Everything a bout The ALlele FREquency Database

OverviewALFRED has been 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data generated in the laboratories of K.K. and J.R. Kidd in the Department of Genetics at Yale, including extensive unpublished data.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 are being entered into ALFRED in a systematic way, with a focus on polymorphisms studied in many different populations. (Researchers wishing to have their data entered into ALFRED should contact us. If suitable data can be sent in appropriate electronic format, it will be much easier to include them in ALFRED, see "Criteria" below.) 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. ALFRED is a work in progress. The structure and functionality of ALFRED are being revised in an ongoing process as time allows improvements to be implemented. We are also routinely adding new data and links to other databases. Those of us on the ALFRED staff hope these data will be useful to others. We welcome comments on content, structure, and the interfaces available. ALFRED is maintained by the ALFRED Staff. ________________________________________Criteria for Data Entry into ALFREDWe feel that gene frequency data are only meaningful if a population sample is reasonably well defined and large enough for a reasonably accurate frequency estimate and if the polymorphism is sufficiently defined to be replicable. Therefore, not all published gene frequency data will be included in ALFRED. Currently, there is no absolute minimum sample size since samples that are small but come from sparsely represented areas and/or have data on multiple polymorphisms can be very useful. (The Nasioi sample is a specific example of such small sample (22 individuals) studied for multiple markers.) We are only including samples that can be reasonably specified as to ethnicity though this includes some highly heterogeneous groups such as "United States whites", which is the equivalent of "mixed European". Because ALFRED focuses on gene frequency variation among populations, we are generally including 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. Similarly, various small sets of data are being entered when we know or expect there are additional data becoming or already available for eventual entry into ALFRED. Our available resources to enter data from the literature are quite limited but if researchers can provide suitable electronic versions of their appropriate data we will be happy to add them to ALFRED. The above criteria for inclusion in ALFRED are subject to change. We welcome comments from the scientific community interested in these data and will attempt to follow any consensus that emerges. ________________________________________Data submission to ALFRED - guidelinesOnly data on well defined population samples that are large enough to yield reasonably accurate frequencies and for polymorphisms sufficiently defined to be replicable can be included in ALFRED. If the submitted data lack any of this information, the data lose much of their value. Therefore, we are looking for the most complete set of information for each population sample. As an aid in your ALFRED submission we have listed below guidelines that you should follow in order to provide the necessary data. In addition to the actual frequencies, we will need further information regarding your publications, samples, loci and sites. Below you will find what type other information we will need to input your data into ALFRED.
PublicationsWe need any citations for publications that contain the allele frequencies that you are submitting.Your data will be linked to these publications. If your data are unpublished the data will be referred to the researcher’s name saying they are unpublished. If they are published in the future, you will need to send us the new citation in order for the data to be linked to the appropriate publication. SampleALFRED distinguishes samples of a population (a particular set of individuals) from the population. This allows future researchers to consider whether differences of whatever sort, shown by different loci, for example, can be attributed to the loci because the same set of individuals was tested for both loci or might be attributed to sampling differences because different sets of individuals were tested. To describe the sample sufficiently, we need to know about certain elements concerning your specific sample. The information you provide will also be used to aid in a complete description of the population from which the sample was collected. The following information is most important:• specific sample information when available (related/unrelated, age, men/women, etc.); • where the sample was collected; • geographic location of sample (city, village, etc.); • precisely who collected the sample (source); • the ethnic make-up of the sample; • the sample size (number of individuals); • any references to articles with published information concerning your particular sample; • language spoken; If the population is not yet described in ALFRED additional information, if available, can also be useful in describing the population. Such information would include: • population name; • subsistence practices; • historical information ; • religion; • any other cultural traditions; • any ethnographic citations. If all of this information is not available, please give the most complete information as possible. Locus: Please provide the official name and symbol for the gene in which the site is located. For the official gene symbol, go to the HGNC website http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl. If you cannot find an official gene symbol for the site, please give us as much information as possible. For intergenic sites it is helpful to have the name of the closest gene and an indication of the distance from the gene 5' or 3'Site (polymorphism): • Specify polymorphism location within the gene if available (e.g. "intron 3"); • Specify nucleotide/amino acid variations if available; • Specify restriction enzyme used to detect this polymorphism if it’s a RFLP; • Give GenBank accession number and/or dbSNP ss# (rs#) if available; • Other additional information used to best describe this site. • Give 10-15 bp flanking sequence on both sides of variant if available. Allele: • For RFLP, use site absent and site present for the two allele names; • For STRP and VNTR, use number of repeats as allele names. If you use fragment size as allele names, please provide typing protocol and specify primer sequences; • For Ins/Del, use insertion and deletion as allele names; • For SNP, use nucleotide variants as allele names. For example, A/G SNP has A and G for the two alleles. Excel Spreadsheet: The excel spreadsheet provided, can be used for sumitting data to the ALFRED Staff at alfred@yale.edu . The information that has be provided in the spreadsheet are as follows: • Sample name: name of sample you used in publication; • Number of chromosomes: number of chromosomes in the population sample; • Locus symbol: official gene symbol; • Site name: site name used in publication; • Allele name: see above; • Frequency: frequency value; • Typed number of chromosomes: number of chromosomes actually typed for that marker in that population sample (may be less than the sample size because of missing data); • Typing method: method used for typing each polymorphism. Sample, locus, and site information can be submitted via a Word file or other comparable word processing file. If you have problems using the excel spreadsheet provided please let us know and we will work with you to come up with a more useful method of submitting your data. If you have any questions, comments or suggestions about any aspect of ALFRED, please feel free to contact us.FOR MORE INFORMATION:http://www.btlogy.blogspot.com/

