Gene SNPs and mutations in clinical genetic testing: Haplotype-based testing and analysis

Jong Eun Lee, Ji Ha Choi, Ji Hyun Lee, Min Goo Lee

Research output: Contribution to journalReview articlepeer-review

64 Scopus citations


Haplotype-based analysis using high-density single nucleotide polymorphism (SNP) markers have gained increasing attention in evaluating candidate genes in various clinical situations. For example, haplotype information is useful for predicting the severity and prognosis of certain genetic disorders. The intragenic cis-interactions between the common polymorphisms and the pathogenic mutations of prion protein (PRNP) and cystic fibrosis transmembrane conductance regulator (CFTR) genes greatly influence the phenotypes and the disease penetrance of hereditary Creutzfeldt-Jakob disease and cystic fibrosis. Merits of haplotype study are more evident in the fine mapping of complex diseases and in identifying genetic variations that influence individual's response to drugs. Knowledge-based approaches and/or linkage analyses using SNP tagged haplotypes are effective tools in detecting genetic associations. For example, haplotype studies in the inflammatory bowel disease susceptibility loci revealed diverse cis and trans gene-gene interactions, which can affect the clinical outcomes. Although currently, we have very limited knowledge on haplotype-phenotypic characterizations of most genes, these examples demonstrate that increased understanding of the clinically relevant haplotypes will provide better results in the diagnosis and possibly in the treatment of both monogenic and polygenic diseases.

Original languageEnglish
Pages (from-to)195-204
Number of pages10
JournalMutation Research - Fundamental and Molecular Mechanisms of Mutagenesis
Issue number1-2
StatePublished - 3 Jun 2005

Bibliographical note

Funding Information:
The authors wish to thank WonSun Han for her editorial assistance. This work was supported by grant 03-PJ10-PG13-GD01-0002 from the Korea Health 21 R&D Project, Ministry of Health & Welfare, Korea.


  • Cystic fibrosis transmembrane conductance regulator
  • Gene-gene interaction
  • Haplotype
  • Mutation
  • Pharmacogenomics
  • Single nucleotide polymorphism


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