OHSU

Primate Genetics Program

Primate GeneticsThe goals of this program are to develop genetic and genomic resources at the ONPRC, in support of both biomedical research and optimal colony management.

 

Colony Genetics and Demographics Unit

The Colony Genetics and Demographics Unit (CGD) oversees the genotyping of all non-human primates (NHPs) at the ONPRC, in order to validate parentage, characterize extended colony pedigrees, and to monitor colony genetic diversity.  These extended pedigrees form a critical foundation for genetic research and animal model development at the ONPRC.  Analyses based on these pedigrees are also used to support colony management personnel in decisions related to the formation of breeding groups, and to inform other management strategies that impact the genetic health and diversity of NHP colonies at the ONPRC.

Amanda Vinson, Ph.D., Director
Samone Khouangsathiene, M.S., Research Associate

Services provided

Parentage determination and population genetic and demographic analyses.  All ONPRC macaques are genotyped to determine parentage and to establish population genetic indices for the colony as a whole. Blood samples are collected from all newborn macaques during regular physical exams, usually conducted during the "round-ups" of outdoor corrals and shelter-houses, or as a routine part of veterinary care for indoor-housed animals.  The blood sample provide DNA both for archiving with the Collaborative Genetics Resource (CGR) unit, and for genotype analysis of new infants and potential parents, conducted by the UC Davis Veterinary Genetics Laboratory (VGL).  Relationships supported by genetic analysis are then used to update pedigrees, which span multiple families and generations.  Parentage analysis has been conducted on 97% of animals housed in outdoor corrals and shelter-housing, and on 65% of indoor-housed animals. Both genotypes and parentage assignments are stored in the Genetic Relationships & Information on Primates database (GRIPdb), which is accessible to all ONPRC staff (see below for a description of GRIPdb).

Population genetic indices include mean kinship values for breeding groups, estimates of relatedness between individuals and groups, and individual measures of genome uniqueness and founder representation.  These measures are used to identify animals (typically males) whose genetic contributions are overrepresented within groups, potentially contributing to loss of genetic diversity within the colony.  The reports for each housing group are provided, along with interpretation and recommendations, to DAR for use in colony management decisions.  Demographic reports are also generated using both census data and parentage data to report trends in reproductive and mortality rates by housing group.  Historical estimates of mortality and birth rates are used in simulations to predict future changes in colony composition, and to assess the long-term effects of different management strategies.

Maintenance of colony genetic and demographic information:  The database tools described below were designed to facilitate use of available data produced by ongoing genetic and demographic analysis within the ONPRC colony.  The information is available through the internal websites listed below, or may be summarized in specialized reports requested by colony management personnel or by research investigators.

1. GRIPdb, a web-based interface for ONPRC genetic, demographic  and phenotypic data:  The GRIP database (http://grip.ohsu.edu) integrates data from the ONPRC Integrated Research Information System (IRIS, used for animal colony administration)  with available genetic demographic and phenotypic data. The dynamic connection between IRIS and GRIPdb allows reporting of extended animal information to users of the GRIPdb interface. This information include:

  • Confirmed (genetic) relationships between NHP parents and offspring, based on genotype information at multiple microsatellite markers;
  • Observed relationships between NHP parents and offspring, based on records obtained from IRIS;
  • Genotype data (allele frequency, genomic location, etc.);
  • Haplotypes data for linked genetic loci;
  • Basic information on each animal, including birth and death dates, ancestral origin, and housing location.

2. MonkeySNP, a web-based portal dedicated to SNP genotype data (also accessible through the GRIPdb interface). To maximize the utility of the growing amount of single-nucleotide polymorphism (SNP) data being generated on animals within our rhesus macaque colony, we developed a web-based portal, “MonkeySNP”, for the purpose of accessing and displaying available data.  We anticipate tremendous growth of this resource as SNP genotypes on colony animals are generated more rapidly using ever-expanding arrays.  The MonkeySNP portal (http://MonkeySNP.ohsu.edu) utilizes the human dbSNP database schema and design, "mirroring" this data but incorporating a more intuitive user interface. Genotypes may be searched by gene symbol, chromosome position or animal population and may be displayed either graphically or in table format.

 

Collaborative Genetics Resource Unit

The Collaborative Genetics Resource Unit (CGR) provides research expertise to support macaque genotype discovery and analysis. The CGR manages an extensive ONPRC non-human primate DNA Bank, and develops the implements high through-put genotyping assays for the study of macaques.  The bioinformatics arm of this group support nextgen sequence analysis methods for genome, transcriptome and epigenome studies. Biostatistics support includes analysis of micro array data, statistical genetics, complex sample survey, meta-analysis, Bayesian data analysis, longitudinal data analysis, and survival analysis. Biostatistics drop-in sessions are held for two hours a day, twice a month at the ONPRC.


Betsy Ferguson, Ph.D., Director
Byung Park, Ph.D., Research Assistant Professor
Beth Wilmot, Ph.D., Staff Scientist
Summer Street, M.S., Research Associate
Ranjani Ramakrishnan, M.S., Bioinformatics Developer/Research Associate
 

Molecular Services provided

Rhesus ancestry SNP assay.  This SNP assay includes 96 Ancestral Informative Markers (AIMs) from over 20 chromosomes. The array is run on an Illumina Bead-Array platform, and Structure analysis (Pritchard et al., 2000) is used to distinguish rhesus macaque ancestral populations.  Pure bred Indian, Chinese and hybrid animals are identified with this assay. 

VNTR genotype assay.  VNTR assays are available to genotype commonly studied alleles in SLC6A4, MAOA and TPH2.  Other assays are developed by request.

DNA bank.  Whole blood and liver samples are collected from all rhesus and Japanese macaques for processing and archiving for genetic research use. Buffy coat cells are isolated from blood samples, liver samples are obtained at necropsy, and DNA samples are extracted from these tissues as needed. All samples are stored in ultra-low freezers and made available to investigators for a fee. Currently the Bank includes over 18,000 archived samples from more than 6,000 NHPs.

Quality control

Quality control is incorporated into each procedure. For the SNP array, the 95% confidence intervals for the ancestral composition is reported for each individual.  Eight characterized Indian and Chinese rhesus DNA controls are included in each assay to insure the reproducibility of genotype calls in each run.  The DNA evaluates DNA samples by UV absorbance to ensure the 260/280 ratio is between1.7-2.0 and that the DNA concentration is between 50-250 ng/?l.

Chargebacks

Charges for rhesus ancestral SNP array analysis are $50/DNA (internal) and $65/DNA (external). Charges for obtaining DNA from the DNA bank is $2/ug DNA for internal use ($4/ug, external). If DNA is extraction from a buffy coat or liver sample is required, a $20 fee is charged directly to the investigator by the MCBSC. That core facility extracts the DNA, with the agreement that 10 ?g is delivered to the investigator and the remaining DNA sample is retained by the Bank.

 

Biostatistical and bioinformatics services provided 

Biostatistical support for data analysis, study design and manuscript submission are arranged as needed.  Drop-In sessions are held bi-monthly to discuss issues on an individual basis.  Workshops are held several times a year to provide educational opportunities to learn and discuss commonly used statistical analyses.

Bioinformatic support is offered for nextgen sequence analysis, also on a fee/service basis.  Whole genome, transcriptome and methlation study analysis are provided.  Short-term network storage is made available for large data sets at the OHSU Advanced Computer Center.

Chargebacks

Charges for statistical services are $60/hour for junior faculty and $100/hour for senior faculty.  Illumina GAII sequence analysis support is $350/lane. Pooled sample read analysis fees are based upon the number of samples run per lane.