BioCarta

Proteomics marketplace and resource center
http://www.biocarta.com/

BIOBASE

Specialized biological databases, mainly from the field of molecular biology, including the TRANSFAC database on transcription factors, their genomic binding sites and their general binding profiles.
BIOBASE is the leading content provider of biological databases, knowledge tools and software for the life science industry. We offer our customers well-structured data, assembled by highly qualified subject-matter experts, organized in an accessible and easily searchable manner that enables researchers to identify connections between disparate pieces of information and to apply that knowledge to their specific topic of interest.

http://www.biobase-international.com/

BIND

Biomolecular Interaction Network Database
Between 1999-2005 Blueprint developed BIND and other bioinformatics resources at Mount Sinai Hospital in Toronto in the laboratory of Principal Investigator, Christopher Hogue.
In 2006 and beyond Blueprint will continue to engage in cutting-edge research, training and development of bioinformatics products and services.

http://www.blueprint.org/

BGEM

The St. Jude Brain Gene Expression Map (BGEM) project is managed by Tom Curran, Ph.D., Patricia Jensen, Ph. D., and Susan Magdaleno, Ph. D. in the Department of Developmental Neurobiology at St. Jude Children’s Research Hospital.Technical expertise is provided by Karen Lehman, Andrew Asbury, Tony Cheung, Tommie Cornelius, Diana Batten, and Christopher Eden. Custom primer design for generating riboprobe template for in situ hybridization analysis is performed in part by The National Center for Biotechnology Information (NCBI). The St. Jude BGEM website is built and maintained by software engineers Nileshwar Dosooye, and Sundeep Shakya and the Bioinformatics programs were written by Perdeep Mehta, Ph.D in the Hartwell Center for Bioinformatics and Biotechnology at St. Jude Children’s Research Hospital. The BGEM project is part of the Gene Expression Nervous System Atlas (GENSAT) funded by the National Institute for Neurological Disorders and Stroke (NINDS), National Institute of Mental Health (NIMH), and National Institute for Drug Abuse (NIDA) at the NIH and the American Lebanese Syrian Associated Charities (ALSAC) at St. Jude Children's Research Hospital.
http://www.stjudebgem.org

Berkeley Drosophila Genome Project

Berkeley Drosophila Genome Project

http://www.fruitfly.org/

BCM Search Launcher

Baylor Human Genome Center

BCM Search Launcher
The Baylor College of Medicine Search Launcher is an on-going project to organize molecular biology-related search and analysis services available on the WWW by function by providing a single point-of-entry for related searches (e.g., a single page for launching protein sequence searches using standard parameters).

