Noonan Syndrome Panel

SEQmethod-seq-icon Our Sequence Analysis is based on a proprietary targeted sequencing method OS-Seq™ and offers panels targeted for genes associated with certain phenotypes. A standard way to analyze NGS data for finding the genetic cause for Mendelian disorders. Results in 21 days. DEL/DUPmethod-dup-icon Targeted Del/Dup (CNV) analysis is used to detect bigger disease causing deletions or duplications from the disease-associated genes. Results in 21 days. PLUSmethod-plus-icon Plus Analysis combines Sequence + Del/Dup (CNV) Analysis providing increased diagnostic yield in certain clinical conditions, where the underlying genetic defect may be detectable by either of the analysis methods. Results in 21 days.

Test code: CA0501

The Blueprint Genetics Noonan Syndrome Panel is a 19-gene test for genetic diagnostics of patients with clinical suspicion of a rasopathy disorder. The panel covers diseases such as cardiofaciocutaneous syndrome, Costello syndrome, LEOPARD syndrome and Noonan syndrome.

Noonan syndrome or disorders mimicking Noonan syndrome are inherited in an autosomal dominant manner. Genetic diagnosis can confirm or modify the clinical diagnosis. Accurate diagnosis is essential when planning the management of these patients. Genetic diagnosis can be used for risk assessment and as a prognostic tool. Noonan Syndrome Panel is included in the Cardiomyopathy Panel and in the Comprehensive Cardiology Panel.

About Noonan Syndrome

Noonan syndrome is one of the most common human syndromes with estimated prevalence of 1 in 1000 to 1 in 2500 live births. It is clinically and genetically heterogeneous condition characterized by cardiovascular abnormalities, distinctive facial features, chest deformity, short stature, and other comorbidities. Among the Noonan syndrome -associated genes, many different genotype-phenotype correlations have been established although no phenotypic features are exclusively associated with one genotype. There are, however, significant differences in the risk of various Noonan syndrome manifestations based on the causative gene.

Availability

Results in 3-4 weeks.

Genes in the Noonan Syndrome Panel and their clinical significance
GeneAssociated phenotypesInheritanceClinVarHGMD
A2ML1Noonan syndromeAD/AR112
BRAF*LEOPARD syndrome, Noonan syndrome, Cardiofaciocutaneous syndromeAD9461
CBLNoonan syndrome-like disorder with or without juvenile myelomonocytic leukemiaAD2433
HRASCostello syndrome, Congenital myopathy with excess of muscle spindlesAD3026
KRAS*Noonan syndrome, Cardiofaciocutaneous syndromeAD4638
LZTR1Schwannomatosis, Noonan syndromeAD1260
MAP2K1Cardiofaciocutaneous syndromeAD1418
MAP2K2Cardiofaciocutaneous syndromeAD1432
NF1*Watson syndrome, Neurofibromatosis, Neurofibromatosis-Noonan syndromeAD2612607
NRASNoonan syndromeAD178
NSUN2Dubowitz syndrome, Non-syndromic intellectual disabilityAD/AR57
PTPN11LEOPARD syndrome, Noonan syndromeAD122129
RAF1LEOPARD syndrome, Noonan syndrome, Dilated cardiomyopathy (DCM)AD3742
RASA2Noonan syndromeAD/AR13
RIT1Noonan syndromeAD2020
RRASNoonan-syndrome like phenotypeAD/AR2
SHOC2Noonan-like syndrome with loose anagen hairAD13
SOS1Noonan syndromeAD4166
SPRED1Legius syndromeAD1271
  • * Some regions of the gene are duplicated in the genome leading to limited sensitivity within the regions. Thus, low-quality variants are filtered out from the duplicated regions and only high-quality variants confirmed by other methods are reported out. Read more.

Gene, refers to HGNC approved gene symbol; Inheritance to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL); ClinVar, refers to a number of variants in the gene classified as pathogenic or likely pathogenic in ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/); HGMD, refers to a number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/ac/). The list of associated (gene specific) phenotypes are generated from CDG (http://research.nhgri.nih.gov/CGD/) or Orphanet (http://www.orpha.net/) databases.

