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. 2017 Oct 23;17:697. doi: 10.1186/s12885-017-3693-7

Table 2.

Individually identified markers with detection ability in ctDNA

No Biomarker Acronym Cancer DNA alteration Assay type (qPCR, ddPCR, BEAMing, NGS, Other) Size Cases (controls) Plasma or Serum Refs
1 14–3-3 sigma 14–3-3 s Breast Methylation qPCR 106 (74) Serum [48]
2 absent in melanoma 1 AIM1; Beta/gamma crystallin domain-containing protein 1 Lung Methylation qPCR 76 (30) Serum [62]
3 ADAM: metallopeptidase with thrombospondin type 1 motif, 1 ADAMTS1 Pancreatic Methylation qPCR 42 Serum [63]
4 Adenomatous Polyposis Coli APC Lung Methylation qPCR 76 (30) Serum [62]
CRC Mutation qPCR 33 (10) Plasma [64]
Testicular Methylation qPCR 73 (35) Serum [47]
CRC Mutation qPCR 191 Plasma [65]
CRC Methylation qPCR 33 Serum [53]
CRC Mutation PCR 104 Serum [66]
Ovarian Methylation qPCR 87 (62) Serum [67]
Renal Methylation PCR 35 (54) Serum [68]
Breast Methylation qPCR 36 (30) Plasma [69]
Lung Methylation qPCR 110 (50) Plasma [70]
Renal Methylation qPCR 27 (15) Plasma [71]
CRC Methylation PCR 60 (100) Plasma [72]
5 ALU repeat Alu 115 bp Breast NA qPCR 39 (49) Plasma [22]
Alu 247 bp Pancreatic NA qPCR 73 (43) Plasma [73]
CRC NA qPCR 50 (35) Plasma [20]
Breast NA qPCR 293 (100) Plasma [19]
Thyroid NA qPCR 176 (19) Plasma [24]
CRC NA qPCR 104 (173) Serum [23]
6 basonuclin 1 BNC1 Pancreatic Methylation qPCR 42 Serum [63]
7 BIN1 BIN1 Breast Methylation qPCR 76 (30) Serum [62]
8 BLU BLU Lung Methylation qPCR 63 (36) Plasma [74]
9 BRAF BRAF (V600E) Melanoma Mutation qPCR 221 Both [17]
Lung Mutation NGS 68 (107) Plasma [75]
LCH Mutation qPCR 30 Plasma [76]
CRC Mutation qPCR 106 Plasma [77]
Thyroid Mutation qPCR 77 Plasma [78]
CRC Mutation BEAMing 503 Plasma [21]
CRC Mutation qPCR 191 Plasma [65]
10 BRCA1 BRCA1 Breast Methylation qPCR 89 Serum [79]
Breast Methylation qPCR 36 (30) Plasma [69]
Ovarian Methylation PCR 50 Serum [80]
Ovarian Methylation PCR 33 (33) Plasma [81]
11 CALCA CALCA Ovarian Methylation PCR 30 (30) Plasma [82]
12 CDH1 CDH1 Ovarian Methylation qPCR 87 (62) Serum [67]
13 CDH13 CDH13 Lung Methylation qPCR 63 (36) Plasma [74]
Lung Methylation qPCR 110 (50) Plasma [70]
14 CDO1 CDO1 Various Methylation qPCR 150 (60) Plasma [83]
15 CHD1 CHD1 Lung Methylation qPCR 76 (30) Serum [62]
16 CST6 CST6 Breast Methylation qPCR 196 (37) Plasma [84]
Breast Methylation qPCR 36 (30) Plasma [69]
17 CHRM2 CHRM2 Gastric Methylation qPCR 58 (30) Serum [85]
18 CYCD2 CYCD2 CRC Methylation qPCR 30 (30) Plasma [86]
19 DAPK1 DAPK1 HNSCC Methylation PCR 40 (41) Serum [87]
