RAF1 at 3p25
  • SOS1 at 2p22-p21
  • KRAS at 12p12.1
  • HRAS at 11p15.5
  • BRAF at 7q34
  • MEK1 at 15q21
  • MEK2 at 19p13.3
  • NRAS at 1p13.2
  • SHOC2 at 10q25
  • CBL at 11q23.3
  • SPRED1 at 15q14

Methodology: The Noonan Spectrum Panel is performed by next generation sequencing using oligonucleotide-based target capture followed by Illumina HiSeq sequencing of the coding regions and splice sites of PTPN11, SOS1, RAF1, KRAS, NRAS, BRAF, MEK1, MEK2, HRAS SHOC2 exon 2, CBL and SPRED1.

Analytical Sensitivity: This assay is greater than 99% sensitive for detecting substitution variants in the sequence analyzed.

Clinical Sensitivity: This test detects pathogenic variants in at least 63% of individuals with a clinical diagnosis of Noonan syndrome as well as 90% of pathogenic variants in individuals with LEOPARD, Cardio facio-cutaneous, or Costello syndromes.

Sample Requirements

Related CME Courses

How to order test

Noonan syndrome (NS) is a genetically heterogeneous condition. Several other conditions which share overlapping genotypes and phenotypes with Noonan syndrome are cardio-facio-cutaneous (CFC) syndrome, LEOPARD syndrome, and Costello syndrome. Together these four syndromes make up Noonan Spectrum Disorders. Clinical features of Noonan Spectrum Disorders include short stature, cardiovascular defects (pulmonary valve stenosis and hypertrophic cardiomyopathy being the most common), development delays, and characteristic facies. Skeletal, hematologic, and cutaneous findings can also be associated with Noonan syndrome and its related disorders. The comprehensive approach of the Noonan Spectrum Panel covers 12 genes associated with Noonan, CFC, LEOPARD, and Costello syndromes. These genes include: PTPN11, SOS1, RAF1, KRAS, HRAS, BRAF, MEK1/MAP2K1, MEK2/MAP2K2, NRAS, SHOC2, CBL and SPRED1. As shown below, these genes are involved in the Ras-MAPK pathway and gain-of–function mutations result in the phenotype associated with Noonan spectrum disorders. CBL and SPRED1 variants in individuals with Noonan syndrome-like features have been reported with additional hematologic or cutaneous features, respectively.

Individuals with a Noonan spectrum disorder can have very variable phenotypes, even among family members. Features of these disorders can also change with age, which may make it difficult to make an accurate clinical diagnosis. To this point, individuals with a clinical diagnosis of one of the Noonan spectrum disorders have had a molecular etiology that is not consistent with their clinical diagnosis. For example, BRAF variants have been reported in individuals with a clinical diagnosis of Noonan syndrome and a SOS1 variant has been reported in an individual with Cardio-facio-cutaneous syndrome (Nystrom et al. 2008). In addition, some of these genes are associated with more than one syndrome (PTPN11, KRAS, and RAF1). As such, molecular diagnostics can help to distinguish between the different Noonan spectrum disorders. Therefore, this comprehensive approach of simultaneously testing all of these genes is beneficial because it provides complete testing while eliminating the need to determine which of these genes to test based on an individual's clinical features, thus reducing the likelihood of missed molecular diagnoses.

Noonan syndrome (NS; OMIM #163950) is an autosomal dominant disorder occurring in about 1 in 1000-2500 live births. It is characterized by short stature, distinct facial features, congenital heart disease, motor delay, learning difficulties or mild intellectual disability, hearing loss, chest deformity, scoliosis, undescend testes, pubertal delay and varied coagulation defects and lymphatic dysplasias (www.GeneTests.org/Gene Reviews). Although these are common manifestations of the condition, this syndrome exhibits both inter- and intrafamilial variation.

