ALFRED: An allele frequency database for anthropology.
- Authors
- Osier, Michael V; Cheung, Kei-Hoi; Kidd, Judith R; Pakstis, Andrew J; Miller, Perry L; Kidd, Kenneth K
- Year
- 2002
- Journal
- American journal of physical anthropology
- PMID
- 12209575
- DOI
- 10.1002/ajpa.10094
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.
No figures extracted from this document.
No chunks — full text not yet ingested.
No entities extracted from this document yet.
No uploaded files.
No citations found.
In this knowledge base
| Title | Year | PMID |
|---|---|---|
| Genetics and alcoholism. | 2013 | 23712313 |
External
| Title | Authors | Journal | Year | Link |
|---|---|---|---|---|
| MHappaMundi: A custom AmpliSeq microhaplotype panel for ancestry inference. | Rodrigues P et al. | — | 2026 | → |
| Using FastID to analyze complex SNP mixtures from indoor dust. | Meiklejohn KA et al. | — | 2023 | → |
| Heterogeneity in disease resistance and the impact of antibiotics in the US. | Cook CJ et al. | — | 2022 | → |
| A systems omics-based approach to decode substance use disorders and neuroadaptations. | Veerappa A et al. | — | 2021 | → |
| FrogAncestryCalc: A standalone batch likelihood computation tool for ancestry inference panels catalogued in FROG-kb. | Rajeevan H et al. | — | 2020 | → |
| Microhaplotypes in forensic genetics. | Oldoni F et al. | — | 2019 | → |
| Ancestry inference of 96 population samples using microhaplotypes. | Bulbul O et al. | — | 2018 | → |
| Dopamine genes are linked to Extraversion and Neuroticism personality traits, but only in demanding climates. | Fischer R et al. | — | 2018 | → |
| Recent Selection on a Class I ADH Locus Distinguishes Southwest Asian Populations Including Ashkenazi Jews. | Gu S et al. | — | 2018 | → |
| The macromorphoscopic databank. | Hefner JT | — | 2018 | → |
| Ancestry prediction in Singapore population samples using the Illumina ForenSeq kit. | Ramani A et al. | — | 2017 | → |
| Ancient DNA reveals selection acting on genes associated with hypoxia response in pre-Columbian Peruvian Highlanders in the last 8500 years. | Fehren-Schmitz L et al. | — | 2016 | → |
| Lactase non-persistence and general patterns of dairy intake in indigenous and mestizo chilean populations. | Fernández CI et al. | — | 2016 | → |
| Recent advances in the study of fine-scale population structure in humans. | Novembre J et al. | — | 2016 | → |
| Haemostaseome-associated SNPs: has the thrombotic phenotype a greater influence than ethnicity? GMT study from Aquitaine including Basque individuals. | Freyburger G et al. | — | 2015 | → |
| Distribution of genetic polymorphisms associated with hepatitis C virus (HCV) antiviral response in a multiethnic and admixed population. | Trinks J et al. | — | 2014 | → |
| Extreme population differences in the human zinc transporter ZIP4 (SLC39A4) are explained by positive selection in Sub-Saharan Africa. | Engelken J et al. | — | 2014 | → |
| Genome-wide mapping of IBD segments in an Ashkenazi PD cohort identifies associated haplotypes. | Vacic V et al. | — | 2014 | → |
| Lactase persistence and dairy intake in Mapuche and Mestizo populations from southern Chile. | Fernández CI et al. | — | 2014 | → |
| Genetics and alcoholism. | Edenberg HJ et al. | — | 2013 | → |
| ALFRED: an allele frequency resource for research and teaching. | Rajeevan H et al. | — | 2012 | → |
| Novelty-seeking DRD4 polymorphisms are associated with human migration distance out-of-Africa after controlling for neutral population gene structure. | Matthews LJ et al. | — | 2011 | → |
| Selection on the human bitter taste gene, TAS2R16, in Eurasian populations. | Li H et al. | — | 2011 | → |
| Theory and methods in cultural neuroscience. | Chiao JY et al. | — | 2010 | → |
| Genetic variation in IL28B and spontaneous clearance of hepatitis C virus. | Thomas DL et al. | — | 2009 | → |
| HGD-Chn: The Database of Genome Diversity and Variation for Chinese Populations. | Hong-Sheng G et al. | — | 2009 | → |
| ALFRED: an allele frequency database for microevolutionary studies. | Rajeevan H et al. | — | 2007 | → |
| Global diversity and evidence for coevolution of KIR and HLA. | Single RM et al. | — | 2007 | → |
| Linguistic tone is related to the population frequency of the adaptive haplogroups of two brain size genes, ASPM and Microcephalin. | Dediu D et al. | — | 2007 | → |
| Significant variation in haplotype block structure but conservation in tagSNP patterns among global populations. | Gu S et al. | — | 2007 | → |
| Effects of traditional and western environments on prevalence of type 2 diabetes in Pima Indians in Mexico and the U.S. | Schulz LO et al. | — | 2006 | → |
| What makes a champion? Explaining variation in human athletic performance. | Brutsaert TD et al. | — | 2006 | → |
| A common inversion under selection in Europeans. | Stefansson H et al. | — | 2005 | → |
| Evolution of the DRD2 gene haplotype and its association with alcoholism in Mexican Americans. | Luo HR et al. | — | 2005 | → |
| Is spatial distribution of the HIV-1-resistant CCR5Delta32 allele formed by ecological factors? | Balanovsky O et al. | — | 2005 | → |
| Linkage disequilibrium patterns vary substantially among populations. | Sawyer SL et al. | — | 2005 | → |
| Use of autosomal loci for clustering individuals and populations of East Asian origin. | Kim JJ et al. | — | 2005 | → |
| Implications of biogeography of human populations for 'race' and medicine. | Tishkoff SA et al. | — | 2004 | → |
| Possible epistatic role of ADH7 in the protection against alcoholism. | Osier MV et al. | — | 2004 | → |
| The evolution and population genetics of the ALDH2 locus: random genetic drift, selection, and low levels of recombination. | Oota H et al. | — | 2004 | → |
| Understanding human DNA sequence variation. | Kidd KK et al. | — | 2004 | → |
| ALFRED: the ALelle FREquency Database. Update. | Rajeevan H et al. | — | 2003 | → |