ALFRED: A Resource for Research and Teaching

1. ALFRED: A Resource for Research and Teaching http://alfred.med.yale.edu/ K. K. Kidd, H. Rajeevan, K.-H. Cheung1, S. Stein, U. Soundararajan, J. R. Kidd, A. J. Pakstis, and P. L. Miller1 Dept. of Genetics and 1Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, 06520-8005, USA. Through 5/31/07 ALFRED is supported by the U.S. National Science Foundation

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 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.

3. ALFRED provides: • Over 89,000 frequency tables, and growing • Over 500 populations with descriptions and links • Over 3,700 sites typed for at least one population • A GIS-based map interface to view populations and frequency data geographically • Easy to use search options including keyword search, publication author search and ALFRED UID search. • Data that can be easily downloaded for analysis • Free ALFRED Newsletter on a regular basis when you register

4. ALFRED Homepage

5. Face Lift for Description Pages Synonym(s) used in the keyword search Display Options *NEW* Data download options

6. Polymorphism linked to recent and previous locus/gene association Users can now locate polymorphisms that have “moved” in recent genome builds. Polymorphism linked to its recent and previous locus association.

7. Population Information Synonym(s) used in the keyword search View population on a geographic map Links to additional population information

8. Finding a Locus/Gene • Search for a locus alphabetically when you don’t know on which chromosome it is located Select the 1st letter of the desired Locus on the left Then select your Locus from the alphabetical list displayed on the right

9. Search for a locus alphabetically when you do know on which chromosome it is located Then select the desired locus from the alphabetical list Select the chromosome on which your locus is located and click “A”

10. Search for a locus by chromosomal position Then select the desired locus by its chromosomal position Select the chromosome on which your locus is located and click “P”

11. Educational Material A few starting points to help with classroom projects Clickable snapshots of ALFRED Continued on next slide

12. Allele frequency data download in PML (Polymorphism Markup Language) format Polymorphism Information Population Information Sample Information Allele frequency data

13. Links available from PharmGKB to ALFRED This link takes you to the Locus information page in ALFRED

14. Links available from dbSNP to ALFRED Scroll down Links take you to the Polymorphism information page in ALFRED Scroll down

15. 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 Programmer Haseena Rajeevan, Ph.D., Systems Programmer Consultants Andrew J. Pakstis, Ph. D., Research Scientist Judith R. Kidd, Ph. D., Research Scientist Kei-Hoi Cheung, Ph. D., Assistant Professor