1. ALFRED: the ALlele FREquency Database
Kenneth K. Kidd and the ALFRED Team
Department of Genetics and Center for Medical Informatics
Yale University School of Medicine
Supported by the U.S. National Science Foundation

2. Introduction What is ALFRED? How to access ALFRED Why is it necessary?
What we are doing now?
What is in ALFRED?

3. What is ALFRED?
ALFRED, the ALlele FREquency Database, is designed to integrate into a single source information on the frequencies of human DNA sequence variants.

4. ALFRED Home Page http://alfred.med.yale.edu/alfred/

5. ALFRED is designed to allow reference of frequencies to:
A specific sampling of an ethnic group.
A specific typing protocol for a specific polymorphism at a specific locus.
Cross reference to the literature for other publications of frequencies based on the same sample or ethnic group.

6. Why is it necessary?
ALFRED is designed to serve as a central repository of frequencies for variation in the human genome–curated and cross referenced to molecular and ethnographic databases–by assembling in one place data that are dispersed very widely in the scientific literature.

7. Why is it necessary?
ALFRED is web-based, publicly available, with easy to download data thus serving as a resource for many types of research projects.
With its graphic displays of data, ALFRED can also serve as an educational resource for physical anthropology and human population genetics.

8. What are we doing now? Data content - Quality control
Criteria - a minimal typed sample size of 20 individuals, minimization of missing data, time-stamped frequency data (i.e., different versions of frequency data are available).

9. What are we doing now? Data integration and accumulation
ALFRED curators are currently uploading allele frequency data from published literature throughout the physical anthropology and population genetics peer reviewed journals.

10. What are we doing now? Data management
ALFRED programmers are currently working on the migration of ALFRED from Access to Oracle in order to handle the rapidly growing database.

11. What is in ALFRED?
ALFRED stores allele frequencies and information on a wide range of loci, polymorphic sites, populations, and samples.

12. Table Summary Numbers As of April 9, 2002

13. Loci Example: Chromosome 22

14. Locus Example: Catechol-O-Methyl Transferase

15. Locus Example: Catechol-O-Methyl Transferase

16. Definition of the Polymorphism
A clear protocol
PCR primers and product sizes for In/Dels and STRPs
PCR primers and fragment sizes after enzyme digestion for RSPs
Unambiguous definition of varying nucleotides based on flanking sequence.

17. Polymorphisms Example: COMT, 3-site haplotype

18. Allele Frequencies Example: COMT, 3-site haplotype

19. Allele Frequencies Example: COMT, 3-site haplotype

20. Populations Example: North America

21. Populations Example: Maya, Yucatan

22. Samples Example: Maya, Yucatan

23. Frequency data retrieval Search

24. Frequency Variation for Four SNPS in 33 Populations
Africa
Europe/Middle East
East Asia
North America
South
America P. S.

25. ALFRED System Implementation
Microsoft Access (migration to Oracle)
Microsoft NT Server with Internet Information Server (IIS)
Scripts Written in Server-side ASP (VB Script)

26. ALFRED System Overview
Input Data Sources
Kidd Lab Data
HAPLO
Program
PhenoDB
Collaborators
Others (e.g.
literature)
Web Server
(ASP)
Client
Browser
External
Data
Resources
ALFRED
ODBC
NT Server

27. ALFRED The ALlele FREquency Database from Kidd Lab
Suggestions and comments are welcome.

28. The ALFRED Team Senior Faculty Curators Programmers Consultants
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
Chen-Chen Yeh, M.S., Research Associate
Rebekah Heinzen, B.A., Research Assistant
Programmers
Michael V. Osier, Ph.D. Candidate, Graduate Student
Haseena Rajeevan, Ph. D., Systems Programmer
Nicholas P. Tosches, M.D., Associate Research Scientist
Lyudmila Druskin, M.D., Postdoctoral Fellow and Associate
Consultants
Andrew J. Pakstis, Ph. D., Research Scientist
Judith R. Kidd, Ph. D., Research Scientist
Kei-Hoi Cheung, Ph. D., Assistant Professor