Table 2.

Subjects 3–7—demographics and molecular analyses

Case No.Age/sexDiagnosisTissue NGSa,cDate of tissue acquisition for NGS and siteAscites/pleural effusion cfDNAbDate of effusate acquisition/cytology positivity/DNA yield
374/malePancreatic adenocarcinoma metastasticNot doneN/AAscitesJuly 2014
HMGA1 amplification (CNV = 3 copies)Cytology positive
CBL amplification (CNV = 3 copies)DNA Yield: 878.2 ng/30 ml
440/femaleColon cancer metastatic to lung, liverKRAS G12DJuly 2014Pleural effusionAugust 2014
APC K1165, I1580fs*69Pelvic massNo CNVs ≥3 copiesCytology negative
Multiple CNVs <3 were found (Supplementary Table S3)ctDNA plasma negative
CDKN1B truncation
FOXP1 A506TDNA Yield: 141.7 ng/30 ml
TP53 P190fs*57
562/femaleRenal cell carcinoma metastatic to pancreas, lungPTEN E114*April 2013AscitesJuly 2014
VHL P71fs*79KidneyNo CNVs ≥3 copiesCytology positive
APC truncation, intron 12Multiple CNVs <3 were found (Supplementary Table S3)DNA Yield: 251.4 ng/30 ml
MLL2 T1246M
658/femaleRectal cancer metastatic to liver, lungNot doneN/AAscitesAugust 2014
YWHAE amplification (CNV = 3 copies)Cytology: Not done
Multiple CNVs <3 were found (Supplementary Table S3)DNA Yield: 119.3 ng/30 ml
755/femaleCirrhosis (control patient)Not doneN/AAscitesAugust 2014
No CNVs ≥3 copiesCytology negative
DNA Yield: 250.7 ng/30 ml
  • aFoundationOne, Cambridge, Massachusetts.

  • bAffymetrix, Santa Clara, California. CNVs with high copy gains and losses in actionable genes are reported.

  • cAmplification infers ≥ 8 copies.

  • dGuardant cfDNA plasma assay.