ALFRED - the ALlele FREquency Database: S. Stein 1, H. Rajeevan 1,U. Soundararajan 1, K-H Cheung 2, J.R. Kidd 1, A.J. Pakstis 1, R. Gadagkar 2, P.L. Miller 2, K.K. Kidd 1 1 Dept. of Genetics and 2 Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, , USA. An Update

Overview ALFRED, the ALlele FREquency Database, is a free, web-accessible, curated compilation of allele frequency data on DNA sequence polymorphisms in anthropologically defined human populations. ALFRED is supported by a grant from the U.S. National Science Foundation to be an international resource for research and teaching in physical anthropology, human population genetics, and any other field that can benefit from easy access to data that are otherwise widely dispersed in the scientific literature.

ALFRED provides: Over 36,000 frequency tables, and growing Over 450 populations with descriptions and links Over 1300 sites typed for at least one population New GIS-based map interface to view populations and frequency data geographically Easy to use Keyword search Data that can be easily downloaded for analysis Free ALFRED Newsletter on a regular basis when you register

ALFRED Homepage ALFRED Homepage

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 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 Information Synonym(s) used in the keyword search View location of population on a geographic map

Frequency search result – tabular format The icon is used throughout ALFRED whenever additional information can be retrieved. Click on the to get additional information

Frequency 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 ALFRED function. It gives users the ability to visualize genetic data on polymorphisms in a geographic context. There are several ways users can interact with the interface including, selecting populations based on their geographic location and displaying data at the location of the population. This interface allows, among other things, users to easily see clinal patterns of frequencies, both worldwide and regionally. Overview What is GIS? GIS: Geographic Information SystemGIS: Geographic Information System –New interface interacts with GIS servers ALFRED uses a GIS package called “ArcIMS” (Arc Internet Mapping Server)ALFRED uses a GIS package called “ArcIMS” (Arc Internet Mapping Server) New interface supports an integrated view that encompasses queries to ALFRED and GIS serversNew interface supports an integrated view that encompasses queries to ALFRED and GIS servers

Map Interface Zoom 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_ _10, rs ) 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 ALFRED Team Senior Faculty Kenneth K. Kidd, Ph.D., Professor of Genetics and Psychiatry (ALFRED P.I.) Perry Miller, M.D., Ph.D., Director of Center for Medical Informatics Curators Shannon Stein, B.S., Research Associate Usha Soundararajan, M.S., Research Assistant Programmers Haseena Rajeevan, Ph.D., Systems Programmer Rohit Gadagkar, M.S., Programmer Consultants Andrew J. Pakstis, Ph. D., Research Scientist Judith R. Kidd, Ph. D., Research Scientist Kei-Hoi Cheung, Ph. D., Assistant Professor Supported by the U.S. National Science Foundation