Information on the Ring Trial Next-generation sequencing

Aim

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

Performance interval

Once per year.

Procedure

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

Method

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.

Criteria

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.

Certificate

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
sebastian.eck@medizinische-genetik.de

Dr. med. Caroline Lehmann
bio.logis Zentrum für Humangenetik
Weststraße 27
09221 Neukirchen
Tel. 0174 7863342
Fax
caroline.lehmann@genetik.diagnosticum.eu