Seminar

Seminar Plan

Single Nucleotide Polymorphisms (SNPs) constitute the major form of variation in the human genome. Data about SNPs are collected in many large-scale, international efforts. Current estimates speak of one SNP per 1000 bases in a human genome, accounting only for those which are frequent in the population. The interest in SNPs stems from the fact that SNPs can direct medical research to genes or pathways related to disease, and sometimes may be causative for disease themselves. Linkage between SNPs, alleles and diseases is studied in genone-wide association (GWA) studies.

• The design, intent, and results of GWA studies which collect such data. Which diseases are under study? How is a significant association determined?

  Literature and other sources:
  • Review by Hardy and Singleton, N Engl J Med 2009
  • Exploring the potential relevance of human-specific genes to complex disease, Cooper, Kehreer-Sawatzki 2010

• The data bases which make such information available (NCBI, HApMap, HGMD). What is the added value they contribute, what is their public/commercial model and long-term perspective?

  Literature and other sources:
  • The HapMap Project and DataBase , project homepage
  • Vorstellung des HapMAp-Projekts, NATURE 2003
  HApMAp-Ergebnisse Phase I, NATURE 2005
  • An utter refutation of the 'Fundamental Theorem of the HapMap', Joseph D Terwilliger, Tero Hiekkalinna, 2006
  • The Human Genome Mutation Database

• Algorithmic issues related to SNPs, such as genomic haplotyping or predicting impact of SNP types in coding and non-coding regions.

  Literature and other sources:
  • An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations, TCBB 2011
  • Genotype determination for polymorphisms in linkage disequilibrium, Yu et al, BMC Bioinformatics,2009