Noonan syndrome is genetically heterogeneous. Variants in PTPN11 have been detected in 50% of individuals with a clinical diagnosis of Noonan syndrome (Tartaglia et al. 2001, 2002). Of the remaining individuals, variants in RAF1, SOS1, and KRAS have been observed in 3-17%, 10%, and 1%, respectively (Pandit et al. 2007, Razzaque et al. 2007, Roberts et al. 2007, Tartaglia et al. 2007, Carta et al. 2006, Schubbert et al. 2006). BRAF and NRAS variants have been reported in individuals with a clinical diagnosis of Noonan syndrome, and SHOC2 variants have been reported in individuals with a clinical diagnosis of Noonan syndrome with loose anagen hair. However, the detection rates for BRAF, NRAS and SHOC2 are unknown at this time (Nystrom et al. 2008, Cordeddu et al. 2009, Cirstea et al. 2010). In addition, variants in CBL and SPRED1 have been identified in a subset of individuals with overlapping features of Noonan syndrome (Martinelli et al. 2010, Niemeyer et al. 2010, Denayer et al. 2011). PTPN11, RAF1, NRAS and SOS1 variants have occurred de novo and have co-segregated with Noonan syndrome within families; however, variable expressivity has been observed. All KRAS and SHOC2 variants described to date have occurred de novo.

LEOPARD syndrome (OMIM# 151100) is an autosomal dominant disorder whose clinical features include multiple lentigines, electrocardiographic conduction abnormalities, ocular hypertelorism, pulmonic stenosis, abnormal genitalia, retardation of growth, and sensorineural deafness (Digilio et al. 2002, Pandit et al. 2007). There is clinical overlap with features of Noonan syndrome (facial anomalies, distinct congenital heart defects, pectus deformity, hearing loss and growth retardation). Variants in exons 7, 12, and 13 of PTPN11 have been detected in the majority of individuals with LEOPARD syndrome (90-100%) (Digilio et al. 2002; Legius et al. 2002). As many as 33% of patients with PTPN11-negative LEOPARD syndrome have variants in RAF1 (Pandit et al. 2007).

Cardio-Facio-Cutaneous syndrome (CFC; OMIM# 115150) is characterized by congenital heart defects and ectodermal anomalies. Sparse, curly, or slow-growing hair and skin abnormalities such as atopic dermatitis and hyperkeratosis with ichthyosis-like lesions are distinguishing. Cardiac features occur in 77% of cases and include atrial septal defects, pulmonic stenosis, and hypertrophic cardiomyopathy. Characteristic facial features include macrocephaly, a large prominent forehead, bitemporal narrowing, down-slanting palpebral fissures, epicanthal folds, hypertelorism, ptosis, exophthalmos, short upturned nose, prominent philtrum, posteriorly rotated, low-set ears, and webbed neck. Mild to severe intellectual disability is observed in 80% of Cardio-facio-cutaneous syndrome cases. Postnatal growth deficiency is common. Cardio-facio-cutaneous syndrome has been reported to share features with Noonan syndrome, Costello syndrome, and Kabuki syndrome. An increased risk of malignancy has not been reported in individuals with Cardio-facio-cutaneous syndrome.

Costello syndrome (CS; OMIM# 218040) is characterized by typical craniofacial features, failure to thrive, developmental delay, cardiac anomalies, skeletal anomalies, and a predisposition to neoplasia. Facial features are coarse and typically include macrocephaly with a prominent forehead, epicanthal folds, down-slanting palpebral fissures, a short nose with a depressed nasal bridge and broad tip, and low-set posteriorly rotated ears with thickened helices and lobes. The cheeks may be full and the mouth large with full lips. The hair is typically curly. Deep palmar and plantar creases, hyperpigmentation and nasal papillomas are evident. Cardiac features are observed in up to 52% of cases and include pulmonary valve stenosis, ventricular septal defect, atrial septal defect, thickening of the intraventricular septum, hypertrophic cardiomyopathy, or rhythm disturbances. Developmental delay ranges from mild to severe and feeding difficulties (poor suck and swallow) are common. Predisposition to malignancy has been observed, with the most common being rhabdomyosarcoma, transitional cell carcinoma of the bladder, and neuroblastoma. Costello syndrome has been reported to share features with Noonan syndrome and Cardio-facial cutaneous syndrome.