20 DCC DCC Lung Methylation qPCR 76 (30) Serum [62]
21 DCLK1 DCLK1 Lung Methylation qPCR 65 (95) Plasma [88]
Lung Methylation qPCR 32 (8) Plasma [89]
22 DKK3 DKK3 Breast Methylation qPCR 604 (59) Serum [90]
23 DLEC1 DLEC1 Lung Methylation qPCR 110 (50) Plasma [70]
HNSCC Methylation PCR 40 (41) Serum [87]
24 DNA (NOS) DNA Lung NA qPCR v Seq 30 (26) Plasma [91]
Various No NGS 77 (35) Plasma [45]
Various No NGS 640 Plasma [16]
Lung No qPCR 65 (44) Plasma [92]
Ovarian No bDNA 36 (41) Serum [93]
25 e-cadherin e-cadherin Colorectal Methylation PCR 60 (100) Plasma [72]
26 EGFR EGFR Lung Mutation NGS 68 (107) Plasma [75]
27 EP300 EP300 Ovarian Methylation PCR 30 (30) Plasma [82]
28 ERBB2 HER2 Lung Mutation NGS 68 (107) Plasma [75]
Breast Amplification qPCR 120 (98) Plasma [14]
Oesphageal Amplification qPCR 41 (34) Plasma [94]
29 ESR ESR Breast Methylation qPCR 106 (74) Serum [48]
Breast Methylation qPCR 36 (30) Plasma [69]
30 FAM5C FAM5C Gastric Methylation qPCR 58 (30) Serum [85]
31 FHIT FHIT Lung Methylation qPCR 63 (36) Plasma [74]
Renal Methylation qPCR 27 (15) Plasma [71]
32 Glyceraldehyde-3-phosphate dehydrogenase GAPDH Breast NA qPCR 200 (100) Serum [26]
Breast NA qPCR 33 (50) Serum [27]
Breast NA qPCR 27 (32) Serum [28]
Breast NA qPCR 33 (32) Serum [29]
33 GNA11 GNA11 Uveal Melanoma Mutation NGS 28 Plasma [34]
34 GNAQ GNAQ Uveal Melanoma Mutation NGS 28 Plasma [34]
35 GPC3 GPC3 Pancreatic Methylation qPCR 30 (30) Plasma [86]
36 GSTP1 GSTP1 Breast Methylation qPCR 89 Serum [79]
Breast Methylation qPCR 36 (30) Plasma [69]
Prostate Methylation PCR 12 (10) Plasma [95]
Prostate Methylation qPCR 31 (44) Plasma [96]
Testicular Methylation qPCR 73 (35) Serum [47]
Renal Methylation PCR 35 (54) Serum [68]
Prostate Methylation PCR 31 (34) Serum [97]
37 HIC1 HIC1 CRC Methylation PCR 30 (30) Plasma [98]
CRC Methylation qPCR 30 (30) Plasma [86]
38 HOXA7 HOXA7 Various Methylation qPCR 150 (60) Plasma [83]
39 HOXA9 HOXA9 Various Methylation qPCR 150 (60) Plasma [83]
40 HOXD13 HOXD13 Breast Methylation qPCR 253 (434) Serum [99]
41 IgH FR3A/VLJH Lymphoma Clonality NGS 75 Plasma [43]
42 ITIH5 Breast Methylation qPCR 604 (59) Serum [90]
43 INK4A INK4A HCC Methylation Seq 66 (43) Plasma [100]
44 KLK10 KLK10 Lung Methylation qPCR 110 (50) Plasma [70]
45 KRAS KRAS Lung Mutation NGS 68 (107) Plasma [75]
CRC Mutation qPCR 52 Plasma [101]
CRC Mutation qPCR 35 (135) Plasma [30]
CRC Mutation qPCR 229 (100) Plasma [102]
CRC Mutation qPCR 106 Plasma [77]
Lung Mutation qPCR 82 (11) Plasma [103]
CRC Mutation BEAMing 503 Plasma [21]
CRC Mutation qPCR 191 Plasma [65]
