1. ALFRED - the ALlele FREquency Database: H. Rajeevan 1, K-H Cheung 2, H. Deng 1, J.R. Kidd 1, S. Stein 1, A.J. Pakstis 1, D. Chudnov 1, P.L. Miller 2, K.K. Kidd 1 1 Dept. of Genetics and 2 Center for Medical Informatics, Dept. of Anesthesiology, Yale University School of Medicine, New Haven, CT, 06520-8005, USA. An Update

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

3. ALFRED provides: Over 20,000 frequency tables, and growing Over 350 populations with descriptions and links Over 950 sites typed for at least one population Populations divided by geographic region for easy browsing Easy to use Keyword search Data that can be easily downloaded for analysis Free ALFRED Newsletter on a regular basis when you register

4. ALFRED ALFRED Data Summary: 22227 frequency tables (one population typed for one site) 1031 polymorphisms 372 populations If you know of any data that should be in ALFRED send us the reference or submit your own data electronically.

5. ALFRED How to Use ALFRED Search by locus name, polymorphism name, population name, or geographic region: From the homepage, click ‘keyword search’ under the search tab Enter the name in the preferred keyword search option Search by ALFRED UID (Unique Identifier): From the homepage, click basic search under the search tab Enter the UID in the ‘Search by UID’ field Search for loci using chromosome number: From the homepage, click ‘loci’ under the search tab Select the desired chromosome number from the list on the left and a list of loci on the chromosome will display on the right Search by browsing the population names: From the homepage, click ‘populations’ under the search tab Select the desired geographic region or sub region from the list on the left and the population located in that region will display on the right There are multiple ways of searching ALFRED, such as:

6. ALFRED Homepage ALFRED Homepage http://alfred.med.yale.edu/ New tabbed menu for easy navigation

7. Polymorphism Information New synonym field This link will directly connect to the corresponding dbSNP record

8. Population Information New synonym field

9. Frequency search result – tabular format Click here to get additional information The icon is used throughout ALFRED whenever additional information can be provided.

10. 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

11. Frequency search result – matrix format Using the keyword search, enter gene names or symbols and population names to retrieve a polymorphism X population matrixUsing the keyword search, enter gene names or symbols and population names to retrieve a polymorphism X population matrix After customizing your matrix you can retrieve the frequencies for your data setAfter customizing your matrix you can retrieve the frequencies for your data set Uncheck check marks to eliminate rows and columns to update matrix Checks indicate data exists in ALFRED

12. Graphical Overview of ALFRED Graphical Overview of ALFRED A. Populations per site A. Populations per site –Ordered by number of population’s typed (Multiple different samples of a population are not distinguished in this summary)

13. B. Sites per population B. Sites per population –Ordered by number of sites typed (Multiple different samples of a population are not distinguished in this summary)

14. 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 Hongyi Deng, M.S., Research Associate Shannon Stein, B.S., Research Associate Usha Soundararajan, M.S., Research Assistant Programmers Haseena Rajeevan, Ph.D., Systems Programmer Daniel Chudnov, M.S., Systems Programmer Rohit Gadagkav, 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