 
 
Noonan Spectrum Genes
Gene Protein OMIM# Locus
PTPN11 PROTEIN-TYROSINE PHOSPHATASE, NONRECEPTOR-TYPE 11 176876 12q24.1
SOS1 SON OF SEVENLESS, DROSOPHILA, HOMOLOG 1 182530 2p22-p21
RAF1 V-RAF-1 MURINE LEUKEMIA VIRAL ONCOGENE HOMOLOG 1 164760 3p25
KRAS KIRSTEN RAT SARCOMA VIRAL ONCOGENE HOMOLOG 190070 12p12.1
NRAS NEUROBLASTOMA RAS VIRAL ONCOGENE HOMOLOG 164790 1p13.2
HRAS HARVEY RAT SARCOMA VIRAL ONCOGENE HOMOLOG 190020 11p15.5
BRAF V-RAF MURINE SARCOMA VIRAL ONCOGENE HOMOLOG B1 164757 7q34
MEK1 MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1 176872 15q21
MEK2 MITOGEN-ACTIVATED PROTEIN KINASE KINASE 2
601263 19p13.3
SHOC2 SUPPRESSOR OF CLEAR, C. ELEGANS, HOMOLOG OF; SHOC2 602775 10q25
CBL CAS-BR-M MURINE ECOTROPIC RETROVIRAL TRANSFORMING SEQUENCE HOMOLOG 165360 11q23.3
SPRED1 SPROUTY-RELATED EVH1 DOMAIN-CONTAINING PROTEIN 1 609291 15q14
 
Epidemiology
  • Noonan syndrome: 1/1000-1/2500
  • LEOPARD, Cardio-facio-cutaneous and Costello syndromes: rare, unknown
  • Both males and females are affected in equal frequency.
  • There is no known association with ethnic origin. 
Inheritance Pattern:
  • Autosomal dominant
  • Children of an affected individual with an identified pathogenic variant have a 50% (1 in 2) risk of inheriting the same variant
Test Indications
  • Diagnostic testing for individuals with a clinical diagnosis or suspicion of Noonan, LEOPARD, Costello, or CFC syndromes.
  • Familial single site testing for parents and siblings who may be at risk for carrying a variant when a familial variant has been identified
  • Prenatal diagnosis when a familial variant has been identified
  • Prenatal testing when cystic hygroma or increase nuchal translucency is noted on ultrasound. Pathogenic variants in PTPN11 have been found in 16% and 2% of pregnancies with a cystic hygroma or increased nuchal translucency, respectively, when chromosome abnormalities have been ruled out (Lee et al, 2008).
  • Loss-of-function variants in PTPN11 have been identified in individuals with metachondromatosis syndrome (MC). 
Test Outcome
  • The detection of a pathogenic variant will offer a definitive diagnosis for an affected individual.
  • A negative test result does not rule out a diagnosis of Noonan, LEOPARD, Cardio-facio-cutaneous or Costello Syndrome. Additional genes that have not yet been identified may also be associated with these syndromes.

Methodology

The Noonan Spectrum Panel is performed by next generation sequencing using oligonucleotide-based target capture (SureSelect, Agilent) followed by Illumina HiSeq sequencing of the coding regions and splice sites of PTPN11, SOS1, RAF1, KRAS, NRAS, BRAF, MEK1, MEK2, HRAS SHOC2, CBL and SPRED1. Variant calls are generated using the Burrows-Wheeler Aligner followed by GATK analysis. Sanger sequencing is used to confirm all clinically significant variants and fill in regions with insufficient coverage.

Analytical Sensitivity

This assay is greater than 99% sensitive for detecting substitution variants in the sequence analyzed. In addition, this assay is 95% sensitive for detecting small insertions or deletions (InDels) (100% for 1-2 bp indels, 92.3% for 3-5 bp indels and 87.5% for >10 bp indels). Indels are not a described variant type for Noonan spectrum syndromes. This test does not examine most non-coding regions that could affect gene expression.