http://searchlauncher.bcm.tmc.edu/

Base4 Bioinformatics

Integrated systems solutions for biotechnology and pharmaceutical development.

http://www.opentext.com/

Bacterial Names with Standing in Nomenclature

List of Prokaryotic names with Standing in Nomenclature Formerly List of Bacterial names with Standing in Nomenclature (LBSN)

http://www.bacterio.cict.fr/

AtlasInfo

Clontech Laboratories, Inc.
Clontech Laboratories provides kits, reagents, and services that help researchers explore questions about gene discovery, regulation, and function. As the newest member of the Takara Bio Group, Clontech joins a company that holds a leadership position in the global market and is committed to improving the human condition through biotechnology. Clontech’s mission is to develop high-quality innovative tools and services to accelerate discovery.

http://atlasinfo.clontech.com/

Atlas of Side-Chain and Main-Chain Hydrogen Bonding is available for biomolecular modellers

University College London was early to recognise the importance of Biochemistry as a scientific discipline. Even during the last quarter of the nineteenth century the study of Physiological Chemistry was being actively pursued within the UCL Department of Physiology. The appointment of the eminent nutritionist Sir Jack Drummond as UCL's first Professor of Biochemistry in 1922 began the process that eventually led to the founding of a separate department of Biochemistry in 1946 and the recognition at UCL of Biochemistry as a distinct and important scientific discipline. Initially the new department only admitted postgraduate students but by 1953 was one of the first departments in the UK to offer a BSc programme in Biochemistry. Emeritus Professor Peter Campbell has compiled a detailed history of the department since its establishment.

http://www.biochem.ucl.ac.uk/

ATCC

ATCC is a global nonprofit bioresource center that provides biological products, technical services and educational programs to private industry, government and academic organizations around the world. Our mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement, validation and application of scientific knowledge.
http://www.atcc.org/

ARP

Antibody Resources Page

http://www.antibodyresource.com/

Anti-Cancer Maps

Public database with viewing tools (NCI).

http://spheroid.ncifcrf.gov/

ANGIS

Australian National Genomic Information Service provides access for biologists to a comprehensive system of bioinformatics software, databases, documentation, training and support, on a subscription basis.
http://www.angis.org.au/

ALFRED

Allele frequency database from the Kidd Lab at Yale Univ.

http://alfred.med.yale.edu/alfred/

addgene

A non-profit organization dedicated to promoting sharing of plasmid constructs described in published literature. Addgene stores original plasmid samples submitted by scientists and distributes them for use in advancing life science research.

http://www.addgene.org/pgvec1

Short and concise introductions to basic concepts in molecular and cell biology and bioinformatics. The main emphasis is placed on making it as easy as possible for the user to understand which tools and databases are available from the EBI and from sites belonging to its collaborators.

http://www.ebi.ac.uk/2can/home.html

BIOTECHNOLOGY IN AUSTRALIA

Biotechnology Australia, a multi-departmental Government agency, was established in 1999.
We are responsible for managing the National Biotechnology Strategy and for coordinating non-regulatory biotechnology issues for the Australian Government.
We also provide balanced and factual information on biotechnology to the Australian community, including through our Biotechnology Online school resource.
Our five partner agencies are:
Department of Agriculture, Fisheries and Forestry
Department of Education, Science and Training
Department of Health and Ageing
Department of Industry, Tourism and Resources
Department of Environment and Heritage

