Updates on “Cancer Genomics and Epigenomics”

Table 1 Genome characterization technologies

Technique	Application	Advantages/remarks	Disadvantages	Ref.
GTG banding	Chromosomal abnormalities, such as translocations, genomic, autosomal trisomies, polyploidy, sex chromosome monosomy and double trisomies	Can only detect rearrangements that involve > 3 Mb of DNA; -low Sensitivity	-Limited to mitotically active cells; -Difficulties in decoding highly rearranged chromosomes	[20,21]
FISH	Gene fusions, aneuploidy, loss of a chromosomal region or a whole chromosome	Can identify genetic changes that are too small. High sensitivity and specificity	Heavily influenced by cellular phenomena and hybridization artifacts	[22,23]
aCGH	Deletions, amplifications, breakpoints, and ploidy abnormalities	Detect 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 seq	Single nucleotide change, small indels (insertions or deletions)	Gold standard platform widely used for SNV detection; --High sensitivity and Specificity	Unable to detect mosaic alleles below a threshold of 15%–20% (Limit of detection 15%–20%); Low discovery power	[25]
NGS	Whole genome sequencing, de novo assembly sequencing, resequencing, and transcriptome sequencing at the DNA or RNA level	Higher sequencing depth enables higher sensitivity (down to 1%); More data produced with the same amount of input DNA; -High sensitivity and Specificity	Expensive method; High rate of sequencing errors	[26,27]
Bisulfite conversion	DNA methylation	Resolution at DNA level. Effective method providing information about cytosine methylation	Beginning with high quality DNA is critical, Impossible to distinguish methylated and hemimethylated cytosine	[28]
MDRE	Restrict CpG methylation analysis only to methylated regions of genome	Easy to use availability and assortment of endonucleases	DNA 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 proteins	Fast well studied. Compatible with array-or sequencing-based analysis, i.e. it is possible to perform genome-wide analysis	Relies on antibody specificity Microarray assay relies on particular probes	[30]

FISH: Fluorescence in situ hybridization; aCGH: Array comparative genomic hybridization; NGS: Next generation sequencing; MDRE: Methylation-dependent restriction enzyme; ChIP-seq: Chromatin immunoprecipitation sequencing; Sanger seq: Sanger sequencing; SNV: Single nucleotide variation.