Table 2.

Genetic Test Methods

Laboratory Test	Description of Methods
Karyotype:	Whole chromosomes from cells in the metaphase stage of cell division are stained and visualized by microscopy.
Fluorescence in situ hybridization (FISH):	Whole chromosomes (metaphase from dividing cells or interphase from non-dividing cells) are hybridized to complementary probes and visualized on a fluorescence microscope.
Polymerase chain reaction (PCR):	DNA is isolated and a specific segment of it is copied a billion-fold for ease of detection and for further analysis. A variant method called reverse transcription PCR (rtPCR) converts RNA into complementary DNA (cDNA) prior to PCR amplification. A variant called quantitative PCR (Q-PCR) can measure the level of target DNA, usually by monitoring product accumulation during each cycle using one or more fluorescent internal probes, and then comparing the time course of product accumulation to a series of standards of known concentration. A fluorescent internal probe combined with “melt curve analysis” detects sequence variants within the amplicon.
DNA sequencing:	The nucleotide sequence is determined by replicating one of the DNA strands and monitoring the order in which labeled nucleotides are added.
Comparative genomic hybridization array (CGH array):	Patient DNA is hybridized to hundreds or thousands of probes arrayed on a solid surface, and gene dosage is determined for each locus on the array, thus identifying deletions, duplications, and gene amplifications. Single nucleotide polymorphism (SNP) arrays can additionally detect copy-neutral loss of heterozygosity (uniparental disomy).
Gene expression array:	Patient RNA is typically amplified and labeled, then mixed with control RNA labeled with a different fluorochrome and hybridized to hundreds or even hundreds of thousands of probes (eg, 60-mers) arrayed on a solid surface. Scans of each spot followed by data analysis permit evaluation of the gene expression profile in the tissue, which can be matched to the pattern of normal or diseased tissues for purposes of diagnosis, or to the pattern of clinical outcome variants to predict response to therapy.