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ALFRED :  the  AL lele  FRE quency  D atabase Kenneth K. Kidd and the ALFRED Team Department of Genetics and Center for Me...
Introduction <ul><li>What is in ALFRED? </li></ul><ul><li>How to access ALFRED </li></ul><ul><li>What is ALFRED? </li></ul...
What is ALFRED? <ul><li>ALFRED,  the ALlele FREquency Database , is designed to integrate into a single source information...
ALFRED Home Page http://alfred.med.yale.edu/alfred/
ALFRED is designed to allow reference of frequencies to: <ul><li>A specific typing protocol for a specific polymorphism at...
Why is it necessary? <ul><li>ALFRED is designed to serve as a central repository of frequencies for variation in the human...
Why is it necessary? <ul><li>ALFRED is web-based, publicly available, with easy to download data thus serving as a resourc...
What are we doing now?   Data content - Quality control <ul><li>Criteria - a minimal typed sample size of 20 individuals, ...
What are we doing now?   Data integration and accumulation <ul><li>ALFRED curators are currently uploading allele frequenc...
What are we doing now?   Data management <ul><li>ALFRED programmers are currently working on the migration of ALFRED from ...
What is in ALFRED? <ul><li>ALFRED stores allele frequencies and information on a wide range of loci, polymorphic sites, po...
Table Summary Numbers As of April 9, 2002
Loci Example: Chromosome 22
Locus Example: Catechol-O-Methyl Transferase
Locus Example: Catechol-O-Methyl Transferase
Definition of the Polymorphism <ul><li>A clear protocol </li></ul><ul><ul><ul><li>PCR primers and product sizes for In/Del...
Polymorphisms Example: COMT, 3-site haplotype
Allele Frequencies Example: COMT, 3-site haplotype
Allele Frequencies Example: COMT, 3-site haplotype
Populations Example: North America
Populations Example: Maya, Yucatan
Samples Example: Maya, Yucatan
Frequency data retrieval Search
Frequency Variation for  Four SNPS in 33 Populations Africa Europe/Middle East East Asia North America South America P. S.
<ul><li>Microsoft Access (migration to Oracle) </li></ul><ul><li>Microsoft NT Server with  Internet Information Server (II...
ALFRED System Overview PhenoDB ALFRED Web Server (ASP) ODBC Client Browser External Data Resources Collaborators HAPLO Pro...
<ul><li>http://alfred.med.yale.edu/alfred/index.asp </li></ul><ul><li>Suggestions and comments are welcome. </li></ul>ALFR...
<ul><li>Senior Faculty </li></ul><ul><li>Kenneth K. Kidd, Ph.D., Professor of Genetics and Psychiatry (ALFRED P.I.) </li><...
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ALFRED PowerPoint Presentation

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Transcript of "ALFRED PowerPoint Presentation"

  1. 1. ALFRED : the AL lele FRE quency D atabase Kenneth K. Kidd and the ALFRED Team Department of Genetics and Center for Medical Informatics Yale University School of Medicine Supported by the U.S. National Science Foundation
  2. 2. Introduction <ul><li>What is in ALFRED? </li></ul><ul><li>How to access ALFRED </li></ul><ul><li>What is ALFRED? </li></ul><ul><li>Why is it necessary? </li></ul><ul><li>What we are doing now? </li></ul>
  3. 3. What is ALFRED? <ul><li>ALFRED, the ALlele FREquency Database , is designed to integrate into a single source information on the frequencies of human DNA sequence variants. </li></ul>
  4. 4. ALFRED Home Page http://alfred.med.yale.edu/alfred/
  5. 5. ALFRED is designed to allow reference of frequencies to: <ul><li>A specific typing protocol for a specific polymorphism at a specific locus. </li></ul><ul><li>A specific sampling of an ethnic group. </li></ul><ul><li>Cross reference to the literature for other publications of frequencies based on the same sample or ethnic group. </li></ul>
  6. 6. Why is it necessary? <ul><li>ALFRED is designed to serve as a central repository of frequencies for variation in the human genome – curated and cross referenced to molecular and ethnographic databases – by assembling in one place data that are dispersed very widely in the scientific literature. </li></ul>