CRC Mutation PCR 104 Serum [66]
46 LINE1 Repeat LINE1 79 bp CRC NA qPCR 50 (35) Plasma [20]
LINE1 300 bp CRC NA qPCR 503 Plasma [21]
Breast NA qPCR 293 (100) Plasma [19]
47 MDG1 MDG1 CRC Methylation PCR 30 (30) Plasma [98]
48 Microsatellite alterations FHIT LoH Lung NA PCR 87 (14) Plasma [104]
FHIT LoH Lung NA PCR 32 (10) Serum [105]
LoH Oesophageal NA PCR 18 (22) Plasma [106]
LoH CRC NA qPCR 33 Serum [53]
3p LoH Lung NA qPCR 64 Plasma [107]
49 mitochondrial DNA mtDNA Breast NA qPCR 60 (51) Plasma [108]
50 MLH1 hMLH1 Breast Methylation qPCR 253 (434) Serum [99]
51 MYC MYC Neuroblastoma Amplification ddPCR 44 Plasma [42]
52 MYF3 MYF3 Pancreatic Methylation qPCR 30 (30) Plasma [86]
53 MYLK MYLK Gastric Methylation qPCR 58 (30) Serum [85]
54 O(6)-methyl-guanine-DNA methyltransferase MGMT Lung Methylation qPCR 76 Serum [62]
CRC Methylation qPCR 33 Serum [53]
Breast Methylation qPCR 89 Serum [79]
55 OPCML OPCML Ovarian Methylation qPCR 87 (62) Serum [67]
56 P14 ARF tumor suppressor protein gene P14 Testicular Methylation qPCR 73 (35) Serum [47]
Renal Methylation PCR 35 (54) Serum [68]
57 P16 cyclin-dependent kinase inhibitor 2A P16, CDKN2A Testicular Methylation qPCR 73 (35) Serum [47]
Renal Methylation PCR 35 (54) Serum [68]
Breast Methylation qPCR 36 (30) Plasma [69]
Lung Methylation qPCR 63 (36) Plasma [74]
Breast Methylation qPCR 253 (434) Serum [99]
HNSCC Methylation qPCR 40 (41) Serum [87]
58 P21 P21 Breast Methylation qPCR 36 (30) Plasma [69]
59 P53 Various Mutation qPCR 20 (16) Plasma [109]
Various NA qPCR 120 (120) Plasma [110]
CRC Mutation qPCR 191 Plasma [65]
CRC Mutation PCR 104 Serum [66]
SCLC Mutation qPCR 51 (123) Plasma [55]
60 PCDHGB7 PCDHGB7 Breast Methylation qPCR 253 (434) Serum [99]
61 Peptidylprolyl isomerase A cyclophilin A, gCYC, PPIA CRC NA qPCR 229 (100) Plasma [102]
62 PIK3CA PIK3CA Breast Mutation qPCR 76 Both [18]
Lung Mutation NGS 68 (107) Plasma [75]
CRC Mutation BEAMing 503 Plasma [21]
CRC Mutation qPCR 191 Plasma [65]
63 Prostaglandin-endoperoxid synthase 2 PTGS2 Renal Methylation PCR 35 (54) Serum [68]
Testicular Methylation qPCR 73 (35) Serum [47]
64 Protocadherin 10 PCDH10 CRC Methylation qPCR 67 Plasma [111]
65 Retinoid-acid-receptor-beta gene RARbeta2 Breast Methylation PCR 20 (25) Plasma [112]
CRC Methylation qPCR 33 Serum [53]
Renal Methylation PCR 35 (54) Serum [68]
Lung Methylation qPCR 63 (36) Plasma [74]
66 RASSF1A RASSF1A Breast Methylation PCR 93 (76) Plasma [113]
Breast Methylation PCR 20 (25) Plasma [112]
Breast Methylation qPCR 39 (49) Plasma [22]
Breast Methylation qPCR 604 (59) Serum [90]
