Information on the Ring Trial Next-generation sequencing
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
Raw data in .fastq format should be analyzed via the normal analysis pipeline of the respective laboratory. The goal is to review the analysis pipeline and the accuracy of variant detection. The variants found in the target regions, both single-nucleotide variants (SNVs) as well as small inserts and deletions (indels), should be submitted via www.bvdh-ringversuche.de in .vcf format. For this trial the correct detection of the variants is necessary, an interpretation of the variants is not required. The mapping of the reads should be performed against the reference genome hg19/GRCh37. The nomenclature of the variants should follow the rules of VCF version 4.2.
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
The evaluation takes into account individual detection limits of the laboratory, such as minimal coverage or maximum length of insertions and deletions.
For successful participation the laboratory will receive a certificate by BVDH, valid for two years. At present no RiLiBÄK certificate is obtainable.
Ring trial management
Dr. Sebastian Eck MVZ Martinsried GmbH Lochhamer Str. 29 82152 Martinsried
Tel. +49 89 895578-607 Fax
Dr. med. Caroline Lehmann bio.logis Zentrum für Humangenetik Weststraße 27 09221 Neukirchen