There are many advantages to using circulating cell-free DNA (ccfDNA) for identifying new variant biomarkers and for monitoring cancer patients after drug treatment. However, data analysis can be difficult. Our Advanced Testing Solution, featuring Biomedical Genomics Workbench and Ingenuity Variant Analysis, combines state-of the-art data analysis and data interpretation into a single offering for the most accurate detection of known pathogenic and actionable variants as well as new potential cancer drivers.
Liquid biopsies are increasingly common in translational research for identification of tumoral heterogeneity, tracking of the evolution of the tumor genome over time and the identification of tumor recurrence and upcoming resistance, which leads to a change in treatment. Clinicians are now using liquid biopsy — or targeted sequencing of circulating cell-free DNA — because it requires a small blood sample from the patient that can easily be retrieved, even where surgery is impossible (e.g. brain tumors). Typically, the benefits of liquid biopsy are offset by the inherent difficulties of data analysis, which requires the identification of variants at a level of 1% and lower. The challenge increases during data interpretation, which requires detection of potential cancer-driver variants.
As part of the Advanced Testing Solution, our new end-to-end workflow features Biomedical Genomics Workbench and Ingenuity Variant Analysis to combine analysis and interpretation of targeted ccfDNA data. It features optimal parameter settings across the complete workflow, to easily help identify and inspect known and new potential pathogenic and actionable cancer variants. Samples from several patients can also be compared afterwards in Ingenuity Variant Analysis to allow the identification of new upcoming pathogenic variants.
The detection of known pathogenic and actionable variants is key in ccfDNA applications. However, because of low coverage or allelic dropout (e.g. via insufficient amplification of the allele during enrichment or on the sequencing machine), those variants often get missed during variant calling.
To make sure that you achieve the highest sensitivity for known pathogenic and actionable variants, our one step data analysis and interpretation workflow takes the list of all variants you want to test for in the ccfDNA sample and reports back even the smallest amounts of sequencing reads supporting the variants.
Identification of new potential cancer driver variants is hard from cfDNA as variants are expected at a level of 1% and lower. Many variant calling pipelines are not able to call variants at this low level and when they can, they are not able to interpret unknown pathogenic cancer driver variants as such when they are not listed in databases like COSMIC and ClinVar.
Our solution allows the detection of variants at a level of 1% and lower and is able to identify new cancer-driver and pathogenic variants by using QIAGEN’s large Knowledgebase of literature curated content.