Clinical Sensitivity

This test detects pathogenic variants in at least 63% of individuals with a clinical diagnosis of Noonan syndrome as well as 90% of pathogenic variants in individuals with LEOPARD, Cardio-facio-cutaneous, or Costello syndromes.

 

Noonan Syndrome

CFC Syndrome LEOPARD Syndrome Costello Syndrome
PTPN11 50% ----- ~90-100% -----
SOS1 10% ----- ----- -----
RAF1 3-17% ----- ~5% -----
KRAS 1% 7% ----- -----
NRAS <1% ----- ----- -----
SHOC2 <1% ----- ----- -----
BRAF UNKNOWN 78% ----- -----
MEK1/MEK2 ----- ~12% ----- -----
HRAS ----- ----- ----- 87%
CBL UNKNOWN ----- ----- -----
SPRED1 UNKNOWN ----- ----- -----

 

PTPN11 variants have been identified in 16% of fetuses with cystic hygroma and 2% of fetuses with increased nuchal translucency. The incidence of variants in the other genes analyzed is unknown at this time (Lee et al. 2008).

 

References

Aoki Y, Niihori T, Kawame H, Kurosawa K, Ohashi H, Tanaka Y, Filocamo M, Kato K, Suzuki Y, Kure S, Matsubara Y (2005) Germline mutations in HRAS proto-oncogene cause Costello syndrome., Nat Genet. Oct;37(10):1038-40.

Bentires-Alk M, Kontaridis MI, Neel BG. (2006) Stops along the RAS pathway in human genetic disease. Nat Med. Mar;12(3):283-5.

Carta C, Pantaleoni F, Bocchinfuso G, Stella L, Vasta I, Sarkozy A, Digilio C, Palleschi A, Pizzuti A, Grammatico P, Zampino G, Dallapiccola B, Gelb BD, Tartagli M. (2006) Garmline missense mutations affecting KRAS Isoform B are associated with a severe Noonan syndrome phenotype. Am J Hum Genet. Jul;79(1):129-35.

Cirstea IC, Kutsche K, Dvorsky R, Gremer L, Carta C, Horn D, Roberts AE, Lepri F, Merbitz-Zahradnik T, König R, Kratz CP, Pantaleoni F, Dentici ML, Joshi VA, Kucherlapati RS, Mazzanti L, Mundlos S, Patton MA, Silengo MC, Rossi C, Zampino G, Digilio C, Stuppia L, Seemanova E, Pennacchio LA, Gelb BD, Dallapiccola B, Wittinghofer A, Ahmadian MR, Tartaglia M, Zenker M. (2010) A restricted spectrum of NRAS mutations causes Noonan syndrome. Nat Genet. Jan;42(1):27-9.

Cordeddu V, Di Schiavi E, Pennacchio L, Ma’ayan A, Sarkozy A, Fodale V, Cecchetti S, Cardinale A, Martin J, Schackwitz W, Lipzen A, Zampino G, Mazzanti L, Digilio MC, Martinelli S, Flex E, Lepri F, Bartholdi D, Kutsche K, Ferrero GB, Anichini C, Selicorni A, Rossi C, Tenconi R, Zenker M, Merlo D, Dallapiccola B, Iyengar R, Bazzicalupo P, Gelb B, Tartaglia M. (2009) Mutation of SHOC2 promotes abberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair. Nat Gen. Sep;41(9):1022-6.

Denayer E, Chmara M, Brems H, Kievit AM, van Bever Y, Van den Ouweland AM, Van Minkelen R, de Goede-Bolder A, Oostenbrink R, Lakeman P, Beert E, Ishizaki T, Mori T, Keymolen K, Van den Ende J, Mangold E, Peltonen S, Brice G, Rankin J, Van Spaendonck-Zwarts KY, Yoshimura A, Legius E. Legius syndrome in fourteen families. Hum Mutat. 2011 Jan;32(1):E1985-98. PubMed PMID: 21089071; PubMed Central PMCID: PMC3038325.

