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WHOLE GENOME SEQUENCE ANALYSIS OF CAYO SANTIAGO RHESUS MACAQUES

​Our lab at UPenn is developing techniques to combine linear mixed modeling (used in heritability analyses) with sparse regression (used in genome-wide association studies) to look for phenotype-genotype associations

​Cayo Santiago is home to a free-ranging colony of rhesus macaques since 1938. The population is​ descended from 409 Indian-origin founders, including 40 adult males and 183 adult females.


I've adapted genomic techniques, previously developed and extensively validated for analyses of variants in human populations, to identify and annotate genomic variations in the Cayo population

Aim One

Align whole genome sequences from population samples to the M. mulatta reference assembly

Aim Two

Identify single nucleotide
​variants (SNVs) 

Aim Three

​Identify structural
​variants (SVs)











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