Fig 7 Carr et al. 2007

Alternative approaches to SNP detection:
Iterative DNA "Re-Sequencing" on Microarrays
(after SM Carr et al. 2008 Comp Biochem Physiol D, Genomics & Proteomics 3,1-11)

    A DNA Re-sequencing microarray is based on a reference sequence of length n bases, represented in a series of n overlapping  ("tiled") oligonucleotide probes. For each probe, three variant probes are included that vary the middle base, one for each of the three alternative DNA code letters. Mis-match at this position most strongly influences binding, so that a genomic DNA fragment with a SNP sequence will stick to only one of the four oligos at any tiled position.   Re-sequencing allows a lengthy contiguous sequence to be determined in one experiment, without multiple PCR and sequencing reactions. Re-sequencing of both strand of a continuous 17Kb sequence like mtDNA requires 2 x 4 x 17,000 = 136,000 oligos [above]. Re-sequencing is useful where analogous sequences are to be read repeatedly ("re-sequenced") from multiple individuals, and is thus particularly well-suited to population genomics

    In the enlargement below, the re-sequencing chip tiles the reference sequence in the first row, and the variants below it. (
A vs CGT, C vs AGT ,
vs AGT, and T vs ACG). The occassional variant stands out clearly: the reference DNA sequence is  AGCC at positions 121-124, and the experimental sequence is AGCT.

Affy chip

All material ©2008 by Steven M. Carr