title: mFast-SeqS as a Monitoring and Pre-screening Tool for Tumor-Specific Aneuploidy in Plasma DNA.
abstract: 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. Comprehensive genome-wide analysis of tumor genomes is greatly facilitated when plasma DNA has increased amounts of ctDNA. In order to develop a fast and cost-effective pre-screening method for the identification of plasma samples suitable for further extensive qualitative analysis, we adapted the recently described FAST-SeqS method. 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. Moreover, since the genome-wide mFAST-SeqS z-scores correlate with the actual tumor content in plasma samples, changes in ctDNA levels associated with response to treatment can be easily monitored without prior knowledge of the genetic composition of tumor samples.
authors.affiliation: Institute of Human Genetics, Medical University of Graz, Graz, Austria.
authors.forename: Jelena
authors.initials: J
authors.lastname: Belic
authors.affiliation: Institute of Human Genetics, Medical University of Graz, Graz, Austria.
authors.forename: Marina
authors.initials: M
authors.lastname: Koch
authors.affiliation: Institute of Human Genetics, Medical University of Graz, Graz, Austria.
authors.forename: Peter
authors.initials: P
authors.lastname: Ulz
authors.affiliation: Institute of Human Genetics, Medical University of Graz, Graz, Austria.
authors.forename: Martina
authors.initials: M
authors.lastname: Auer
authors.affiliation: Institute of Molecular Biotechnology, Technical University of Graz, Graz, Austria.
authors.forename: Teresa
authors.initials: T
authors.lastname: Gerhalter
authors.affiliation: Institute of Human Genetics, Medical University of Graz, Graz, Austria.
authors.forename: Sumitra
authors.initials: S
authors.lastname: Mohan
authors.affiliation: Department of Urology, Medical University of Graz, Graz, Austria.
authors.forename: Katja
authors.initials: K
authors.lastname: Fischereder
authors.affiliation: Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria.
authors.forename: Edgar
authors.initials: E
authors.lastname: Petru
authors.affiliation: Division of Oncology, Medical University of Graz, Graz, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Bauernhofer
authors.affiliation: Institute of Human Genetics, Medical University of Graz, Graz, Austria.
authors.forename: Jochen B
authors.initials: JB
authors.lastname: Geigl
authors.affiliation: Institute of Human Genetics, Medical University of Graz, Graz, Austria.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Speicher
authors.affiliation: Institute of Human Genetics, Medical University of Graz, Graz, Austria. ellen.heitzer@medunigraz.at.
authors.forename: Ellen
authors.initials: E
authors.lastname: Heitzer
mesh_terms: D000782:Aneuploidy; D001943:Breast Neoplasms / Q000097:blood / Q000175:diagnosis / Q000235:genetics*; D004273:DNA, Neoplasm / Q000097:blood / Q000235:genetics*; D005260:Female; D055106:Genome-Wide Association Study; D019073:HT29 Cells; D006801:Humans; D016014:Linear Models; D061986:MCF-7 Cells; D008297:Male; D009154:Mutation; D011471:Prostatic Neoplasms / Q000097:blood / Q000175:diagnosis / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004273:DNA, Neoplasm
keywords: Cancer; Circulating tumor DNA (ctDNA); Copy number alterations (CNA); Liquid biopsy; Plasma-Seq; mFAST-SeqS