Watch saturated fats and calories too

Boston -- In December, New York City passed a law to phase out the use of trans fat in restaurants. Other cities, including Boston and Chicago, might follow suit. According to Alice H. Lichtenstein, DSc, Gershoff professor of nutrition science and policy at the Friedman School of Nutrition Science and Policy at Tufts University, the ban is a step in the right direction, but restaurateurs need to replace partially hydrogenated fat with unsaturated fat. If they choose saturated fat it would diminish the health benefits of this new initiative. Another new regulation that requires some restaurants to provide calorie information as prominently as price might be even more important, notes Lichtenstein.
"There is no biological need for trans fat and intake is associated with adverse health outcomes. However, the media attention on the trans fat announcement to the exclusion of the calorie labeling is unfortunate. Two-thirds of Americans are overweight or obese. The New York City Department of Health and Mental Hygiene has proposed that the calorie content of food items be displayed as prominently as the price, at the point of purchase," says Lichtenstein, also director of the Cardiovascular Nutrition Laboratory at the Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts.
"That means," Lichtenstein continues, "that if you are wavering between placing an order for a small versus a medium order of French fries, both the price and the number of calories per serving will be displayed. People will become more aware of the caloric cost of the foods they order, and the next step on a public health level would be to educate the consumer on the amount of calories their body needs per day. This way, they will be able to put the numbers they see on the board or menu into perspective. Because the amount of food and beverages we eat that is prepared outside the home is so large, even if this regulation just covers a fraction of food service establishments, it can have a tremendous impact on caloric intake."
"Trans fat," says Lichtenstein, "is a double whammy, because like saturated fat, it raises levels of LDL or 'bad cholesterol,' but it also lowers levels of HDL or 'good' cholesterol." Most of the trans fats we eat are formed during the partial hydrogenation of oils used in fried foods and commercial baked goods. Partially hydrogenated oils provide processed foods with longer shelf lives and therefore greater economic profitability.
"But, trans fat is just one part of the diet. In general, people are still eating far more saturated fat than trans fat, and both need to be reduced in order to maintain optimal cholesterol levels and promote heart health," says Lichtenstein. "And the big giant – total calories – is always looming in the background."
In one study to assess the effects of consuming different types of oils on cholesterol levels, led by Lichtenstein and published earlier this year, fifteen adult volunteers with moderately high LDL cholesterol were fed each of four diets with a different source of primary fat, including partially hydrogenated soybean oil (trans fat), palm oil (50 percent saturated fat), non-hydrogenated soybean oil (only 16 percent saturated fat), and canola oil (only 7 percent saturated fat).
The results, published in the American Journal of Clinical Nutrition (AJCN), reported that after a trial of 35 days on each diet, participants consuming the partially hydrogenated soybean oil and palm oil diets had levels of LDL cholesterol that were 12 and 14 percent higher, respectively, than when consuming the non-hydrogenated soybean oil diet. An even greater difference was observed when the partially hydrogenated soybean oil and palm oil diets were compared to the canola oil diet. While participants were on the partially hydrogenated soybean oil and palm oil diets their LDL levels were 16 and 18 percent higher, respectively, than when on the canola oil diet.
"On the basis of this and other work, it's clear that phasing out partially hydrogenated oils (trans fats) will improve diet in some ways, "says Lichtenstein, corresponding author on the AJCN study. "However, just decreasing trans fat intake without changing other dietary habits, such as minimizing saturated fat intake and controlling total calorie intake, will result in some real disappointments with respect to both heart health and obesity."
Lichtenstein recommends that other cities monitor the successes and challenges of the trans fat ban in New York City before implementing their own regulations, and also advises that the focus on the new regulations shift to the mandate to display calorie labeling in food service establishments, and educating people about their total daily caloric requirements.
###
Vega-Lopez S, Ausman LM, Jalbert SM, Erkkila AT, Lichtenstein AH. "Palm and partially hydrogenated soybean oils adversely alter lipoprotein profiles compared with soybean and canola oils in moderately hyperlipidemic subjects." American Journal of Clinical Nutrition. 2006 (July);84(1):54-62.
If you are interested in learning more about this topic, or speaking with a faculty member at the Friedman School of Nutrition Science and Policy at Tufts University, or another Tufts health sciences researcher, please contact Siobhan Gallagher at 617-636-6586.
The Gerald J. and Dorothy R. Friedman School of Nutrition Science and Policy at Tufts University is the only independent school of nutrition in the United States. The school's eight centers, which focus on questions relating to famine, hunger, poverty, and communications, are renowned for the application of scientific research to national and international policy. For two decades, the Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University has studied the relationship between good nutrition and good health in aging populations. Tufts research scientists work with federal agencies to establish the USDA Dietary Guidelines, the Dietary Reference Intakes, and other significant public policies