During tissue-typing for transplantation, certain diploid combinations of allele pairs fail to be resolved with current typing methods. Haplotype-Specific Extraction, HSE, establishes haplotypes from individual patient's samples and permits the unambiguous typing of such combinations without knowledge of familial information, thus enabling more accurate and efficient HLA typing. ? ? HSE physically separates a diploid sample into its haploid components without requiring amplification: Magnetic beads are selectively attached to polymorphic sites and used to isolate the targeted fragments from a heterozygous mixture. Genomic DNA from blood, buccal swabs or tissue will be separated by HSE and analyzed directly with kits and assays already in use for HLA typing. ? ? During Phase I we will extract and type fragments of 50,000 -100,000 base pairs in less than three hours and demonstrate the resolution of ambiguous allele combinations. HSE will be tested on 100+ ambiguous and non-ambiguous DNA samples provided by seven collaborating institutions. ? ? We will attempt to prove HSE as a generic haplotyping method that directly provides long-distance linkage without requiring familial information or statistical methods. This is relevant for certain studies investigating disease genes on the HLA-/MHC-Iocus, as well as for other loci. HSE can accelerate efforts to create a haplotype map. ? ?
| Dapprich, Johannes; Ferriola, Deborah; Magira, Eleni E et al. (2008) SNP-specific extraction of haplotype-resolved targeted genomic regions. Nucleic Acids Res 36:e94 |
| Nagy, M; Entz, P; Otremba, P et al. (2007) Haplotype-specific extraction: a universal method to resolve ambiguous genotypes and detect new alleles - demonstrated on HLA-B. Tissue Antigens 69:176-80 |
