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Figure 3 | Journal of Translational Medicine

Figure 3

From: A strategy for detection of known and unknown SNP using a minimum number of oligonucleotides applicable in the clinical settings

Figure 3

Principle of fluorimetric detection of SNP by proportional hybridization to oligonucleotide arrays in homozygous and heterozygous conditions. Portrait of proportional hybridization (of differentially labeled reference (Cy3) and test (Cy5) sample to overlapping oligos encompassing an arbitrarily chosen "consensus" sequence (consensus oligos = CO) or variant-specific oligos (Va1 and Va2...., see Figures 1 and 2). The homozygous reference sample consists of two alleles identical to the consensus sequence (HLA-A*0101). Differentially fluorescence-labeled reference and test samples are co-hybridized to an array slide spotted with the 18-nucleotide overlapping consensus oligos and variant oligos. Four consensus oligos representing a "conserved" region (k) were used to normalize the data set (see text). Reference sample consistently hybridizes to CO and never to Va oligos. Hybridization of test sample will determine variability in ratio of fluorescence intensity as portrayed by the digital images from a GenePix scanner. Possible combinations are: I) a,a type homozygosity (row I); II) b,b homozygosity (row II); III) a,b heterozygosity with one known allele (row III) and one unknown allele (row VII); IV) b,c heterozygosity with two known alleles (row IV), one known and one unknown allele (row V) and two new alleles (row VI). Question marks represent the hypothetical discovery of new allele(s).

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