Vervet Monkey: Whole Genome Sequencing
Background[edit]

The vervet monkey is a very common primate. The largest natural populations reside in Africa. The animal was introduced in the Caribbean, possibly by slave traders, and flourished there. Fifty individuals from this Caribbean population were used to seed a colony at the University of California, Los Angeles. The colony has been in existence for forty generations and presently numbers about 800 individuals.
Potential Project[edit]
The vervet monkey is a model for a variety of human traits. In a project currently underway, Nelson Freimer (UCLA) is funded to generate whole genome shotgun sequence of vervet monkeys for the purpose of SNP discovery. The funded mandate is to sequence one individual from each of five different populations at approximately 10x coverage and 20 individuals from each of the same five populations at approximately 2x coverage. The SNP discovery results could be used to design a vervet specific SNP genotyping chip which could be used, for example, to conduct a GWAS in the UCLA vervet colony and other well phenotyped colonies.
The potential project currently under discussion involves replacing the proposed SNP chip development and genotyping effort with low pass sequencing (2-4x) of 500-800 individuals in the UCLA vervet colony. One appealing feature of the colony is that, except for rare de novo events, most variants should appear in several individuals -- greatly increasing the proportion of all variants that can be discovered using low pass sequencing.
Key Individuals[edit]
- Nelson Freimer (University of California, Los Angeles)
- George Weinstock (Washington University Department of Genetics)