Virtual DNA analysis--a new tool for combination and standardised evaluation of SSO, SSP and sequencing-based typing results

Tissue Antigens. 1998 Jun;51(6):587-92. doi: 10.1111/j.1399-0039.1998.tb03000.x.

Abstract

In order to obtain reliable information on HLA types, DNA typing with sequence-specific oligonucleotide/primer (SSO/SSP) typing sets or sequencing-based typing (SBT) is increasingly performed. The quality of the evaluation depends on the presence of a complete listing of all typed alleles as well as on the ability of detecting all corresponding alleles/allele pairs. We have developed the concept of virtual DNA analysis (VDA), which is able to combine all types of SSO/SSP/SBT results and evaluate this typing in combination according to the latest published allele sequence lists. The concept is based on the target DNA recognised by the respective typing techniques. All SSO/SSP or SBT results are transformed to a virtual sample DNA, which subsequently is analysed. Evaluation of generic or allele-specific DNA typing or the combination of both is supported. Due to this flexible approach, all kinds of SSO/SSP sets, as far as the respective SSO/SSP sequences are available, can be entered and evaluated immediately. The combination of collected data of different typing sets and procedures leads to the highest possible typing resolution. If more than one possible allele combination persists, the program reduces the result to the most specific common denominator in a stepwise manner. VDA offers the possibility of re-evaluation of former SSO/SSP/SBT results, alone or in combination. No solutions are omitted. This might be a first step towards standardisation of evaluating DNA-based HLA typing results or transfer of the respective typing data for later evaluation.

MeSH terms

  • Databases, Factual
  • Evaluation Studies as Topic
  • Genotype
  • HLA Antigens / genetics*
  • Histocompatibility Testing / methods*
  • Humans
  • Polymerase Chain Reaction / methods*
  • Polymerase Chain Reaction / standards*
  • Sequence Analysis, DNA*
  • Software*

Substances

  • HLA Antigens