ALFRED: A Resource for Research and Teaching

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.

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

Through 5/31/07 ALFRED is supported by the U.S. National Science Foundation

OverviewALFRED, 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.

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

ALFRED Homepage

Face Lift for Description Pages

Display Options

*NEW* Data download options

Synonym(s) used in the keyword search

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.

Population Information

View population on a geographic map

Synonym(s) used in the keyword search

Links to additional population information

Finding a Locus/Gene• Search for a locus alphabetically when you don’t

know on which chromosome it is locatedSelect the 1st letter of the desired Locus on the left

Then select your Locus from the alphabetical list

displayed on the right

• Search for a locus alphabetically when you do know on which chromosome it is located

Select the chromosome on which your locus is located

and click “A”

Then select the desired locus from the

alphabetical list

• Search for a locus by chromosomal position

Select the chromosome on which your locus is located

and click “P”

Then select the desired locus by its chromosomal

position

Educational Material

Clickable snapshots of ALFRED

A few starting points to help with classroom projects

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Allele frequency data download in PML (Polymorphism Markup Language) format

Polymorphism Information

Population Information

Sample Information

Allele frequency data

Links available from PharmGKB to ALFRED

This link takes you to the Locus information page in

ALFRED

Links available from dbSNP to ALFRED

Links take you to the Polymorphism information page

in ALFRED

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The ALFRED TeamThe ALFRED Team

Senior FacultyKenneth K. Kidd, Ph.D., Professor of Genetics and Psychiatry (ALFRED P.I.)Perry Miller, M.D., Ph.D., Director of Center for Medical Informatics

CuratorsShannon Stein, B.S., Research AssociateUsha Soundararajan, M.S., Research Assistant

ProgrammerHaseena Rajeevan, Ph.D., Systems Programmer

ConsultantsAndrew J. Pakstis, Ph. D., Research ScientistJudith R. Kidd, Ph. D., Research ScientistKei-Hoi Cheung, Ph. D., Assistant Professor