title: Rapid Identification of Plasma DNA Samples with Increased ctDNA Levels by a Modified FAST-SeqS Approach.
abstract: BACKGROUND
  Recent progress in the analysis of cell-free DNA fragments [cell-free circulating tumor DNA (ctDNA)] now allows monitoring of tumor genomes by noninvasive 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 prescreening 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.
  
  
  METHODS
  We adapted the recently described Fast Aneuploidy Screening Test-Sequencing System (FAST-SeqS) method, which was originally established as a simple, effective, noninvasive screening method for fetal aneuploidy from maternal blood.
  
  
  RESULTS
  We show that our modified FAST-SeqS method (mFAST-SeqS) can be used as a prescreening tool for an estimation of ctDNA percentage. With 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% mutant alleles. Plasma samples with an mFAST-SeqS z-score >5 showed results that were highly concordant with those of copy number profiles obtained from our previously described plasma-Seq approach.
  
  
  CONCLUSIONS
  Advantages of this approach include the speed and cost-effectiveness of the assay and that no prior knowledge about the genetic composition of tumor samples is necessary to identify plasma DNA samples with >10% ctDNA content.
authors.affiliation: Institute of Human Genetics.
authors.forename: Jelena
authors.initials: J
authors.lastname: Belic
authors.affiliation: Institute of Human Genetics.
authors.forename: Marina
authors.initials: M
authors.lastname: Koch
authors.affiliation: Institute of Human Genetics.
authors.forename: Peter
authors.initials: P
authors.lastname: Ulz
authors.affiliation: Institute of Human Genetics.
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.
authors.forename: Sumitra
authors.initials: S
authors.lastname: Mohan
authors.affiliation: Department of Urology.
authors.forename: Katja
authors.initials: K
authors.lastname: Fischereder
authors.affiliation: Department of Obstetrics and Gynecology, and.
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.
authors.forename: Jochen B
authors.initials: JB
authors.lastname: Geigl
authors.affiliation: Institute of Human Genetics.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Speicher
authors.affiliation: Institute of Human Genetics, ellen.heitzer@medunigraz.at.
authors.forename: Ellen
authors.initials: E
authors.lastname: Heitzer
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000782:Aneuploidy; D016022:Case-Control Studies; D004247:DNA / Q000097:blood*; D005260:Female; D005821:Genetic Techniques; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008297:Male; D008875:Middle Aged; D009369:Neoplasms / Q000097:blood* / Q000235:genetics / Q000473:pathology; D009360:Neoplastic Cells, Circulating; D011471:Prostatic Neoplasms / Q000097:blood / Q000235:genetics / Q000473:pathology; D012016:Reference Values; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA