Circulating DNA as biomarker in breast cancer

Schwarzenbach, Heidi; Pantel, Klaus

doi:10.1186/s13058-015-0645-5

Breast Cancer Research

Table 1 Selected studies on circulating DNA in plasma and serum of patients with breast cancer

From: Circulating DNA as biomarker in breast cancer

Number of patients	Target of analysis	Methods	Clinical relevance	Reference
52 M0, 26 benign	Mitochondrial DNA quantification	qPCR	Detection of cancer	[12]
			Deregulated DNA levels
			Diagnosis
51 M0, 28 M1, 13 benign	Nucleosome quantification	ELISA	Monitoring for therapy response	[14]
51 M0, 28 M1, 13 benign	Nucleosome quantification	ELISA	Deregulated nucleosome levels	[14]
31 M0, 32 M1, 20 benign	DNA, nucleosome quantification	PicoGreen, ELISA	Detection of cancer progression	[13]
			Elevated nucleosome/DNA levels
			Diagnosis
64 M0	DNA quantification	qPCR	Monitoring for MRD	[22]
64 M0	DNA quantification	qPCR	Inverse relationship with DTC status	[22]
100 Stage I–IV	DNA quantification	Fluorometer	Detection of cancer	[19]
			Elevated DNA levels
			Diagnosis
61 M0, 33 benign	DNA quantification	qPCR	Screening for early detection and follow-up	[20]
			Deregulated DNA levels
			Diagnosis
83 M0	DNA integrity	qPCR	Detection of cancer progression	[24]
83 M0	DNA integrity	qPCR	Diagnosis	[24]
65 M0, 47 M1, 12 benign	DNA integrity	qPCR	Detection of cancer	[25]
65 M0, 47 M1, 12 benign	DNA integrity	qPCR	Diagnosis	[25]
82 M0, 201 M1	DNA integrity	qPCR	Detection of cancer	[26]
			Correlation with progression-free and overall survival
			Diagnosis and prognosis
65 M0	DNA integrity	qPCR	Monitoring for therapy response	[27]
25 M0	Mutations	PCR-SSCP and direct sequencing	Detection of cancer	[5]
25 M0	Mutations	PCR-SSCP and direct sequencing	Diagnosis	[5]
313 M0	Mutations	Digital PCR	Correlation with recurrence-free and overall survival	[33]
313 M0	Mutations	Digital PCR	Prognosis	[33]
17 M1	Mutations	Next-generation sequencing	Detection of metastasis	[34]
17 M1	Mutations	Next-generation sequencing	Diagnosis	[34]
33 M0	Mutations	Digital PCR	Detection of cancer	[35]
33 M0	Mutations	Digital PCR	Diagnosis	[35]
30 M1	Mutations	Targeted sequencing	Detection of metastasis	[36]
30 M1	Mutations	Targeted sequencing	Monitoring for therapy response	[36]
2 M0	Mutations	Whole exome sequencing	Detection of acquired drug resistance in advanced cancer	[37]
65 M0	SNP/CNV	Array	Detection of cancer during routine follow-up	[31]
			Correlation with MRD
			Diagnosis
58 M1	Copy number	Whole-genome sequencing	Dynamic variation of DNA range in metastasis	[38]
65 M0, 58 M1	Copy number	Digital PCR	Screening for the acquisition of HER2 amplification in metastasis	[29]
102 M0, 32 benign	LOH	PCR	Correlation with overall and disease-free survival	[21]
102 M0, 32 benign	LOH	PCR	Diagnosis and prognosis	[21]
62 M0	LOH, Methylation, Mutations	Microsatellite, PCR-SSCP, MSP	Detection of tumor progression	[3]
62 M0	LOH, Methylation, Mutations	Microsatellite, PCR-SSCP, MSP	Diagnosis	[3]
35 M0	Methylation	MSP	Detection of cancer	[4]
35 M0	Methylation	MSP	Diagnosis	[4]
428 M0	Methylation	MethyLight PCR	Correlation with overall and disease-free survival	[39]
428 M0	Methylation	MethyLight PCR	Therapy-independent prognosis	[39]
101 M0, 58 M1	Methylation	OS-MSP	Detection of metastasis	[40]
101 M0, 58 M1	Methylation	OS-MSP	Diagnosis	[40]
336 M0	Methylation	OS-MSP	Correlation with overall survival	[41]
336 M0	Methylation	OS-MSP	Prognosis	[41]
80 M1	Methylation	MSP	Correlation with CTC status	[42]
148 M0	Methylation	MethyLight PCR	Monitoring for therapy response	[43]
52 M0	Methylation	MSP	Monitoring for therapy response	[44]
110 M0	Methylation	MSP	Detection of estrogen receptor-negative status	[45]
120 M0, 100 benign	Methylation	MSP	Detection of cancer	[46]
120 M0, 100 benign	Methylation	MSP	Diagnosis	[46]
155 M0	Methylation	MSP	Detection of metastasis	[47]
			Correlation with overall and disease-free survival
			Diagnosis and prognosis
79 M0	Methylation	MSP	Correlation with CTC status	[48]
79 M0	Methylation	MSP	Diagnosis	[48]
100 M0	Methylation	MSP	Correlation with protein expression	[50]
100 M0	Methylation	MSP	Diagnosis	[50]
203 M0	Methylation	MSP	Association with DNA repair capacity	[51]
203 M0	Methylation	MSP	Diagnosis	[51]
304 M0 234 benign	Methylation	Pyrosequencing	Modest difference in methylation patterned	[52]

This table represents a selection of cell-free DNA analyses in plasma or serum of patients with breast cancer and is not meant to be comprehensive. It is based on our own view of studies that offer substantial clinical insight
CNV copy number variation, CTC circulating tumor cell, DTC disseminated tumor cell, ELISA enzyme-linked immunosorbent assay, HER2 human epidermal growth factor receptor 2, LOH loss of heterozygosity, M0 patients with primary breast cancer, M1 patients with metastatic breast cancer, MRD minimal residual disease, MSP methylation-specific polymerase chain reaction, OS-MSP one-step methylation-specific polymerase chain reaction, PCR-SSCP polymerase chain reaction-single strand conformation polymorphism, qPCR quantitative real-time polymerase chain reaction, SNP single-nucleotide polymorphism

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ISSN: 1465-542X

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