QIAGEN Competes in AMP-Led Project Comparing Vendors’ Bioinformatics Pipelines to Analyze Cancer Panel Data


QIAGEN Digital Insights

QIAGEN Competes in AMP-Led Project Comparing Vendors’ Bioinformatics Pipelines to Analyze Cancer Panel Data

The recent AMP Europe 2018 conference was a wonderful chance to catch up with old friends and establish new relationships—our team provided demos at the booth and we had a wonderful symposium. We also participated in a fun challenge, known as “Innovation Lab: Battle of the Bioinformatics Pipeline.” According to this story by Julia Karow in GenomeWeb, the aim of the exercise was “to provide commercial vendors of NGS analysis and interpretation pipelines with sequencing data from real patient samples, generated by a routine molecular diagnostics laboratory, and to see how similar or different their results would be.”

QIAGEN was one of three vendors who participated, using Biomedical Genomics Workbench data analysis platform and Qiagen Clinical Insight (QCI) Interpret software to identify mutations in tumor sequence data, down to a level of 5 percent. Participants were instructed to name and annotate the variants, state their allele frequencies and interpret them according to a five-tier classification system ranging from “benign” to “clinically significant.”

The session was organized and led by Winand Dinjens, head of molecular diagnostics in the Department of Pathology at Erasmus University Medical Center (Erasmus MC) Rotterdam, whose lab also analyzed the data, to establish a benchmark against which the other outcomes were compared. During the session, all three vendors presented their results and compared them to those of Erasmus MC. Though there was plenty of overlap amongst the three vendors’ results, none were identical. The session concluded with all participants agreeing that context (of a patient’s disease) is important in variant interpretation, and that laboratories must define their own thoughtful criteria to effectively frame a clinical report.

We are honored to have been included in the #AMPEurope2018 challenge, and that Biomedical Genomics Workbench and QCI were part of the process. We are also very proud of our team’s positive results—this is our third such challenge,  1) ECP 2017 and 2) AG MolPath, and we welcome the chance to compete again!