Overview
Welcome! to the newly designed and implemented web interface of ALFRED.
ALFRED was conceived and developed by Prof. Kenneth K. Kidd and Dr. Judith R. Kidd & Kidd Lab in the Department of Genetics at Yale. It aims to provide allele frequency data on human population samples, making this information readily accessible for scientific research and educational use.The ALFRED database includes published allele frequency data that has been systematically curated and added to the database over the past 20 years.
ALFRED the database was designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases. Initially, ALFRED contained primarily data generated in the laboratories of K.K. and J.R. Kidd in the Department of Genetics at Yale, including extensive unpublished data. Data from the published literature were entered into ALFRED in a systematic way, with a focus on polymorphisms studied in many different populations.
ALFRED is distinct from such databases as dbSNP, which catalogs sequence variation. ALFRED's focus is on allele frequencies in diverse anthropologically defined populations. It is not a compendium of human DNA polymorphisms but of frequencies of selected polymorphisms with an emphasis on those that have been studied in multiple populations. All of the data in ALFRED are considered to be in the public domain and available for use in research and teaching.
The new version of the ALFRED web interface is currently a work in progress. We are continually revising its structure and functionality as time permits for ongoing improvements. Please note that we are not adding new data to the database at this time.
Criteria for Including Data in ALFRED
We believe gene frequency data are meaningful only when the population sample is well-defined and large enough to provide a reasonably accurate estimate, and when the polymorphism is sufficiently defined to be replicable. As a result, not all published gene frequency data are included in ALFRED. There is no strict minimum sample size; even small samples from underrepresented regions or those with data on multiple polymorphisms can be valuable. For example, the Nasioi sample, which consists of 22 individuals studied across multiple markers, is a case in point. We include samples that can be reasonably specified in terms of ethnicity, though this sometimes encompasses broadly defined groups like "United States whites," which effectively represents "mixed European" populations.
Because ALFRED focuses on gene frequency variation among populations, we included frequency estimates only for polymorphisms that have been studied in at least six distinct population samples. Of course, there are exceptions, especially if a sample generally studied for multiple polymorphisms that meet the ">6 populations" criterion also has data on some unique polymorphisms.
ALFRED UID
Every record in ALFRED has a unique identifier (UID). The UIDs are a text string consisting of three parts: a table identifier, a record number, and a check character. The Table Identifier is a two character symbol representing the table the record belongs to, such as PO for POpulation, SI for SIte, and so on. The Record Number is an internal identifier for the specific record. The Check Character is a simple checksum for the digits in the Record Number. The Check Character is determined by summing the digits of the Record Number, taking the modulo 26 of that number, and representing the resulting number as an upper case ASCII character (A-Z). For example, SI014100G is the UID for the rsnumber rs1126670. UIDs are stable for a particular record, providing a dependable means for users to access data.
Use of ALFRED
Help is available within ALFRED, and we hope the search procedures are fairly intuitive. If you encounter any issues or find that something is not working as expected, we welcome your feedback. Below are some tips to help you quickly get an overview of what ALFRED has to offer.
There are several great ways of searching ALFRED. The following search options are available from the tabbed menu provided for easy browsing.
UID Search
Searches for detailed information using UID. Unique IDentifiers (UIDs) are used in ALFRED to access specific records from various tables. UIDs are stable for a particular record, providing a dependable means for users to access data.
Loci Search
Follow the links Chromosome - Locus - Polymorphism
Selecting a locus would bring you to Locus Information page,
and selecting a site from the displayed list would bring you to
Polymorphism Information page.
Population Search
Follow the links Geographic Region - Population Selecting a population would bring you to Population Information page. Information regarding population samples are also provided in this page.
Keyword Search
The Keyword Search function helps a user to query the database using keywords. Fields available for keyword search are official gene symbols, ALFRED loci names, dbSNP rs#s, GDB IDs for loci, population names, ALFRED sample names, ALFRED polymorphism names and ALFRED geographic names.
ALFRED Publications
1. Cheung KH, Miller PL, Kidd JR, Kidd KK, Osier MV, Pakstis AJ. "ALFRED: a Web-accessible allele frequency database".Pac Symp Biocomput 2000.:639-50.
pdf file of article
2. Cheung KH, Osier MV, Kidd JR, Pakstis AJ, Miller PL, Kidd KK. "ALFRED: an allele frequency database for diverse populations and DNA polymorphisms.".Nucleic Acids Res. 28(1):361-3. (2000)
pdf file of article
3. Osier MV, Cheung KH, Kidd JR, Pakstis AJ, Miller PL, Kidd KK. "ALFRED: an allele frequency database for diverse populations and DNA polymorphisms--an update." Nucleic Acids Res. 29(1):317-9. (2001)
pdf file of article
4. Osier MV, Cheung KH, Kidd JR, Pakstis AJ, Miller PL, Kidd KK. "Expansion of ALFRED, the ALlele FREquency Database." Am J Phys Anthropol. Annual Meeting Issue: Supplement 34:94. (2002)
5. Osier MV, Cheung KH, Kidd JR, Pakstis AJ, Miller PL, Kidd KK. "ALFRED: an allele frequency database for Anthropology." Am J Phys Anthropol. 119:77-83. (2002)
pdf file of article
6. Osier MV, Cheung KH, Rajeevan H, Pakstis AJ, Kidd JR, Miller PL, Kidd KK. "ALFRED(ALlele FREquency Database): A Resource for genetic anthropology and human population genetics." Human Origins & Disease . CSHL Meeting Abstracts of Papers. 43. (2002)
7. Rajeevan H, Osier MV, Cheung KH, Deng H, Druskin L, Heinzen R, Kidd JR, Stein S, Pakstis AJ, Tosches NP, Yeh CC, Miller PL, Kidd KK. "ALFRED ? the ALlele FREquency Database ? update." Nucleic Acids Research..31(1):270-271.(2003) pdf file of article
8. Kidd KK, Rajeevan H, Osier MV, Cheung KH, Deng H, Druskin L, Heinzen R, Kidd JR, Stein S, Pakstis AJ, Tosches NP, Yeh CC, Miller PL. "ALFRED ? the ALlele FREquency Database ? update." Am J Phys Anthropol. Annual Meeting Issue: Supplement S36:128. (2003)
9. Rajeevan H, Cheung KH, Gadagkar R, Stein S, Soundararajan U, Kidd JR, Pakstis AJ, Miller P, Kidd KK. "ALFRED: An allele frequency database for Microevolutionary Studies." Evolutionary Bioinformatics Online.2005:1 (2005) pdf file of article
10.Rajeevan H, Soundararajan U, Kidd JR, Pakstis AJ, Kidd KK. "ALFRED: an allele frequency resource for research and teaching." Nucleic Acids Research.40(D1): D1010-D1015.(2012) pdf file of article