Medical Sequencing Data

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

Mock Ups

Image:PhenSort.gif