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PTPN11-Related Disorders via the PTPN11 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
Order Kits
TEST METHODS

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
373 PTPN11$940.00 81406 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity
This test will detect causative mutations in ~50% of NS patients, ~90% of LS patients, and ~60% of MC patients.

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 PTPN11$690.00 81479 Add to Order
Pricing Comment

# of Genes Ordered

Total Price

1

$690

2

$730

3

$770

4-10

$840

11-30

$1,290

31-100

$1,670

Over 100

Call for quote

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Features

Noonan Syndrome (NS, OMIM 163950) is a relatively common developmental disorder that is characterized by dysmorphic facial features, growth and congenital heart defects, and musculoskeletal abnormalities. Cardiac abnormalities are found in up to 80% of patients and include pulmonary valve stenosis, atrial septal defect, atrioventricular canal defect, and hypertrophic cardiomyopathy. Musculoskeletal abnormalities include short stature, chest deformity with sunken or raised sternum, and short webbed neck. Several additional abnormalities have been described and include renal, genital, hematological, neurologic, cognitive, behavioral, gastrointestinal, dental, and lymphatic findings. Intelligence is usually normal; however, learning disabilities may be present. NS is characterized by an extensive clinical heterogeneity, even among members of the same family. Diagnosis is often made in infancy or early childhood. Symptoms often change and lessen with advancing age. Infants with NS are at risk of developing juvenile myelomonocytic leukemia (JMML OMIM 607785). The prevalence of NS is estimated at 1 in 1000 to 1 in 2,500 births worldwide (Allanson et al. Am J Med Genet 21:507-514, 1985; Romano et al. Pediatrics 126:746-759, 2010). LEOPARD Syndrome (multiple Lentigines, Electrocardiographic-conduction abnormalities, Ocular hypertelorism, Pulmonary stenosis, Abnormal genitalia, Retardation of growth, sensorineural Deafness, OMIM 151100) is a rare congenital developmental disorder characterized by skin pigmentation anomalies including multiple lentigines and café au lait spots, hypertrophic cardiomyopathy, pulmonary valve stenosis, and deafness. Other less common features include short stature, mild mental retardation, and abnormal genitalia (Legius et al. J Med Genet 39:571-574, 2002; Sarkozy et al. J Med Genet 41:e68, 2004). See also (Gelb and Tartaglia, GeneReviews, 2010). Metachondromatosis (MC OMIM 156250) is a rare skeletal dysplagia characterized by multiple exostoses mainly in the hands and feet. Additional features include enchondromas of the iliac crest and metaphyseal region of the long bones of the lower extremities, and periarticular calcifications. The exostoses may result in peroneal-nerve symptoms, which are relieved by surgery. The original exostoses may regress spontaneously with age, while new ones may develop. Although skeletal radiological findings of MC resemble those of Multiple Enchondromatosis (OMIM 166000), the two conditions can be easily distinguished. In MC, the exostoses point toward the nearby joints. In addition, they do not result in shortening of affected long bones, bowing, joint deformity, or joint dislocation, as is the case in Multiple Enchondromatosis (Kennedy Radiology 48:117-118, 1983; Bassett et al. J Bone Joint Surg Am 67:811-814, 1985).

Genetics

Noonan Syndrome (NS) is caused by gain of function mutations in various genes within the RAS/MAPK pathway, including PTPN11. These mutations appear to activate the gene product (SHP2 protein). To date, seven RAS/MAPK genes (PTPN11, SOS1, RAF1, KRAS, SHOC2, BRAF and NRAS) have been involved in patients with NS. PTPN11 mutations are the most common cause of NS, and account for ~ 50% of all cases genotyped (Allanson and Roberts, GeneReviews, 2011). Over 70 mutations were reported. Most causative mutations are missense. A few small deletion or insertion mutations have been reported (Tartaglia et al. Am J Hum Genet 78:279-290, 2006). Except for two large genomic duplications that included the entire PTPN11 gene (Shchelochkov et al. Am J Med Genet 146A:1042-1048, 2008; Graham et al. Am J Med Genet 149A:2122-2128, 2009), no gross defects or rearrangements in PTPN11 have been reported in patients with NS. Although de novo mutations are found in a substantial fraction of patients, familial cases have been reported. In these families, NS is inherited in an autosomal dominant manner with variable expressivity (Romano et al. Pediatrics 126:746-759, 2010).