Digilio MC, Conti E, Sarkozy A, Mingarelli R, Dottorini T, Marino B, Pizzuti A, Dallapiccola B. (2002) Grouping of multiple-lentigines/LEOPARD and Noonan syndromes on the PTPN11 gene. Am J Hum Genet. Aug;71(2):389-94.

Estep AL, Tidyman WE, Teitell MA, Cotter PD, Rauen KA (2006) HRAS mutations in Costello syndrome: detection of constitutional activating mutations in codon 12 and 13 and loss of wildtype allele in malignancy. Am J Med Genet A. Jan 1;140(1):8-16.

Gripp KW, Lin AE, Stabley DL, Nicholson L, Scott CI Jr, Doyle D, Aoki Y, Matsubara Y, Zackai EH, Lapunzina P, Gonzalez-Meneses A, Holbrook J, Agresta CA, Gonzalez IL, Sol-Church K (2006) HRAS mutation analysis in Costello syndrome: genotype and phenotype correlation. Am J Med Genet A. Jan 1;140(1):1-7.

Kerr B, Delrue MA, Sigaudy S, Perveen R, Marche M, Burgelin I, Stef M, Tang B, Eden T, O'sullivan J, De Sandre-Giovannoli A, Reardon W, Brewer C, Bennett C, Quarrell O, McCann E, Donnai D, Stewart F, Hennekam R, Cave H, Verloes A, Philip N, Lacombe D, Levy N, Arveiler B, Black G (2006) Genotype-phenotype correlation in Costello syndrome; HRAS mutation analysis in 43 cases. J Med Genet. Jan 27.

Lee K, Williams B, Roza K, Ferguson H, David K, Eddleman K, Stone J, Edelmann L, Richard G, Gelb B, Kornreich R (2008) PTPN11 analysis for the prenatal diagnosis of Noonan syndrome in fetuses with abnormal ultrasound findings. Clin Genet. 2008 Aug 26.

Lequis E, Schrander-Stumpel C, Scholleen E, Pulles-Heintzberger C, GewiliqM, Fryns JP. (2002) PTPN11mutations in LEOPARD syndrome. J Med Genet. Aug;39(8):571-4.

Martinelli S, De Luca A, Stellacci E, Rossi C, Checquolo S, Lepri F, Caputo V, Silvano M, Buscherini F, Consoli F, Ferrara G, Digilio MC, Cavaliere ML, van Hagen JM, Zampino G, van der Burgt I, Ferrero GB, Mazzanti L, Screpanti I, Yntema HG, Nillesen WM, Savarirayan R, Zenker M, Dallapiccola B, Gelb BD, Tartaglia M. Heterozygous germline mutations in the CBL tumor-suppressor gene cause a Noonan syndrome-like phenotype. Am J Hum Genet. 2010 Aug 13;87(2):250-7. Epub 2010 Jul 8. PubMed PMID: 20619386; PubMed Central PMCID: PMC2917705.

Niemeyer CM, Kang MW, Shin DH, Furlan I, Erlacher M, Bunin NJ, Bunda S, Finklestein JZ, Sakamoto KM, Gorr TA, Mehta P, Schmid I, Kropshofer G, Corbacioglu S, Lang PJ, Klein C, Schlegel PG, Heinzmann A, Schneider M, Starý J, van den Heuvel-Eibrink MM, Hasle H, Locatelli F, Sakai D, Archambeault S, Chen L, Russell RC, Sybingco SS, Ohh M, Braun BS, Flotho C, Loh ML. Germline CBL mutations cause developmental abnormalities and predispose to juvenile myelomonocytic leukemia. Nat Genet. 2010 Sep;42(9):794-800. Epub 2010 Aug 8. PubMed PMID: 20694012.

Niihori T, Aoki Y, Narumi Y, Neri G, Cave H, Verloes A, Okamoto N, Hennekam RC, Gillessen- Kaesbach G, Wieczorek D, Kavamura MI, Kurosawa K, Ohashi H, Wilson L, Heron D, Bonneau D, Corona G, Kaname T, Naritomi K, Baumann C, Matsumoto N, Kato K, Kure S, Matsubara Y (2006) Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome. Nat Genet. Mar;38(3):294-6.

