Haplotype Specific Extraction (HSE)

Used for:

  • Transplantation tissue typing
  • Forensics
  • Disease association studies

Haplotype-Specific Separation of Parental Alleles:

HSE is available for haplotyping applications.  HSE is being used to determine long range haplotypes in disease association studies.  HSE separation primers can be designed for any polymorphic site, including single nucleotide polymorphisms.

Resolution of Out-of-Phase Sequencing Artifacts:

By separating a sample into its parental alleles, difficult to sequence regions, caused by single or multi-base differences in repetitive elements between the parental alleles (such as STRs) can be simply and completely resolved by HSE and standard sequencing.


SNP-specific analysis and separation of diploid genomic DNA into its haploid components by selectively targeting heterozygous SNPs or other polymorphisms with allele-specific primers.

  • Determines unambiguous molecular linkage and haplotypes without need for familial information or inference
  • Directly builds on associated SNP data to reduce ambiguity & complexity and detect rare linked variants
  • Identifies new SNPs and alleles

We support customers using the HaploPrepTM family of reagents on Qiagen’s EZ1 robot for tissue typing applications (solid organ and bone marrow transplantation).  HSE resolves all known ambiguities in HLA typing for all five major HLA loci.

  • HLA-A
  • HLA-B
  • HLA-C

Haplotype Specific Extraction primers are also available for KIR typing as well as other commonly typed loci.