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
Introduction

What is ALFRED?

How to access ALFRED

Why is it necessary?

What we are doing now?

What is in ALFRED?
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.
ALFRED Home Page
http://alfred.med.yale.edu/alfred/
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.
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.
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.
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).
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.
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.
What is in ALFRED?

ALFRED stores allele frequencies and
information on a wide range of loci,
polymorphic sites, populations, and
samples.
Table Summary Numbers
As of April 9, 2002
Loci
Example: Chromosome 22
Locus
Example: Catechol-O-Methyl Transferase
Locus
Example: Catechol-O-Methyl Transferase
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.
Polymorphisms
Example: COMT, 3-site haplotype
Allele Frequencies
Example: COMT, 3-site haplotype
Allele Frequencies
Example: COMT, 3-site haplotype
Populations
Example: North America
Populations
Example: Maya, Yucatan
Samples
Example: Maya, Yucatan
Frequency data retrieval
Search
Frequency Variation for
Four SNPS in 33 Populations
Africa
Europe/Middle East
East Asia
North South
P. S. America America
ALFRED System Implementation

Microsoft Access (migration to Oracle)

Microsoft NT Server with
Internet Information Server (IIS)

Scripts Written in Server-side ASP
(VB Script)
ALFRED System Overview
Input Data Sources
Kidd Lab Data
Collaborators
External
Data
Resources
HAPLO
Program
ALFRED
PhenoDB
ODBC
NT Server
Web Server
(ASP)
Others (e.g.
literature)
Client
Browser
ALFRED
The ALlele FREquency Database
from Kidd Lab
http://alfred.med.yale.edu/alfred/index.asp
Suggestions and comments are welcome.
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
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