ALFREDALFRED -- the the ALALlele lele FREFREquency quency

DDatabase:atabase:

ALFREDALFRED -- the the ALALlele lele FREFREquency quency

DDatabase:atabase:

S. Stein1, H. Rajeevan1,U. Soundararajan1, K-H Cheung2, J.R. Kidd1, A.J. Pakstis1, R. Gadagkar2, P.L. Miller2, K.K. Kidd1

1Dept. of Genetics and 2Center for Medical Informatics, Yale University School of Medicine,

New Haven, CT, 06520-8005, USA.

An UpdateAn Update

OverviewOverviewALFREDALFRED,, thethe ALALlelelele FREFREquencyquency DDatabaseatabase,,

is a free, web-accessible, curated is a free, web-accessible, curated compilation of allele frequency data on DNA compilation of allele frequency data on DNA

sequence polymorphisms in anthropologically sequence polymorphisms in anthropologically defined human populations. ALFRED is supported defined human populations. ALFRED is supported

by a grant from the U.S. National Science by a grant from the U.S. National Science Foundation to be an international resource for Foundation to be an international resource for

research and teaching in physical anthropology, research and teaching in physical anthropology, human population genetics, and any other field human population genetics, and any other field

that can benefit from easy access to data that are that can benefit from easy access to data that are otherwise widely dispersed in the scientific otherwise widely dispersed in the scientific

literature.literature.

http://alfred.med.yale.edu/

ALFREDALFRED provides: provides:

Over 36,000 frequency tables, and growingOver 36,000 frequency tables, and growing

Over 450 populations with descriptions and linksOver 450 populations with descriptions and links

Over 1300 sites typed for at least one populationOver 1300 sites typed for at least one population

New GIS-based map interface to view New GIS-based map interface to view populations and frequency data geographicallypopulations and frequency data geographically

Easy to use Keyword searchEasy to use Keyword search

Data that can be easily downloaded for Data that can be easily downloaded for analysisanalysis

Free ALFRED Newsletter on a regular basis Free ALFRED Newsletter on a regular basis when you registerwhen you register

ALFREDALFRED Homepage Homepage http://alfred.med.yale.edu/

Genotypes• ALFRED now displays genotype information for selected

polymorphisms• The symbol “G” will appear for a site-population combination

when genotype numbers are available• Searching with the keyword “Genotype” will retrieve the list of

sites with genotype information

Click on the “G” to get additional genotype information

Polymorphism InformationPolymorphism Information

Display frequency data at the location of the population/sample on a geographic map

Synonym(s) used in the keyword search (rs#’s are now included)

This link will directly connect to the corresponding dbSNP record

Population InformationPopulation Information

Synonym(s) used in the keyword search

View location of population on a geographic map

Frequency search result – tabular formatFrequency search result – tabular formatThe icon is used throughout ALFRED whenever The icon is used throughout ALFRED whenever

additional information can be retrieved.additional information can be retrieved.

Click on the to get additional information

Frequency search result – graphical viewFrequency search result – graphical view

Clicking here will give you population information

Clicking here will give you sample information

Haplotype frequencies displayed as a stacked-bar histogram with the legend for colors at the bottom of the page Allele

Legend

GIS-based Map Interface

The GIS-based map interface is the newest The GIS-based map interface is the newest ALFREDALFRED function. It function. It gives users the ability to visualize genetic data on polymorphisms in gives users the ability to visualize genetic data on polymorphisms in

a geographic context. There are several ways users can interact a geographic context. There are several ways users can interact with the interface including, selecting populations based on their with the interface including, selecting populations based on their

geographic location and displaying data at the location of the geographic location and displaying data at the location of the population. This interface allows, among other things, users to easily population. This interface allows, among other things, users to easily

see clinal patterns of frequencies, both worldwide and regionally. see clinal patterns of frequencies, both worldwide and regionally.

OverviewOverview

What is GIS?• GIS: Geographic Information SystemGIS: Geographic Information System

– New interface interacts with GIS serversNew interface interacts with GIS servers

• ALFREDALFRED uses a GIS package called “ArcIMS” (Arc Internet uses a GIS package called “ArcIMS” (Arc Internet Mapping Server)Mapping Server)

• New interface supports an integrated view that New interface supports an integrated view that encompasses queries to encompasses queries to ALFREDALFRED and GIS servers and GIS servers

Map InterfaceZoom for a more detailed view Triangles represent various

populations

Select site, sample or population

Use directional buttons to navigate the map

Selection of populations based on their location• Select a group of populations (click and drag a rectangle

around the desired group of populations)• Click “Retrieve data for selected populations”• List of populations selected with population information is

displayed at the bottom of the page

Display frequency data as pie charts• Display frequency data at the location of the

population/sample• Example below displays the distribution of allele

frequencies for a TaqMan (C_8829451_10, rs1229966) site

Population names can be hidden for a clearer view of the pie charts

Chromosomal Position• On the locus information page, the polymorphisms are listed in

order following the latest dbSNP build available from NCBI

Locus symbol

Chromosomal band position

Ordered by chromosomal position

The The ALFREDALFRED Team TeamThe The ALFREDALFRED Team Team

Senior FacultySenior FacultyKenneth K. Kidd, Ph.D., Professor of Genetics and Psychiatry (ALFRED P.I.)Kenneth K. Kidd, Ph.D., Professor of Genetics and Psychiatry (ALFRED P.I.)Perry Miller, M.D., Ph.D., Director of Center for Medical InformaticsPerry Miller, M.D., Ph.D., Director of Center for Medical Informatics

CuratorsCuratorsShannon Stein, B.S., Research AssociateShannon Stein, B.S., Research AssociateUsha Usha Soundararajan, M.S., Research AssistantSoundararajan, M.S., Research Assistant

ProgrammersProgrammersHaseena Rajeevan, Ph.D., Systems ProgrammerHaseena Rajeevan, Ph.D., Systems ProgrammerRohit Gadagkar, M.S., ProgrammerRohit Gadagkar, M.S., Programmer

ConsultantsConsultantsAndrew J. Pakstis, Ph. D., Research ScientistAndrew J. Pakstis, Ph. D., Research ScientistJudith R. Kidd, Ph. D., Research ScientistJudith R. Kidd, Ph. D., Research ScientistKei-Hoi Cheung, Ph. D., Assistant ProfessorKei-Hoi Cheung, Ph. D., Assistant Professor

Supported by the U.S. National Science FoundationSupported by the U.S. National Science Foundation