Exome Complete: Congenital Platelet Disorders

Clinical information

Congenital Platelet Disorders (CPDs) are a heterogeneous group of rare diseases caused by mutations in genes related to the formation and/or function of platelets. The most common CPDs include Bernard-Soulier Syndrome, caused by mutations in GP1BA, GP1BB, and GP9, and Glanzmann Thrombasthenia, caused by mutations in ITGA2B and ITGB3. Currently, around 60 types of CPDs have been recognized, caused by molecular defects in more than 70 different genes. CPDs disrupt primary hemostasis and are associated with increased bleeding tendency. They can present with a wide range of bleeding symptoms, with mucocutaneous bleeding such as epistaxis or menorrhagia being the most common. Additionally, some CPDs may be associated with specific syndromic features, such as hearing loss, renal disease, or albinism, while others may predispose to the development of malignant tumours.

Genetic testing for these disorders provides crucial information for establishing a precise diagnosis and accurate classification. Additionally, it allows for genetic counselling, improves the prognosis and management of these patients, and contributes to research and therapy development.

Indication for Study

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

Diagnostic Utility

Identifying genetic variants associated with 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 sequencing of the entire human exome, which comprises the protein-coding genomic regions (exons) and flanking intronic regions of all genes. Subsequently, a virtual gene panel selected based on the study's pathology (see gene panel section) is used to limit and focus the genetic analysis on genes related to the patient's phenotype.

Especially in the study of complex phenotypes or in cases with difficulty evaluating identified variants, trio analysis (patient and two direct relatives) is recommended. This strategy can simplify and strengthen analyses, providing information on disease inheritance.

Lastly, NGS-detected candidate mutation(s) are confirmed by traditional Sanger sequencing to reach an unequivocal result. Specific primer design may be necessary to analyse the exact region where the variant is located.

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

Gene Panel

CPDs genetic study analyses 87 genes. The genes in the panel have been carefully selected from scientific literature, mutation databases, and our own experience. It is important to note that this panel is periodically updated based on current knowledge, allowing for modification of candidate gene selection and result reanalysis. However, upon request from the responsible physician, analysis of other genes not included in the virtual panel but related to specific clinical features can be performed. This is possible due to complete exome sequencing.

Limitations

This test does not detect:

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

This test may not reliably detect:

• Indels exceeding 50 bp
• Single-exon deletions or duplications
• Variants within pseudogene/duplicated segments

Reference Values

N/A

Diagnostic Algorithm

N/A

Turnaround Time

8 weeks

Specimen information

Sample: Whole blood

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

Minimum essential volume: 3 ml

Stability:

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

Transport instructions: Preferably at room temperature

Reason for rejection: Coagulated or incorrectly identified sample

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 for sample collection specifications

Administrative information

BST Code: LRD2829

Test Description: Whole Exome Study

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

Section: Congenital Coagulopathies

BST Fee: Check the updated fees by clicking here.

On the molecular study request form, the Other box must be ticked, specifying the whole exome study and providing (attaching) available phenotypic data.

References

• Palma-Barqueros V, Revilla N, Sánchez A, Zamora Cánovas A, Rodriguez-Alén A, Marín-Quílez A, González-Porras JR, Vicente V, Lozano ML, Bastida JM, Rivera J. Inherited Platelet Disorders: An Updated Overview. Int J Mol Sci. 2021 Apr 26;22(9):4521. doi: 10.3390/ijms22094521. PMID: 33926054; PMCID: PMC8123627.
• 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