New functionality available in the hereditary disorders workflows!

Monika Opalek, PhD

March 31, 2023

We have added new functionality for report generation among NGS panel, WES and WGS hereditary disorders workflows (fastq input file). The Manual Filtering option allows new report generation with genes of choice, without the need to rerun the analysis.

Each human genome differs on average in ~5 million positions from the reference. Therefore, the annotated variants need to be carefully filtered to provide relevant information, in particular, the variants which can be connected with the phenotype of interest. 

Within our workflows, we use multiple filters to eliminate irrelevant variants. First, we remove the low quality variants that are likely to be sequencing errors. Common variants (i.e. frequency above 5% in the human population) and those with low impact on gene product (i.e. synonymous mutations) are also excluded. The analysis is then narrowed down to genes specified by the user in the gene panel. 

The report shows a maximum of 50 variants. These include all variants classified as pathogenic or likely pathogenic in the ClinVar database, and variants that gained the highest pathogenicity score in the ACMG classification.

The new Manual Filtering function allows you to select the genes to be included in the final report from all those that have passed the filtering. You can now decide whether you want to limit the final report to a few of the most relevant variants, expand it, or add selected genes of interest. All without the need for additional analysis. The Manual Filtering is available for the following workflows:

  • NGS panel hereditary disorders ACMG report (input: fastq)
  • WES hereditary disorders ACMG report (input: fastq)
  • WGS hereditary disorders ACMG report (input: fastq)

Watch the video tutorial below and customise your report!

https://youtu.be/C8uOELEuXY0
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