HLA-B AND HLA-C INTRON SEQUENCING BEYOND INTRON 3
JB Stein, MD McGinnis, P Krausa Forensic Analytical Inc.

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HLA intron sequences not only provide insight into evolution of HLA polymorphism, but are a useful resource for the design and implementation of molecular based typing approaches. Many DNA based strategies for HLA Class I typing use specific primer sites located in introns adjacent to target exons. For example, in developing Sequencing Based typing (SBT) strategies, we utilized intron sequence information from a representative panel of alleles, to identify useful primer sites for DNA sequencing into exons of interest. For HLA Class I, exons 2 and 3 are the major regions of functional polymorphism, and hence the adjacent introns 1, 2, and 3 have been sequenced and well characterized for many alleles. However, intron sequence information beyond intron 3 is scarce. HLA Class I polymorphisms that lead to reduced or abrogated expression have been found in exons other than 2 and 3, and it is therefore important to analyze these regions. The capability to analyze polymorphism within exons 4-8 of HLA Class I loci requires characterization of additional introns to locate suitable priming sites. This study presents sequencing data from introns 4 to 7 using a panel of HLA-B and –C alleles obtained from sequenced and workshop cell lines. The information generated further extends a database resource of known HLA intron sequences and increases our understanding of HLA polymorphism.