Post on 21-Jan-2016
description
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