Table 1.

Summary of the features of currently available methods for CNV detection.

Platform	resolution	TAT(days)	Alterations	Analytical method	Advantage	Disadvantage	Ref
Karyotyping	5～10 Mb	2～21	CNV, SV	Qualitative	A gold standard	Highly dependent on the expertise of technicians and cytogeneticists	[59]
FISH	80–200 kb	3～5	CNV, SV	Qualitative	A gold standard that serves as a means of verification of known tumor sites	Expensive, customization limited by the types of genomic variation, depending on subjective assessment	[37,38]
CMA	20–100 kb	3～14	CNV, LOH	Quantitative	Cost-effective, significant advantages in detecting genomic variations greater than 100 Kb,	Limited by the types of genomic variation and the use of hybridization-based assays in repeat-rich and duplicated regions	[40,60,61]
CNV-seq	～100 kb	5～14	CNV, SV, LOH, SNV, Indel	Quantitative	High throughput, excellent compatibility, enabling the detection of large fragments of CNVs at a whole-genome scale.	Cannot detect ROH	[62]
WGS	≥1 bp	5～14	CNV, SV, LOH, SNV, Indel	Quantitative	High throughput, comprehensive evaluation of all tumor variation information	Expensive, long turnaround time, heavy computational requirements	[63]
WES	≥1 bp	5～14	CNV, SV, LOH, SNV, Indel	Quantitative	High throughput, cost-efficient, and analytic-effective manner	Cannot detect pathogenic CNVs located within non-coding regions associated with human disease	[64]
dPCR	≥1 bp	2～5	CNV, SV, LOH, SNV, Indel	Absolute quantification	Higher accuracy and reproducibility	Limited or biased by a probe design	[65,66]

Abbreviations: CNV, copy number variations; SV, structural variants; FISH, fluorescence in situ hybridization; CMA, CNV microarrays; LOH, loss of heterozygosity; ROH, runs of homozygosity; SNV, single nucleotide variants; WGS,whole genomic sequencing; WES, whole exome sequencing; dRCR, droplet PCR.