Tag Archives: Andreas Scherer

NGS-based Clinical Testing (Part VI)

reporting incidental genetic findings

With a properly defined wet-lab and bioinformatics process, we are able to zero in on clinically relevant variants. How does a lab report on the outcome of their analysis? We find that most laboratories conduct their variant classification based on the guidelines formulated by the American College of Medical Genetics (ACMG) for inherited diseases. The ACMG guidelines for variant classification… Read more »

NGS-Based Clinical Testing (Part V)

Quality Managment

Quality Management in Clinical Testing Any validated bioinformatics pipeline must be continuously monitored. Quality management in clinical testing labs ensures that any divergence from predefined quality metrics during the analysis of clinical samples is investigated. For example: There is an insufficient number of sequence reads that passed the predefined base quality score threshold The number of variants identified in a… Read more »

NGS-based Clinical Testing (Part IV)

clinical testing

After the Wet Lab process has been completed, the bioinformatics analysis of the sequencing data work begins. The next three blogs will focus on three aspects of this process. The building blocks of a bioinformatics pipeline, documentation and validation (today’s topic) Quality Management (Part V) Clinical Reporting (Part VI) The Building Blocks of an NGS Pipeline The bioinformatics process to analyze… Read more »

NGS-based Clinical Testing (Part III)

DNA sequencing

Getting the NGS wet bench process right is not a small undertaking. Targeted NGS assays such as multigene panels or exome sequencing allow for the targeted analysis of genomic regions that are of particular interest. For every sample type, e.g. blood, formalin-fixed paraffin-embedded specimens, saliva etc, there must be a detailed protocol in place outlining how each sample type is going… Read more »

NGS-based Clinical Testing (Part II)

ngs-based clinical testing

We have come a long way since next-generation sequencing (NGS) evolved as a set of technologies in the 1970s. The higher throughput and rapid reduction of costs associated with NGS have lead to the accelerated adoption of clinical testing that we are experiencing today. Currently, it is applied to analyze inherited diseases, tumors, hematologic malignancies and infectious diseases. It is also… Read more »