Blueprint Genetics offers a comprehensive Noonan syndrome panel that covers classical genes associated with cardiofaciocutaneous syndrome, Costello syndrome, LEOPARD syndrome and Noonan syndrome. The genes are carefully selected based on the existing scientific evidence, our experience and most current mutation databases. Candidate genes are excluded from this first-line diagnostic test. The test does not recognise balanced translocations or complex inversions, and it may not detect low-level mosaicism. The test should not be used for analysis of sequence repeats or for diagnosis of disorders caused by mutations in the mitochondrial DNA.

Please see our latest validation report showing sensitivity and specificity for SNPs and indels, sequencing depth, % of the nucleotides reached at least 15x coverage etc. If the Panel is not present in the report, data will be published when the Panel becomes available for ordering. Analytical validation is a continuous process at Blueprint Genetics. Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. All the Panels available for ordering have sensitivity and specificity higher than > 0.99 to detect single nucleotide polymorphisms and a high sensitivity for indels ranging 1-19 bp. The diagnostic yield varies substantially depending on the used assay, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be cost-effective first line test if your patient’s phenotype is suggestive for a specific mutation profile. Detection limit for Del/Dup analysis varies through the genome from one to six exon Del/Dups depending on exon size, sequencing coverage and sequence content.

The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. The highest relevance in the reported variants is achieved through elimination of false positive findings based on variability data for thousands of publicly available human reference sequences and validation against our in-house curated mutation database as well as the most current and relevant human mutation databases. Reference databases currently used are the 1000 Genomes Project (http://www.1000genomes.org), the NHLBI GO Exome Sequencing Project (ESP; http://evs.gs.washington.edu/EVS), the Exome Aggregation Consortium (ExAC; http://exac.broadinstitute.org), ClinVar database of genotype-phenotype associations (http://www.ncbi.nlm.nih.gov/clinvar) and the Human Gene Mutation Database (http://www.hgmd.cf.ac.uk). The consequence of variants in coding and splice regions are estimated using the following in silico variant prediction tools: SIFT (http://sift.jcvi.org), Polyphen (http://genetics.bwh.harvard.edu/pph2/), and Mutation Taster (http://www.mutationtaster.org).

Through our online ordering and statement reporting system, Nucleus, the customer can access specific details of the analysis of the patient. This includes coverage and quality specifications and other relevant information on the analysis. This represents our mission to build fully transparent diagnostics where the customer gains easy access to crucial details of the analysis process.

In addition to our cutting-edge patented sequencing technology and proprietary bioinformatics pipeline, we also provide the customers with the best-informed clinical report on the market. Clinical interpretation requires fundamental clinical and genetic understanding. At Blueprint Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical statement. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals, even without training in genetics.

Variants reported in the statement are always classified using the Blueprint Genetics Variant Classification Scheme modified from the ACMG guidelines (Richards et al. 2015), which has been developed by evaluating existing literature, databases and with thousands of clinical cases analyzed in our laboratory. Variant classification forms the corner stone of clinical interpretation and following patient management decisions. Our statement also includes allele frequencies in reference populations and in silico predictions. We also provide PubMed IDs to the articles or submission numbers to public databases that have been used in the interpretation of the detected variants. In our conclusion, we summarize all the existing information and provide our rationale for the classification of the variant.

A final component of the analysis is the Sanger confirmation of the variants classified as likely pathogenic or pathogenic. This does not only bring confidence to the results obtained by our NGS solution but establishes the mutation specific test for family members. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. Furthermore, in the case VUS we do not recommend use of genetic information in patient management or genetic counseling. For some cases Blueprint Genetics offers a special free of charge service to investigate the role of identified VUS.

We constantly follow genetic literature adapting new relevant information and findings to our diagnostics. Relevant novel discoveries can be rapidly translated and adopted into our diagnostics without delay. These processes ensure that our diagnostic panels and clinical statements remain the most up-to-date on the market.

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ICD & CPT codes

CPT codes

SEQ81442
DEL/DUP81479


ICD codes

Commonly used ICD-10 codes when ordering the Noonan Syndrome Panel

ICD-10Disease
Q87.1Noonan syndrome
Q87.8Costello syndrome
Q87.1LEOPARD syndrome
Q87.89Cardiofaciocutaneous syndrome

Accepted sample types

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 5μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.