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Copyright ©The Author(s) 2020.
World J Clin Oncol. Nov 24, 2020; 11(11): 890-897
Published online Nov 24, 2020. doi: 10.5306/wjco.v11.i11.890
Table 1 Genome characterization technologies
TechniqueApplicationAdvantages/remarksDisadvantagesRef.
GTG bandingChromosomal abnormalities, such as translocations, genomic, autosomal trisomies, polyploidy, sex chromosome monosomy and double trisomiesCan only detect rearrangements that involve > 3 Mb of DNA; -low Sensitivity-Limited to mitotically active cells; -Difficulties in decoding highly rearranged chromosomes[20,21]
FISHGene fusions, aneuploidy, loss of a chromosomal region or a whole chromosomeCan identify genetic changes that are too small. High sensitivity and specificityHeavily influenced by cellular phenomena and hybridization artifacts[22,23]
aCGHDeletions, amplifications, breakpoints, and ploidy abnormalitiesDetect DNA copy changes simultaneously at multiple loci in a genome- sensitivity was estimated to be 96.7% - specificity was 99.1%Inappropriate for the detection of mosaicism, balanced chromosomal translocations, and inversions[24]
Sanger seqSingle nucleotide change, small indels (insertions or deletions)Gold standard platform widely used for SNV detection; --High sensitivity and SpecificityUnable to detect mosaic alleles below a threshold of 15%–20% (Limit of detection 15%–20%); Low discovery power[25]
NGSWhole genome sequencing, de novo assembly sequencing, resequencing, and transcriptome sequencing at the DNA or RNA levelHigher sequencing depth enables higher sensitivity (down to 1%); More data produced with the same amount of input DNA; -High sensitivity and SpecificityExpensive method; High rate of sequencing errors[26,27]
Bisulfite conversionDNA methylationResolution at DNA level. Effective method providing information about cytosine methylationBeginning with high quality DNA is critical, Impossible to distinguish methylated and hemimethylated cytosine[28]
MDRERestrict CpG methylation analysis only to methylated regions of genomeEasy to use availability and assortment of endonucleasesDNA methylation assay is circumscribed by the use of a particular enzyme[29]
ChIP-seq-Analyze protein interactions with DNA; -ChIP-seq combines chromatin immunoprecipitation (ChIP) with NGS for identification of binding sites of DNA-binding proteinsFast well studied. Compatible with array-or sequencing-based analysis, i.e. it is possible to perform genome-wide analysisRelies on antibody specificity Microarray assay relies on particular probes[30]
Table 2 Circulating tumor cell isolation techniques
TechnologyPlatformMethodsRef.
Physical propertiesDensity gradient, physical filter, dielectric, photoacoustic microfluidicSize, density[35,36]
High-throughput imagingImaging cytometryScanning of cells on the slide[36]
Leukocyte depletionBatch cell lysis; microfluidic CTC-iChip; immunomagnetic separationNegative depletion of leukocytes[37]
Antibody captureCell search; magsweeper; microfluidic CTC-chipSelection for tumor-specific markers[37]
Functional characteristicsEpispot assay, invasion assayProtein secretion, cell migration[38]
NanotechnologyImmunomagnetic nanobeads, nano-structures substrates in microchipNanomaterials able to increase interactions with CTCs and specific antibodies, and to enable their electrical conductivity[39]