Interspecies hybridization on DNA resequencing microarrays:
efficiency of sequence recovery and accuracy of SNP detection
in human, ape, and codfish mitochondrial DNA genomes
sequenced on a human-specific MitoChip

(SMC Flynn & SM Carr. BMC Genomics, 8:339)

    We investigated the efficiency of sequence recovery and accuracy of SNP identification for 15,452 bp of homologous chimpanzee, gorilla, and codfish mitochondrial (mtDNA) genomes resequenced on a human-specific microarray. Efficiencies of calls made at high-confidence in both ape species were 99.59% and 97.89 %, however SNP identification error rates increased from 0.067 to 0.247 per SNP between the chimpanzee and gorilla genomes.  Resequencing of fish mtDNA correctly called <4% of the genome, in short inter-ordinally conserved islands.  Differential binding of experimental DNAs to the 25-base SNP-specific oligonucleotides on the microarray is strongly affected by the density of mismatches. In ape genomes where 33% and 46% of 25bp regions contain 3 or more interspecific SNPs, efficiency declines log-linearly with respect to sequence divergence, and accuracy of SNP identification drops precipitously. The experiments support design of a multi-species microarray that could sequence homologous but distantly-related mtDNA genomes simultaneously, without interference from interspecific cross-hybridization.

© 2007 by Steven M. Carr