ALFRED: An allele frequency database for anthropology - PubMed (original) (raw)
ALFRED: An allele frequency database for anthropology
Michael V Osier et al. Am J Phys Anthropol. 2002 Sep.
Abstract
The deluge of data from the human genome project (HGP) presents new opportunities for molecular anthropologists to study human variation through the promise of vast numbers of new polymorphisms (e.g., single nucleotide polymorphisms or SNPs). Collecting the resulting data into a single, easily accessible resource will be important to facilitate this research. We created a prototype Web-accessible database named ALFRED (ALelle FREquency Database, http://alfred.med.yale.edu/alfred/) to store and make publicly available allele frequency data on diverse polymorphic sites for many populations. In constructing this database, we considered many different concerns relating to the types of information needed for anthropology, population genetics, molecular genetics, and statistics, as well as issues of data integrity and ease of access to data. We also developed links to other Web-based databases as well as procedures for others to make links to the data in ALFRED. Here we present an overview of the issues considered and provisional solutions, as well as an example of data already available. It is our hope that this database will be useful for research and teaching in a wide range of fields, and that colleagues from various fields will contribute to making ALFRED an important resource for many studies as yet unforeseen.
Copyright 2002 Wiley-Liss, Inc.
Similar articles
- ALFRED: an allele frequency database for diverse populations and DNA polymorphisms--an update.
Osier MV, Cheung KH, Kidd JR, Pakstis AJ, Miller PL, Kidd KK. Osier MV, et al. Nucleic Acids Res. 2001 Jan 1;29(1):317-9. doi: 10.1093/nar/29.1.317. Nucleic Acids Res. 2001. PMID: 11125124 Free PMC article. - ALFRED: an allele frequency database for diverse populations and DNA polymorphisms.
Cheung KH, Osier MV, Kidd JR, Pakstis AJ, Miller PL, Kidd KK. Cheung KH, et al. Nucleic Acids Res. 2000 Jan 1;28(1):361-3. doi: 10.1093/nar/28.1.361. Nucleic Acids Res. 2000. PMID: 10592274 Free PMC article. - Developments of geriatric autopsy database and Internet-based database of Japanese single nucleotide polymorphisms for geriatric research (JG-SNP).
Sawabe M, Arai T, Kasahara I, Esaki Y, Nakahara K, Hosoi T, Orimo H, Takubo K, Murayama S, Tanaka N; Tokyo Metropolitan Geriatric Medical Center; Japan Science and Technology Agency. Sawabe M, et al. Mech Ageing Dev. 2004 Aug;125(8):547-52. doi: 10.1016/j.mad.2004.06.005. Mech Ageing Dev. 2004. PMID: 15336912 - Generic design of Web-based clinical databases.
Anhøj J. Anhøj J. J Med Internet Res. 2003 Nov 4;5(4):e27. doi: 10.2196/jmir.5.4.e27. J Med Internet Res. 2003. PMID: 14713655 Free PMC article. Review. - Central mutation databases--a review.
Porter CJ, Talbot CC, Cuticchia AJ. Porter CJ, et al. Hum Mutat. 2000;15(1):36-44. doi: 10.1002/(SICI)1098-1004(200001)15:1<36::AID-HUMU9>3.0.CO;2-D. Hum Mutat. 2000. PMID: 10612820 Review.
Cited by
- Heterogeneity in disease resistance and the impact of antibiotics in the US.
Cook CJ, Fletcher JM. Cook CJ, et al. Econ Hum Biol. 2022 Dec;47:101155. doi: 10.1016/j.ehb.2022.101155. Epub 2022 Jul 27. Econ Hum Biol. 2022. PMID: 35944452 Free PMC article. - Dopamine genes are linked to Extraversion and Neuroticism personality traits, but only in demanding climates.
Fischer R, Lee A, Verzijden MN. Fischer R, et al. Sci Rep. 2018 Jan 29;8(1):1733. doi: 10.1038/s41598-017-18784-y. Sci Rep. 2018. PMID: 29379052 Free PMC article. - Theory and methods in cultural neuroscience.
Chiao JY, Hariri AR, Harada T, Mano Y, Sadato N, Parrish TB, Iidaka T. Chiao JY, et al. Soc Cogn Affect Neurosci. 2010 Jun;5(2-3):356-61. doi: 10.1093/scan/nsq063. Soc Cogn Affect Neurosci. 2010. PMID: 20592044 Free PMC article. Review. - Ancestry inference of 96 population samples using microhaplotypes.
Bulbul O, Pakstis AJ, Soundararajan U, Gurkan C, Brissenden JE, Roscoe JM, Evsanaa B, Togtokh A, Paschou P, Grigorenko EL, Gurwitz D, Wootton S, Lagace R, Chang J, Speed WC, Kidd KK. Bulbul O, et al. Int J Legal Med. 2018 May;132(3):703-711. doi: 10.1007/s00414-017-1748-6. Epub 2017 Dec 16. Int J Legal Med. 2018. PMID: 29248957 Free PMC article. - ALFRED: an allele frequency resource for research and teaching.
Rajeevan H, Soundararajan U, Kidd JR, Pakstis AJ, Kidd KK. Rajeevan H, et al. Nucleic Acids Res. 2012 Jan;40(Database issue):D1010-5. doi: 10.1093/nar/gkr924. Epub 2011 Oct 28. Nucleic Acids Res. 2012. PMID: 22039151 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources