Table 1.

Biomarkers and Available Technologies for Future Ductal Carcinoma in Situ Studies

Category	Available technologies	Assayed biomarkers	Advantages	Disadvantages
DNA	Sanger sequencing	Mutations	Low cost, easy setup and analysis	Low throughput, primer dependent, large input requirement, high error rate
	Next-generation sequencing	Mutations, copy number alterations, rearrangements, epigenetics	High resolution, sensitive	High cost, difficult analysis pipeline
	Single-cell sequencing	Mutations, copy number alterations, rearrangements, epigenetics	Single-cell resolution, can assess heterogeneity	High cost, difficult setup and analysis pipeline
	PCR	Mutations, rearrangements	Low-input material requirement, sensitive	Low throughput, primer dependent, high error rate
	Microarray (SNP, CGH)	Mutations, copy number alterations, rearrangements	High throughput	Restricted to predetermined alterations, prone to batch effects
	Karyotyping	Rearrangements	Low cost	Time-consuming, difficult setup, low resolution
	FISH	Copy number alterations, rearrangements	Quantitative, specific	Probe dependent, sensitivity
RNA	RT-PCR	mRNA, miRNA, lncRNA	Easy setup and analysis, low-input material requirement, specific	Low throughput, primer dependent
	NanoString	mRNA, miRNA (DNA and protein assays also available)	Reproducibility, sensitivity	Proprietary technology, high cost
	Microarray	mRNA, miRNA, lncRNA	High throughput	Restricted to predetermined alterations
	Next-generation sequencing	mRNA, miRNA, lncRNA	High resolution, sensitive	High cost, difficult analysis pipeline
	Single-cell RNA sequencing	mRNA, miRNA, lncRNA	Single-cell resolution, can assess heterogeneity	High cost, difficult setup and analysis pipeline
Protein	Immunohistochemistry	Protein expression, posttranslational modifications, metabolites	Low cost, easy setup and analysis, preserves histologic information	Tissue-preparation variability, antibody dependent, semiquantitative
	ELISA	Protein expression, posttranslational modifications, metabolites	Easy setup and analysis, low cost	Antibody dependent
	Western blot	Protein expression, posttranslational modifications, metabolites	Easy setup and analysis, low cost	Antibody dependent, semiquantitative
	Flow cytometry	Protein expression, posttranslational modifications, metabolites	Live cell setting, single-cell resolution	High cost, difficult setup and analysis pipeline, cell surface proteins only
	Mass spectrometry	Protein expression, posttranslational modifications, metabolites	Antibody independent, sensitive, specific	High cost, difficult setup and analysis pipeline

CGH, comparative genomic hybridization; ELISA, enzyme-linked immunosorbent assay; FISH, fluorescence in situ hybridization; lncRNA, long noncoding RNA; SNP, single-nucleotide polymorphism.