ALFRED - the ALlele FREquency Database:

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ALFRED - the ALlele FREquency Database
An Update
H. Rajeevan1, K-H Cheung2, H. Deng1, J.R. Kidd1,
S. Stein1, A.J. Pakstis1, D. Chudnov1, P.L.
Miller2, K.K. Kidd1
1Dept. of Genetics and 2Center for Medical
Informatics, Dept. of Anesthesiology, Yale
University School of Medicine, New Haven, CT,
06520-8005, USA.
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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/
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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

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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.
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How to Use ALFRED
There are multiple ways of searching ALFRED, such
as

• 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

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ALFRED Homepage http//alfred.med.yale.edu/
New tabbed menu for easy navigation
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Polymorphism Information
New synonym field
This link will directly connect to the
corresponding dbSNP record
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Population Information
New synonym field
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Frequency search result tabular format

• The icon is used throughout ALFRED
  whenever additional information can be provided.

Click here to get additional information
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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
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Frequency search result matrix format

• Using 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 set

Uncheck check marks to eliminate rows and columns
to update matrix
Checks indicate data exists in ALFRED
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Graphical Overview of ALFRED

• A. Populations per site
• Ordered by number of populations typed
• (Multiple different samples of a population are
  not distinguished in this summary)

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

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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