Monkey Gene Mapping Study Aims to Reduce Use of Animals in Medical Experiments

As part of a worldwide effort to reduce, refine, and replace animals in medical experiments, researchers have completed the first gene map of the cynomolgus monkey Macaca fascicularis, one of the most important nonhuman primate animal models.

Investigators at Roche Pharma Research and Early Development (Basel, Switzerland) and Roche NimbleGen (Madison, WI, USA) used a whole-genome shotgun sequencing approach to map the genome of a M. fascicularis female of Mauritian origin.

In shotgun sequencing, DNA is broken up randomly into numerous small segments, which are sequenced using the chain termination method to obtain reads. Multiple overlapping reads for the target DNA are obtained by performing several rounds of this fragmentation and sequencing. Computer programs then use the overlapping ends of different reads to assemble them into a continuous sequence. The practical work was performed using the Genome Sequencer FLX System from Roche’s 454 Life Sciences division (Branford, CT, USA).

Results published in the August 23, 2011, online edition of the journal Genome Research revealed that shotgun sequencing in combination with other latest generation sequencing techniques had enabled discovery of about 2.1 million potential single-nucleotide polymorphisms based on occurrence of a dimorphic nucleotide at a given position in the genome sequence. More than 20,000 transcripts in the cynomolgus monkey genome were predicted and used to build a M. fascicularis-specific gene expression microarray on the Roche NimbleGen 12x135K platform. This novel microarray design for in-depth expression profiling will be of tremendous value in preclinical drug safety research.

Comparative expression analysis of liver samples from 36 animals of different geographic origin resulted in the identification of over 700 genes with highly variable expression while the majority of the genome showed relatively stable expression with low inter-animal variation.

Senior author Dr.Ulrich Certa, head of molecular toxicology at Roche Pharma Research and Early Development, said, “The flexibility and accuracy of the NimbleGen expression microarray platform allowed us to develop a novel microarray based on our genome sequencing effort. For the first time, gene expression can be monitored with high-specificity in this animal model to answer mechanistic or safety related questions based on transcriptional responses. Furthermore, we plan to design additional arrays for copy-number-variation and SNP (single nucleotide polymorphism) analysis on the NimbleGen array platform. These combined efforts will hopefully improve the translational value of nonhuman primate experiments for humans. As in humans, it might become possible in the future to discover polymorphisms in drug-response genes that differentiate poor and good metabolizers, for instance.”

Related Links:
Roche Pharma Research and Early Development
Roche NimbleGen
Roche’s 454 Life Sciences Division