Exome Complete: Noonan Syndrome and RASopathies

Clinical information

RASopathies are a group of genetic diseases caused by mutations in genes that encode proteins of the RAS/MAPK pathway. This group of pathologies, in addition to Noonan syndrome, also includes: neurofibromatosis type 1, Costello syndrome, Legius syndrome, Noonan-like disorder with loose anagen hair, Noonan syndrome with multiple lentigines (also known as LEOPARD syndrome), cardiofaciocutaneous syndrome, capillary-arteriovenous malformation syndrome, and hereditary gingival fibromatosis. Many of these genetic disorders share common clinical features such as abnormal facial features, short stature, varying degrees of cognitive impairment, cardiovascular anomalies, skeletal anomalies, and a predisposition to benign and malignant neoplasms. However, it has been reported that patients with RASopathies may also present with various coagulation and platelet-related disorders, leading to an increased risk of bleeding and hematomas.

Genetic testing for these pathologies provides crucial information for establishing an accurate diagnosis and precise classification. Additionally, it allows for genetic counselling, improvement of patient prognosis and management, and contributes to research and the development of therapies.

Study indication

Confirmation of clinical or analytical suspicion of the disease. This test is particularly indicated in cases of diseases with different candidate genes or with a phenotype lacking a clear genetic basis.

Diagnostic utility

Identification of genetic variants related to the clinical suspicion of a hereditary bleeding disorder.

Method

Whole Exome Sequencing (WES) for the identification of pathogenic variants. WES involves capturing fragmented DNA, derived from whole blood, through hybridisation of specific probes. This test allows for the sequencing of the entire human exome, comprising the protein-coding genomic regions (exons) and the flanking intronic regions of all genes. Subsequently, a virtual gene panel selected based on the study pathology (see gene panel section) is used to limit and focus the genetic analysis on those genes related to the patient's phenotype.

Especially in the study of complex phenotypes or in cases of difficult interpretation of identified variants, trio analysis (patient and two direct family members) is recommended. This strategy can simplify and reinforce the analyses, providing information on the inheritance of the disease.

Finally, the candidate mutation(s) detected by NGS are confirmed by traditional Sanger sequencing to reach an indisputable result. Specific primers may need to be designed to analyse the specific region where the variant is located.

If no candidate mutation potentially causing the disease is identified, complementary studies may be considered and discussed with the requesting medical team.

Gene panel

The genetic study of Noonan syndrome and other RASopathies analyses 27 genes. The genes in the panel have been carefully selected from scientific literature, mutation databases, and personal experience. It is important to note that this panel is periodically updated based on current knowledge, allowing for modifications in the selection of candidate genes and reanalysis of results. However, upon request of the responsible physician, other genes that are not included in the virtual panel and may be related to specific clinical features can be analysed. This is possible thanks to complete exome sequencing.

Limitations

This test does not detect:

• Complex structural variants such as inversions
• Genetic conversions
• Balanced translocations
• Repetitive nucleotide expansions
• Variants in deep intronic regions

This test may not reliably detect:

• Indels larger than 50 bp
• Single exon deletions or duplications
• Variants within pseudogene/duplicated segment regions

Reference values

Not applicable

Diagnostic algorithm

Not applicable

Turnaround time

8 weeks

Specimen information

Sample: Total blood

Tube: EDTA K3 tube 5-10 ml if it is a blood sample

Minimum required volume: 3 ml

Stability:

• At room temperature: 4 days
• In refrigeration: 10 days

Transport instructions: Preferably at room temperature

Reasons for rejection: Coagulated sample and/or incorrectly identified

Other accepted sample types:

• Purified DNA: minimum 300 ng (30 ng/µL). The recommended volume is a minimum of 60 µl
• Buccal mucosa: contact the laboratory to consult sample collection specifications

Administrative information

BST Code: LRD2829

Test Description: Whole Exome Study

Synonyms: Complete exome sequencing, WES, genetic-based disease molecular study.

Section: Congenital Coagulopathies

BST Rate: Check the updated rates by clicking here.

On the molecular study request form, the Other box must be checked, specify that the complete exome study is requested, and fill in (attach) the available phenotypic data.

References

• Longo JF, Carroll SL. The RASopathies: Biology, genetics and therapeutic options. Adv Cancer Res. 2022;153:305-341. doi: 10.1016/bs.acr.2021.07.007. Epub 2021 Aug 7. PMID: 35101235.
• Di Candia F, Marchetti V, Cirillo F, Di Minno A, Rosano C, Pagano S, Siano MA, Falco M, Assunto A, Boccia G, Magliacane G, Pinna V, De Luca A, Tartaglia M, Di Minno G, Strisciuglio P, Melis D. RASopathies and hemostatic abnormalities: key role of platelet dysfunction. Orphanet J Rare Dis. 2021 Dec 2;16(1):499. doi: 10.1186/s13023-021-02122-7. PMID: 34857025; PMCID: PMC8638204.
• Human Molecular Genetics, Volume 25, Issue R2, 1 October 2016, Pages R123-R132, https://doi.org/10.1093/hmg/ddw191
• Aoki Y, Niihori T, Inoue S, Matsubara Y. Recent advances in RASopathies. J Hum Genet. 2016 Jan;61(1):33-9. doi: 10.1038/jhg.2015.114. Epub 2015 Oct 8. PMID: 26446362.
• Protocolo Nextera Flex for Enrichment Reference Guide (1000000048041) de Illumina.

Base de dades de mutacions

• Human Gene Mutation Database: http://www.hgmd.cf.ac.uk
• Leiden Open Variation Database: https://databases.lovd.nl/shared/genes
• Genome Aggregation Database: https://gnomad.broadinstitute.org
• 1000 Genomes Database: https://www.internationalgenome.org