  7. 7. Why is it necessary? <ul><li>ALFRED is web-based, publicly available, with easy to download data thus serving as a resource for many types of research projects. </li></ul><ul><li>With its graphic displays of data, ALFRED can also serve as an educational resource for physical anthropology and human population genetics. </li></ul>
  8. 8. What are we doing now? Data content - Quality control <ul><li>Criteria - a minimal typed sample size of 20 individuals, minimization of missing data, time-stamped frequency data (i.e., different versions of frequency data are available). </li></ul>
  9. 9. What are we doing now? Data integration and accumulation <ul><li>ALFRED curators are currently uploading allele frequency data from published literature throughout the physical anthropology and population genetics peer reviewed journals. </li></ul>
  10. 10. What are we doing now? Data management <ul><li>ALFRED programmers are currently working on the migration of ALFRED from Access to Oracle in order to handle the rapidly growing database. </li></ul>
  11. 11. What is in ALFRED? <ul><li>ALFRED stores allele frequencies and information on a wide range of loci, polymorphic sites, populations, and samples. </li></ul>
  12. 12. Table Summary Numbers As of April 9, 2002
  13. 13. Loci Example: Chromosome 22
  14. 14. Locus Example: Catechol-O-Methyl Transferase
  15. 15. Locus Example: Catechol-O-Methyl Transferase
  16. 16. Definition of the Polymorphism <ul><li>A clear protocol </li></ul><ul><ul><ul><li>PCR primers and product sizes for In/Dels and STRPs </li></ul></ul></ul><ul><ul><ul><li>PCR primers and fragment sizes after enzyme digestion for RSPs </li></ul></ul></ul><ul><li>Unambiguous definition of varying nucleotides based on flanking sequence. </li></ul>
  17. 17. Polymorphisms Example: COMT, 3-site haplotype
  18. 18. Allele Frequencies Example: COMT, 3-site haplotype
  19. 19. Allele Frequencies Example: COMT, 3-site haplotype
  20. 20. Populations Example: North America
  21. 21. Populations Example: Maya, Yucatan
  22. 22. Samples Example: Maya, Yucatan
  23. 23. Frequency data retrieval Search
  24. 24. Frequency Variation for Four SNPS in 33 Populations Africa Europe/Middle East East Asia North America South America P. S.
  25. 25. <ul><li>Microsoft Access (migration to Oracle) </li></ul><ul><li>Microsoft NT Server with Internet Information Server (IIS) </li></ul><ul><li>Scripts Written in Server-side ASP (VB Script) </li></ul>ALFRED System Implementation
  26. 26. ALFRED System Overview PhenoDB ALFRED Web Server (ASP) ODBC Client Browser External Data Resources Collaborators HAPLO Program Others (e.g. literature) Input Data Sources NT Server Kidd Lab Data
  27. 27. <ul><li>http://alfred.med.yale.edu/alfred/index.asp </li></ul><ul><li>Suggestions and comments are welcome. </li></ul>ALFRED The AL lele FRE quency D atabase from Kidd Lab
  28. 28. <ul><li>Senior Faculty </li></ul><ul><li>Kenneth K. Kidd, Ph.D., Professor of Genetics and Psychiatry (ALFRED P.I.) </li></ul><ul><li>Perry Miller, M.D., Ph.D., Director of Center for Medical Informatics </li></ul><ul><li>Curators </li></ul><ul><li>Chen-Chen Yeh, M.S., Research Associate </li></ul><ul><li>Rebekah Heinzen, B.A., Research Assistant </li></ul><ul><li>Programmers </li></ul><ul><li>Michael V. Osier, Ph.D. Candidate, Graduate Student </li></ul><ul><li>Haseena Rajeevan, Ph. D., Systems Programmer </li></ul><ul><li>Nicholas P. Tosches, M.D., Associate Research Scientist </li></ul><ul><li>Lyudmila Druskin, M.D., Postdoctoral Fellow and Associate </li></ul><ul><li>Consultants </li></ul><ul><li>Andrew J. Pakstis, Ph. D., Research Scientist </li></ul><ul><li>Judith R. Kidd, Ph. D., Research Scientist </li></ul><ul><li>Kei-Hoi Cheung, Ph. D., Assistant Professor </li></ul>The ALFRED Team
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