Melanoma Methylation qPCR 84 (68) Plasma [114]
Lung Methylation qPCR 76 (30) Serum [62]
Testicular Methylation qPCR 73 (35) Serum [47]
CRC Methylation qPCR 33 Serum [53]
Ovarian Methylation qPCR 87 (62) Serum [67]
Renal Methylation PCR 35 (54) Serum [68]
Lung Methylation qPCR 63 (36) Plasma [74]
Lung Methylation qPCR 110 (50) Plasma [70]
HCC Methylation PCR 40 (20) Serum [115, 116]
HCC Methylation PCR 50 (50) Serum [117]
Renal Methylation PCR 27 (15) Plasma [71]
Breast Methylation qPCR 253 (434) Serum [99]
CRC Methylation PCR 30 (30) Plasma [98]
Renal Methylation qPCR 157 (43) Serum [118]
Ovarian Methylation PCR 50 Serum [80]
Ovarian Methylation PCR 30 (30) Plasma [82]
67 RUNX3 RUNX3 Ovarian Methylation PCR 87 (62) Serum [67]
68 Septin 9 Septin 9 CRC Methylation qPCR 97 (172) Plasma [119]
CRC Methylation qPCR 378 (285) Plasma [120]
CRC Methylation qPCR 60 (24) Plasma [121]
CRC Methylation qPCR 55 (1457) Plasma [58]
Lung Methylation qPCR 70 (100) Plasma [122]
CRC Methylation qPCR 135 (341) Plasma [123]
CRC Methylation qPCR 50 (94) Plasma [124]
CRC Methylation qPCR 44 (444) Plasma [59]
69 SFN SFN Breast Methylation qPCR 253 (434) Serum [99]
70 SFRP5 SFRP5 Ovarian Methylation qPCR 87 (62) Serum [67]
71 SHOX2 SHOX2 Lung Methylation qPCR 188 (155) Plasma [125]
Lung Methylation qPCR 118 (212 Plasma [126]
72 SOX17 SOX17 Breast Methylation qPCR 114 (60) Plasma [127]
Various Methylation qPCR 150(60) Plasma [83]
73 SLC26A4 SLC26A4 Thyroid Methylation qPCR 176 (19) Plasma [24]
74 SLC5A8 SLC5A8 SLC26A4 Thyroid Methylation qPCR 176 (19) Plasma [24]
75 SRBC SRBC Pancreatic Methylation qPCR 30 (30) Plasma [86]
76 TAC1 TAC1 Various Methylation qPCR 150 (60) Plasma [83]
77 human telomerase reverse transcriptase DNA hTERT CRC NA qPCR 35 (135) Plasma [30]
HCC NA qPCR 70 (30) Plasma [31]
HCC NA qPCR 60 (29) Plasma [32]
HNSCC NA qPCR 200 Plasma [33]
78 TFPI2 TFPI2 Ovarian Methylation PCR 87 (62) Serum [67]
79 THBD-M THBD-M CRC Methylation qPCR 107 (98) Plasma & Serum [128]
80 TIMP3 TIMP3 Renal Methylation PCR 35 (54) Serum [68]
Breast Methylation qPCR 36 (30) Plasma [69]
81 TMS TMS Pancreatic Methylation qPCR 30 (30) Plasma [86]
82 UCHL1 UCHL1 HNSCC Methylation PCR 40 (41) Serum [87]
83 Von Hippel Lindau gene VHL CRC Methylation qPCR 30 (30) Plasma [86]
Pancreatic Methylation qPCR 30 (30) Plasma [86]
Renal Methylation qPCR 157 (43) Serum [118]
84 ZFP42 ZFP42 Various Methylation qPCR 150 (60) Plasma [83]

CRC colorectal cancer, HNSCC head and neck squamous cell carcinoma, HCC hepatocellular carcinoma, LCH Langerhans cell histocytosis, SCLC small cell lung cancer