By Angela Brooks and David ChapmanBy Angela Brooks and David Chapman

Mentor: Dr. Garry LarsonMentor: Dr. Garry Larson

Molecular Medicine, City Of HopeMolecular Medicine, City Of Hope

Southern California Bioinformatics Institute 2004

OutlineOutline

ObjectiveObjective Biological Background Biological Background Programming ProjectProgramming Project Database DesignDatabase Design SIBXP Screen ShotsSIBXP Screen Shots Future TasksFuture Tasks AcknowledgementsAcknowledgements

SIBXPSIBXP – – SIBSIB e eXPXPerimenteriment

A relational database that contains all important A relational database that contains all important components of PCR experiments performed in components of PCR experiments performed in the labthe lab

SIB is an existing database that contains the SIB is an existing database that contains the data obtained from the PCR experimentsdata obtained from the PCR experiments

PCR Experiments

Experimental Outcomes

SIBXP Database SIB Database

What is the goal of the study?What is the goal of the study?

Alleles – alternative forms of a geneAlleles – 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 riskIdentify alleles that contribute to cancer risk

BreastBreast ProstateProstate

http://www.el-minjas.com/alleles.gif

Affected Sibling Pairs (ASP)Affected Sibling Pairs (ASP)

To help search for disease causing alleles, the To help search for disease causing alleles, the study examines siblings that have the same type study examines siblings that have the same type of cancer.of cancer.

If there is evidence of If there is evidence of linkagelinkage, the sibling pairs , the sibling pairs will share alleles more often then by chance will share alleles more often then by chance alone.alone.

Brothers with prostate cancer

Why SIBXP?Why SIBXP?

Important to keep track of all experiments Important to keep track of all experiments Knowledge of what has been analyzed and Knowledge of what has been analyzed and

what has yet to be analyzedwhat has yet to be analyzed There are many associated components to There are many associated components to

an experiment that you need to keep track an experiment that you need to keep track ofof

Polymerase Chain Polymerase Chain Reaction(PCR) – Detecting Reaction(PCR) – Detecting

genetic markersgenetic markers

PCR creates multiple copies which PCR creates multiple copies which amplifies a specific region in a DNA amplifies a specific region in a DNA templatetemplate The amplification makes it easier to detect the The amplification makes it easier to detect the

region of DNAregion of DNA PCR experiments are used to detect PCR experiments are used to detect

genetic markersgenetic markers Genetic markers help to detect the alleles that Genetic markers help to detect the alleles that

can contribute to cancer riskcan contribute to cancer risk

Genetic MarkersGenetic 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 TrackingPCR Experiment Tracking

In order to track PCR experiments that In order to track PCR experiments that detect the genetic markers you need to detect the genetic markers you need to know:know: What marker you are detectingWhat marker you are detecting Ingredients that are added in the PCR Ingredients that are added in the PCR

reaction – cocktailreaction – cocktail What human DNA template you are usingWhat human DNA template you are using Experimental DetailsExperimental Details

Programming ProjectProgramming Project

Create a software solution to enable Create a software solution to enable researchers to track PCR experiments. researchers to track PCR experiments.

Lab currently uses Excel spreadsheets to Lab currently uses Excel spreadsheets to track experiments.track experiments. Lab notes are referred to as “cooksheets”Lab notes are referred to as “cooksheets”

What is a cooksheet?What is a cooksheet?

A cooksheet is the term the lab technicians use A cooksheet is the term the lab technicians use for the set of data they use to keep track of PCR for the set of data they use to keep track of PCR experiments.experiments. It is in essence a “recipe” of ingredients and It is in essence a “recipe” of ingredients and

conditions for the experiment.conditions for the experiment. Cooksheets keep track of:Cooksheets keep track of:

DNA samples usedDNA samples used PrimersPrimers Reagents (such as TAQ polymerase and buffer)Reagents (such as TAQ polymerase and buffer) Thermal cycler conditionsThermal cycler conditions Gel ExperimentsGel Experiments

Actual Cooksheet

Stored as Excel Spreadsheet

Current System Current System ShortcomingsShortcomings

The current system is unsatisfactory for the The current system is unsatisfactory for the following reasons:following reasons: Time consuming to create new cooksheetsTime consuming to create new cooksheets Errors can be easily introducedErrors can be easily introduced Retrieving data is cumbersomeRetrieving data is cumbersome Data cannot be cross-referencedData cannot be cross-referenced Cooksheets are not dynamically linked to the Cooksheets are not dynamically linked to the existingexisting

SIB databaseSIB database Preferred or standard conditions for PCR cannot be Preferred or standard conditions for PCR cannot be

easily ascertainedeasily ascertained

Programming SolutionProgramming Solution

Use a relational database.Use a relational database. Incorporate experimental data into Incorporate experimental data into

SIB DBSIB DB SIB DB back end is administered with SIB DB back end is administered with

Microsoft SQL ServerMicrosoft SQL Server Program front end with Active Server Program front end with Active Server

Pages (web interface)Pages (web interface)

Why use a relational Why use a relational database?database?

Ensures data consistency & integrityEnsures data consistency & integrity Using a relational database will allow Using a relational database will allow

users to cross-reference data setsusers to cross-reference data sets Cooksheet creation can be partially Cooksheet creation can be partially

automatedautomated

Entity Relationship Diagram for SIB XP

Consists of: 23 Tables & 148 Fields

Project TimelineProject Timeline

Weeks 1-4 Weeks 1-4 Gather requirementsGather requirements Analyze cooksheetsAnalyze cooksheets Produce specification documentationProduce specification documentation

SIB XP DocumentationSIB XP Documentation

Created rapid prototype of interface in Power PointCreated rapid prototype of interface in Power Point Weeks 5-6Weeks 5-6

Create database tablesCreate database tables Implement “front end” user interface in ASPImplement “front end” user interface in ASP

Future TasksFuture Tasks

Continue implementationContinue implementation Test and debugTest and debug Add additional featuresAdd additional features

Special Thanks To…Special Thanks To…

City of Hope City of Hope PersonnelPersonnel Garry LarsonGarry Larson Yan DingYan Ding Louis GellerLouis Geller Dave KoDave Ko Catheryn LundbergCatheryn Lundberg Guillermo RivasGuillermo Rivas Bryan PacadaBryan Pacada

SoCalBSI MembersSoCalBSI Members ProfessorsProfessors Fellow InternsFellow Interns

NIH and NSF for NIH and NSF for fundingfunding

SourcesSources

Database information: Database information: http://support.microsoft.comhttp://support.microsoft.com http://his.osu.edu/help/database/terms.cfmhttp://his.osu.edu/help/database/terms.cfm