Exploratory Analysis of Exploratory Analysis of Disease DataDisease Data& & Introduction to UNC’s GIS Introduction to UNC’s GIS Reference LibraryReference Library

Prepared originally by Kristen HamptonPrepared originally by Kristen Hampton

Updated and maintained by Ben Allshouse and othersUpdated and maintained by Ben Allshouse and others

Types of InvestigationsTypes of Investigations

Disease mappingDisease mapping– Summation of spatial and spatio-temporal variation Summation of spatial and spatio-temporal variation

in disease riskin disease risk

Geographical Correlation AnalysisGeographical Correlation Analysis– Relationship between heath outcomes and Relationship between heath outcomes and

environmental risk factorsenvironmental risk factors

Disease clusteringDisease clustering– Raised incidence of disease in an areaRaised incidence of disease in an area– Non-random spatial pattern of disease relative to Non-random spatial pattern of disease relative to

non-casesnon-cases

Disease MappingDisease Mapping

(Zucker, J.R. Changing Patterns of Autochthonous Malaria Transmission in the United States: A Review of Recent Outbreaks. Emerging Infectious Diseases. 1996;2(1):37-43.)

Geographical Correlation Geographical Correlation AnalysisAnalysis

(Glass, G.E. et al. Infectious Disease Epidemiology and GIS: A Case Study of Lyme Disease. Geo Info Systems. 1992;2(10):65-69.)

Disease ClusteringDisease ClusteringGCA – Point Source StudyGCA – Point Source Study

Hypothesis of Hypothesis of disease etiologydisease etiology

LayersLayers– RoadsRoads– PumpsPumps– Case event dataCase event data

John Snow’s 1854 Map of Cholera and the Broad Street Pump

(McLeod, K.S. Our sense of Snow: the myth of John Snow in medical geography. Social Science & Medicine. 2000;50:923-935.)

ID Application of GISID Application of GIS

““Continuum of diseases”Continuum of diseases”

– Highly applicable to ‘environmental’ diseases, such Highly applicable to ‘environmental’ diseases, such as malaria and other vector-borne diseasesas malaria and other vector-borne diseases

– Limited applicability to non-communicable Limited applicability to non-communicable diseases, such as MS, with weak or non-existent diseases, such as MS, with weak or non-existent environmental componentsenvironmental components

– In between are HIV and other STDs with In between are HIV and other STDs with moderately strong links to the environmentmoderately strong links to the environment

(Tanser, F.C. et al. The application of geographical information systems to important public health problems in Africa. Int. J Health Geographics. 2002;1:4.)

I-95 Syphilis StudyI-95 Syphilis Study

(Cook et al. What’s driving an epidemic? The Spread of Syphilis Along an Interstate Highway in Rural North Carolina. Am. J of Public Health. 1999 Mar;89(3):369-373.)

I-95 Syphilis StudyI-95 Syphilis Study

(Cook et al. What’s driving an epidemic? The Spread of Syphilis Along an Interstate Highway in Rural North Carolina. Am. J of Public Health. 1999 Mar;89(3):369-373.)

IssuesIssues

ConfoundingConfounding

Resolution / Aggregation levelResolution / Aggregation level– Patient confidentialityPatient confidentiality– Spatial accuracySpatial accuracy– Ecological Fallacy (individual v. group)Ecological Fallacy (individual v. group)

Temporal relationship between exposure and Temporal relationship between exposure and diseasedisease

Exploratory Analysis of Exploratory Analysis of HIV in North CarolinaHIV in North Carolina

Screening and Tracing for Acute HIV Screening and Tracing for Acute HIV Transmission (STAT)Transmission (STAT)– Collaboration between UNC-CH CFAR and NC DHHSCollaboration between UNC-CH CFAR and NC DHHS– Developed a system using HIV biomarkers to determine Developed a system using HIV biomarkers to determine

the time of transmission (incident cases)the time of transmission (incident cases)– All HIV test samples sent to state labs are staged with All HIV test samples sent to state labs are staged with

the STAT protocolthe STAT protocol

Records are mapped according to self-Records are mapped according to self-reported zip code of residencereported zip code of residence– Sample data for 1 year:Sample data for 1 year:

110,000 mappable records110,000 mappable records

500 prevalent cases500 prevalent cases

100 incident cases100 incident cases

GoalGoal

Given a table of patient records with disease Given a table of patient records with disease X in North Carolina, create choropleth maps ofX in North Carolina, create choropleth maps of

i. i. case count,case count,

ii.ii. density of cases per square mile, anddensity of cases per square mile, and

iii.iii. population density (persons per square population density (persons per square mile)mile)

by zip code, shown with major highways. by zip code, shown with major highways.

Road ClassificationMajor Highway

No. of Cases

0

1

2

3

4 - 9

Patient ID Street Address City State Zip Gender1 ----- ----- NC ----- 12 ----- ----- NC ----- 1

Information NeededInformation Needed

Tabular Disease Data (Given*)Tabular Disease Data (Given*)– *.dbf (dbase) or *.txt (text) file formats*.dbf (dbase) or *.txt (text) file formats

GIS DataGIS Data– Polygon shapefile of NC zip codesPolygon shapefile of NC zip codes– Line shapefile of NC roadsLine shapefile of NC roads

Attribute DataAttribute Data– Zip code area and populationZip code area and population

* All disease data introduced in this exercise is fictional * All disease data introduced in this exercise is fictional and for demonstration purposes only.and for demonstration purposes only.

ResourcesResources

http://www.lib.unc.edu/reference/gis/http://www.lib.unc.edu/reference/gis/

Amanda HenleyAmanda Henley

GIS Reference Librarian, Davis LibraryGIS Reference Librarian, Davis Library

ahenley@refstaff.lib.unc.eduahenley@refstaff.lib.unc.edu

ArcGIS desktop HelpArcGIS desktop Help

Data ConfidentialityData Confidentiality

Health data is confidentialHealth data is confidential– Issue of privacy for health dataIssue of privacy for health data– As a researcher you must seek training about, and As a researcher you must seek training about, and

proactively protect data confidentialityproactively protect data confidentiality Environmental data is confidential as wellEnvironmental data is confidential as well

– Privacy issue also applies to any environmental data Privacy issue also applies to any environmental data that can be associated with an individualthat can be associated with an individual

How will you protect data confidentiality in this How will you protect data confidentiality in this course?course?– Identify data that might be confidential (address, Identify data that might be confidential (address,

etc.)etc.)– Take action to protect it (do not send it to others, do Take action to protect it (do not send it to others, do

not discuss it or use it in a way that would allow not discuss it or use it in a way that would allow others to identify/target individuals, erase the data others to identify/target individuals, erase the data after you use it, always ask yourself what else you after you use it, always ask yourself what else you can do)can do)

ExerciseExercise

HandoutHandout– Searching UNC’s GIS DatabaseSearching UNC’s GIS Database

Additional ExercisesAdditional Exercises– Adding X,Y Coordinates of Polygon CentroidsAdding X,Y Coordinates of Polygon Centroids– Creating Raster Density Maps from Point LayersCreating Raster Density Maps from Point Layers– Geocoding a Table of AddressesGeocoding a Table of Addresses