Genotype-phenotype correlations are slowly being made. In particular, several groups have shown that pulmonary stenosis is more common in NS patients with PTPN11 mutations, while hypertrophic cardiomyopathy is more common in patients without PTPN11 mutations (Romano et al. 2010).

LEOPARD Syndrome is caused by defects in three genes within the RAS/MAPK: PTPN11, RAF1 and BRAF (Digilio et al. Am J Hum Genet 71:389-394, 2002; Pandit et al. Nat Genet 39:1007-1012, 2007; Sarkozy et al. Hum Mutat 30:695-702, 2009). Unlike NS, LEOPARD Syndrome mutations act through a dominant negative effect, which appears to disrupt the function of the wild-type gene product (SHP2 protein) (Jopling et al. PLOS Genetics 3:e225, 2007). Ten different PTPN11 mutations, all missense, have been reported in patients with LEOPARD. PTPN11 mutations are the most common cause of LEOPARD syndrome, and account for over 90% of all cases genotyped. Parents of LEOPARD patients are often asymptomatic, and de novo mutations are common. However, familial cases have been reported. In these families, affected relatives are diagnosed only after the birth of a visibly affected child, and the disease is transmitted in an autosomal dominant manner with variable penetrance and expressivity (Gelb and Tartaglia, GeneReviews, 2010). Genotype-phenotype correlations have been proposed (see for example Limongelli et al. Am J Med Genet A 146:620-628, 2008).

Metachondromatosis (MC) is caused by loss-of-function mutations in PTPN11. Recently, 13 heterozygous PTPN11 mutations were reported. At this time, PTPN11 mutations are the only known cause of MC. Mutations were found in ~ 60% if the MC families that have been studied, suggesting that PTPN11 mutations are a common cause of the disorder and that MC is genetically heterogeneous (Sobreira et al. PLoS Genet 6:e1000991, 2010; Bowen et al. PLoS Genet 7:e1002050, 2011). Mutations are distributed along the entire coding region of the gene and include missense, splicing, small deletions and complex rearrangements. MC is inherited in an autosomal dominant manner with incomplete penetrance.

Somatic PTPN11 mutations account for ~ 34% of non-syndromic Juvenile Myelomonocytic Leukemia (JMML) (Tartaglia et al. Nat Genet 34:148-150, 2003).

Testing Strategy

PTPN11 testing for NS, LS and MC involves bidirectional DNA sequencing of all coding exons and splice sites of the PTPN11 gene. The full coding sequence of each exon plus ~ 20 bp of flanking DNA on either side are sequenced. We will also sequence and single exon (Test #100) in family members of patients with a known mutation or to confirm research results.

Indications for Test

Patients with clinical features of NS, LS and MC and their family members are candidates for this test. Clinical features of Cardio-Facio-Cutaneous Syndrome (CFCS, OMIM 115150) overlap with those for NS and Costello Syndrome (CS OMIM 218040). CFCS patients who test negative for the mutations in BRAF, MAP2K1, MAP2K2 and KRAS genes may be candidates for NS (PTPN11, SOS1, RAF1, KRAS, SHOC2, BRAF and NRAS) genes or CS (HRAS gene) testing. Conversely, NS or CS patients who test negative for those genes may be candidates for all or a portion of CFCS testing (BRAF, MAP2K1, MAP2K2 and KRAS genes).

