In WP2 we will develop a standardized format for data analysis pipelines at the laboratory level, based on bioinformatics expertise and hardware infrastructures to manage the massive sets of data produced by WGS, in collaboration with WP3 for the development of a data sharing infrastructure at the national level.
Best practice guidelines defining a standardized format for WGS clinical interpretation and reporting will be established on a national level including all Dutch clinical genetic centres (VKGL/VKGN), and will be in compliance with international guidelines such as ESHG/EuroGenTest guidelines for NGS-based diagnostics.32


  • 2.1: Harmonize ICT development at the individual laboratory level (M27)
  • 2.2: Harmonize reporting of WGS data (M27)

Description of Work

To harmonize infrastructure dealing with the analysis of large WGS datasets, we will develop standardized data analysis software pipelines, which will assess sequence variant identification and quantitative analysis for detection of copy number variation. In addition, we will develop standardized variant filter strategies as well as standards for diagnostic variant interpretation. The latter will include tools for clinical variant assessment, standardized (HPO-based) phenotyping, clinical validation of interpretation pipelines, knowledge resources and reporting; Related hereto, we will develop standards for diagnostic data sharing in collaboration with WP3.


  • D2.1 Best practice guidelines for WGS interpretation and reporting (M36)