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Table 1 Characteristics of Eligible Studies

From: Accuracy of analysis of cfDNA for detection of single nucleotide variants and copy number variants in breast cancer

Author Year Case Age (range) Stage Detection Method Data sources Sampling time Gene Mutation Type TP FP FN TN
gDNA (tissue) cfDNA (plasma)
Beaver JA 2014 29 60 (38–77) EBC dPCR dPCR Reported in text baseline PIK3CA SNV 13 0 1 15
Beaver JA (2) 2014 29 60 (38–77) EBC dPCR dPCR Reported in text post-surgery PIK3CA SNV 10 3 0 16
Dawson SJ 2013 30 66 (43–85) MBC TAm-Seq/PE-WGS dPCR,TAm-Seq Reported in text mid-therapy PIK3CA SNV 9 0 1 20
Dawson SJ(2) 2013 30 66 (43–85) MBC TAm-Seq/PE-WGS dPCR,TAm-Seq Reported in text mid-therapy TP53 SNV 15 0 1 14
Higgins MJ 2012 48 62(39–84) MBC BEAMing BEAMing Data-extrapolated unavailable PIK3CA SNV 14 8 6 20
Rothe F 2014 17 48(35–62) MBC Ion PGM Ion PGM Reported in text mid-therapy PIK3CA SNV 4 1 2 15
Rothe F (2) 2014 17 48(35–62) MBC Ion PGM Ion PGM Reported in text chemotherapy TP53 SNV 5 0 1 16
Spoerke J 2016 156 unavailable MBC dPCR dPCR Data-extrapolated baseline PIK3CA SNV 54 8 15 79
Higgins MJ 2011 51 unavailable MBC sequencing BEAMing Data-extrapolated unavailable PIK3CA SNV 14 12 0 25
Kodahl AR 2018 29 unavailable MBC dPCR dPCR Reported in text unavailable PIK3CA SNV 20 0 4 5
Garcia-Saenz JA 2015 37 unavailable ABC (IV 84%) dPCR dPCR Data-extrapolated unavailable PIK3CA (p.E545K) SNV 4 2 0 31
Garcia-Saenz JA (2) 2015 37 unavailable ABC (IV 84%) dPCR dPCR Data-extrapolated unavailable PIK3CA (p.H1047R) SNV 6 2 4 25
Board RE 2010 30 64 (39–88) MBC ARMS ARMS Data-extrapolated unavailable PIK3CA SNV 0 0 14 16
Board RE(2) 2010 43 59(43–79) MBC ARMS ARMS Data-extrapolated mid-therapy PIK3CA SNV 8 1 2 32
Oshiro C 2015 313 ≤50:121;
> 50:192 		EBC real-time PCR dPCR Reported in text preoperative PIK3CA SNV 85 0 25 203
Frenel,JS 2015 7 60 (29–78) MBC PGM PGM Reported in text mid-therapy PIK3CA SNV 2 0 0 5
Frenel,JS (2) 2015 7 61 (29–78) MBC PGM PGM Reported in text mid-therapy TP53 SNV 4 0 2 1
Liang,DH 2016 23 55.5(55.5 ± 13.1) ABC (IV/ high-risk III) NGS Digital Sequencing Reported in text mid-therapy PIK3CA SNV 4 1 2 16
Liang,DH (2) 2016 23 55.5(55.5 ± 13.1) ABC (IV /high-risk III) NGS Digital Sequencing Reported in text mid-therapy TP53 SNV 8 1 7 7
Schiavon G 2015 31 58(WT);69(MT) ABC dPCR dPCR Reported in text relapsed or progressed ESR1 SNV 3 0 1 27
Takeshita T 2017 35 56.4 (31–84) MBC dPCR dPCR Reported in text mid-therapy ESR1 SNV 1 4 5 25
Madic J 2015 31 unavailable MBC Hiseq and 454 Hiseq and 454 Reported in text baseline TP53 SNV 21 1 5 4
Nakauchi C 2016 17 57.7(32–80) MBC Ion-PGM Ion-PGM Reported in text recurrent and primary PIK3CA SNV 3 2 1 11
Nakauchi C (2) 2016 17 57.7(32–80) MBC Ion-PGM Ion-PGM Reported in text recurrent or primary TP53 SNV 4 1 2 10
Sefrioui D 2015 7 55(41–71) MBC dPCR dPCR Reported in text mid-therapy ESR1 SNV 4 0 3 14
Janku F 2015 107 58 (20–84) ABC PBDS, MPD, Ion Torrent BEAMing Reported in text mid-therapy PIK3CA SNV 12 8 2 85
Chung JH 2017 14 58 (32–85) ABC (IV 94%) HiSeq 2500/ 4000 HiSeq 2500 or 4000 Reported in text mid-therapy PIK3CA SNV 3 1 0 11
Chung JH(2) 2017 14 58 (32–85) ABC (IV 94%) HiSeq 2500/ 4000 HiSeq 2500 or 4000 Reported in text mid-therapy TP53 SNV 4 2 0 8
Chung JH(3) 2017 14 58 (32–85) ABC (IV 94%) HiSeq 2500/4000 HiSeq 2500 or 4000 Reported in text mid-therapy ESR1 SNV 4 3 1 9
Chung JH(4) 2017 14 58 (32–85) ABC (IV 94%) HiSeq 2500/ 4000 HiSeq 2500 or 4000 Reported in text mid-therapy CCND1 CNV 1 0 4 9
Chung JH(5) 2017 14 58 (32–85) ABC (IV 94%) HiSeq 2500/4000 HiSeq 2500 or 4000 Reported in text mid-therapy MYCN CNV 1 0 0 13
Liang DH(3) 2016 23 55.5(55.5 ± 13.1) ABC (IV/high -risk III) NGS Digital Sequencing Reported in text mid-therapy ERBB2 CNV 2 0 1 20
Liang DH(4) 2016 23 55.5(55.5 ± 13.2) ABC (IV/high -risk III) NGS Digital Sequencing Reported in text mid-therapy EGFR CNV 1 2 1 19
Page K. 2011 30 unavailable MBC Quantitative PCR Quantitative PCR Reported in text baseline HER2 CNV 5 0 8 5
  1. Abbreviation: gDNA genomic DNA, cfDNA cell free DNA, EBC early breast cancer, dPCR digital PCR, FFPE Formalin-fixed paraffin-embedded, MBC metastatic breast cancer, TAm-Seq tagged-amplicon deep sequencing, PE-WGS paired-end whole-genome sequencing, BEAMing beads, emulsion, amplification, magnetics, ARMS Amplification Refractory Mutation Testing System, WT wild type, MT mutation type, ABC advanced breast cancer, NGS Next generation sequence, PBDS PCR-based DNA sequencing
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