Nystrm AM, Ekvall S, Berglund E, Bjrkqvist M, Braathen G, Duchen K, Enell H, Holmberg E, Holmlund U, Olsson-Engman M, Annern G, Bondeson ML (2008) Noonan and Cardio-faciocutaneous syndromes: two clinically and genetically overlapping disorders. J Med Genet. May 2.

Pandit B, Sarkozy A, Pennacchio LA, Carta C, Oishi K, Martinelli S, Pogna EA, Schackwitz W, Ustaszewska A, Landstrom A, Bos JM, Ommen SR, Esposito G, Lepri F, Faul C, Mundel P, López Siguero JP, Tenconi R, Selicorni A, Rossi C, Mazzanti L, Torrente I, Marino B, Digilio MC, Zampino G, Ackerman MJ, Dallapiccola B, Tartaglia M, Gelb BD (2007) Gain-of-function RAF1 mutations cause Noonan and LEOPARD syndromes with hypertrophic cardiomyopathy. Nat Genet. Aug;39(8):1007-12.

Razzaque MA, Nishizawa T, Komoike Y, Yagi H, Furutani M, Amo R, Kamisago M, Momma K, Katayama H, Nakagawa M, Fujiwara Y, Matsushima M, Mizuno K, Tokuyama M, Hirota H, Muneuchi J, Higashinakagawa T, Matsuoka R. (2007) Germline gain-of-function mutations in RAF1 cause Noonan syndrome. Nat Genet. Aug;39(8):1013-7.

Roberts AE, Araki T, Swanson KD, Montgomery KT, Schipiro TA, Joshi VA, Li L, Yassin Y, Tamburino, AM, Neel BG & Kucherlapati RS. (2007) Germline gain-of-function mutations in SOS1 cause Noonan syndrome. Nat Genet. Jan;39(1):70-4.

Rodriguez-Viciana P, Tetsu O, Tidyman WE, Estep AL, Conger BA, Cruz MS, McCormick F, Rauen KA (2006) Germline mutations in genes within the MAPK pathway cause cardio-faciocutaneous syndrome. Science. Mar 3;311(5765):1287-90.

Schubbert S, Zenker M, Rowe SL, Boll S, Klein C, Bollag G, van der Burgt I, Musante L, Kalscheuer V, Wehner LE, Nguyen H, West B, Zhang KY, Sistermans E, Rauch A, Niemeyer CM, Shannon K, Kratz CP (2006) Germline KRAS mutations cause Noonan syndrome. Nat Genet. Mar;38(3):331-6.

Tartaglia M, Mehler EL, Goldberg R, Zampino G, Brunner HG, Kremer H, van der Burgt I, Crosby AH, Ion A, Jeffery S, Kalidas K, Patton MA, Kucherlapati RS, Gelb BD (2001) Mutations in PTPN11, encoding the protein tyrosine phosphatase SHP-2, cause Noonan syndrome. Nat Genet. Dec;29(4):465-8.

Tartaglia M, Kalidas K, Shaw A, Song X, Musat DL, van der Burgt I, Brunner HG, Bertola DR, Crosby A, Ion A, Kucherlapati RS, Jeffery S, Patton MA, Gelb BD (2002) PTPN11mutations in Noonan syndrome: molecular spectrum, genotype-phenotype correlation, and phenotypic heterogeneity. Am J Hum Genet. Jun;70(6):1555-63.

Tartaglia M, Pennacchio LA, Zhao C, Yadav KK, Fodale V, Sarkozy A, Pandit B, Oishi K, Martinelli S, Schackwitz W, Ustaszewska A, Martin J, Bristow J, Carta C, Lepri F, Neri C, Vasta I, Gibson K, Curry CJ, Siguero JP, Digilio MC, Zampino G, Dallapiccola B, Bar-Sagi D, Gelb BD (2007) Gain-of-function SOS1 mutations cause a distinctive form of Noonan syndrome. Nat Genet. 2007 Jan;39(1):75-9.


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