Process and Timeline

From blood to variants

When a blood sample is received, DNA is extracted, amplified and submitted for sequencing. The sequencing results are quality controlled, variants are identified and the common ones removed by filtering. Variants that pass the filtering process are presented to the Multi Disciplinary Team for assessment in the context of Human Phenotype Ontology (HPO) terms appended to the patient record.

A negative report will be issued if no ‘clearly pathogenic’ or ‘likely pathogenic’ variants are identified.  If ‘clearly pathogenic’ or ‘likely pathogenic’ variants are identified then confirmation by Sanger sequencing will follow and, if confirmed, a positive report will be issued. Reports are issued to the referring clinician.

The target turn-around time of 4 months is envisaged but positive results require additional laboratory time because a ‘variant specific’ assay needs to be ordered.

Scientific vigilance

The GRID platform will be regularly re-assessed and relevant new genes involved in primary immune disorders will be added.

‘Clearly pathogenic’ and ‘likely pathogenic’ variants will be submitted to publicly accessible databases linked to the Human Phenotype Ontology terms to improve the accuracy of future reporting if the same variant is observed in another genetically independent patient.

Quality metrics

The GRID panel can screen in parallel 279 genes known to be causative of primary immune disorders.

This gene panel covers for each of the 279 genes not only the coding regions (exons) but also the extra flanking regions upstream and downstream each gene and all the known damaging mutations associated to immune deficiencies.

Sequencing results from each patient undergo a series of quality checks (QCs) before the list of variants is generated. Some QCs include sample identity check and genomic ethnicity analysis.

This test has 100% sensitivity obtained using a wide a range of single nucleotide variants (SNVs), insertions and deletions (INDELs) and copy number variations (CNVs), including multi-exons or multi-gene deletions.

Further metrics:

  • Average depth across all panel: 200X fold.
  • Coverage of the 3Mb target region at 20X fold: 98.9%.
  • Coverage per gene will be provided in the patient report.
  • Minimum depth for reporting: 20X.