In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.
BACKGROUND
Genomic approaches in large animal models (canine, ovine etc) are challenging due to insufficient genomic information for these species and the lack of availability of corresponding microarray platforms. To address this problem, we speculated that conserved interspecies genetic sequences can be experimentally detected by cross-species hybridization. The Affymetrix platform probe redundancy offers flexibility in selecting individual probes with high sequence similarities between related species for gene expression analysis.


RESULTS
Gene expression profiles of 40 canine samples were generated using the human HG-U133A GeneChip (U133A). Due to interspecies genetic differences, only 14 +/- 2% of canine transcripts were detected by U133A probe sets whereas profiling of 40 human samples detected 49 +/- 6% of human transcripts. However, when these probe sets were deconstructed into individual probes and examined performance of each probe, we found that 47% of human probes were able to find their targets in canine tissues and generate a detectable hybridization signal. Therefore, we restricted gene expression analysis to these probes and observed the 60% increase in the number of identified canine transcripts. These results were validated by comparison of transcripts identified by our restricted analysis of cross-species hybridization with transcripts identified by hybridization of total lung canine mRNA to new Affymetrix Canine GeneChip.


CONCLUSIONS
The experimental identification and restriction of gene expression analysis to probes with detectable hybridization signal drastically increases transcript detection of canine-human hybridization suggesting the possibility of broad utilization of cross-hybridizations of related species using GeneChip technology.
Grigoryev
Dmitry N
DN
Division of Pulmonary and Critical Care Medicine, Center for Translational Respiratory Medicine, Johns Hopkins University, 5501 Hopkins Bayview Circle, Baltimore, MD 21224, USA. dgrigor1@jhmi.edu
Ma
Shwu-Fan
SF
Simon
Brett A
BA
Irizarry
Rafael A
RA
Ye
Shui Q
SQ
Garcia
Joe G N
JG
D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D004285:Dogs; D020224:Expressed Sequence Tags; D005786:Gene Expression Regulation; D015723:Gene Library; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
D015345:Oligonucleotide Probes; D012333:RNA, Messenger