ALFRED 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

IntroductionIntroduction What is in ALFRED? What is in ALFRED? How to access ALFRED How to access ALFRED What is ALFRED? What is ALFRED? Why is it necessary? Why is it necessary? What we are doing now? What we are doing now?

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

ALFRED Home Page ALFRED Home Page

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

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

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 America SouthAmericaP.S.

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

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

ALFRED The ALlele FREquency Database from Kidd Lab 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 InformaticsCurators Chen-Chen Yeh, M.S., Research Associate Rebekah Heinzen, B.A., Research AssistantProgrammers 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 AssociateConsultants Andrew J. Pakstis, Ph. D., Research Scientist Judith R. Kidd, Ph. D., Research Scientist Kei-Hoi Cheung, Ph. D., Assistant Professor