ALFRED: an Allele Frequency Resource for Research and Teaching

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2011 Nov 1

PMID 22039151

Citations 40

Authors

Haseena Rajeevan

Usha Soundararajan

Judith R Kidd

Andrew J Pakstis

Kenneth K Kidd

Affiliations

Soon will be listed here.

Abstract

ALFRED (http://alfred.med.yale.edu) is a free, web accessible, curated compilation of allele frequency data on DNA sequence polymorphisms in anthropologically defined human populations. Currently, ALFRED has allele frequency tables on over 663,400 polymorphic sites; 170 of them have frequency tables for more than 100 different population samples. In ALFRED, a population may have multiple samples with each 'sample' consisting of many individuals on which an allele frequency is based. There are 3566 population samples from 710 different populations with allele frequency tables on at least one polymorphism. Fifty of those population samples have allele frequency data for over 650,000 polymorphisms. Records also have active links to relevant resources (dbSNP, PharmGKB, OMIM, Ethnologue, etc.). The flexible search options and data display and download capabilities available through the web interface allow easy access to the large quantity of high-quality data in ALFRED.

Citing Articles

CYP2C gene polymorphisms in North African populations.

Messaoudi M, Pakstis A, Boussetta S, Ben Ammar Elgaaied A, Kidd K, Cherni L Mol Biol Rep. 2024; 51(1):1145.

PMID: 39532754 DOI: 10.1007/s11033-024-10093-8.

Contribution of infectious diseases to the selection of ADH1B and ALDH2 gene variants in Asian populations.

Deiana G, Sun R, Huang J, Napolioni V, Ciccocioppo R Alcohol Clin Exp Res (Hoboken). 2024; 48(5):855-866.

PMID: 38462538 PMC: 11073917. DOI: 10.1111/acer.15288.

Unappreciated subcontinental admixture in Europeans and European Americans and implications for genetic epidemiology studies.

Gouveia M, Bentley A, Leal T, Tarazona-Santos E, Bustamante C, Adeyemo A Nat Commun. 2023; 14(1):6802.

PMID: 37935687 PMC: 10630423. DOI: 10.1038/s41467-023-42491-0.

Anti-Inflammatory Effects of Peripheral Dopamine.

Moore S, de Castro P, Yaqub D, Jose P, Armando I Int J Mol Sci. 2023; 24(18).

PMID: 37762126 PMC: 10530375. DOI: 10.3390/ijms241813816.

Native American genetic ancestry and pigmentation allele contributions to skin color in a Caribbean population.

Ang K, Canfield V, Foster T, Harbaugh T, Early K, Harter R Elife. 2023; 12.

PMID: 37294081 PMC: 10371226. DOI: 10.7554/eLife.77514.

References

Yoshiura K, Kinoshita A, Ishida T, Ninokata A, Ishikawa T, Kaname T . A SNP in the ABCC11 gene is the determinant of human earwax type. Nat Genet. 2006; 38(3):324-30. DOI: 10.1038/ng1733. View

Nadkarni N, Weale M, von Schantz M, Thomas M . Evolution of a length polymorphism in the human PER3 gene, a component of the circadian system. J Biol Rhythms. 2005; 20(6):490-9. DOI: 10.1177/0748730405281332. View

Rajeevan H, Osier M, Deng H, Druskin L, Heinzen R, Kidd J . ALFRED: the ALelle FREquency Database. Update. Nucleic Acids Res. 2003; 31(1):270-1. PMC: 165490. DOI: 10.1093/nar/gkg043. View

Phillips C, Salas A, Sanchez J, Fondevila M, Gomez-Tato A, Alvarez-Dios J . Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Genet. 2008; 1(3-4):273-80. DOI: 10.1016/j.fsigen.2007.06.008. View

Rosenberg N, Pritchard J, Weber J, Cann H, Kidd K, Zhivotovsky L . Genetic structure of human populations. Science. 2002; 298(5602):2381-5. DOI: 10.1126/science.1078311. View

Cheung K, Osier M, Kidd J, Pakstis A, Miller P, Kidd K . ALFRED: an allele frequency database for diverse populations and DNA polymorphisms. Nucleic Acids Res. 1999; 28(1):361-3. PMC: 102486. DOI: 10.1093/nar/28.1.361. View

Kosoy R, Nassir R, Tian C, White P, Butler L, Silva G . Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Hum Mutat. 2008; 30(1):69-78. PMC: 3073397. DOI: 10.1002/humu.20822. View

Gourraud P, Feolo M, Hoffman D, Helmberg W, Cambon-Thomsen A . The dbMHC microsatellite portal: a public resource for the storage and display of MHC microsatellite information. Tissue Antigens. 2006; 67(5):395-401. DOI: 10.1111/j.1399-0039.2006.00600.x. View

Ruitberg C, Reeder D, Butler J . STRBase: a short tandem repeat DNA database for the human identity testing community. Nucleic Acids Res. 2000; 29(1):320-2. PMC: 29767. DOI: 10.1093/nar/29.1.320. View

10.

Soranzo N, Bufe B, Sabeti P, Wilson J, Weale M, Marguerie R . Positive selection on a high-sensitivity allele of the human bitter-taste receptor TAS2R16. Curr Biol. 2005; 15(14):1257-65. DOI: 10.1016/j.cub.2005.06.042. View

11.

Pakstis A, Speed W, Kidd J, Kidd K . Candidate SNPs for a universal individual identification panel. Hum Genet. 2007; 121(3-4):305-17. DOI: 10.1007/s00439-007-0342-2. View

12.

Sherry S, Ward M, Kholodov M, Baker J, Phan L, Smigielski E . dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2000; 29(1):308-11. PMC: 29783. DOI: 10.1093/nar/29.1.308. View

13.

Sanchez J, Phillips C, Borsting C, Balogh K, Bogus M, Fondevila M . A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis. 2006; 27(9):1713-24. DOI: 10.1002/elps.200500671. View

14.

Li J, Absher D, Tang H, Southwick A, Casto A, Ramachandran S . Worldwide human relationships inferred from genome-wide patterns of variation. Science. 2008; 319(5866):1100-4. DOI: 10.1126/science.1153717. View

15.

van Baal S, Kaimakis P, Phommarinh M, Koumbi D, Cuppens H, Riccardino F . FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide. Nucleic Acids Res. 2006; 35(Database issue):D690-5. PMC: 1747180. DOI: 10.1093/nar/gkl934. View

16.

Pemberton T, Jakobsson M, Conrad D, Coop G, Wall J, Pritchard J . Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India. Ann Hum Genet. 2008; 72(Pt 4):535-46. PMC: 2495051. DOI: 10.1111/j.1469-1809.2008.00457.x. View

17.

Shriver M, Mei R, Parra E, Sonpar V, Halder I, Tishkoff S . Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation. Hum Genomics. 2005; 2(2):81-9. PMC: 3525270. DOI: 10.1186/1479-7364-2-2-81. View

18.

Sayers E, Barrett T, Benson D, Bolton E, Bryant S, Canese K . Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2009; 38(Database issue):D5-16. PMC: 2808881. DOI: 10.1093/nar/gkp967. View

19.

Li H, Pakstis A, Kidd J, Kidd K . Selection on the human bitter taste gene, TAS2R16, in Eurasian populations. Hum Biol. 2011; 83(3):363-77. DOI: 10.3378/027.083.0303. View

20.

Hewett M, Oliver D, Rubin D, Easton K, Stuart J, Altman R . PharmGKB: the Pharmacogenetics Knowledge Base. Nucleic Acids Res. 2001; 30(1):163-5. PMC: 99138. DOI: 10.1093/nar/30.1.163. View