The utility of the targeted NGS gene panel in a clinical setting
This project applies the validated 200 gene NGS panel to the patient population with relevant hematological symptoms.

The study aims to recruit approximately 100 patients and is primarily targeted to Nordic populations but can be extended to Baltics and Europe.

Back­ground

Because of the heterogeneity of the genetic background, it takes time for many patients with hematological disorders to reach a specific diagnosis, even when the disease is caused by mutations in known disease genes. Next generation sequencing (NGS) techniques have resulted in rapid identification of genes involved in hematological disorders and provided new possibilities for diagnostic testing.

Aim

This project aims to implement and evaluate the clinical utility of the NGS cytopenia panel and make a reliable estimate of the prevalence of known gene defects in this patient cohort.

Patient recruitment

The project will be applying the validated NGS panel to a population with relevant phenotypes (1). Patient population will also include patients with unknown cause of primary cytopenia with splenomegaly and/or other hematological and/or immunological dysfunctions. The project is aiming at recruiting approximately 100 patients from the Nordic populations, but could be extended to Baltics and Europe. More information for collecting and shipping samples for the study can be found in the following attached word file. Please follow these instructions carefully.

Pro­ject plan

The analyses will be performed at the Institute for Molecular Medicine Finland, FIMM, University of Helsinki or in Helsinki University Hospital, Finland. The project will be utilizing the previously developed and validated NGS gene panel for 200 genes (detailed info see the word file attached) and previously developed analysis workflows (2). Target enrichment will be done in the batches of 8 samples utilizing the custom modified whole exome enrichment kit (TwistBiosciences) including the probes for the previously selected 200 genes. Sequencing will be done utilizing the NovaSeq 6000 sequencers (lllumina).

All identified pathological and likely pathological variants will be validated by capillary sequencing, and pathogenic and likely pathogenic GBA variants will be further validated by targeted capillary sequencing of a long PCR product enabling analysis of the functional GBA gene without the homologous pseudogene.

Results of the analysis will be reported back to the doctor sending the sample.

The project timeframe is from 1st December 2018 to 31st March 2021.

Ref­er­ences:

1. Motta et al. A multicentre observational study for early diagnosis of Gaucher disease in patients with Splenomegaly and/or Thrombocytopenia. Eur J Haematol. 2016 Apr;96(4):352-9. doi: 10.1111/ejh.12596.

2. Sulonen AM, Ellonen P, Almusa H, Lepisto M, Eldfors S, Hannula S, Miettinen T, Tyynismaa H, Salo P, Heckman C, Joensuu H, Raivio T, Suomalainen A, Saarela J. Comparison of solution based exome capture methods for next generation sequencing. Genome Biol. 2011 Sep 28;12(9):R94. PMID: 21955854