Team II Comparative Genomics Group

Team 2: Comparative Genomics

Team Members: Kara Keun Lee, Courtney Astore, Kristine Lacek, Ujani Hazra, Jayson Chao

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Objectives

• Identify kinds of strains (outbreak vs. sporadic)​

• Construct phylogeny demonstrating which isolates are related and which differ​

• Determine source of outbreak​

• Map virulence and antibiotic resistence features of outbreak isolates​

• Compile recommendations for outbreak response and treatment

Overview of Techniques

When performing phylogenomics, there are many options by which one can classify similarities and differences across the genome. Our approach utilizes tools from three different techniques.

SNP-based

SNP stands for Single Nucleotide Polymorphism, meaning that certain alleles have two or three possibilities as to which base is at a given locus. As SNPs accumulate through de novo mutations and are passed down through generations, comparing a given isolate's SNPs to other isolates and a reference genome allow ascertainment of phylogenetic distance between samples. Tools have been developed to compare bases position by position (SNP-calling) and create matrices to compute relatedness between samples based on common SNPs. Generalized Algorithm Overview:

• Pre-processing and read cleaning
• Mapping
• SNP calling against reference genome
• Phylogeny generation based on SNP profiles