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. For each 25-base
probe, 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 to
include
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 the magnified view
below, 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.