Exome-seq: #Genomics #Quality #Genetics

26 March 2018

So proud to announce that we qualified above the mean and got a green label in the external quality assessment of NextGen DNA Sequencing by European Molecular Genetics Quality Network (EMQN).

Even though IGAtech provides service to research only, last November we participated NGS vGermline scheme designed to test the whole analytical process of a molecular diagnostics laboratory in order to validate our exome-seq workflow.



Must admit that initially we aspired to participate to vSomatic scheme as well, but couldn’t agree on the panel to test, so we decided not to dissipate energy and withdraw from the somatic scheme. 

This is how it went: we received the DNA from EMQN and had 6 weeks to process the sample using our standard NGS procedure for germline testing, and deliver back FASTQ, BAM and VCF files that were subjected to the quality assessment.

Since we could submit up to 3 different sets of data, we decided to perform target enrichment using Agilent SureSelect All Exon (48Mb) and Focused Exome (16Mb). We prepared libraries, sequenced on HiSeq2500, 125bp paired-end mode and analyzed data with our pipeline for the detection of human germline sequence variants. The pipeline was previously validated on the well characterized reference material “genome in a bottle”. I promise I’ll write a separate post on the pipeline because it deserves it.

It took a little patience to get the EMQN feedback, but finally results were GREAT!

Congratulations to all the team and special thanks to Eleonora, Giorgia, Alessandro and Simone! Great job guys!!!