Complete MHC haplotype sequencing for common disease gene mapping

Area of Science:

• Genomics
• Human Genetics
• Molecular Biology

Background:

• Systematic mapping of genetic variants is crucial for understanding common disease susceptibility.
• The major histocompatibility complex (MHC) is associated with over 100 diseases.
• A fully informative polymorphism map requires comprehensive genome sequencing.

Purpose of the Study:

• To sequence two common, autoimmune disease-associated MHC haplotypes in their entirety.
• To define the complete variation content between these two haplotypes.
• To provide a definitive resource for constructing informative genetic maps.

Main Methods:

• Sequencing of two major histocompatibility complex (MHC) haplotypes (HLA-A3-B7-Cw7-DR15 and HLA-A1-B8-Cw7-DR3) using bacterial artificial chromosome (BAC) cloning.
• Utilizing consanguineous cell lines PGF and COX for sequencing.
• Annotation of sequences to include all described splice variants of expressed genes.

Main Results:

• Generated 4.75 Mb of contiguous sequence for each of the two MHC haplotypes.
• Identified over 18,000 variations between the two sequenced haplotypes.
• Determined average SNP densities ranging from <1 to >60 SNPs per kilobase.

Conclusions:

• Complete and accurate sequence data from large-insert cloned DNA of polymorphic regions like the MHC is a definitive resource for genetic mapping.
• This approach overcomes limitations of PCR amplification in certain chromosome regions.
• The generated data will facilitate the construction of informative genetic maps for disease susceptibility studies.