Table 2.

Advantages and disadvantages of various diagnostic technologies for the diagnostic assessment of HD ALL.

Method	Advantages	Disadvantages
DNA index measurement	• Fast, cheap, and easy • Can to a certain extent identify multiple abnormal clones to a certain extent	• Provides only a rough estimate of the DNA content but no information about chromosomal composition of the respective clones • Cannot differentiate between classical and nonclassical HD forms
Cytogenetics	• Provides information about types and numbers of chromosomes	• Relies on the availability of blast cell metaphases • Information derives only from single dividing cells
Fluorescence in situ hybridization (FISH)	• Allows interphase screening • Provides information about composition and size of cell clones	• Utilized to screen for selected relevant chromosomes only • Cannot elucidate the chromosomal composition of the entire genome
CGH/SNP array analysis	• Provides a representative genome-wide profile of all large- and small-scale copy number alterations as well as their allelic pattern	• Cannot distinguish between monoclonal and/or bi-clonal forms of hyperhaploid and nonclassical HD forms
Whole-exome sequencing (WES)	• Provides exome-wide information about copy number as well as sequence alterations	• Primarily a research tool • Mutations hardly diagnostically or therapeutically relevant in HD
Whole-genome sequencing (WGS)	• Provides genome-wide information about all relevant copy number, structural, and sequence alterations simultaneously • Could replace all other methods, in principle	• Cannot distinguish between monoclonal and/or bi-clonal forms of hyperhaploid and nonclassical HD forms • Not yet implemented for routine diagnostics
Gene expression (GEP) analysis	• Reflects chromosome copy number changes • May be utilized for mutation calling • Can identify fusion genes • Uncovers the close relationship between mono- and/or bi-clonal nonclassical HD and hyperhaploid forms	• Diagnostically not relevant • Primarily a research tool
Optical genome mapping	• Provides genome-wide information about copy number and structural abnormalities • Reveals allele-specific patterns • May eventually replace karyotype, FISH, and array analyses	• Research tool only • Not yet implemented in the diagnostic work-up • Cannot detect sequence variants