A Rapid Method for HLA-typing by Haplotyping

DESCRIPTION (provided by applicant): 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.