By Angela Brooks and David Chapman Mentor: Dr. Garry Larson Molecular Medicine, City Of Hope Southern California Bioinformatics Institute 2004

Outline Objective Objective Biological Background Biological Background Programming Project Programming Project Database Design Database Design SIBXP Screen Shots SIBXP Screen Shots Future Tasks Future Tasks Acknowledgements Acknowledgements

SIBXP – SIB eXPeriment A relational database that contains all important components of PCR experiments performed in the lab A relational database that contains all important components of PCR experiments performed in the lab SIB is an existing database that contains the data obtained from the PCR experiments SIB is an existing database that contains the data obtained from the PCR experiments PCR Experiments Experimental Outcomes SIBXP Database SIB Database

What is the goal of the study? Alleles – alternative forms of a gene Alleles – alternative forms of a gene Alternative forms of a region of DNA Alternative forms of a region of DNA Ultimate goal: Ultimate goal: Identify alleles that contribute to cancer risk Identify alleles that contribute to cancer risk Breast Breast Prostate Prostate

Affected Sibling Pairs (ASP) To help search for disease causing alleles, the study examines siblings that have the same type of cancer. If there is evidence of linkage, the sibling pairs will share alleles more often then by chance alone. Brothers with prostate cancer

Why SIBXP? Important to keep track of all experiments Important to keep track of all experiments Knowledge of what has been analyzed and what has yet to be analyzed Knowledge of what has been analyzed and what has yet to be analyzed There are many associated components to an experiment that you need to keep track of There are many associated components to an experiment that you need to keep track of

Polymerase Chain Reaction(PCR) – Detecting genetic markers PCR creates multiple copies which amplifies a specific region in a DNA template PCR creates multiple copies which amplifies a specific region in a DNA template The amplification makes it easier to detect the region of DNA The amplification makes it easier to detect the region of DNA PCR experiments are used to detect genetic markers PCR experiments are used to detect genetic markers Genetic markers help to detect the alleles that can contribute to cancer risk Genetic markers help to detect the alleles that can contribute to cancer risk

Genetic Markers Look for genetic markers that are close to locus of interest Microsatellites/minisatellites Length polymorphism. Short repeated sequences of DNA Usually found in non-protein coding regions of DNA i.e. CACACACACACACACACA SNPs – Single Nucleotide Polymorphism A single nucleotide base, at a specific location, that shows variation in the population i.e. AT CA AT CA Polymorphism? What’s that? A difference in DNA sequence among individuals.

PCR Experiment Tracking In order to track PCR experiments that detect the genetic markers you need to know: In order to track PCR experiments that detect the genetic markers you need to know: What marker you are detecting What marker you are detecting Ingredients that are added in the PCR reaction – cocktail Ingredients that are added in the PCR reaction – cocktail What human DNA template you are using What human DNA template you are using Experimental Details Experimental Details

Programming Project Create a software solution to enable researchers to track PCR experiments. Create a software solution to enable researchers to track PCR experiments. Lab currently uses Excel spreadsheets to track experiments. Lab currently uses Excel spreadsheets to track experiments. Lab notes are referred to as “cooksheets” Lab notes are referred to as “cooksheets”

What is a cooksheet? A cooksheet is the term the lab technicians use for the set of data they use to keep track of PCR experiments. A cooksheet is the term the lab technicians use for the set of data they use to keep track of PCR experiments. It is in essence a “recipe” of ingredients and conditions for the experiment. It is in essence a “recipe” of ingredients and conditions for the experiment. Cooksheets keep track of: Cooksheets keep track of: DNA samples used DNA samples used Primers Primers Reagents (such as TAQ polymerase and buffer) Reagents (such as TAQ polymerase and buffer) Thermal cycler conditions Thermal cycler conditions Gel Experiments Gel Experiments

Actual Cooksheet Stored as Excel Spreadsheet

Current System Shortcomings The current system is unsatisfactory for the following reasons: The current system is unsatisfactory for the following reasons: Time consuming to create new cooksheets Time consuming to create new cooksheets Errors can be easily introduced Errors can be easily introduced Retrieving data is cumbersome Retrieving data is cumbersome Data cannot be cross-referenced Data cannot be cross-referenced Cooksheets are not dynamically linked to the existing SIB database Cooksheets are not dynamically linked to the existing SIB database Preferred or standard conditions for PCR cannot be easily ascertained Preferred or standard conditions for PCR cannot be easily ascertained

Programming Solution Use a relational database. Use a relational database. Incorporate experimental data into SIB DB Incorporate experimental data into SIB DB SIB DB back end is administered with Microsoft SQL Server SIB DB back end is administered with Microsoft SQL Server Program front end with Active Server Pages (web interface) Program front end with Active Server Pages (web interface)

Why use a relational database? Ensures data consistency & integrity Ensures data consistency & integrity Using a relational database will allow users to cross-reference data sets Using a relational database will allow users to cross-reference data sets Cooksheet creation can be partially automated Cooksheet creation can be partially automated

Entity Relationship Diagram for SIB XP Consists of: 23 Tables & 148 Fields

Project Timeline Weeks 1-4 Weeks 1-4 Gather requirements Gather requirements Analyze cooksheets Analyze cooksheets Produce specification documentation Produce specification documentation SIB XP Documentation SIB XP Documentation SIB XP Documentation SIB XP Documentation Created rapid prototype of interface in Power Point Created rapid prototype of interface in Power Point Weeks 5-6 Weeks 5-6 Create database tables Create database tables Implement “front end” user interface in ASP Implement “front end” user interface in ASP

Future Tasks Continue implementation Continue implementation Test and debug Test and debug Add additional features Add additional features

Special Thanks To… City of Hope Personnel City of Hope Personnel Garry Larson Garry Larson Yan Ding Yan Ding Louis Geller Louis Geller Dave Ko Dave Ko Catheryn Lundberg Catheryn Lundberg Guillermo Rivas Guillermo Rivas Bryan Pacada Bryan Pacada SoCalBSI Members Professors Fellow Interns NIH and NSF for funding

Sources Database information: Database information: