Bioinformatics: analysis of HLA sequence data.

High resolution HLA typing is a requirement for the selection of matched donors in hematopoietic cell transplantation. The high resolution typing method that provides the most accurate and complete identification of HLA genotypes is sequencing-based typing (SBT). For each sample being tested, SBT defines the exact nucleotide sequence of the coding regions of both alleles at a given HLA locus. Identification of the underlying genotype of the sample can then be made by computerized sequence comparison with all possible HLA allele combinations at that locus. The use of SBT to identify the complete nucleotide sequence of a given HLA gene also enables the direct detection of previously undefined alleles. Since different HLA alleles may differ by a single nucleotide, the accurate assignment of an HLA genotype by SBT is absolutely dependent on the correct identification of the nucleotide at each position for a given sample. However, automated sequence analysis of heterozygous samples may result in the ambiguous assignment of nucleotides at a given position. In addition, ambiguous assignments may result from the sequencing of two different samples that express different HLA alleles but whose sequence profiles appear exactly the same. Both of these ambiguous situations can be resolved by the application of the multi-sequence analysis (MSA) method described here.