Medical Sequencing Data

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Medical Sequencing Data

Some combination of phenotype and genotype ... Details unknown. Worthwhile to design ?

Major Types of information

  • Subjects
    • Anonymous individuals
      • Family history
      • Age
      • Sex
      • Ethnicity
    • Pools of people
  • Environmental data
    • Location (zip code would be great)
    • Medications they are taking
    • Exercise, nutrition ...
  • Genotype info
    • Microarray based
      • SNPs
      • Haplotype blocks
      • Copy number polymorphism
    • Sequence based
      • Random reads
      • PCR products
      • larger clones
      • single haplotype vs. diploid
  • Phenotype
    • Disease presence/absence or severity
    • ADR - Adverse Drug Reaction
    • Single physiological measure
      • Enzyme activity, measure of amount of substance
    • Parallel Measures
      • Microarray measurements, etc...

Some Other Database Entities

  • GenotypeTest - records what regions of genome probed.
  • Study
    • External URL
    • Publications
    • Contacts
    • A group of subjects
    • A set of phenotype and genotype tests

Existing Genotype/Phenotype Web Databases

http://www.pharmgkb.org/ - Requires registration for much data. Fan & Jim registered
http://globin.bx.psu.edu/genphen/ - Belinda, Ross and Webb's work, mostly covers hemoglobins