Gene

Official Gene Symbol OMIM ID
PTPN11 176876
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Tests

Name
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Panel
Comprehensive Fetal and Neonatal Loss Panel
Fetal Concerns Sequencing Panel
Noonan Spectrum Disorders/Rasopathies Sequencing Panel

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Allanson JE, Hall JG, Hughes HE, Preus M, Witt RD. 1985. Noonan syndrome: the changing phenotype. Am. J. Med. Genet. 21: 507-514. PubMed ID: 4025385
  • Allanson, Judith E MD , Roberts, Amy E MD. (2011). "Noonan Syndrome." PubMed ID: 20301303
  • Bassett, G. S., Cowell, H. R. (1985). "Metachondromatosis. Report of four cases." J Bone Joint Surg Am 67(5): 811-4. PubMed ID: 3873457
  • Bowen, M. E., et.al. (2011). "Loss-of-function mutations in PTPN11 cause metachondromatosis, but not Ollier disease or Maffucci syndrome." PLoS Genet 7(4): e1002050. PubMed ID: 21533187
  • 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. The American Journal of Human Genetics 71: 389–394. PubMed ID: 12058348
  • Gelb BD, Tartaglia M. 2010. LEOPARD Syndrome. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301557
  • Graham JM, Kramer N, Bejjani BA, Thiel CT, Carta C, Neri G, Tartaglia M, Zenker M. 2009. Genomic duplication of PTPN11 is an uncommon cause of Noonan syndrome. American Journal of Medical Genetics Part A 149A: 2122–2128. PubMed ID: 19760651
  • Kennedy. Metachondromatosis. Radiology 48:117-118, 1983 PubMed ID: 6602353
  • Legius E, Schrander-Stumpel C, Schollen E, Pulles-Heintzberger C, Gewillig M, Fryns J-P. 2002. PTPN11 mutations in LEOPARD syndrome. J. Med. Genet. 39: 571–574. PubMed ID: 12161596
  • 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. Nature Genetics 39: 1007–1012. PubMed ID: 17603483
  • Romano AA, Allanson JE, Dahlgren J, Gelb BD, Hall B, Pierpont ME, Roberts AE, Robinson W, Takemoto CM, Noonan JA. 2010. Noonan syndrome: clinical features, diagnosis, and management guidelines. Pediatrics 126: 746-759. PubMed ID: 20876176
  • Sarkozy A, Conti E, Digilio MC, Marino B, Morini E, Pacileo G, Wilson M, Calabrò R, Pizzuti A, Dallapiccola B. 2004. Clinical and molecular analysis of 30 patients with multiple lentigines LEOPARD syndrome. Journal of Medical Genetics 41: e68–e68. PubMed ID: 15121796
  • Shchelochkov OA, Patel A, Weissenberger GM, Chinault AC, Wiszniewska J, Fernandes PH, Eng C, Kukolich MK, Sutton VR. 2008. Duplication of chromosome band 12q24.11q24.23 results in apparent Noonan syndrome. Am. J. Med. Genet. A 146A: 1042–1048. PubMed ID: 18348260
  • Sobreira, N. L., et.al. (2009). "Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene." PLoS Genet 6(6): e1000991. PubMed ID: 20577567
  • Tartaglia M, Niemeyer CM, Fragale A, Song X, Buechner J, Jung A, Hählen K, Hasle H, Licht JD, Gelb BD. 2003. Somatic mutations in PTPN11 in juvenile myelomonocytic leukemia, myelodysplastic syndromes and acute myeloid leukemia. Nature genetics 34: 148–150. PubMed ID: 12717436
  • Tartaglia, M., et.al. (2006). "Diversity and functional consequences of germline and somatic PTPN11 mutations in human disease." Am J Hum Genet 78(2): 279-90. PubMed ID: 16358218
Order Kits
TEST METHODS

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org).  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 20 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Deletion/Duplication Testing Via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

Ordering Options


myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
REQUISITION FORM
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.

DNA

(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.

CELL CULTURE

(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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