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Recent progress in the analysis of cell-free DNA fragments (cell-free circulating tumor DNA, ctDNA) now allows monitoring of tumor genomes by non-invasive means. However, previous studies with plasma DNA from patients with cancer demonstrated highly variable allele frequencies of ctDNA. The comprehensive analysis of tumor genomes is greatly facilitated when plasma DNA has increased amounts of ctDNA. Therefore, a fast and cost-effective pre-screening method to identify such plasma samples without previous knowledge about alterations in the respective tumor genome could assist in the selection of samples suitable for further extensive qualitative analysis. To address this, we adapted the recently described FAST-SeqS method, which was originally established as a simple and effective, non-invasive screening method for fetal aneuploidy from maternal blood. We show that our modified FAST-SeqS method (mFAST-SeqS) can be used as a pre-screening tool for an estimation of the ctDNA percentage. Using a combined evaluation of genome-wide and chromosome-arm specific z-scores from dilution series with cell line DNA and by comparisons of plasma-Seq profiles with data from mFAST-SeqS, we established a detection limit of 10% or more of mutant alleles. Plasma samples with an mFAST-SeqS z-score above 5 showed highly concordant results compared to copy number profiles obtained from our previously described plasma-Seq approach.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001001313 Illumina MiSeq 10
EGAD00001001314 Illumina MiSeq 125
Publications Citations
Rapid Identification of Plasma DNA Samples with Increased ctDNA Levels by a Modified FAST-SeqS Approach.
Clin Chem 61: 2015 838-849
Comprehensive characterization of cell-free tumor DNA in plasma and urine of patients with renal tumors.
Genome Med 12: 2020 23