Carr et al.
              2007 Comp Biochem Physiol D, Fig. 7

DNA Re-Sequencing Microarrays
(SM Carr et al. 2008. Comp. Biochem Physiol. D, Genomics & Proteomics 3,1-11)

    A DNA Re-sequencing microarray allows a contiguous sequence of 30 ~ 300Kbp to be determined in a single experiment. The microrarray is designed from a known reference sequence, and allow the homologous sequence to be read repeatedly from additional individuals ("re-sequenced"). Re-sequencing is thus particularly well-suited to population genomics.

    The microarray represents a reference sequence of length n bases as a series of 4 x n overlapping ("tiled") oligonucleotide probes ("oligos"). For
each 25-base oligo , three variant probes are included that vary the middle base, one for each of the three alternative DNA code letters. Miss-match at this position will prevent binding, so that a genomic DNA fragment with a SNP sequence will stick to only one of the four oligos at any tiled position. [Click here for further details]. The example shows a 15,452bp human mtDNA sequence in a 320 row x 488 column array that includes both the sense and antisense strands. Each nucleotide position is represented in a vertical block of 4 cells in 5 rows (ACGT + a blank). In each block, the cell with the strongest relative intensity of DNA binding identifies the base present at that position. In magnified view, the sequence of bases in each of four blocks is easily read as the left-to-right order of successive brightest 'spots'.

     Where homologous mtDNA sequences differ by > 20%, it is possible to include reference DNA sequences from several species on the same microarray, and determine the sequences of experimental DNA from multiple individuals simultaneously. The ArkChip is a high-throughput, cost-effective platform for conducting several commercial and conservation projects simultaneously.


All figures and text material 2013 by Steven M. Carr