63automated enzymatic reactions that produce genotype specifi c diagnostic products.
Very small quantities of these products, typically 5–10 nanoliter, are transferred
with the SpectroJET nanoliter dispensing system onto the high density SpectroCHIP
array for subsequent automated analysis with the SpectroREADER mass spectrom-
eter. Because DNA is composed of four bases (A, T, G and C) and each has a unique
mass, the mass of the resultant diagnostic product can be used to unambiguously
identify the sample’s genotype. The SpectroTYPER software then calculates,
records, compares and reports the genotypes at the rate of 3 s/per sample.
There is a proof of concept of the use of pooled DNA as a means of effi ciently
screening SNPs and prioritizing them for further study. This approach reduces the
fi nal number of SNPs that undergo full, sample-by-sample genotyping as well as
the quantity of DNA used overall. Genotyping of the individual samples shows that
the average margin of error in frequency estimate is ~4 % when pools are used.
These fi ndings clearly demonstrate the potential of pooling techniques and their
associated technologies as an initial screen in the search for genetic associations.
BeadArray Technology
BeadArray technology (Illumina) combines fi ber optic bundles and specially pre-
pared beads that self-assemble into an array. Each fi ber optic bundle contains
thousands to millions of individual fi bers depending on the diameter of the bundle.
Table 2.3 Technologies for SNP analysis
Digital genetic analysis (DGA)
DNA chips and microarrays
DNA sequencing
Electrochemical DNA detection
Hybridization assays
Allele-specifi c oligomer hybridization
Array hybridization assays, e.g., MASDA (mutiplexed allele-specifi c diagnostic assay)
Hybridization with PNA probes
Mass spectrometry (MS)
Matrix assisted laser desorption ionization time of fl ight MS (MALDI-TOF MS)
Competitive oligonucleotide single base extension (COSBE)
Nanotechnology-based methods
PCR-based methods
PCR-CTPP (confronting two-pair primers)
Degenerate oligonucleotide primed (DOP)-PCR
TaqMan real-time PCR
Smart amplifi cation process version 2
Peptide nucelic acid (PNA) probes
Pyrosequencing
Restriction-fragment-length polymorphism (RFLP)
Zinc fi nger proteins
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