Information on the EQA test NGS: Bioinformatics

The interlaboratory test NGS Data Analysis aims to evaluate the bioinformatics analysis pipeline of the participating laboratories.

Once per year.

The participants receive raw NGS data in the .fastq format to perform the analysis with. The detected variants can be submitted using the standard variant call format (.vcf). The NGS raw data were generated from Whole Exome sequencing. The source material is available for download and contains:

• 4 .fastq files with the sequenced reads
• 1 .bed file with the target regions

The necessary NGS data files in .fastq format are available for download on the BVDH website. The reads stem from a whole exome sequencing experiment. During registration, the participant has to select with which version of the human reference genome (with the respective patch version) the test scheme will be processed, hg19 or hg38. The regions for analysis are provided in a .bed file, all analysis must be restricted to the regions specified in the file, all regions in the file have to be analyzed. The reads need to be analyzed using the standard laboratory pipeline. Detected variants (both single nucleotide variants SNVs and small insertions and deletions) in the target regions need to be reported in a .vcf file that may be uploaded to the BVDH website. For this scheme variants need to be correctly identified, an interpretation of results is not necessary. For the correct nomenclature the rules of the VCF format 4.2 or higher need to be employed.

We will check the variants by comparison with the real variants of the reference material. The VCF uploaded by the participants via www.bvdh-ringversuche.de is evaluated according to the following criteria:

• Number of correctly detected SNVs
• Number of correctly detected insertions
• Number of correctly detected deletions
• Number of false-positive variants detected
• Correct nomenclature of variants according to VCF version 4.2

During analysis, if the employed analysis pipeline uses a minimal coverage to call variants, the participants may specify the cutoff and the value will then be taken in account during evaluation.

For successful participation the laboratory will receive a certificate by BVDH, valid for two years. At present no RiLiBÄK certificate is obtainable.

Julian Schulz M.Sc.
MVZ Martinsried GmbH
Lochhamer Str. 29
82152 Martinsried